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F O S T E R , C E D R I C 1 6 9 2 T S

Welcome to Biology! 1

Puzzling Observation

Proposed Explanation

Planned Test

Predicted Result

Conclusion

Observed Result of Test

then ...

Therefore ...

And/But ...

and ...

If ...

The Man in the Mirror

Alzheimer’s Disease: Plaques in a Brain vs. a Normal Brain

The Scientific Method offers solutions

Humans in the living world.Species Diversity

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EssEntials

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2 Essential Biology

the Case of the nonpaying tenant It was a day I always looked forward to – my father and I went to visit Uncle Hans in Mastic Beach, Long Island. Hans was my father’s uncle, and we all enjoyed spending time together at the beach. We regretted that we saw him only once a year during the holidays. Uncle Hans had lived through World War II, built his own house, told many stories, and always liked seeing us on our visits. When I was a child, he was generous with candy and treats whenever we visited, which made it a fun time.

When we arrived at his house this time, we knocked on his door, but no one answered. We knocked again and finally went to the back door. There was Uncle Hans, sitting at the kitchen table, staring at the wall. We gestured to him, and he opened the back door, with- out much of a greeting. How strange that he was not smiling and hugging us as we entered.

Hans instead greeted us with a complaint: “That man is using my stuff. I told him to leave, but he won’t go.” “Who?” asked my father. “Why, the tenant in my house – he’s not paying rent, he does what he pleases, and he won’t leave me alone,” explained an exasperated Hans. My father and I were very concerned . . .Who was this nonpaying tenant and why had we not heard about him?

But how odd; Hans had lived alone in his one-family house for many years. Had he taken in a boarder? We did not think that he really needed the money. Uncle Hans took us around the house, showing us all the mess the tenant was making: he was sloppy, used all of Uncle Hans’ dishes, ate his food, and didn’t pay his share of the grocery bills. We could see that the place had deteriorated since our last visit, and Hans had always been so neat.

At this point, my father and I were angry. How could this be happening? Why had our family not helped Uncle to take legal action to remove this tenant? It was elder abuse and we would not tolerate disrespect to seniors. “Uncle, where is this man right now? We will have a word with him!” I exclaimed.

“I’ll show you. He’s living in this room.” Uncle Hans took us to what I thought was the bathroom. It was curious, and my father and I quixotically looked at each other. I think that we both knew that something was not right. No one lives in a bathroom.

Uncle Hans took us into the small room, but there was no one there. It was an empty bathroom with a towel on the mirror. Hans pulled off the towel and yelled into the mirror, “There he is! – That old man is using my toothpaste, my toothbrush, and my cologne, and he’s not paying any rent or anything. He is everywhere I go; now let’s get him out of here.” My father said sadly to Hans, “that old man is you.”

ChECk in

From reading this chapter, you will be able to:

• Using the opening story or an example from your own experience, explain how biology affects soci- ety and our everyday lives.

• Define biology, biophilia, and biological literary and explain how biology is an interdisciplinary, multi- faceted science.

• Describe the characteristics of life. • Using the postulates of the Linnaean classification system and the hierarchical order of life as sup-

port, defend the statement that there is a high degree of order in living organisms. • Trace the development of evolutionary thought and explain the evidence for natural selection. • Outline the steps of the scientific method.

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Chapter 1: Welcome to Biology! 3

Getting to know Biology Hans was his own nonpaying tenant due to dementia brought on by Alzheimer’s disease and aging. Changes in his brain chemistry, namely the accumulation of certain chem- icals, caused Hans to become confused and prevented him from recognizing his own image in the mirror. Alzheimer’s disease is associated with tangles or masses of proteins that form plaques along nerves in the brains of its victims. These plaques prevent proper transmission of nerve signals (Figure 1.1). Protein buildups cause fragmented thoughts and brain processes. There are many possible causes of Alzheimer’s disease, ranging from traumatic head injuries and cardiovascular disease to genetics (family history). In fact, mutations of a certain gene are closely linked with higher risks of developing Alzheimer’s disease.

Age-related dementia is a common symptom in elderly populations, but its prev- alence does not make it less tragic. One in eight elders is afflicted with some degree of dementia due to aging, and Alzheimer’s disease is the sixth leading cause of death among seniors. Nearly half of all seniors who are 85 years old and older experience Alzheimer’s disease symptoms. The disease impacts their quality of life, their families, and their ability to contribute successfully to our society.

Everyone has an idea about the definition of biology, the study of life, but to really feel its effects in our everyday lives is another matter. Hans lives with his biology each day, struggling and trying to cope with its effects. Scientists work to study diseases to help people like Hans by finding cures or treatments for symptoms. Physicians treat conditions such as dementia but rely on research findings that scientists develop to help them fight the effects of diseases. Biology has many facets, affecting each of us uniquely.

Alzheimer’s disease

Progressive mental deterioration brought on by aging. The disease is associated with protein masses or tangles that form plaques along the nerves in the brains of the victims.

Biology

Study of living creatures.

ChECk Up sECtion

There are many examples of diseases caused by the aging process affecting our society. Lifestyle changes can help people cope with these challenges. Use our case in the story to research Alzheimer’s disease. Explain two benefits and two drawbacks to the solutions you propose for coping with Alzheimer’s disease. How do you see changes due to age-related diseases affecting our society in the near future?

Healthy Alzheimer’s

Figure 1.1 Amyloid beta protein plaques on a nerve cell. Plaques block the transmission of nerve messages in the brain of Alzheimer’s patients.

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4 Essential Biology

Biology encompasses many levels of study – from diseases to the basic unit of life, the cell, to how living beings interact with each other and their environment. It is a com- plex and exciting field, changing frequently as new species are discovered, new medical devices are developed, and old ways of looking at environmental problems are updated with new understandings and shifts in focus. Although many of you reading this chapter are not actively pursuing a career in one of the sciences, almost everyone has an interest in the natural world and the organisms we find in it. In fact, the affinity we share for other living creatures is termed biophilia, a term first coined by E. O. Wilson, a famous American biologist. Biophilia drives a questioning of how life works and how it relates to the world around us:

“How do birds fly south for the winter?” “Why are we thirsty in the morning, after we wake up?” “How does the Dionaea muscipula (Venus flytrap) trap flies?” “Why does the Amorphophallus titanum (corpse flower) emit a horrible odor (Figure 1.2)?”

These questions and many others like them are important in understanding our relation to other living creatures and to the planet. They are based on principles in science that draw from fields outside of biology. A bird flies south in the fall because of visual and smell cues, but also because certain of the chemicals in its brain give it an ability to detect the Earth’s magnetism (physics) to guide it. We are thirsty because we require water, with the right amount of salt, to bathe our cells (chemistry). The carnivorous diet of the Venus fly- trap allows it to live in soils that are nutrient poor (geology). The odor of the corpse flower attracts sweat bees and beetles, which help spread its pollen to other flowers (ecology).

Asking questions such as those above helps to develop biological literacy, which comprises the many aspects of knowing about life: the facts, skills, ideas, and ways of thinking that enable a citizen to make decisions about and use biology and its technol- ogy. Everyone should be biologically literate. One does not need to perform specified tasks or understand complex instrumentation to be biologically literate. Biological lit- eracy just means thinking like a scientist; that is the best descriptor of a biologically literate person.

Cell

The structural and functional unit of an organism.

Biophilia

The affinity human beings share with other living creatures.

Biological literacy

Is the ability to interpret, negotiate, and make meaning from the many aspects of knowing about life to make decisions and use biology and its technology.

Figure 1.2 Amorphophallus titanum (corpse flower). The corpse flower has a smell similar to that of a decomposing animal.

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Chapter 1: Welcome to Biology! 5

Because biology is interrelated with concepts and terms branching from other areas, both science and non-science, we say that biology is interdisciplinary. This means that it draws from many fields of knowing. Science is often seen as a group of separate subjects, among them biology, geology, physics, and chemistry, but these subjects often over- lap. The distinction between biology and other fields was discussed by the geographer Halford Mackinder in 1887, who stated, “The truth of the matter is that the bounds of all the sciences must naturally be compromises, knowledge . . . is one. Its division into subjects is a concession to human weakness.” Biology should be understood in relation to the many fields that comprise it.

This chapter explores the scientific process used to understand big ideas in biology. We begin the textbook with a look at the characteristics of life, at how the Earth and its inhabitants came to be in the present, and at how scientists in all disciplines arrive at understandings about their fields of study; then in the next chapter, we will explore some of the chemistry and physics principles that drive life processes.

There are many branches of biology, each studying different aspects of the living world. A few include microbiology, the study of organisms not seen with the naked eye (99% of all living things); pathology, the study of diseases; anatomy, the study of structure, or how an organism appears; physiology, the study of function, or how an organism works; genetics, the study of inheritance and how characteristics are passed on between the generations; and ecology, the study of organisms and their interactions with the environment. Organization above the organism level is studied by macrobiol- ogy, which investigates how organisms interact with each other and within the envi- ronment. Macrobiology looks at animal behavior and nonliving environmental factors such as water in living systems, for example. Its emphasis is on human impacts within the greater ecosystem (or environment). Issues such as global climate change, acid rain deposition, overpopulation, and endangered species are macrobiology issues. Each of these studies is based on the same seven shared characteristics of living systems described in the next section.

What is life? All living things are composed of chemicals. Individually, the chemical substances are not living; however, in combination, they are the building blocks of life. What constitutes life? How does life differ from nonlife? What is it mean to be alive?

The difference between life and nonlife can be found in the organization of the substances that make up life. For instance, as substances become more complex, new properties emerge that are distinct from those of nonliving objects. There is no single difference between life and nonlife. Instead, there are a host of properties that biolo- gists use to distinguish living from nonliving systems. These properties constitute the characteristics of life:

1) Order: Living organisms have a high degree of order, with complexity that is still being discovered and understood through increased testing and observation techniques. Consider the diatoms, a group of algae that contain intricate walls of silicon dioxide (the same material that sand is made of), arranged in a mosaic structure (Figure 1.3). Their ornate organization is a visual testament to how complex can be the arrangement of a simple living organism. Life is ordered in such a way that is can be divided into smaller and smaller categories. It has a hierarchical order, arranged from the smallest unit of life, the cell to a whole living organism.

Interdisciplinary

Involves two or more areas of knowledge.

Macrobiology

The study of how organisms interact with each other and within the environment

Ecosystem

A system that involves interaction of a biological community with its physical environment.

Characteristics of life

The seven features (adaptation, order, response to stimuli, growth, development, and use of energy, homeostasis, reproduction, metabolism, diversity) that differentiate between life and nonlife.

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6 Essential Biology

2) Homeostasis: Living systems maintain a steady state, termed homeostasis. They respond to and exchange materials with their outside environment to keep internal conditions stable. Temperature and salt and sugar levels in the blood are all maintained to promote stable workings within a living organism. Look to the simple Stentor roeseli in Figure 1.4, a single-celled creature that looks like a nonliving trumpet used in ancient battles. The Stentor carefully controls its internal environment by sensing chemical levels in its watery surroundings and then pumping out excess water through specialized internal pumps. Its nonliving appearance masks its many living characteristics.

3) Growth, Development, and Energy Use: All organisms acquire and use energy from their surroundings to grow and develop. A tree, an elephant, a mouse, and a single-celled bacterium each take in substances to obtain energy. They then con- duct a series of chemical reactions, which are together termed metabolism. These reactions form new materials to grow and make changes in their structures. As

Figure 1.3 Diatom cell wall structure. Note the complexity and almost artistic quality of the walls of the diatom.

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Figure 1.4 Stentor roeseli, a protozoan, resembles a trumpet.

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Homeostasis

The steady state maintained by living systems.

Metabolism

The sum total of chemical reactions taking place in cells.

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Chapter 1: Welcome to Biology! 7

shown in Figure 1.5, a human fetus grows larger and more complex as it develops in its mother’s womb. This ability to acquire energy, grow, and develop makes living systems able to change.

4) Response to Stimuli: Living organisms are able to react to the world around them. Consider the mating behavior of Rana pipiens, the prevalent North Amer- ican frog species. When a male Rana mates with a female, he jumps onto her back, and this initiates a croak reflex; the bottom frog croaks, indicating that she is actually a male (Figure 1.6)! The croak response tells the other male frog to get off, “I am a Male frog!” This signal allows more selective behavior by male frogs, helping them to determine male from female and thus prevents a possible altercation between two males.

Organisms respond to internal stimuli in addition to those in the environ- ment. In order to maintain homeostasis, body systems monitor internal chemical balance, temperature, and even pressure and position. Maintaining balance, as when we are walking, requires cues from our eyes, inner ear structures, known as the semicircular canals, and specialized receptors found throughout our bod- ies that sense position, known as proprioceptors.

5) Adaptation: Populations of living things adapt to their surroundings and evolve or change as a group, with some organisms surviving and reproducing more

Figure 1.6 Two glass frogs (teratohylamidas) mating. A male grabs hold of his female mate, stimulating her to produce eggs and his own sperm to be released.

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Figure 1.5 Growth of a human fetus. The human embryo grows rapidly to a seven-month fetus in this ultrasound image.

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Adaptation

Populations of living things adapt to their surroundings and evolve or change as a group.

Response to stimuli

Ability to react to the various changes of the environment.

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8 Essential Biology

successfully than others. Consider the case of the English peppered moths in England, which contain a light, Bistonbetularia f. typical, and a dark variety, Bis- tonbetularia f. carbonaria. In the preindustrial era, more light moths were found across England. Light-colored moths blended with the light-colored trees of the countryside. However, as soot and pollution from factories created a darker environment during the Industrial Revolution of the 1800s, light- colored moths stood out, attracting predators. Thus, their numbers declined, and the dark vari- ety became dominant. The dark moths blended in better with the changed back- grounds, helping them to survive more successfully. English peppered moths adapted to the Industrial Revolution by having two varieties that fluctuated with changing conditions (Figure 1.7). In Chapter 7, modern trends in English moth populations will be discussed further to elaborate upon adaptation of species in current times.

6) Diversity: The adaptation and evolving of organisms described in the above section resulted in a great variety of living creatures. Scientists have classified roughly 8.7 million nonbacterial species now living on the Earth. Living sys- tems, considered a group, are diverse. A great deal of biodiversity – the variety of life forms in a given area – has yet to be uncovered because there are so many areas of the Earth that have not been sampled – deep sea vents, volcano interiors, and many polar regions, to name a few. The latest reports in Nature magazine state that almost 90% of marine and land species remain undiscov- ered. Unfortunately, the rate of extinction of species has increased a thousand fold in the past century, with about 20 species becoming extinct every minute in tropical rainforests. Some species may never be discovered before they become extinct.

Coral reefs are one of the most diverse ecosystems of the world, containing almost 25% of all marine species and yet occupying only about 0.1% of the surface of the ocean. Like tropical rainforests, coral reefs are being seriously threatened by environmental and other changes that disrupt and sometimes destroy their fragile ecosystems.

7) Reproduction: Living systems are able to reproduce themselves. While there is a great deal of variety of organisms, they all transmit the same set of hereditary

Figure 1.7 English peppered moth: light variety hiding on an oak tree branch.

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Biodiversity

Variety of life forms in a particular habitat.

Reproduction

The process of making new offspring.

Diversity

The adaptation and evolving of organisms showing a great deal of variety.

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Chapter 1: Welcome to Biology! 9

material from generation to generation. Hereditary material is composed of genes, made of the chemical DNA (deoxyribonucleic acid). DNA is the genetic material of a cell that contains the instructions to life. Organisms use DNA to guide their growth and development. Genetic material is passed on to new off- spring each generation.

While the same material is used among all of the species, how does one species differ from another? Why is a maple tree different from an oak tree? How is a baby duck similar to its mother (see Figure 1.8)? The answer lays in the subtle differences in the details of DNA’s structure. Just minor differences in portions of DNA make organisms of different species, very different from each other. In fact, the genetic material of humans and chimpanzees is 99% the same, but small differences in hereditary codes cause big differences in the physical features of humans and chimps. Genetically, each human is 99.9% the same as all other humans, but small differences in the 0.1% of remaining DNA make each of us unique. Guidance by our genetic material helps us to carry out our life functions in a world with forces that often fight against us. Uncle Hans had bits of DNA that coded for plaques in his brain, which led to his problems with dementia. Often, simple changes inherited in our cells can lead to the many characteristics that make us unique.

All living things share each of the seven characteristics discussed in this section of the text. While there is incredible diversity in life across the Earth, all organisms need to be able to carry out these life functions to survive. This is one of the central themes of biology.

order in a Universe of Chaos organizing Biodiversity: hierarchy of life One characteristic of life is that it is ordered: it is composed of building materials that are very similar across organisms. In organisms, atoms are the smallest units of matter that maintain the properties of the larger sample. Atoms organize to form molecules,

Figure 1.8 The genetic trail. Baby ducks have hereditary information passed onto them from their parents.

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Atoms

Are the smallest units of matter that can exist and maintain the properties of the larger sample.

Molecules

Atoms bonded together.

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10 Essential Biology

which are two or more atoms chemically combined. Water is an example of a molecule; it is composed of two hydrogen atoms attached to one oxygen atom. Some molecules join together to form macromolecules, which are the building blocks of living things: proteins, lipids (fats), carbohydrates, and nucleic acids. Proteins make up the structures and perform many functions in cells. Lipids store energy in the longer term for use by cells, and carbohydrates provide instant energy. Nucleic acids are the hereditary materi- als passed on from parents to offspring. Figure 1.10 shows the organization of chemical substances into a living cell. These macromolecules organize into living systems in such a manner as to produce life. Based on their chemistry, macromolecules orient them- selves to form organelles, which are structures that carry out specific functions in living systems. Organelles organize together inside a membrane or a cell wall to form a cell, the fundamental unit of life.

There are over 200 types of different cells in the human body, each with unique structures and functions. Groups of cells that have similar structure and perform similar functions are called tissues. In humans, muscle, nerve, epithelial (covering), and connec- tive tissues make up our structures. Tissues unite to form organs, which are specialized body parts. Organs carry out specific functions for an organism. For example, the kid- neys filter blood, and the small intestines absorb food. Organs working together, such as the bladder, kidneys, and ureter tubes, make up an organ system. The digestive system, which processes food entering the body, is made up of several organs: the liver, gallblad- der, intestines, stomach, and pancreas. Together the organ systems form a whole, living creature known as an organism.

As indicated in Figure 1.10, a group of organisms of the same species living in a given area is known as a population. A population of fungi in a forest is studied and counted as a discreet unit. Two or more populations in an area are termed a community. To extend our example, the community (or biocenoses) would include the pine trees, fungi, insects, birds, and chipmunks found in a forest. A community’s interactions with the non- living environment (air and water) comprise an ecosystem. The many effects of nonliving factors on a forest community are dynamic and often quite complex. All of the different ecosystems of the Earth interacting with their environment make up the biosphere.

Interactions of organisms with each other are graphically described as food chains and food webs. These show the way energy flows within an environment, with food chains showing energy flows from one organism to another, and food webs showing the

Figure 1.9 Robert Hooke’s drawings of cork cells looked much like the image repro- duced here from his Micrographia, 1665.

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Macromolecules

Molecules containing large number of atoms, which are the building blocks of living things.

Organelles

Structures that carry out specific functions within cells.

Membrane

A sheet-like structure that acts as a boundary in an cell.

Tissues

Groups of cells having similar structure and performing similar functions.

Organs

Specialized body parts that carry out specific functions for organisms.

Organ System

A group of organs working together performing a united function.

Population

A group of organisms of the same species living in a given area.

Organism

Living creature formed as a whole by organ systems.

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Chapter 1: Welcome to Biology! 11

Organism Population

Biocenoses

Ecosystem

Bioma

Atom

Molecule

Cell organelles

Cell

Tissue

Organ

System of organs

B i o s p h e r e

Figure 1.10 Organizational levels of living systems. Life is ordered in a hierarchy, with increasing complexity from atoms and molecules to organ systems and whole organisms.

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interaction of many organisms’ energy flows with each other. Food chains are actually threads in a larger food web. An example of each is given in Figure 1.11.

taxonomy: the science of Classification The science of classifying the vast biodiversity described earlier is called taxonomy. Attempts to classify organisms into logical groups began thousands of years ago, as far back as the ancient Greek philosopher Aristotle, who organized life according to a scale of complexity, called scala naturae, meaning stairway of Nature. Aristotle’s scheme is shown in Figure 1.12.

Later, in the 1800s, Carolus Linnaeus, a naturalist, standardized a naming system for living creatures that is still used today. Linnaeus’ system of naming is known as

Community

A group of living organisms living in the same area or having a particular characteristic in common.

Biosphere

All of the different ecosystems of the Earth interacting with their environment make up the biosphere.

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12 Essential Biology

BOx 1.1 PREDICTIng SEx BEHAvIORS

Food resources are not the only valuable commodity in life systems. Organ- isms compete for the limited resource of the opposite sex. Either in a for- aging scenario or in finding a mate, many organisms search far and wide for resources. In the process, organisms maximize their energy intake, using the nutrients of a particular area or “patch.” Ecologists mathematically predict how long a creature will remain in a “patch” of resources based on a few fac- tors. In searching for a female, for example, weaker, smaller, and, of course, more desperate amphibian males will hold onto females (the resource they are trying to obtain) during copulation (sex) to a point of drowning them! Mathematical models show that smaller amphibians will have a difficult time finding another mate, so it “pays” for them to stay atop a female. Being able to predict and even modify behaviors in animals is called the study of behav- ioral ecology.

Figure 1.11 Different ways to show feeding relationships. A simple food chain in Chesapeake Bay on the left. Moreover, a simplified food web in the open water on the right. Both show various pathways of energy flow through living organisms in the environment. Decomposers eventually consume all living organisms. From Biological Perspectives, 3rded by BSCS.

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Taxonomy

The science of classifying the vast biodiversity.

Food web

A network of interdependent and interlocking food chains.

Food chain

Interactions of organism with each other through the transfer of nutrients and energy.

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Chapter 1: Welcome to Biology! 13

Figure 1.12 Scala naturae. Aristotle’s “Ladder of Life,” with humans shown as dominant and more important than all other life.

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14 Essential Biology

binomial nomenclature, in which organisms are given a unique scientific name, com- posed of two parts: the first name is based on the organism’s genus, which is a group of individuals of the same species, and the second name is its species, which is a group of individuals similar enough to be able to reproduce with one another to produce live, fertile young. For example, Drosophila melanogaster is the fruit fly that belongs to the Drosophila genus and the melanogaster species. Note that the scientific name is always italicized or underlined, and the genus is capitalized. A scientific name may be shortened to the first letter of the genus, capitalized, and the full species name, both italicized: D. melanogaster. Drosophila are well known in biology for their simple hereditary make-up and their easy use in the field of genetics. Their mating ritual is shown in Figure 1.13.

A kingdom is the largest grouping used in Linnaeus’ binomial nomenclature. Con- sider the red maple tree, Acer rubrum: Its species, rubrum, is the smallest grouping, and its genus, Acer, is the next largest. A group of genera is known as a family and a group of families is known as an order. Red maples are the members of the Aceraceae family, which are characterized by having watery, sugary sap. The Aceraceae family order is Sapindales, which are soapberry, usually wooden, plants. A group of related orders is known as a class. A red maple’s class is Dicotyledonae, which means that all of these organisms have an embryo with two seed leaves (cotyledons). When a number of similar classes are grouped together, they form a phylum. The red maple phylum is termed Magnoliophyta. Many phyla grouped together form a kingdom. Magnolio- phyta is grouped with other phyla into the plant kingdom. An easy way to remember the sequence of this classification scheme, from broadest to most specific, is by using the saying: “King Phillip Came Over From German Shores,” with the first letter of each word corresponding to the first letter of Kingdom, Phylum, Class, Order, Family, Genus, and Species. The complete biological classification of red maples is shown in Figure 1.14. Humans, such as Uncle Hans, are Homo sapiens. How would you classify Hans? What is his genus? species? phylum? kingdom?

Organisms are also classified based on their domain. There are three known domains in which all organisms fit: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are sin- gle-celled organisms that contain “naked” DNA, meaning that their genetic material is not found within an enclosed nucleus, which is the control center of the cell. DNA and cell structures of Bacteria and Archae are different from each other, classifying them as separate domains. Traditionally, organisms lacking a distinct nucleus and organelles

Figure 1.13 Drosophila’s fruit flies mating. ‘Dancing Mate Ritual’ Drosophila fruit flies engage in sexual foreplay through dancing to attract a mate. This leads to copulation (sex).

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Binomial nomenclature

Naming convention for living creatures, in which organisms are given unique scientific name, composed of two parts. The first indicates the genus and the second the species.

genus

A group of individuals of the same species.

Species

A group of individuals similar enough to be able to reproduce with one another to produce live, fertile young.

Class

A group of related orders.

Phylum

Number of similar classes grouped together.

Kingdom

The highest grouping under which living organisms are classified.

Family

A group of genera consisting of organisms related to each other.

Order

Used in the classification as a group of families.

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Figure 1.14 Classification schemes of red maples.

Kingdom: Plant

Phylum: Magnoliophyta

Class: Magnoliopsida

Order: Sapindales

Family: Aceraceae

Genus: Acer

Species: rubrum L.

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were called prokaryotes, but this classification is now informal. Both Bacteria and Archae are prokaryotes.

Over 99% of all organisms are classified as either Bacteria or Archaea. They inhabit all areas of the Earth, from boiling sulfur lakes to frozen arctic ice to the insides of our large intestines. Bacteria are heavier by mass (this is called biomass) than all other living organisms combined. Oddly, this is a world unseen by humans and yet it is vast, vibrant, and changing. Bacteria and Archaea live in such varied conditions that they are said to be omnipresent: on average, there are 100,000,000 bacteria (including Archaea) per square centimeter of surface at any place on the Earth.

Eukarya, or eukaryotes, are organisms containing organelles and a distinct, true nucleus with genetic material contained therein. Eukarya are composed of four different groups. The simplest Eukarya are the protists or Protista, a diverse group composed of both single-celled and multi-celled organisms, ranging from Amoeba to Paramecium to Euglena, as shown in Figure 1.15. A drop of pond water usually contains all of these creatures. Some protists are producers – they are able to produce their own food. Others, known as heterotrophs or consumers, acquire energy by eating other organisms. Protista are the oldest, evolutionarily, of all the groupings of eukaryotes.

The fungi (singular, fungus) are eukaryotes that secrete chemicals to break down other living or once-living materials. This allows fungi to consume these substances.

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Figure 1.15 a. Amoeba, b. Paramecium, and c. Euglena. Microorganisms depicted belong to the Protista kingdom. Each has characteristics that make them unique. An Amoeba appears blob-like, often engulfing prey as it moves; The Paramecium captures food as it beats its hair-like projections, creating waves to bring prey in toward it; A Euglena is able to make its own food from sunlight as well as capture prey.

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Bacteria

Single-celled organisms that have cell walls but lack an enclosed nucleus and organelles.

Archaea

Microorganisms that are similar to bacteria in size and structure but different in molecular organization.

Eukarya

One of the three domains of the biological classification system.

Domain

A division of organisms ranking above a kingdom in the systems of classification based on similarities in DNA and not based on structural similarities.

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Mushrooms are a common example of fungi, which are able to decompose dead organ- isms, but unable to make their own food (Figure 1.16).

Alternatively, all plants are able to obtain food by converting sunlight’s energy to chemical energy through the process of photosynthesis. Carbon dioxide and water are rearranged by plants to produce the simple sugar, glucose, and oxygen, using sunlight as a source of energy. Plants are multicellular eukaryotes, with an ability to live on land, or in freshwater or saltwater. Their ability to survive without the need of energy from other organisms makes them producers, able to produce their own food (Figure 1.17).

Animals require the energy of other living creatures to survive. Animals are multicel- lular eukaryotes, which consume other organisms. Examples include herbivores, which eat plants, scavengers, which consume dead remains, parasites, which draw energy from a host organism while it is alive, and carnivores, which eat meat to survive. Ani- mals are motile (able to move) in carrying out their life functions such as in obtaining food sources; plants are immotile and require other means to acquire food sources. For

Figure 1.16 The Death Cap Mushroom. This is a deadly poisonous fungus. It likely killed Roman Emperor Claudius and Holy Roman Emperor Charles VI. It contains tox- ins that damage the liver and kidneys leading to fatalities.

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Figure 1.17 Plants: A Giant Redwood in Yosemite National Park. Giant Redwoods are the largest trees on the Earth, with stems reaching over 75 meters (250 feet) tall.

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Eukaryote

Organisms that contain organelles and a distinct, true nucleus with genetic material contained therein.

Protista

A diverse group composed of both single-celled and multi-celled organisms.

Producer

Organisms with the ability to make their own food.

Heterotrophs

Also called consumers, these organisms acquire energy by eating other organisms.

Fungi

Eukaryotic organisms that secrete chemicals to break down other living or once-living materials.

Prokaryote

Organisms that lack a distinct nucleus and organelles.

nucleus

Control center of the cell.

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Chapter 1: Welcome to Biology! 17

example, cheetahs, to obtain their prey are able to run up to 70 miles per hour, while plants use sunlight to obtain needed sugars (see Figure 1.18).

The three-domain classification scheme described earlier divides life into five differ- ent general kingdoms: Bacteria-Archaea, Protists, Fungi, Plants, and Animals. Figure 1.19 shows the five kingdoms of life. Although there is general consensus about how individual organisms should be classified, it is good to remember that classification schemes are human constructs, able to be reconsidered and changed. Molecular techniques are able to show new relatedness of organisms; the information from molecular data results in changing classifica- tions almost every day. If anything, the new information increases the debate within the sci- entific community, but debate is an important part of the development of scientific findings.

asking hard Questions How did slime molds and muscle cells develop so that they can efficiently fulfill their intended function? Why do living systems sometimes fail, as in the case of Uncle Hans’ dementia? Why do cells die and why do all living things die? These are difficult ques- tions with answers that have been thought about over the millennia. Today, because of the contributions of many earlier scientists and philosophers and an impressive and ever-growing body of evidence, we know that the theory of evolution, the process of changes in species over time, explains how life developed. Theodosius Dobzhansky (1900–1975), the modern evolutionary biologist, explained that “Nothing makes sense in biology except in the light of evolution.” We will begin our exploration of the answers to the questions that opened this section, along with hundreds of others, by tracing a little of the history of thought about how life began and progressed.

the Development of Evolutionary thinking Buffon and the Founding of Descent with Modification

While Aristotle developed a classification system of living creatures, it took over 2,000 years to accept that organisms could change over time. French scientist Georges-Louis de Buffon (1707–1788) was among the first to challenge commonly held views of the time by arguing that species were not the same as they when they first developed ages ago.

Figure 1.18 a. Cheetah running after prey; b. Maple tree in a field. While plants use sunlight to obtain energy, animals such as the cheetah pursue their prey to obtain energy. The cheetah runs after prey and a maple tree in a forest obtains light. Each performs life functions.

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Plants

Living organisms that are able to obtain food by converting sunlight’s energy to chemical energy through the process of photosynthesis.

Animals

Living organisms that feed on organic matter (other living creatures) for survival. Animals are multicellular eukaryotes and motile in nature.

Evolution

The process of changes in a species over a period of time.

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18 Essential Biology

Figure 1.19 Three domain systems. All three domains have a common ancestor. Bacteria and Archaea are more closely related and evolved earlier than Eukarya. Note Whittaker’s Five Kingdom System of Classification. From Biological Perspectives, 3rded by BSCS.

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Figure 1.19 (continued) ©

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He posed the degeneration hypothesis, stating that “There are lesser families conceived by Nature and produced by Time . . . improvement and degeneration are the same thing, for both imply an alteration of the original constitution.” De Buffon, despite an unclear mechanism, was the first to state that changes in species occurred over time, explaining the vast diversity of life.

Fossil Record

The evidence for evolution came from geologists, however. The gradual processes of wind, rain, and water flow lead to the deposition of sand and rocks in layers upon layers over the ages. Within these layers were remnants of life forms, discovered by early geol- ogists. Geologist James Hutton (1726–1797) proposed that the Earth had been devel- oped over a period of time through these geologic processes. This proposal contradicted

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20 Essential Biology

Christian theologists, who calculated the Earth’s maximum age to be 6,000 years based on Biblical records and analysis.

English surveyor, William Smith (1769–1839) noted, in his studies of caves, mines, and canals, that strata or layers of soil contained fossils of former life. The f ossil record – the distribution of fossils in the Earth’s layers – gave ample evidence for the changes organisms underwent over time. He stated that the deeper the rock layer is, the older it is (see Figure 1.20 for a depiction). However, it was not until the pieces of this fossil record were put together that a theory of the evolution of life was developed.

Changes and Catastrophes

Charles Darwin’s grandfather, Erasmus Darwin (1731–1802), questioned whether organisms were similar to their original forms during the Biblical creation period. Charles Darwin had never met his grandfather nor even held him in high regard, but Erasmus’ ideas were similar to those developed much later by Charles. Both saw that animals may change in response to their environments and that offspring inherit those changes.

However, a number of theorists contributed to Darwin’s ideas of evolution. Georges Cuvier (1769–1832), studied the fossil record, noting that 99% of all species that seemed to have lived were now extinct due to a variety of catastrophes. Catastrophism explained that new species formed after each destructive event, leading to a blossoming of new organisms. This idea shook the foundations of creationism because it held that forms of life were different from those found in the Garden of Eden of the Bible.

Inheriting Acquired Traits

Like Cuvier, Jean Baptist Lamarck (1744–1829) noted that older rocks contained the fossils of simpler forms of life than newer rocks. Lamarck was the first to propose that individuals inherit traits from their parents. His hypothesis claimed that there was a nat- ural progression or “evolution” dependent on the inheritance of acquired traits. Organ- isms acquired the traits of their parents through the use and disuse of those structures. For example, if trees became taller, their fruit would be higher, so giraffes adapted to the increased height by stretching their necks to reach their food. Those longer necks were passed down to their offspring (see Figure 1.21). Lamarck’s view of evolution is

Fossil record

The distribution of fossils on the layers of Earth.

Catastrophism

The theory that explained that new species formed after sudden and violent catastrophes.

Figure 1.20 Rock layers of the Earth. As layers of gravel and sand accumulate, fossils of once living organisms become embedded in the layers. These fossil layers can be dated to show the age of the fossils. Radioactive dating shows that older layers are found deeper in the Earth. A. From BSCS Biology: A Human Approach, 2nd Edition by BSCS.

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termed the inheritance of acquired traits through use or disuse of those traits. Lamarck was wrong because organisms cannot inherit characteristics of their parents developed during a parent’s lifetime. For example, if a father loses his arm, his child is not more likely to be born without an arm. While Lamarck is now often disregarded because of his errors, he laid the foundation for Darwin’s evolution because he noted that organisms do adapt based upon the environment of their ancestors.

Darwin’s Voyage: Natural Selection

Charles Darwin (1809–1882), author of the 1859 book On the Origin of Species, was the first to develop a full view of evolutionary theory. Through his voyages as a youth to the Galapagos Islands off the coast of Ecuador, he noted a variety of beak shapes and sizes in 13 different genera of finches. Each beak seemed “adapted” for the type of food on its particular island. One species of finch, for example, used a stick to pull insects out of bark but another pecked more easily through the softer wood. While all of the finches were of the same genus, they had minor differences based on their unique environments. These observations led Darwin to conclude that the environment had an effect on finch beak anatomy, seen in Figure 1.22.

It is safe to say that Darwin’s voyage and the conclusions he made were influenced by the ideas of other, previous scientists, including perhaps his grandfather. His contri- bution is that he developed a synthesis of his own ideas and data with those of his fel- low scientists, to comprise a working theory of how life developed over time. Darwin’s theory of evolution can be summed into five steps:

1) All organisms overpopulate in any given area 2) Organisms then compete for the limited resources available to them due to that

overpopulation 3) Individuals of a population have variations or differences that are inherited from

generation to generation 4) Some organisms have an advantage in their variation over other organisms 5) An intense struggle for survival follows, leading to a “survival of the fittest”

members of the population.

This process causes a change in the characteristics of organisms over time. It naturally selects out those best adapted to a particular situation and removes those individuals that are less well adapted. This process is termed natural selection and leads to the changes

Figure 1.21 Giraffes’ necks are inherited; however, long necks did not develop because giraffes stretched them. Instead, they were a mutation that benefitted giraffes, enabling them to reach food at greater heights.

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variation

Differences that are inherited from generation to generation.

natural selection

The process whereby organisms better adapt to their environment survive and produce more off spring.

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22 Essential Biology

or evolution of species over time. There were changes in dragonflies over their history in the fossil record (Figure 1.23).

Evolution and Economic Systems

The ideas of scientists, like those of everyone, are influenced by their social and histori- cal contexts. Darwin’s description of the process of natural selection appears similar to a process seen in capitalist economies. To illustrate, a Wal-Mart Supercenter opens up on a street corner near a small deli. The deli cannot compete with Wal-Mart’s lower prices, so it goes out of business. Similarly, the process of natural selection was well described in economic terms during Darwin’s time by Adam Smith’s (the 1750s), Thomas Mal- thus’ (the 1790s), and David Ricardo’s (the 1820s) theories of money and capitalism. It is surmised that growing up in a capitalist economic system in England of the 1800s influenced the development of Darwin’s ideas, laying the foundation for his theory of biological natural selection and evolution.

These economists argued that an economic system of free markets and capitalism leads to a survival of the fittest businesses based on competition. They state that some businesses survive that are better able to outcompete others, doomed to fail. Their views claimed that businesses freely compete with each other for limited resources, with some being better suited than others, and thus a “struggle for the survival of the fittest” busi- ness. England in the 1800s was more purely capitalistic than any nation in the Western World today and probably best emulated nature in its natural selection of organisms. Darwin’s ideas developed in a society that functioned in such a way that it influenced his own ideas and theory building.

Figure 1.22 A. Anatomy of finch beaks. Darwin observed 13 different genera of finches on the Galapagos Islands. The shapes and sizes of each finch enable different feeding styles, with some able to eat insects and others leaves or fruit. This image shows a female medium ground finch from the Galapagos Islands. B. The map traces Darwin’s trip to the Galapagos Islands. From Biological Perspectives, 3rded by BSCS. C. Darwin’s origin of species was published in 1872. A portrait of Darwin is seen here.

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Wallace Also Came Up with Evolution but Supports Darwin’s Efforts Alfred Wallace (1823–1913), a British geographer, worked independently

of Darwin in developing his ideas on evolution from his knowledge of animal species in the tropics. In 1858, he became convinced that a process of evolu- tion of organisms led to the diversity of animals he studied in the Amazon and in Southeast Asia. He was poor and a social activist, staunchly critical of the injustices he saw in capitalism of 19th-century England. Wallace actively wrote and spoke on the reality of evolution and published a review in 1867 “Creation by Law,’” which defended Darwin’s thinking on evolution.

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Chapter 1: Welcome to Biology! 23

One might argue that society was “ready” for the theory of evolution. Perhaps another person besides Darwin would have developed this theory in such an economy – to link capitalism to organismal change over time. Society had influenced Darwin, and Darwin has obviously influenced science and society. If he had not grown up within a capitalist economy, his world outlook might not have enabled the development of the theory of evolution.

Darwin’s ideas were met with much opposition, especially from religious leaders, but his work revolutionized scientific thinking. “The theory of evolution,” according to Ernst Mayr, “is quite rightly called the greatest unifying theory on biology.” It explains all of the biodiversity seen in our world and the worlds that came before us; it shows how characteristics develop over time that are suited for one era but not necessarily for another; and it explains how Nature can lead to great life developments but also to mis- takes. Perhaps there is a need for Alzheimer’s disease to decrease the surplus population; perhaps Alzheimer’s genes are an error that is recent because humans in the past did not live as long as they now do; perhaps Uncle Hans is a victim of evolutionary develop- ments that occurred long before his own life. Regardless, evolutionary thinking explains many of our questions, while many remain unanswered.

scientific thinking scientific literacy All of the scientists mentioned in the previous section used scientific thinking to con- tribute to the community of ideas. Each of us is able to apply scientific thinking in our everyday lives to make decisions. Time after time, we encounter biology in statements made by the media or discussed with friends: “Echinacea prevents colds,” “Smoked meats cause cancer,” “Alzheimer’s disease is caused by aluminum pots,” and “Gay is genetic.” All of these assertions require scientific analysis.

How do we practice science? It starts with science literacy, which is the comprehen- sion of scientific concepts, processes, values, and ethics, and their relation to technology and society. In order to be able to really use biology, students should practice the science and its process. Science is not easily defined, but it is comprised of three parts: First, it is a body of knowledge, a set of facts that is extensive but continually changing as

Figure 1.23 Dragonfly size changed over time. The era of large insects ended as birds outcompeted larger insect species. Insects such as the dragonfly adapted with smaller sized forms of dragonflies increasing in dominance as time progressed.

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Science literacy

The comprehension of scientific concepts, processes, values, and ethics, and their relation to technology and society.

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24 Essential Biology

new information becomes available. When Linnaeus classified organisms in his system of taxonomy, he constantly had to rearrange their order to add new species because so many were being discovered at the same time. Today, science facts are still changing rapidly with new technology and ideas.

Second, scientific thinking is based on a method. The scientific method has certain, specified steps, as shown in Figure 1.24. It is important to note that the scientific method is more complex than is shown in Figure 1.24. Many scientific discoveries occur by accident and many investigations require retracing of steps. Third, science is a way of thinking critically, being able to judge a claim and change one’s reasoning about it if deemed necessary. The term “critical” comes from the Greek kriticos, to discern, or use judgment. Critical thinking takes practice and requires us to use all aspects of science from knowledge and method to reasoning about an issue at hand. The questions at the start of this section can be best answered using critical thinking.

Science, on the whole, is a way of thinking about the universe – a way of finding out the truth about phenomena. Inquiry is defined as the critical thinking used behind science. Inquiry follows a logical sequence of steps to arrive at truth but is also haphaz- ard, backtracking in ideas and reformulating strategies. Science based on inquiry can be compared with the game of chess. Thomas Henry Huxley (1825–1895), an English biologist, described inquiry in the following excerpt from 1868:

The chessboard is the world, the pieces are the phenomena of the universe, and the rules of the game are what we call the laws of Nature. The player on the other side is hidden from us. We know that his play is always fair, just and patient. But we also know, to our cost, that he never overlooks a mistake; or makes the smallest allow- ance for ignorance. To the man who plays well, the highest stakes are paid, with that sort of overflowing generosity with which the strong shows delight in strength. And one who plays ill is checkmated – without haste, but without remorse.

Figure 1.24 Scientific method steps.

Observation

Question

1 2 3 4 Possible explanations (hypotheses)

Experiments carried out for each hypothesis

1 and 4 rejected

Experiments

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4 predictions made

4 experiments

All predictions confirmed

Hypothesis 3 confirmed

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Inquiry

Critical thinking used behind science to arrive at the truth.

Scientific method

A procedure that has characterized natural science for centuries.

Critical thinking

The analysis and evaluation of an issue to form a judgment

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Science inquiry’s unique process is well captured in this analogy to a chess game. Sometimes, you win and sometimes you lose, based on whether you play the game well enough to find out the truth behind your questions. Science is complex and multifaceted and requires creativity and practice. The purpose of the next section is to describe the process of scientific thinking and give you the skills to more critically evaluate scientific claims.

induction/Deduction Evaluating a scientific question requires a piecing together of the facts. Science inquiry, like chess, requires both induction and deduction. Induction is a gathering of pieces of data to form a general conclusion, much as the fictional detective Sherlock Holmes investigates a crime scene. Deduction is the process of using a general premise to test and gather data, and eventually draw a conclusion. Both induction and deduction are used in the scientific method.

hypothesis testing Scientists begin with a “hunch,” probably based on observations, about natural pro- cesses. Using inductive reasoning (stringing together the set of observations), scientific thinking may be ready to form a more solid guess about the phenomenon. A surfer may notice that changes in the ocean are happening, perhaps wondering if acid rain can lead to destruction of marine life. She or he might then look into what others know about the topic. A critical review of the existing literature should follow the selection of the prob- lem to be studied. A critical review should be just that – looking at strengths and flaws in other studies, the methods and mathematics determining the conclusions, and new ways to investigate one’s questions.

A surfer should know enough about his or her research problem to form a hypothesis, or possible explanation for the natural phenomenon. Any hypothesis should make sense and be based on a critical review of research. In the example, perhaps acid rain was shown to hurt diatom or algae populations in the ocean. Perhaps the surfer read that diatoms produce almost 80% of the world’s oxygen and realized the importance of diatoms in our ecosystem.

A hypothesis must be empirically testable, meaning that the results must be measur- able and logical and should address a question about a natural phenomenon. It should seek to explain and further science. A hypothesis is an unchecked idea and is really only a starting point in the scientific method. Forming tests of the idea is the true measure of the value of any hypothesis. A hypothesis is only an educated guess and as such is subject to change.

Experimentation Next, a test of the hypothesis is devised. There are many kinds of tests used in a scien- tific investigation, but the most powerful is the experiment. An experiment is a planned intervention, which analyzes the effects of a particular variable. The surfer’s hypoth- esis, for example, requires that the effects of acid rain on diatom oxygen production be measured. A control group, which is the group given normal conditions, should be developed. In this case, diatoms could be placed in a test tube to develop under simulated normal marine conditions.

Next, at least one experimental group of diatoms should grow in a more acidic environment. An experimental group has one changed factor. That factor is termed the independent variable, which is the condition that the experimenter alters. In the diatom

Hypothesis

A possible or proposed explanation based on limited evidence for a natural phenomenon.

Experiment

A planned intervention that analyzes the effects of a particular variable.

Control group

A group in a study or experiment not receiving treatment by researchers and used as a benchmark to measure how other tested subjects do.

Experimental group

A group in a study or experiment that receives the test variable.

Independent variable

A variable that is altered by the experimenter.

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26 Essential Biology

experiment, what did we change? Yes, the acid levels. The dependent variable is the factor that is modified as a result of the independent variable having been changed. In other words, it varies or depends on the independent variable – it is what is measured through the course of an experiment. What was the dependent variable for the diatom experiment? Yes, oxygen production by diatoms. Simply put, the dependent variable always reveals the results of the experiment because it isolates the effects of one partic- ular condition. A well-designed experiment seeks to keep all of the variables the same except for the independent variable. These are termed control variables, which are those factors that remain the same for all of the groups under study. The better controlled an experiment is, the stronger will be the study results. Careful preparation before an exper- iment is conducted may control the conditions.

Data analysis Information collected from an experiment is analyzed to form conclusions. Data analysis is the process of evaluating information obtained by an investigation. This may be either a qualitative or a quantitative process. Qualitative analysis is the reporting and use of data that are non-numerical in scope. It usually studies very few subjects or data pieces but looks at those in great depth. Observing changes in an ecosystem but taking notes on a chipmunk’s behavior or tracing the movement of chemicals within a corn field may be qualitative studies.

Quantitative analysis is defined as the reporting and use of numerical data. This is a traditional scientific analysis and shows patterns from which to draw conclusions. Quantitative studies allow generalization of the results to a larger population. It requires a large number of individuals or units to sample. To illustrate, many trials of diatom testing need to be performed to make a conclusion that acid rain affects diatom oxygen production in marine environments. Small numbers of trials could lead to results that are just flukes. Enough numbers of individuals must be tested in quantitative studies for adequate statistical analyses. Quantitative analysis is what separates science from the many forms of pseudoscience.

Math Gives Biology power: statistics Statistics is the study of the collection, organization, analysis, and interpretation of data. Quantitative analyses use statistics to analyze data. Statistics drives biological research by giving credibility to the claims a study makes from its data. For example, if dia- tom oxygen release is cut due to higher acid levels, “By how much?” and “Is it really significant?” should be questions asked and answered by the scientific community. Without math, scientists have little power to make recommendations or generalizations, as expressed by Galileo, the Italian natural philosopher of the 1600s. He understood that mathematics is the language of science.

“Philosophy is written in this grand book, the universe . . . It is written in the language of mathematics, and its characters are triangles, circles, and other geo- metric figures without which it is humanly impossible to understand a single word of it.”

– Galileo Galilei

Experiments are set up using a null hypothesis, which is the opposite (or absence of relationship) of the experiment’s hypothesis. A null hypothesis, represented as Ho, asserts

Dependent variable

The results of the experiment.

Data analysis (Qualitative and Quantitative)

The process of evaluating information that is obtained by investigation. The reporting and use of non-numerical data is qualitative data analysis while reporting and use of numerical data is quantitative data analysis.

null hypothesis

The hypothesis that asserts that there is no effect or change due to a potential treatment.

Statistics

The study of the collection, organization, analysis and interpretation of data.

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Chapter 1: Welcome to Biology! 27

that there is no effect or change due to a potential treatment. If the hypothesis states that variable #1 affects variable #2, the null hypothesis would state that variable #1 does not affect variable #2. When the null hypothesis is not supported by an experiment, then the real hypothesis can be accepted.

Statistically, the chance of error for supporting or failing to support a hypothesis is also calculated for an experiment’s conclusions. The significance level is defined as a level of error that is likely, given the statistical analysis. It is written in the form of a dec- imal number and gives the percentage chance that the results are in error. For example, a significance level of .05 is equal to a 5% chance that the results are in error.

Many scientific investigations use the correlation, which is defined as a simple rela- tionship between two variables. Variable “a” is somehow related to variable “b” as rep- resented by the letter r, a correlation coefficient. Correlation coefficients range in value between −1.0 and 0 and +1.0, with the negative values representing negative correlations and the positive values representing positive correlations. The two variables increase or decrease in tandem with one another in positive correlations and vary in opposing direc- tions in negative correlations. Note that the closer the correlation to positive or negative 1.0 is, the stronger will be the linear relationship between two variables.

Correlations may show relationships but this does not tell anything about how the two factors are related or even if the relationship is important. In fact, variables other than the two given in a correlation may influence the relationship. Perhaps oxygen pro- duction in diatoms, for example, is not affected by acidity, but that acidity correlates with another chemical in the water. That chemical might be the real cause of the rela- tionship between acid rain and oxygen production.

A more powerful statistical test, known as the ANOVA (Analysis of Variance), was developed, which identifies and isolates the independent variable to avoid such prob- lems described in correlations. The ANOVA compares the mean (average) results of three or more groups in an experimental design. Very briefly, it is a process of isolating variables, showing the effects of the independent variable without effects of experimen- tal error. ANOVA methods are beyond the scope of this text, but determining the effects of the independent variable is the point of any experiment or data analysis.

Results and Discussion Publishing results involves objectively reporting the data and statistics of an experi- ment. A discussion of the results returns the investigation back to the subjective realm. The discussion interprets the data, explaining statistics based on the accepted literature, and makes recommendations for future research. It uses the intuitions of the scientist. It is the part of an investigation that is most creative and sometimes even speculative. However, it must be embedded in valid information – the information derived from the mathematics of the results. Conclusions are drawn from the analysis of the results in the discussion section.

Research findings first undergo a peer-review process, in which fellow scientists evaluate the research to determine if it is worthy of publication. A critical analysis of the results of research enables scientists to determine whether the results should be pub- lished for review and use to the scientific community as a whole. Published research enables other scientists to repeat the experiment and to rerun tests to determine the validity of the claims. Hypotheses are reformulated when results are unexpected or when confronting errors in the design of the study. In this way, research is continually chang- ing and investigations are constantly being reformulated.

Significance level

The percentage chance that the results of a study are wrong.

Correlation

Relationship between two variables.

AnOvA (Analy- sis of variance)

Is a powerful statistical method that compares the means of three or more groups.

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28 Essential Biology

BOx 1.2: AlzHEIMER’S DISEASE AnD SMEll: IS THERE A lInK?

Is Alzheimer’s disease able to be detected early in its development through a simple smell test? A question like this was posed by a variety of media outlets in 2004. Even Dr. Oz claimed that scientists could predict if a person will get Alzheimer’s disease based on a smell test. Below is an excerpt of a report in Senior Journal describing the smell test for Alzheimer’s disease. Use your critical thinking skills to judge the claims made, based on the accepted methods for scientific research described in this chapter.

December 13, 2004 – The inability to identify the smell of lemons, lilac, leather, and seven other odors predicts which patients with minimal to mild cognitive impairment (MMCI) will develop Alzheimer’s disease, according to a study presented today at the American College of Neuropsychopharmacology (ACNP) annual meeting. For patients with MMCI, the odor identification test was found to be a strong predictor of Alzheimer’s disease during follow-up, and compared favorably with reduction in brain volumes on MRI scan and memory test performance as potential predictors.

“Early diagnosis of Alzheimer’s disease is critical for patients and their families to receive the most beneficial treatment and medications,” says lead researcher D.P. Devanand, MD, Professor of Clinical Psychiatry and Neurology at Columbia University and Co-Director of the Memory Disorders Center at the New York State Psychiatric Institute. “While currently there is no cure for the disease, early diagnosis and treatment can help patients and their families to better plan their lives.”

Smell identification test results from Alzheimer’s disease patients, MMCI patients and healthy elderly subjects were analyzed to select an optimal subset of fragrances that distinguished Alzheimer’s and MMCI patients who developed the disease from healthy subjects and MMCI patients who did not develop Alzheimer’s. Results of the 10-smell test, which can be administered in five to eight minutes, were analyzed in Dr. Devanand’s study, which evalu- ated 150 patients with MMCI every six months and 63 healthy elderly subjects annually, with average follow-up duration of five years. Inability to identify 10 specific odors (derived from the broader study) proved to be the best predictors for Alzheimer’s disease: strawberry, smoke, soap, menthol, clove, pineapple, natural gas, lilac, lemon, and leather. from http://seniorjournal.com/ NEWS/Alzheimers/4-12-13LemonSmell.htm

Reflection Questions

1) What was the control in the experiment? What was the dependent vari- able? What was the independent variable?

2) Are there other factors that may contribute to a person’s inability to smell these 10 scents?

3) For question #2, how does senescence affect olfactory (smell) abilities? What other age-related factors may lead to a decreased sense of smell?

4) Does the media report give statistical evidence for the ability of smell tests to predict Alzheimer’s disease? Is it strong or weak? Why?

5) What recommendations for future studies do you recommend to validate or debunk the study shown in Box 1.2?

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http://seniorjournal.com/NEWS/Alzheimers/4-12-13LemonSmell.htm

Chapter 1: Welcome to Biology! 29

summary The chapter began with dementia problems faced by an aging gentleman, Uncle Hans, who faces the challenge of his life due to the natural processes of aging. Through under- standing life’s characteristics and organization, we can better understand Hans’ plight. While evolution and natural selection have made living systems better adapted, diseases such as Alzheimer’s persist. New discoveries of ways to combat illnesses, made by using the techniques of scientific inquiry, hold promise for the future. Development of greater scientific literacy in our populace should help people to better understand the chal- lenges we all face. Our biophilic relationship with other living things should help us to appreciate our link to them. Do dogs as well as humans get Alzheimer’s disease as they age? Did Alzheimer’s exist before modern times, when people did not live long enough to develop age-related problems? These kinds of questions can be answered through studying biology.

ChECk oUt

summary: key points

• Biology affects our lives in many ways, from diseases such as Alzheimer’s to cures and solutions. • All living systems have shared characteristics that set them apart from nonliving systems. • Life’s organization increases in complexity and connects living systems with each other and with their

nonliving environment. • Taxonomic systems classify organisms, many of which have not yet been discovered. • Many scientists contributed to the development of evolutionary thinking. • The process of natural selection and evolution has led to today’s biodiversity and continues to

change species. • Research findings need to be based on properly controlled experiments and mathematical analysis

for their results to be validated.

Adaptation Alzheimer’s disease Animals ANOVA, Analysis of Variance Atoms Archae Bacteria Biodiversity

Biological literacy Biology Binomial nomenclature Biophilia Biosphere Catastrophism Cell Characteristics of life

KEy TERMS

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30 Essential Biology

Class Community Control group Correlation Critical thinking Data analysis, Qualitative and Quantitative Dependent variable Diversity Domain Ecosystem Eukarya Eukaryote Evolution Experiment Experimental group Family Food chain Food web Fossil record Fungi Genus Heterotroph Homeostasis Hypothesis Independent variable Interdisciplinary Inquiry Kingdom Macrobiology Macromolecules

Membrane Metabolism Molecules Natural selection Nucleus Null hypothesis Order Organelles Organism Organs Organ System Phylum Plants Population Producer Prokaryote Protista Reproduction Response to stimuli Science literacy Scientific method Significance level Species Statistics Species Taxonomy Tissues Type I error Type II error Variation

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Chapter 1: Welcome to Biology! 31

Multiple Choice Questions

1. Many people feel a deep bond with their beloved dog. Which term best describes this relationship? a. biology b. biological literacy c. biophilia d. biodiversity

2. The maintaining of a steady carbon dioxide level in the blood is accomplished by: a. adaptation b. diversity c. homeostasis d. complement

3. Which is NOT a characteristic of living systems? a. adaptation b. order c. reproduction d. size

4. Humans and chimpanzees are _____% related genetically. a. 1 b. 10 c. 50 d. 99

5. The statement, “The basic unit of life is the cell” is most likely a statement from this scientist. a. Lamarck b. Darwin c. Hutton d. Hooke

6. Which term includes all of the others? a. Class b. Order c. Hutton d. Hooke

7. The Galapagos tortoise, Geochelone elephantopus, is classified in the: a. class Geochelone b. phylum Geochelone c. genus elephantopus d. species elephantopus

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32 Essential Biology

8. A scientist discovers a multicellular, eukaryotic creature in the arctic, which is able to break down mosses in its root system but is not able to make food from sunlight. In which kingdom should the scientist place this organism? a. Animalia b. Fungi c. Plant d. Archaea

9. Which organism is able to obtain energy directly from dead moss in its surroundings? a. other moss b. fungi c. plants d. all of the above

10. An experiment studies human evolution, showing that sunlight leads to changes in skin color as a result of different levels of sunlight. Which is the dependent variable in the experiment? a. human evolution b. sunlight c. skin color d. both a and b are dependent variables

short answer

1. Describe how Alzheimer’s disease creates an imbalance in society and in the bodies of those afflicted.

2. List three ways a person can best become biologically literate.

3. A rock is not considered life, based upon the cell theory. Choose one postulate of the cell theory to defend why a rock is not life.

4. Name two kingdoms described in the six-kingdom system of taxonomy. Describe two differences between the two kingdoms. How are the two kingdoms the same?

5. Explain the drawbacks of a long, rectangular cell within living systems, in terms of the forces placed upon these systems.

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Chapter 1: Welcome to Biology! 33

6. Describe the development of evolutionary thinking through recent history. Be sure to include contributors: de Buffon, Adam Smith, Darwin, Lamarck, and William Smith.

7. Devise an experiment that tests the effects of changing salt concentrations on regeneration of brain cells in Alzheimer’s patients. Define the independent variable, dependent variable, and controls you put in place for your investigation.

8. Which smells predict whether a person will develop Alzheimer’s disease? Name four smells and explain why correlations such as between smell and Alzheimer’s disease are “weak research results.”

9. If a medical test’s results claim that there is a significance level of .15, explain how this may affect a patient’s interpretation of those results.

10. Compare and contrast the goals of the results and discussion sections of a scientific investigation. Be sure to include one way the sections have goals in common and one way the sections are different.

Biology and society Corner: Discussion Questions 1. Alzheimer’s disease will affect a growing aging population in the United States over

the next 25 years. Predict how this will impact healthcare, the economy, and family life patterns.

2. How does better scientific literacy improve a society’s overall health and wellness? 3. In a democratically elected government, people vote for policy changes through

electing their officials. If some people are not scientifically literate, should they still be allowed to vote? Why or why not? What measures would you consider ethical, if any, to ensure that the voting public is educated?

4. The rate of species loss is occurring at the greatest pace in human history. What are the dangers to increasing species loss? For human society? For natural ecosystems?

5. Write a plan to help those families afflicted with Alzheimer’s disease. What are two ways the government can improve the quality of their lives? Name two ways families can best cope with this illness.

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34 Essential Biology

Figure – Concept map of Chapter 1 big ideas

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Unit 1 that’s Life

Chapter 2 Chemistry Comes alive

Chapter 3 the Cell as a City

Chapter 4 energy Drives Life

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Chemistry Comes alive 2

O– O N

Na Cl

Village in China

NO2 ions travel throughout organisms There are many shapes of chemicals

Chemicals react as they travel through living organisms

Acids rise from the stomach into the esophagus

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38 Unit 1: That’s Life

the Case of the Mysterious Killer: a 用硝酸处理; 硝化 nightmare “It is frightening – a force killing us off almost every day and we can’t stop it,” thought Jin, a villager in Lin Xian, China. People of the village lived in fear for their lives in this sleepy town, about 250 miles south of Beijing, China’s capital city. Jin feared that the deadly force would strike down her little boy, only 8 years old. Everyone awaited the report from the detectives, who came from Beijing to help, and rumors were spreading that the killer was found!

“Why had Lin Xian been targeted? Why was it happening to us?” thought Jin. She remembers her brother getting killed by the force. First, it attacked his throat, and he could not eat. Soon he wasted away, unable to move and in pain every moment. Jin remembered how she hated the force and could not bear to see her brother hurt.

The force was something villagers could not see, but it could sneak up on them at any time. Jin had seen so many succumb to this killer and she knew how it started. When it hurt people, she watched, but she never spoke of it. Maybe by talking about it, she thought, it would find her. “Why was she able to avoid it?”“Did she never meet it in the forest?” “Was she just lucky, or was there some she had been spared, but not her brother?” So many thoughts raced through Jin’s mind as she waited and waited for the detectives to come to town.

Legend had it that over 2000 years ago, a curse had been placed on Lin Xian. There were many explanations as to why townspeople were attacked by the force, but no one really knew. Almost a quarter of all villagers died of the force eventually, and everyone blamed the cursed past of their ancestors. When the detectives finally reached town, Jin watched everything they were doing.

Detectives looked through the fields and forests, asked villagers about their food and how they lived. They had instruments and devices to fight the force, but no one really knew what was going to happen. “Perhaps it was too late and the force was growing too strong,” thought Jin.

It took a long time; however, one day, Jin heard from one of the gossips that the detec- tives had found something. Some of the detectives came into her hut with a verdict. They looked very serious – the look on their faces meant they had information: They told her about the force – “It was 用硝酸处理; 硝化 (in English: nitrates).” They explained that the villagers, including her brother, had actually been dying from a disease – cancer of the esophagus (the muscular tube moving food from the throat to the stomach), probably caused by a chemical called nitrates, found in the food.

CheCK in

From reading this chapter, you will be able to:

• Explain how chemicals can affect living systems. • Describe the structure of matter, beginning with the atom, its forms, and combinations in living

systems. • Explain how substances react with each other, including the types of chemical bonds, types of reac-

tions, and characteristics of water that make it critical to living systems. • Describe the role of organic chemicals in life processes, explaining why carbon is an ideal building

block and enumerating the types of macromolecules.

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Chapter 2: Chemistry Comes Alive 39

Detectives explained to Jin that food being grown by villagers was low in a sub- stance called molybdenum, a soil nutrient for plants needed in only small amounts. Crops in the field pulled up more nitrates from soil to make up for low molybdenum levels. Nitrates in plants were being converted into nitrites and then into nitrosamines in the stomachs of residents; and nitrosamines are linked to various cancers, including esophageal and stomach.

They explained to Jin that low molybdenum levels also reduced vitamin C produced by plants. Low levels of vitamin C in the villagers’ diets encouraged the conversion of nitrates into nitrites in our bodies, further increasing the risk of cancer. The detectives had a plan: (1) Villagers were going to be given vitamin C tablets to decrease their pro- duction of nitrites and (2) Villagers would coat their corn and wheat seeds with molybde- num to drive down plant nitrate levels. Jin, in an emotional reaction, said a short prayer for the victims of the deadly force…

CheCK Up seCtion

Chinese detectives (scientists) in the story above studied the link between cancer and the high levels of nitrates in the food supply of Lin Xian. As a result of the recommendations by scientists, nitrite levels in vegetables have dropped 40% and vitamin C levels have risen 25% over the past two decades. Long-term results on esophageal cancer rates remain to be seen.

Choose a particular chemical that you find interesting that is found in our food supply. Research and explain how that chemical acts to cause benefits and/or harm to our environment and to the organisms living in our environment.

atoms and elements that Make Up Life The Chinese scientists in the story found that nitrates in the crops of local food grow- ers caused the high rate of esophageal cancer in Lin Xian. What are nitrates? How do they form? How do their nitrosamine products cause diseases? We can answer all these questions and more by studying some key principles of chemistry, which is the study of matter. The nature of matter, which is defined as anything that has mass and occupies space, was studied throughout human history. Chemistry studies the composition and properties of matter, and the reactions by which matter is changed from one form to another. In order to understand the composition of both living and nonliving things, we need to begin with the smallest components, and then build a hierarchy. Chemicals drive the life functions described in the previous chapter. They form relationships with each other, build substances within living systems, and guide and direct all of an organism’s activities. We begin with the simplest substance – an element – and its most basic unit – an atom.

This chapter moves from the composition of atoms to the ways in which atoms com- bine to form molecules. It looks at different types of chemical reactions, the bonds they form, and particularly how some chemicals change the environment of living systems as they donate hydrogen atoms. The larger chemicals of life will then be studied in the section called organic chemistry. A look to the foods we eat and their chemical make-up reveals that proteins, sugars, and fats play key roles in our health, alongside other chem- icals such as nitrates depicted in our story.

Matter

Anything that has mass and occupies space.

Chemistry

Study of matter.

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40 Unit 1: That’s Life

elements Matter is composed of pure substances: nitrogen and oxygen, components of nitrates, are examples of pure substances, as are silver, lead, and iron (see Figure 2.1). Pure sub- stances, known as elements, are those that cannot be broken down by ordinary chemical means. There are 92 naturally occurring elements. The Periodic Table of Elements, shown in Figure 2.2, displays all the elements, both those that are naturally occurring and those artificially made in laboratories. Elements are ordered on the table by increas- ing weight, shown with special abbreviations for each element (e.g. O = oxygen; N = nitrogen; Au = Gold; Fe = Iron; and Pb = lead). Note that some chemical symbols derive from Latin, with Au emanating from the Latin word aurum for the precious metal, gold; and Fe arising from the Latin word Ferrum, meaning iron.

atoms and subatomic particles The smallest unit of any element that retains the unique properties of that element is the atom. The term atom comes from a word in Greek that means “indivisible.” The characteristics of an element include: (1) how it acts with other elements and (2) how it appears at certain temperatures. These chemical and physical properties make each atom and element unique.

Element

Substances that cannot be broken down by ordinary chemical means.

Atom

The smallest component of any element that retains the unique properties of that element.

(a) (b)

Figure 2.1 Examples of Elements. Elements are found in all matter, ranging from silver tea sets to iron beams, lead air gun pellets, and ammonia.

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Chapter 2: Chemistry Comes Alive 41

Atoms are made of three subatomic particles: protons, which are positively (+) charged units (charge refers to the amount of electricity a chemical possesses), found in the central region of an atom known as the nucleus; neutrons, or neutral particles (0) with a zero charge that are also found in the nucleus; and negatively (−) charged particles called electrons, which move in orbits around the nucleus. An atom is considered neg- atively charged when it possesses a greater number of electrons than protons; and posi- tively charged when it possesses a greater number of protons than electrons. The chart in Figure 2.3 shows the make-up of a variety of atoms: protons, electron, and neutrons (use the acronym PEN to help you remember the parts of an atom).

Electrons move around a nucleus in energy shells, which are layers of electron orbits circling the nucleus of an atom. The shell nearest the nucleus contains up to two elec- trons, and any additional shells contain a maximum of eight electrons. Electrons in the outermost shell form bonds (or chemical relationships) with other atoms.

The more energy an electron has, the farther from the nucleus its orbital shell. For example, an electron in shell #4 has more energy than electrons in shell #1. It takes energy to move an electron to higher shells because there is a force of attraction between an electron and its nucleus. Negatively charged electrons are attracted to the positively charged nucleus, and this attraction, in part, keeps subatomic particles together. While atoms are indivisible, their electron components can exchange with electrons of another atom, allowing atoms to react with each other. Electrons hold energy, which is exchanged during chemical reactions.

Proton

A subatomic particle found in the nucleus, which is positively charged.

Neutron

Particles with zero charge found in the nucleus.

Electron

A negatively charged subatomic particle found in the orbit.

Figure 2.2 The Periodic Table of Elements. The table shows the atomic mass and number of all of the elements known to humans.

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Li Be

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K Ca Sc Ti V Cr Mn Fe

Rb Sr Y Zr Nb Mo Tc Ru

Cs Ba Hf Ta W Re Os

Fr Ra Rf Ha Sg Ns Hs

B C N O F Ne

Al Si P S Cl Ar

KrBrSeAsGeGaZnCuNiCo

Rh Pd Ag Cd In Sn Sb Te I Xe

RnAtPoBiPbTlHgAuPtIr

YbTmErHoDyTbGdEuSm

Pu Am CmNp

Ce Pr Nd Pm

Th Pa U Bk Cf Es Fm Md No

3 4

11 12

19 20 21 22 23 24 25 26 27 28 29 30 31

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14 15 16 17 18

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58 59 60 61 62

90 91 92 93 94

37 38 39

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87 88 104 105 106 107 108 109

Hydrogen

Magnesium

Molybdenum

Rutherfordium Neilsbohrium

Lithium Beryllium

Sodium

Potassium Calcium Scandium Titanium Vanadium Chromium

Rubidium Strontium Ytirium Zirconium Niobium

Cesium Barium Hafnium Tantalum Tungsten

Francium Radium Hahnium Seaborgium Hassium Meitnerium

Manganese Iron Cobalt

Technetium Ruthenium Rhodium

Rhenium Osmium Iridium

Nickel Copper Zinc Gallium Germanium

Boron Carbon

Aluminum Silicon

Palladium Silver Cadmium Indium Tin

Platinum Gold Mercury Thalium Lead

Helium

Nitrogen Oxygen Fluorine Neon

Phosphorus Sulfer Chlorine Argon

Arsenic Selenium Bromine Krypton

Antimony Tellurium Iodine Xenon

Bismuth Polonium Astaline Radon

LutetiumYiterbiumThuliumErbiumHolmiumDysprasiumTerbium

Berkelium Californium Einsteinium Fermium Mendelevium Nobelium Lawrencium

GadoliniumEuropiumSamariumPromethiumNeodymiumPraseodymiumCerium

Thorium Protactinium Uranium Neptunium Plutonium Americium Curium

Lanthanum

Actinium

Hydrogen

Lanthanides

Actinides

IIA

IIIB IVB VB VIB VIIB VIIIB IB IIB

IIIA IVA VA VIA VIIA

VIIIA

P e

ri o

d Group

Atomic # -

Name -

Symbol -

Atomic - weight

Alkali metals Alkaline earth metals Transition metals Rare earth metals Other metals Non-metals Halogens Noble (inert) gases

Neutron

Particles with zero charge found in the nucleus.

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42 Unit 1: That’s Life

Rutherford’s Gold Foil Experiment

As shown in Figure 2.3, there is a great deal of empty space between the electrons in an orbit and its nucleus. In fact, Ernst Rutherford, in his famous Gold Foil experiment, demonstrated that the atom is more than 90% empty space between orbiting electrons and the nucleus. In 1911, Rutherford published the results of his experiment, in which he shot helium atom particles through a solid but very thin sheet of gold foil (see Fig- ure 2.3). He found that over 90% of helium particles passed through the gold foil. This experiment demonstrated that matter is mostly empty space. Because all living and non- living things are made up of atoms, it is theoretically possible for a person to walk through a door, with his or her atoms aligned with a door’s empty space. Will you try to walk through a closed door and take the chance of passing through?

Atomic Number and Atomic Mass

Elements are numbered on the periodic table according to their atomic number, which corresponds to the number of protons in an atom. For example, nitrogen (N), which is a main component of nitrates, has an atomic number equal to 7, meaning that there are 7 protons in nitrogen. Another example is found in table salt, which contains the ele- ment Na or sodium. Na has an atomic number 11, indicating that it contains 11 protons. The atomic number also gives the number of electrons (when protons and electrons are equal, there is no charge on the atom, overall), because protons and electrons balance out to give an overall neutral charge to an atom. Thus, nitrogen’s atomic number of 7 tells you that it has 7 electrons and 7 protons. Sodium thus has 11 electrons and 11 protons.

Hydrogen

Helium Lithium Beryllium

Boron

Carbon Nitrogen

Oxygen

Fluorine Neon

Neutron

Proton Electron Period 1 and 2 Elements

Gold foil

Alpha particles

Figure 2.3 a. Protons, Electrons, and Neutrons in a variety of atoms. B. Rutherford’s Gold Foil Exper- iment: Rutherford shot alpha particles through a very thin sheet of gold foil. He measured the number of particles that made it through the gold foil, finding that roughly 90% passed through the foil. This indicated that the atom is mostly empty space. In our story, nitrogen and oxygen forming nitrates (our killer) are mostly empty space.

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Gold Foil experiment

Also called Rutherford’s gold foil experiment, is a series of experiments that showed an atom’s structure.

Atomic number

The number of protons in the nucleus of an atom.

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Chapter 2: Chemistry Comes Alive 43

Elements are identified by their atomic number, and no two different elements have the same atomic number. Chemists have also defined the atomic mass of an atom. Mass is a physics term that indicates the amount of matter in a substance. Atomic mass is the total matter within an atom; in other words, the mass of an atom is the combined weights of the subatomic parts that have weight. Protons and neutrons each have an atomic mass of 1 amu (atomic mass unit), but electrons have a negligible mass (1/1836 of an amu) and are not considered when calculating an atomic mass. For example, nitrogen has an atomic mass of 14, meaning that together, protons and neutrons in a nitrogen atom make up 14 amu units. Because nitrogen has 7 protons, based on its atomic number, it must have 7 neutrons to make up the total of 14 units. A rule of thumb is that atomic mass minus atomic number equals the number of neutrons in an atom. Nitrogen has a mass of 14 and a number of 7 (14 − 7 = 7 neutrons). What is the number of protons, electrons, and neutrons in a sodium atom? Use the Periodic Table to figure out its subatomic particle composi- tion. Sodium contains 23 protons and neutrons together comprising its atomic mass, but only 11 protons, from its atomic number. Thus, it contains 12 neutrons (23 − 11 = 12 neu- trons). Note that the number of protons and neutrons in an atom are often not the same.

Ions

Frequently, atoms in living systems occur in the form of ions, which are particles with a charge. A charge, either positive or negative, occurs because of the addition or sub- traction of electrons from an atom. If, for example, sodium loses one electron, as occurs when it is immersed in water in an organism’s cells, it loses a negative charge because an electron is negative. Sodium therefore becomes slightly more positive by one unit and is called the Na+1 ion. The “+1” is written as Na+, for short. What happens when an atom gains an electron? It adds negative charges, one for each electron added. When chloride is immersed in water, it gains one electron and becomes the Cl−1ion. These ions are called “charged” because they have a number associated with their atom. The number equals the amount of charge an ion has. For example, Na+1 has a charge of positive one.

You can compare the formation of ions to a party scene. In a party, when a negative person enters the room, the party feels a little more negative. When the negative person leaves the party, the party becomes a little happier – a little more positive. While ions are not humans, this is the same principle behind how ions form. Ions are very important in life processes because most substances in living systems are immersed in water and form ions. In the form of ions, atoms interact with one another. The sodium and chlorine ions described in the examples are important for proper nerve and muscle functions in humans. Nitrates, which caused so many problems for Jin in our story, are ionic substances. Their extra electrons make them reactive with substances within the body, often causing harm.

Isotopes

Sometimes, atoms of the same element (those containing the same atomic number) have different atomic masses. These atoms are known as isotopes, which have the same num- ber of protons but differing numbers of neutrons. For example, atoms of oxygen all contain sets of protons, as shown in Figure 2.4, but they can contain different numbers of neutrons. Isotopes, due to increased numbers of neutrons, are often less stable than their original atoms. Often, isotopes break down spontaneously, giving off energy known as radiation. Radioactive isotopes decompose spontaneously, losing particles and energy in the process. They can also cause cancer because of the destructive effects of radiation on cells. Isotopes of each other have the same physical characteristics as normal atoms and therefore act the same as one another in living systems.

Atomic mass

The mass of an atom is the combined weights of the subatomic parts that have weight.

Isotope

Are atoms of the same element having different atomic masses.

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While some isotopes can cause disease, others are used in the study of natural phe- nomena. For example, isotopes of oxygen are analyzed in ice cores to obtain historical climate data, giving an idea about the temperature of the Earth long ago. There exist three stable, naturally occurring isotopes of oxygen: oxygen-16, oxygen-17, and oxy- gen-18. The atomic number for oxygen is 8, so there are 8 protons and 8 electrons in oxygen-16. Using our formula for determining the number of neutrons, how many neutrons does oxygen-16 contain? Yes, 8 neutrons are found in oxygen-16. Oxygen-17 contains one extra neutron, bringing its total to 9 neutrons and raising the atomic mass to 17. Oxygen-18 has two extra neutrons, bringing its total to 10 neutrons and its atomic mass to 18. These three isotopes of oxygen occur in the Earth’s atmosphere in the follow- ing proportions: Oxygen-16, 99.759%; Oxygen-17, 0.037%; and Oxygen-18, 0.204%. When combined with hydrogen, they form water (H2O). Water containing the lighter isotope evaporates more readily than those containing the heavier isotopes; and heavier isotopes condense more readily as rainfall. Heavier isotopes of oxygen in water fall more easily as rainfall. Isotope proportions are measured in ice cores to determine the age of ice layers and the historic climate conditions of the Earth.

Other isotope examples include deuterium and tritium, which are less stable forms of the hydrogen atom. They are used in research to trace substances as they move in living systems. Radioactive isotopes are also needed for medical research, with Iodine-131 and Radium-226 used for cancer treatments. Isotopes of carbon are also studied to obtain the ages of once living material such as cloth and paper. Radioactive isotopes deteriorate at a certain rate, called a half-life, with half of the material changed into another substance in that period. For example, radioactive Carbon-14 has a half-life of roughly 5730 years. The proportion of C-14 left in a substance indicates the age of the material.

Figure 2.4 Isotopes of Carbon travel through living systems. Atoms with the same atomic number (the number of protons in the nucleus) but different numbers of neu- trons are isotopes. From Biological Perspectives, 3rd ed by BSCS.

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Chapter 2: Chemistry Comes Alive 45

Exposure to Radiation

Many substances that are radioactive occur naturally. To illustrate, radioactive carbon is found in trace amount throughout the Earth’s atmosphere, and radioactive potassium is found in human bones. These isotopes give off small, harmless amounts of energy. However, some isotopes, such as radium-226 and uranium-238, decay and give off large amounts of dangerous energy. In nature, they occur in such small quantities that their effects are limited; however, in nuclear weapons, they are very destructive.

About 80% of the radiation to which living systems are exposed comes from the environment, primarily emanating from outer space cosmic rays, and is natural and harmless. Sources for the other 20% are cell phones, TVs, old fallout from past nuclear testing still in the soil, nuclear power plant leaks, and medical testing such as X-rays and CT scans. In fact, the radiation in one chest X-ray equals the natural exposure an air- plane passenger receives on one round trip flight from New York to California. In the air, your body is exposed to more galactic cosmic rays at higher altitudes than on the Earth’s surface. Airline workers have higher rates of cancer than the general public, indicating the negative effects of such exposure. While medical technicians are protected by law from excess exposure in their jobs, no such legal protection yet exists for airline workers.

BIoEthICs Box 2.1

The study of radiation and radioactive isotopes began by Marie Curie (1867– 1934), who discovered its existence while studying geology. She died from the radiation found in the substances with which she worked. Several scientists continued Curie’s work. Albert Einstein (1874–1955), a theoretical physicist, while never conducting experiments to split the atom, expressed mathemati- cally that such a process would produce large amounts of energy. In his famous equation, E = mc2, in which E stands for energy released, m for mass of a sub- stances, and c the speed of light (which is large: 3.0 × 108 meters per second), the relationship between matter and energy is shown. When applied by scien- tists, the discovery of nuclear fission and the atomic bomb was possible. Huge amounts of energy are released using very small masses of nuclear material. Is the use of nuclear weapons ever justified? Was it right to use the atomic bomb on Japan? Is Curie’s discovery of radiation and Einstein’s work leading to nuclear weaponry good or bad for society? Name an example of a benefit from their research.

Einstein was disturbed by the use of force to control people. He wrote a famous poem describing the horrors of groupthink and mind control by authorities to express his angst:

By sweat and toil unparalleled At last a grain of the truth to see? Oh fool! To work yourself to death. Our party make truth by decree. Does some brave spirit dare to doubt? A bashed-in skull’s his quick reward. Thus teach we him, as ne’er before, To live with us in sweet accord.

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the elements of Living systems Although living systems are complex, 96% of all living matter is made up of combina- tions of carbon, oxygen, hydrogen, and nitrogen (use the acronym COHN to help you remember this combination). Almost 99.9% of all living things are composed of only 10 different atoms! The chart in Figure 2.5 gives the relative proportions of all the elements found in the human body. Many of the elements found in lesser proportions in living sys- tems, however play vital roles. As described earlier, sodium and chlorine have specific functions. Calcium is also an element found in small quantities that regulates enzyme activity, maintains our body temperature, and coordinates movement. Small disruptions in these minor elements may initiate serious imbalances. Heart failure may result from small changes in sodium, potassium, or calcium levels (see Figure 2.6).

substances Combine to Form Complex systems From atoms to Molecules In the last section, we looked at the atom, the smallest discrete unit of a pure substance. However, both nonliving and living systems are combinations of larger chemicals, so we will look now at how atoms from pure substances combine with those from other pure substances to form new materials. Substances combine with one another through chemical reactions, and when atoms combine, a molecule is formed. Molecules may be the combinations of the same atom or different atoms. Molecules made up of different atoms are known as compounds. We can describe the formation of a molecule in a chem- ical equation. For example, the chemical equation for forming nitrates in our story is:

N + 3O ➔ NO3−

On the left-hand side of a chemical reaction, the substances are termed reactants because they react with one another. N and O are reactants that form the nitrates in the soil in

Figure 2.5 The Most Common Elements in the Human Body: Carbon, Oxygen, Hydrogen, and Nitrogen comprise about 95–96% of all living organisms. From Biological Perspectives, 3rd ed by BSCS.

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Molecules

Atoms bonded together.

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Chapter 2: Chemistry Comes Alive 47

Lin Xian. The substance or substances that appear on the right-hand side of a chemical equation are termed products because they are produced or formed from the reactants. NO3− is the chemical formula for nitrate, and it may have led to disease in our story.

Nitrates (NO3) are also found naturally occurring in the Earth’s crust. They are needed for plant growth and development and are found in fertilizers, foods, and even explosives. Nitrogen and oxygen alone are harmless and in fact comprise over 90% of the atmosphere we breathe. However, when they react with each other to form nitrates, they may be toxic molecules linked to cancer in high doses in our foods. How do atoms that make up a molecule combine to form new substances with unique properties?

Valence electrons: how Matter is Combined? Chemicals combine using their outermost electrons. The chemical behavior of any atom is determined by distribution of electrons around it. Electrons in the outermost shell of an atom are called valence electrons. Valence electrons dictate the chemical activity of an atom. Chemical reactions occur when atoms share or exchange their valence elec- trons, forming bonds. Figure 2.7 gives an example of the exchange of valence electrons between three atoms of oxygen and one atom of nitrogen. The nitrogen atom obtains three electrons by forming bonds with three separate oxygen atoms, forming a molecule of nitrate. The molecule of nitrate in Figure 2.7 shows that nitrogen shares one electron with each of the oxygen atoms to complete their valence shells. Why does this process occur in such a regular and predictable manner?

Figure 2.6 Ions Flowing along a Nerve. Ions conduct nerve transmissions that sustain biological processes ranging from the beating of one’s heart to thinking and breathing. The arrows show the direction in which chemicals travel to produce a nerve transmission. Disruptions in ion flow cause many problems, including heart failure.

Na+

Node of Ranvier

Stimulus Stimulus

Na+

Na+Na+

Na+ Na+

Na+Na+

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Valence electrons

Electrons present in the outermost shell of an atom.

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Factors influencing Chemical reactions Three factors govern chemical reactions:

1) The octet rule: atoms react to obtain eight electrons in their valence shell; 2) Electronegativity: the ability of an atom to attract electrons to itself varies; and 3) Electrons occur in pairs, which are represented as lines or bonds when mole-

cules are drawn.

Let’s apply these three rules of chemical reactions. As shown in Figure 2.7, a nitrogen atom has five electrons in its valence shell. In order to satisfy the octet rule, the atom needs three more electrons to complete its outer shell. Oxygen atoms have six electrons in their valence shells. Each oxygen atom requires two electrons to complete its valence. Thus, nitrogen shares a pair of electrons with three separate oxygen atoms. A free pair of elec- trons also rotates around the nitrogen atom, thus completing a full set of eight electrons around each of the atoms in the molecule. Nitrogen has a greater electronegativity than oxygen atoms, which pulls electrons into nitrogen’s orbit more readily. In fact, nitrates form a special kind of molecule known as a polyatomic ion. Polyatomic ions are molecules that contain a number of atoms that together form a charge, with positive or negative, on their overall structure. Some common polyatomic ions are listed in Figure 2.8.

Another simpler chemical example, HF, hydrogen fluoride, is found in toothpaste. This molecule arrangement enables hydrogen to share its electrons with fluoride to allow

Polyatomic ion

A special kind of ion, composed of more than one atom, forming a charge.

Figure 2.7 Bonds Form to Make Nitrates (NO3). Nitrogen and oxygen satisfy the octet rule when they combine; forming bonds that shift in a variety of structures. All of these structures have the same chemical formula but feature shifting electrons.

N +

–

O O N

O N

O –

resonance structures

–

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Figure 2.8 The Most Common Polyatomic Ions.

Common polyatomic ions

Ion

NH4 +

NO2 –

NO3 –

SO3 2–

SO4 2–

PO4 3–

HPO4 2–

H2PO4 –

OH–

CN–

HSO4 –

ammonium nitrite nitrate sulfite sulfate

phosphate hydrogen phosphate dihydrogen phosphate

hydroxide cyanide

hydrogen sulfate (bisulfate is a widely used common name)

CO3 2–

HCO3 –

CIO–

CIO2 –

CrO4 2–

O2 2–

MnO4 –

Cr2O7 2–

CIO3 –

CIO4 –

C2H3O2 –

carbonate hydrogen carbonate (biscarbonate is a widely used common name) hypochlorite chlorite

chromate peroxide

permanganate dichromate

chlorate perchlorate acetate

Name Ion Name

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Electronegativity

The ability of an atom to attract electrons to itself.

octet rule

A chemical rule that reflects how atoms react to attain eight electrons in their valence shell.

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Chapter 2: Chemistry Comes Alive 49

both atoms to satisfy the octet rule. For example, fluoride, the most electronegative atom on the Periodic Table, pulls electrons so strongly that it unevenly shares an electron with hydrogen. Because fluoride has seven electrons in its valence, the extra electron from hydrogen completes its outer shell. Hydrogen is satisfied with the sharing of one electron because it takes only one pair of electrons to complete its shell. Hydrogen and helium are exceptions to the octet rule, because a single pair of electrons in their outer shell completes their valence. The first shell of any atom holds two electrons while all higher shells hold eight. Fluoride’s strong electronegativity is what makes toothpaste able to kill oral bacteria, which cause dental caries (cavities). Fluoride literally pulls off electrons from key chemical reactions occurring within bacteria, preventing them from multiplying and causing damage to enamel. There is also some evidence that fluoride remineralizes the enamel on teeth, strengthening it and preventing cavities.

On the other side, some atoms are nonreactive, meaning that they have little ability to exchange electrons. These are known as noble gases – helium, neon, argon, krypton, xenon, and radon; they have full valence shells and little importance in living organisms. Radon, the last in our list, has importance as a chemical causing human health hazards. Radon is found in rock and soil particles from radioactive decay of the element, radium. After prolonged exposure to radon, which often seeps into basements, lung cancer may develop.

type of Chemical Bonds Atoms gain, lose, or share electrons with one another to form chemical bonds, which are defined as electron relationships between atoms. Each bond contains energy in its arrangement of electrons between two atoms. Relationships between atoms are based on how electrons are exchanged. The more “pull,” or electronegativity, an atom has for electrons, the more time electrons will spend around that particular atom. Thus, in the example of HF described earlier, which atom should hold the greatest time with the exchanged electrons? Yes, Fluoride, because it is most electronegative.

Let’s explore the four major forms of bonding: covalent, polar covalent, ionic, and hydrogen bonds.

Covalent Bonds

Covalent bonds result from the equal sharing of electrons between atoms. We say that bonds are covalent when the bonding atoms have the same electronegativity, or the same pull, on the shared electrons. In cases such as carbon dioxide, in which there is an even pull on the electrons due to shape, there is also an equal sharing of electrons around the atoms of the molecule. The relationship could be compared to one in which both partners share all of the expenses and there is an even give-and-take between the two. Covalent bonding shares electrons completely evenly around the nuclei of the atoms comprising the molecule.

Polar Covalent Bonds

Unequal sharing of electrons between atoms is known as polar covalent bonding. While electrons move around both atoms, they are not shared equally between atoms in a polar covalent bond. One atom has a greater attraction for electrons, or greater electronega- tivity, than another. This results in a slight positive charge on the atom that has less time spent with its shared electrons and a slight negative charge on the atom that has more time spent with its shared electrons. NO3−, or the nitrate ion, is an example of polar cova- lent bonding. Nitrogen has less of a connection with its electrons and has a relatively positive charge, while oxygen has more of a connection with electrons in its outer shell and therefore has a relatively negative charge.

Chemical bond

Relationship between atoms.

Covalent bond

Bonds that result from the equal sharing of electrons between atoms.

Polar covalent bond

The unequal sharing of electrons between atoms.

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Ionic Bonds

Ionic bonds result from the complete transfer of electrons from one atom to another. A sharing of electrons does not occur in ionic bonding. An example is table salt (NaCl). Sodium gives one electron to chlorine and a bond forms to satisfy the octet rule for both. Atoms that compose a molecule in ionic bonding can have very different properties than the molecules they form. Sodium is a pliable metal and chlorine is a poisonous gas, but together they form table salt.

In an ionic relationship, one atom is a “taker” and one atom is a “giver.” The taker is known as an anion, and the giver is known as a cation. In the case of table salt, sodium is a cation because it gives away one electron, and chlorine is an anion because it receives the electron. Anions become relatively negative in their charge because they have additional electrons, and cations become positive because they lose electrons. (You may recall the difference using the idea that cats (cations) are very positive to have as house pets).

When a molecule loses electrons, we say that the substance is oxidized. In the exam- ple of NaCl, Na loses an electron and is therefore oxidized in the ionic formation of a bond. Reduction is the opposite of oxidation and is defined as any reaction that causes the gaining of electrons. When a molecule gains electrons, we say that it is reduced. In the forming of NaCl, Cl is reduced because it receives an electron from Na. In our story, the dreadful disease was linked to the oxidation of villagers’ cells by nitrosamine free radicals, the most likely force causing cancer in Lin Xian.

Ionic relationships are unstable because one atom is gaining and the other is losing electrons. In relationships that you know about: do you know a cation-type person? Do you know an anion? Are you one or the other type? This kind of bonding often breaks apart. Charges therefore occur on each atom in ionic bonds. This causes an attraction between other substances with opposite charge. For example, sodium ions having a pos- itive charge are likely to attract a water molecule, which has a negative charge.

Hydrogen Bonds

Hydrogen bonds are fleeting bonds that form between atoms of different structures. Hydrogen bonds are defined as attractions between a hydrogen atom and another atom with higher electronegativity; in other words, they are based on attraction between posi- tive and negative charges. Hydrogen in one water molecule may form bonds with atoms in other substances. For example, water forms hydrogen bonds with Na+, when the pos- itive charge of sodium attracts to the relatively negative charge of the oxygen in a water molecule. Atoms within water have polar covalent bonding, with one oxygen atom hold- ing more tightly to electrons than hydrogen atoms. Hydrogen has a more positive charge within a water molecule and oxygen a more negative charge. The relative positive charge of hydrogen atoms attracts them to negatively charged ions. Hydrogen atoms will also find other bonds with negative oxygen atoms within water and therefore link water mol- ecules to each other. When water molecules stick together due to hydrogen bonding, it is known as cohesion or cohesive forces. Cohesion is shown in Figure 2.9.

The Importance of Water

We have already discussed some of the characteristics that make water so import- ant biologically. It enables living processes to occur, all of which require a watery environment. Water allows many life functions to occur: (1) dissolving of ions; (2) hydration of plants; and (3) moderating of weather. Thus, hydrogen bonds formed by water described in the previous section are biologically very important. Let us elaborate on each of these.

Ionic bond

Bonds that result from complete transfer of electrons from one atom to another.

hydrogen bond

Are fleeting bonds that form between hydrogen atoms and atoms of different structures. These bonds are based on attraction between positive and negative charges.

Cohesion (or cohesive forces)

The force that is formed when water molecules stick together due to hydrogen bonding.

Anion

Negatively charged ion.

Cation

Positively charged ion.

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1) Water is a solvent. Living cells are made of 60–80% water and dissolved sub- stances. All movement within cells occurs in a watery environment. Dissolved materials are found within that watery world. When salt or sugar disappears in water, we say it has dissolved. The salt or sugar dissolves as a result of hydrogen bonds forming a wall of water around the dissolved ions. The resulting salty or sugary liquid is known as a mixture. The substance that is dissolved is called a solute and the substance doing the dissolving is termed a solvent. At the molecular level, when salt is added to a cup of water, as shown in Figure 2.9, sodium loses its valence electron to chlorine, and sodium becomes a positively charged ion. Then, a wall of water forms around the sodium ion, with relatively negative oxygen atoms surrounding the positive sodium ion. The ability of some molecules to dis- solve is important for living systems to function, as we will see in later sections.

solvent

Substance that does the dissolving.

Atoms in crystal of salt

(a)

(b) (c)

Salted water

Condensation Precipitation

Transpiration

Evaporation Percolation

Figure 2.9 Water Has Many Features. a. Salt dissolving in water. Water surrounds salt’s ions, making them “disappear” to the human eye. b. Transpiration in plants, an example of cohesion. Bonds form between water molecules, causing them to be “sticky”, which allows them to be pulled up a plant. c. Cohesion (stickiness) between water molecules is caused by hydrogen bonding. These water striders (Gerris) walk on water.

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solute

The component in a solution that is dissolved in the solvent.

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2) Water is cohesive. We saw in the preceding section that hydrogen bonds can link water molecules. In plants, roots absorb water by pulling it from the soil and into their cells. The cohesive forces of water molecules form a “sticky” line from the roots and soil all the way up to the top of the plant. Figure 2.9 shows tran- spiration, the continuous replacement of water molecules that evaporate from the leaves by water molecules continually moving upward from the soil. This characteristic of water molecules allows them to reach great heights in plants, upward of 300 feet in the case of giant sequoia trees. Water transport in plants will be discussed in more detail in Chapter 9.

3) Moderating Temperature. Water stores a great deal of energy because of its many hydrogen bonds. Energy is stored within each of its hydrogen bonds. Because of its stored energy, water has a high specific heat, the amount of energy required to raise the temperature of 1 gram of water 1 degree Celsius. This property, along with its ability to cohere, makes it critical to living systems.

Without water living systems would not have developed and could not sur- vive. Water moderates temperatures at coasts. When the weather is hot, hydro- gen bonds in water absorb the heat and make the surrounding area less warm. When it is cold out, water’s hydrogen bonds release heat, adding warmth to regions near it. Wild changes in the Earth’s temperature do not occur because of the effects of water’s specific heat on moderating temperature. This was a factor allowing life to develop on our planet. In fact, because of water’s unique properties, life could develop within its oceans and lakes.

Usually, as temperatures cool, substances freeze and become denser or heavier. At 4 degrees Celsius (the freezing point of water in degrees Celsius is 0), water is at its heavi- est. However, after this point, as it gets colder, it gets lighter. Ice floats because it forms a crystalline lattice structure that has more space between its molecules at zero degrees Celsius than at any other temperature. Ice serves as an insulator to the water underneath, from the colder air above. In this way, ice floating prevented the freezing of oceans and lakes from the bottom up, as would occur if water were denser at its coldest temperature. Life could thus develop within watery environments at deeper levels and be protected from freezing that was occurring at the top. Water also moderates body temperature due to sweating. The hottest molecules on an organism’s surface evaporate, leaving only the cooler molecules of water. For life to exist as we know it, another planet would need to have water or another chemical with its unique properties to support and sustain life.

acids and Bases The cohesive forces of water make it a biologically important molecule, but that is not the end of the story. Water also moderates the internal environment of living systems. Within a watery environment, ions of hydrogen from water form in different amounts. For exam- ple, when hydrogen is immersed in water; it changes into a positively charged ion, H+. The amount of hydrogen ions in water changes the properties of water. Water has the ability to give up its hydrogen ions or take on more hydrogen ions depending on the conditions around it. In other words, at any time, a water molecule may surrender a hydrogen atom to its surroundings, or it may absorb one. Different parts of our bodies and even different parts of our cells require the right amount of hydrogen atoms to enable life functions.

When water yields more hydrogen into its surroundings, the resulting liquid is termed an acid, and when water absorbs more hydrogen from its surroundings, the resulting liq- uid is called a base. The amount of hydrogen in a solution is measured on a pH (power of hydrogen) scale. The scale ranges from 0 to 14, with pure water set at a pH of 7, shown in Figure 2.10. The pH scale shows the amount of acidity or base in a substance. This is so important because conditions for cells require pH homeostasis to survive.

Acid

The resulting liquid when water yields more hydrogen into its surroundings.

Base

The resulting liquid when water absorbs more hydrogen from its surroundings.

ph scale

A numeric scale that specifies the acidity or alkalinity of an aqueous solution.

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Recall that the term homeostasis is defined as maintaining stable internal condi- tions, from Chapter 1, including the proper pH.

The pH scale is based on the logarithmic amounts of hydrogen ions (H+) dissolved in water, meaning that each pH value represents a ten-fold increase or decrease in the amount of hydrogen ions. Water has the ability to break down into H+ and H− ions. Thus, the lower the number on the pH scale is, the greater will be the acidity and the greater the amount of hydrogen ions found in solution. The higher the number on the pH scale, the more basic (or less acidic) will be the solution and the fewer hydrogen ions. The numbers of OH− ions increase as a substance becomes more basic. Pure water, at a pH of 7, has a concentration of hydrogen ions that is 10−7 or .0000001 out of all the water molecules in solution. Pure water has an equal amount of H+ and OH− ions. A concentration of 0.001

Figure 2.10 The pH Scale. This scale shows the acidic or basic level of some com- mon substances. The pH of a substance is based on the number of hydrogen ions it forms in a solution.

–1

–2

–3

–4

–5

–6

–7

–8

–9

–10

–11

–12

–13

–14

H+ ion concentration

Acidic

Alkaline

Hydrochloric acid

Stomach acid

Lemon juice

Cola, vinegar, beer, wine

Tomatoes, grapes

Coffee, rainwater

Urine Saliva (6.5) Pure water

Tears, blood (7.5)

Sea water, egg whites

Baking soda

Great Salt Lake

Household ammonia

Bicarbonate of soda

Household bleach (12.5)

Oven cleaner (13.5)

Sodium hydroxide

Neutral

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(10−3) would equal a pH of 3. At this pH level, it is considered very acidic, and there are many more hydrogen ions in such water than at a neutral pH.

As shown in Figure 2.11, while water is able to dissociate into both hydrogen (H+) and hydroxide (OH−) ions, certain chemicals added to water influence the number of H+ and OH− ions in the solution. When a base is added to water, hydroxide ions (OH−) increase in proportion and hydrogen ions decrease. An example of a strong base is NaOH (lye), which dissociates into OH− and Na+. NaOH breaks into Na+ and OH− (hydroxide). Hydroxide is able to absorb hydrogen ions and form water, lessening acidity: OH− + H+ yields H2O. Hydroxide ions absorb hydrogen to and from water, lessening the proportion of H+ in solution. Alternatively, HCl (hydrochloric acid) is a strong acid, which breaks apart and donates hydrogen to surroundings, making the solution acidic. Our stomach environment contains a low pH of between 2 and 3. A strongly acidic environment is needed to destroy the many bacteria and other pathogens that enter our bodies from the food we eat. Without such acidity, invaders would easily attack us from the inside out. Ulcers or open wounds in the intestines and esophagus sometimes form due to the extreme acidity leaking out of the stomach into these neighboring areas.

Acidity can become a chronic problem for some people – for example, gastroesoph- ageal reflux disease (GERD) occurs when acid from the stomach travels up into the esophagus and causes damage. People suffering from GERD may take an antacid, in the form of the bicarbonate ion, HCO3−, to lessen the acidity. There are also surgical procedures to reduce the negative effects of acidity in the esophagus. In fact, many cases of untreated GERD lead to a condition called Barrett’s esophagus, which is a change in the cells’ structure in the esophagus due to stomach acid. Approximately 10% of people with Barrett’s esophagus eventually develop esophageal cancer. In our story, nitrates caused this dreaded disease, but many factors may lead to cancer.

The bicarbonate ion in antacids used to treat GERD both gives off and absorbs hydrogen ions to stabilize pH of a solution. Bicarbonate uses special reactions, which occur in both directions, either toward products or reactants, to stabilize pH. Many reac- tions involving acid and base formation act in this way. Chemists use double arrows when showing chemical reactions that move in both directions. These reactions are called reversible reactions. One example of a reversible reaction is found in the blood, which maintains very stringent acid and base levels, called the carbonic acid-bicarbonate buffer system (Figure 2.12). A buffer maintains a certain pH. The blood’s buffer system is an example of homeostasis, maintaining internal balance within a fairly narrow range.

Figure 2.11 Dissociation of Water. Water breaks apart into hydrogen and hydroxide ions. From Biological Perspectives, 3rd ed by BSCS.

electric

2 molecules of water

2 molecules of hydrogen

4OH–4H2O 2H2 +

1 molecule of oxygen

energy

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Figure 2.12 Acid–Base Buffering System in Blood. Carbonic acid acts as a buffer to maintain the pH of blood. At times it releases hydrogen ions and at other times it absorbs hydrogen ions. This buffering action regulates the hydrogen ion levels in blood and therefore pH.

CO2 + H2O

Carbon dioxide

Carbonic acid

Bicarbonate ion

Water

H2CO3 H +

+ CO3 –

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Water, acids, and bases play an important role stabilizing the internal conditions of living systems. Chemical reactions take place within a stable environment but a guided by rules of chemistry that dictate their behavior. In the next section, we will explore how these chemicals come together to form larger molecules of life, the macromolecules. They are built with the same basic atoms described earlier, but use carbon as their backbone build- ing material. Macromolecules are the most active chemicals or “living molecules” in cells.

Why Carbon? Life forms found on the Earth range from microscopic, unicellular organisms to those as large and complex as the blue whale. While water is an important component of all organisms, accounting for over two-thirds of their mass, carbon is the backbone. Complex carbon-based molecules are the molecules of life. A building is made of many materials, but its building blocks are usually uniform and have similar units. Our building block is the carbon atom.

Why carbon? Unlike many other atoms, it is very stable because it is generally neu- tral, sharing electrons equally. Carbon has four valence electrons and therefore forms four bonds with neighboring atoms (see Figure 2.13). This is a lot of bond potential. More bonds mean more connections with other atoms, more complexity in their arrange- ments, greater strength, and more possible structures. Scientists have isolated 13 million organic chemicals compared to only 300,000 inorganic (noncarbon) chemicals. Often, organic molecules form even larger numbers of compounds because they form isomers of one another. Isomers are substances with the same number and types of atoms as each other, but with different arrangements in their structure.

With such a large number of compounds, it might seem an impossible task to under- stand them. Fortunately, while they can undergo many different reactions, only one por- tion of the molecule, known as the functional group, is actually involved in reactions. Each functional group has a unique arrangement of atoms that acts a specific way in chemical reactions. Therefore, all of the compounds forming a particular functional group will react in the same way under a given set of conditions. A list of functional groups from our story is provided in Figure 2.14. Nitrates, seen in our story earlier in the

Functional group

A group of atoms that are involved in reactions.

Figure 2.13 Why Carbon? Carbon forms four bonds with its neighbors to satisfy the octet rule. It is a stable and generally neutral atom, which makes it an ideal building block.

Carbon ATOM

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Figure 2.14 Functional Groups of Organic Molecules Including –NH2, and N–N=O (nitrosamine).

amine

nitrosamine

NN O

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chapter, and their related nitrites and nitrosamines, are important and even destructive functional groups in living systems.

Functional groups are often very reactive, exchanging “free” or extra electrons with other substances. Nitrates are functional groups that react easily with other compounds to form nitrosamines. Some studies indicate that bacteria in human guts cause the dan- gerous nitrosamines to form from nitrates we consume from our foods. Substances con- taining free electrons, such as nitrates, are termed free radicals. Note the extra sets of electrons in the chemicals that scientists believed were plaguing Lin Xian in Figure 2.14.

In order to obtain extra electrons, free radicals oxidize (take away electrons) other substances and cause damage to parts of the body, including DNA in the nucleus and blood vessel walls. Antioxidants, as is obvious by the name, prevent oxidation of foods. Damage to DNA leads to many problems, including genetic defects, heart disease, and cancer. Damage to blood vessel walls can lead to clotting, stroke, heart attack, and other ailments. Antioxidants, which are found in many fruits and vegetables, prevent or slow damage from free radicals, so diet may play a role in disease prevention.

Recall that the scientists in our story recommended vitamin C to combat the effects of nitrosamines in Lin Xian. Foods high in antioxidants include garlic, blueberries, rasp- berries, onions, broccoli, carrots, and leafy greens. All of these high-antioxidant foods are fruits and vegetables. Vitamins A, C, and E (the acronym ACE will help you remem- ber), all have antioxidant properties, are found in these foods to help fight disease.

Macromolecules Organic molecules form an incredible array of substances, from penicillin to petroleum products. In living systems, larger carbon-based substances, called macromolecules, carry out life’s functions. There are four types of macromolecules in living organisms: carbohy- drates, lipids, proteins, and nucleic acids (see Figure 2.17). Each of these macromolecules has specific roles in our life functions. They are able to form large strings of molecules that both support and carry out life’s functions. They are assembled and disassembled for use by cells.

Building Up and Breaking Down Macromolecules How do these large macromolecules become so large and how do they break down once again? Through a process that is common to all of these chemicals: Dehydration synthesis and hydrolysis. Dehydration synthesis occurs when organic molecules link sub- units together. This forms larger and larger molecules. During this process, a molecule of water is lost, allowing open bonds to become unstable and link up between nearby organic molecules. In Figure 2.15, the removal of a water molecule from two separate macromolecules leads to a bond formed between them.

Alternatively, macromolecules break down through the process of hydrolysis. Hydrolysis literally means the splitting of a chemical (lysis), using water (hydro). When water is added to the joined macromolecules (polymer) in Figure 2.15, two bonds form out of the one bond that originally joined them. Water breaks the two apart and hydrox- ide from the water molecule separates the macromolecules.

Take your hands and repeat the slogan, lifting your fingers up when saying: “Dehy- dration synthesis builds up,” and point your fingers down when saying: “Hydrolysis breaks down.” This slogan will help you to remember the difference between the two processes. We now explore each of the macromolecules, keeping in mind that they are all built up and broken down by these same processes.

Carbohydrates

Carbohydrates are the “instant energy” macromolecule. They contain loads of readily available energy in the many covalent bonds linking their subunits. Carbohydrates are

Macromolecules

Molecules forming the building blocks of living things.

Carbohydrate

Organic compounds providing “instant energy” for living tissues.

Lipid

Neutral fats, phospholipids, and steroids found in food and in living systems.

Protein

The most common macromolecule in living systems.

Nucleic acid

The genetic material of a cell.

Dehydration synthesis

A process in which hydroxyl and hydrogen atoms are removed from two organic compounds that merges them into one (covalent) bond.

hydrolysis

The breakdown of a compound due to its reaction with water.

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made up of a consistent ratio of atoms: one carbon to two hydrogen to one oxygen atom. This 1:2:1 ratio forms ring-shaped structures that are the building blocks of carbohy- drates, called monosaccharides, or simple sugars. Common monosaccharides are glu- cose, galactose, and fructose (see Figure 2.16).

When two monosaccharides combine, they form disaccharides. Some examples include sucrose, lactose, and maltose. Sucrose is table sugar, lactose is milk sugar, and maltose is beer sugar. Glucose and fructose join together to form sucrose. Sucrose is shown in Figure 2.16.

The combination of three or more monosaccharides is known as a polysaccharide. Polysaccharides are long chains of simple sugars, with tremendous ability to store energy in the many bonds between the rings. The animal storage form of carbohydrate energy occurs mainly in glycogen, which is abundantly found in the liver and muscles. When energy is needed, the liver breaks off a piece of the polysaccharide for the body to use. In plants, the primary storage form of carbohydrate energy is starch. Starch is found throughout the plant’s structure. Through photosynthesis, energy from sunlight is converted and stored as starch in roots, stems, and leaves. Seeds contain partic- ularly high amounts of starch because they provide energy for the next generation of growing plants. The most abundant polysaccharide in plants is cellulose, which comprises much of the structure in stems and bark. Some polysaccharides are shown in Figure 2.16.

H — N+ — C — C

H H

+Glycine Alanine

R group Carboxyl

group Amino group

Monomer Monomer Polymer Water

R group

O–

H H

H — N+ — C — C

CH3 O

O– H — N+ — C — C

H H

N — C — C

O CH3

O– + H2O

Glycylalanine (a dipeptide)

Peptide bond α-amino

end α-carboxyl

end

Figure 2.15 Dehydration Synthesis and Hydrolysis of Two Generic Monomers.

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Disaccharide

A class of sugars formed when two monosaccharaides combine.

Monosaccharide

Ring-shaped structures that are the building blocks of carbohydrates.

2.1 LACtosE INtoLErANCE

Lactose, or milk sugar, is a way mammals give energy to their young in the form of milk. Between 30 and 50 million people in the U.S. are unable to digest lactose and therefore milk and milk products. Lactose-intolerant people experience bloating, indigestion, cramping, and diarrhea when ingesting lac- tose-containing foods. The evolution of lactose intolerance is evident in that people who come from the regions of the world that did not have domestica- tion of animals (and thus did not use cow’s, goat’s, or the milk of another mam- mal as a food source) tend to have greater rates of lactose intolerance. Perhaps in these societies, the benefits of being able to drink milk were not present, thus not putting pressure on such populations to be able to digest lactose. Humans are, indeed, the only adult organisms that drink milk. However, recent studies report that lactose-intolerance problems may be more than 50% mis- diagnosed. Other causes of the symptoms listed are often the culprit. It may be that lactose intolerance is an easy answer to more complex health issues.

Polysaccharide

The combination of three or more monosaccharides.

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Lipids

Lipids are neutral fats (fats, waxes, and oils), phospholipids, and steroids found in our food and in our bodies. Lipids are stored in fat cells for use as long-term energy storage. They are found in all of our cell membranes – up to 50% of those membranes are made up of a type of lipid. They serve as hormones to help cells communicate, as components of cell parts, and as stabilizers or cushions for organs and tissues.

Much like carbohydrates, lipids contain carbon, hydrogen, and oxygen. However, they have a much higher amount of carbon and hydrogen than carbohydrates. Indeed, lipids are long chains of carbon skeletons with many bonds of hydrogen attached. When considering the large number of bonds, it is clear that energy storage, in the long term, is a main function of lipids. They are often used to cushion organs and are found side-by- side with the other macromolecules, as shown in Figure 2.17.

Oil and water do not mix – a chemical rule that shows how lipids work. Lipids are electrically neutral, meaning that they do not contain a charge. Water, on the other hand, is charged, as it contains polar covalent bonds. Charged substances mix with each, while neutral or uncharged substances mix only with other uncharged substances. Uncharged chemicals are known as hydrophobic, which translates into “water fearing” because of this rule. Water’s charge drives hydrophobic substances away. Instead, substances that are charged dissolve in water and thus mix with water. These substances are known as hydrophilic, which means “water loving.” Water is hydrophilic, which means that it sticks together in a cohesive way.

The hydrophobic nature of lipids drives their behavior within living systems. Lip- ids avoid water and other charged particles because of this aversion. In cells, lipids will arrange themselves away from water environments to form a cell’s shape. Lipids

Figure 2.16 Carbohydrates Have Varied Types. Monosaccharides (glucose), Disaccharides, Polysaccharides (starch or glycogen). Several glucose molecules join together to form cellulose through dehydration synthesis.

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hydrophobic

Compounds that do not dissolve in water (also called, water fearing).

hydrophilic

Compounds that have the tendency to dissolve in or mix with water.

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self-assemble, or arrange themselves, in accordance with the watery world surrounding them. This characteristic is important because lipids compose cell membranes, which self-assemble to surround cells. The cell membrane, for example, has a lipid layer on the inside of its membrane, which arranges itself away from the watery regions.

While lipids have similar behaviors overall, they are classified into three categories: neutral fats (triglycerides), phospholipids, and steroids.

Triglycerides

Neutral fats, or triglycerides, are composed of three large fatty acids joined together by a short-chained glycerol molecule, as shown in Figure 2.18. The fats found beneath our skin, called subcutaneous fat, around our organs, and in our cells are neutral fats. There are many kinds of neutral fats; however, based on their bonding, they may be classified a few ways, as shown in Figure 2.18. Saturated fats are neutral fats that are literally saturated with as many hydrogen atoms as is possible in the carbon skeleton. Saturated fats come primarily from consuming animal products. Saturated fats are linked to heart disease and hardening of the arteries, called atherosclerosis. When a neutral fat con- tains only one double bond, it eliminates two hydrogen atoms from the carbon skeleton, forming a monounsaturated fat. This kind of neutral fat is associated with heart health because they are thought to eliminate fats from the walls of blood vessels and improving blood flow. Neutral fats are shown in Figure 2.18. Polyunsaturated fats are neutral fats that contain more than one double bond, as indicated by the name “-poly.” Double bonds reduce the overall number of hydrogen atoms on the carbon skeleton. These fats are also associated with heart health, but monounsaturated fats are best. Unsaturated fats are associated with plants and plant products.

Figure 2.17 The Four Types of Macromolecules. These molecules join together to form larger substances.

OOO

C C

C C H

C H H

H H

C O

HH N

H H

C3 H7 O2 N1

An amino acid

C6 H12 O6

Glucose a sugar

C C

N C H

C6 H12 O2 A fatty acid

C4 H5 O2 N2 A nitrogenous base

(a) (b)

OH HC

C C CC

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y Phospholipid

A lipid composed of both a charged phosphate group and fatty acid chains.

steroid

A type of fat that stabilizes the structure of cell membranes.

Neutral fat

A fat that is composed of three large fatty acids joined together by a short-chained glycerol molecule.

saturated fat

Neutral fats that are literally saturated with as many hydrogen atoms as is possible in the carbon skeleton.

Atherosclerosis

Condition in which saturated fats are linked to heart disease and hardening of the arteries occurs.

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Phospholipids

Phospholipids are another category of the lipid group. They are composed of both a charged phosphate group and fatty acid chains. Figure 2.18 also shows the structure of phospholipids, which looks like a lollipop: it contains a circular phosphate head, with three negative charges attached to two sticks, or chains of fatty acids. In cell membranes, phospholipids arrange to form the bulk of its structure. The role of phospholipids in cells and in cell transport will be discussed in the next chapter.

Steroids

Cell membranes also contain steroids, a type of fat that stabilizes their structure. As shown in Figure 2.18, these fats are very different in shape from the other types: they contain four flat hydrocarbon rings, which are made naturally by animals. Cholesterol is one example of a steroid. While some forms of cholesterol aid in disease-causing buildups of plaques on the walls of blood vessels (described earlier), it also serves an important role as a component of cell membranes. Steroids are also needed in the body as hormones, such as male and female sex hormones, testosterone, and estrogen. They

Figure 2.18 Types of Lipids: Triglyceride is a neutral fat. Phospholipids in cell membranes, and cholesterol, a type of steroid.

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are also beneficial in use in different therapies to bring down inflammation, such as treatments for asthma and in back pain relief.

Proteins

The most common macromolecule in living systems is protein. Proteins play a diverse role in our bodies, making up everything from hair, nails, and skin to having functions in chem- ical reactions within cells. The basic building block of proteins is the amino acid. Amino acids are composed of a central carbon bonded together with a hydrogen atom, a carboxyl group (–COOH), an amino group (–NH2), and a variable group. Almost all of the amino acids in proteins come from a list of 20, similar in structure to those found in Figure 2.19. The variable group (those groups found atop of amino acids in Figure 2.19) determines the type of the amino acid because all of the other parts are the same. The amino group in an amino acid becomes nitrates in the body, the chemical discussed in our opening story.

The amino group, as a functional group, also serves in several chemical reactions as a way to form bonds between amino acids. When two amino acids combine to form larger proteins, a molecule of water is lost and a peptide bond forms. Peptide bonds form as a result of the H and OH leaving adjacent amino acids (see Figure 2.19). Through hydrolysis, water is added to break the two apart once again.

As a molecule of protein adds amino acids, it grows into a longer string of amino acids called a polypeptide. How proteins are organized is shown in Figure 2.20. The simple string structure is called its primary structure. Much like a power cord attach- ing your computer, this string has a long shape. However, the variable groups along the string of amino acids contain charges and chemical characteristics that allow them to bond with one another along the string. When bonding occurs, it results in two shapes at the secondary level of organization: an alpha helix and a beta-pleated sheet. An alpha helix is like a slinky, coiled together with bonds holding the structure. Take the power cord on your computer and wrap it around your finger. This is what the alpha helix

Amino acid

The building blocks of proteins.

Polypeptide

A long string of amino acids formed as molecules of protein adds amino acids.

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Figure 2.19 Amino Acids Are the Building Blocks of Proteins. This figure shows the basic amino acid structure, three types of amino acids, and several amino acids com- bining to form larger proteins (tripeptide). There are only 20 amino acid types used to make up all proteins in living organisms. From Biological Perspectives, 3rd ed by BSCS.

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looks like. Beta-pleated sheets resemble a blanket and are found as keratin fibers in hair, clotting proteins in blood, and even as spider web silk. When secondary level polypep- tides fold, forming more complex shapes as compared with lower levels, it is known as a tertiary protein. Proteins fold to give a distinct shape and function to them. Tertiary pro- teins combine with one another to form a unique shape called the quaternary structure. An example of a quaternary protein is the hemoglobin molecule which carries oxygen throughout animal systems. Its unique quaternary structure allows oxygen to be carried in large amounts.

Quaternary proteins may occur as either fibrous or globular. Fibrous proteins are structural, meaning that they do not dissolve in water but remain solid support in parts of organisms. Fibrous proteins appear as strands, such as collagen, which maintain cell structure, and keratin, which protects skin and nails in humans. Chemically active proteins that carry out life functions are termed globular proteins. Globular proteins are water soluble, meaning that they dissolve in water. They are “functional” proteins because they have specialized shapes that attach to other chemicals to perform reactions. Consider auxins, which are plant hormones that cause cells to grow, developing the root and vessel systems. Other globular proteins include antibodies to fight infection and clotting factors to prevent bleeding.

Figure 2.20 Proteins and Hierarchy of Structures of Proteins. Proteins are organized from simple strings of amino acids at the primary level to more complex structures at higher levels within the hierarchy.

N HC

O H

C C

CC C

C C

H H

Primary structure

Amino acids

Secondary structure Quaternary structure

Tertiary structure Hydrogen bond

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Fibrous protein

Structural compound that does not dissolve in water but remains solid support in parts of organisms.

Globular protein

A type of protein that is water soluble.

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Enzymes

Another example of a globular protein is an enzyme, which is a specialized protein that speeds up chemical reactions. Enzymes are also called catalysts, which are substances that help chemical reactions to occur. Special shapes on each enzyme, called active sites, allow for binding to other chemicals, called substrates, to either bring substrates together or break them apart. Enzymes can be compared to a match-maker, or a med- dling in-law, who breaks up or sets up their family members. Figure 2.21 shows the action of an enzyme in both cases, bringing forth a chemical reaction. When enzymes bind to substrates, they facilitate a reaction – they make it happen more quickly. Much like a match-maker, enzymes cannot make something happen that otherwise chemically would be impossible. Enzymes lower the activation energy required for the reaction to take place by bringing substrates together. Otherwise, the process might take much lon- ger to occur. However, enzymes cannot force the substrates together. For example, lac- tose in our intestines does not get digested without the presence of the lactase enzyme. Lactase breaks down the lactose milk sugar into glucose, able to be absorbed by cells. Other enzymes include amylase, which breaks down carbohydrates in our mouths, and telomerase, which adds to our DNA to prevent damaged ends. Telomerase is associ- ated with slowing the aging process, discussed later in the text. In each of these cases, enzymes are reusable, unchanged after reacting with substrates, and readily available once they facilitate a reaction.

Enzyme names usually end in –ase, with a prefix that indicates the type of sub- strate the enzyme acts upon. For example, lactose was mentioned as a form of milk protein. When lactase, the enzyme for lactose, acts upon milk, it causes milk to become digested into a form able to be utilized by animals. Enzymes often require specific environmental conditions to work: temperature, pH, and salt concentrations affect enzymatic activity.

Decomposing bacteria require the right pH to perform their role in breaking down living organisms. The optimal pH for decomposing bacterial enzymes is much higher than in peat bogs, allowing preservation of dead organisms in those environments. Bac- teria could not act to break down the dead organisms because bacterial enzymes often do not work in an acidic bog.

Enzyme

Specialized protein that speeds up chemical reactions.

Active site

Special shapes on enzymes that allow for binding to other chemicals.

substrate

A compound on which an enzyme acts.

Activation energy

The minimum amount of energy that the must be possessed by the reacting species to undergo a specific reaction.

Figure 2.21 Action of an Enzyme on Substrates. A. Enzymes lower the activation energy required to get chemicals to react. In the graph, substrates start at a higher energy level and after the reaction have less energy. B. An enzyme joins together substrates to form a new product. Enzymes also break down substrates. Lactase is an enzyme that breaks apart the lactose carbohydrate in milk. From Biological Perspectives, 3rd ed by BSCS.

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Nucleic acids

Nucleic acids are the genetic material of a cell. Genetic material stores information that (1) controls the cell and (2) passes that information on to new generations of cells. The main types of nucleic acids are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). DNA contains the information code that directs cellular activities in living organ- isms. RNA comprises a set of messenger molecules that carry out the orders given by DNA. In some viral types, RNA is the primary hereditary code, but this is rare. DNA and RNA each play a major role in the formation of proteins. Their code gives rise to proteins, which perform many vital functions for cells.

Nucleic acids are long macromolecules, composed of repeating units of nucleotides, as shown in Figure 2.22. Each nucleotide is made up of three parts: a five-carbon sugar, a phosphate group (PO4−3), and a nitrogenous base. There are four nitrogenous bases, adenine, guanine, cytosine, and thymine. The arrangement of these bases in strings of sequences makes up the genetic information code. That code gives unique directives to cells and organisms.

• The details of the genetic code will be discussed in Chapter 5.

ATP, or adenosine triphosphate, is a special nucleotide, holding large amounts of energy available for cell functions. It is composed of one adenine base combined with a ribose sugar forming an adenosine group. Adenosine has three phosphate groups attached to it, forming the ATP molecule, with energy contained within its phosphate bonds. The phosphate’s energy within ATP drives cellular reactions, building up and breaking down the macromolecules, as shown in Figure 2.23.

The phosphate groups are held together by high-energy bonds, denoted by squiggly lines. Phosphate bonds are unstable because of their high energy, causing these bonds to

readily break and make energy available for cellular needs. When water is added to an ATP molecule, for example, hydrolysis occurs, releasing a free inorganic phosphate (Pi) along with energy and ADP, or adenosine diphosphate (ATP with one less phosphate group). ADP is recycled back and forth with ATP, as energy is formed and released in accordance with cell needs. This reaction is shown in the following chemical equation.

ATP + H2O ➔ ADP + Pi + energy

ATP provides immediate and accessible energy for all cell functions. Its role is vitally important in almost every biological process.

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Figure 2.22 Nucleotide Structure. A phosphate, sugar, and base comprise the basic unit of nucleic acids, the nucleotide. From Biological Perspectives, 3rd ed by BSCS.

Nitrogenous base

A nitrogen containing molecule having the same chemical properties as a base.

Adenosine triphosphate (AtP)

A special nucleotide that holds readily available energy for cell functions.

Deoxyribo- nucleic acid (DNA)

A long macromolecule containing the information code that directs cellular activities in living organisms.

ribonucleic acid (rNA)

A nucleic acid present in living cells.

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Figure 2.23 Macromolecules Are Broken Down and Built Up during Metabolic Reactions. ATP (adenosine triphosphate) is used to make and break bonds. The energy from ATP, in high-energy phosphate bonds, drives cellular reactions. Autotrophs make their own food, and heterotrophs eat other life for food exchange mat- ter and energy to perform their life functions. From Biological Perspectives, 3rd ed by BSCS.

ArE NItrAtEs so BAD For us? WhAt – BoLoGNA too!

Just as in the opening story, is there a killer lurking in our own diets? Should we be cautious about eating processed meats, for example, which contain nitrates like the food in Jin’s village? There is a link between processed meats and can- cer. Sodium nitrate has been added to processed meats such as bologna, hot dogs, ham, and bacon for years (Figure 2.24). It acts as a preservative, prevents botulism and provides longer refrigerator life.

Because of nitrates’ link to various digestive cancers, as described in our opening story, in the 1970s, the US government set a limit of 120 part per mil- lion (ppm) for the amount of sodium nitrate allowable in processed meat. As also shown in Lin Xian, scientists also learned that adding 550 ppm of vitamin C or erythorbic acid (a relative of vitamin C) can prevent the formation of nitrosamines (known to cause cancer in lab animals) by bacteria in animal guts. Therefore, more recently, meat-packaging companies have been adding vitamin C to meats to protect from nitrosamine formation.

Sodium nitrate itself is not bad – we get it from vegetables too – like celery, lettuce, beets, radishes, and spinach, which absorb it from the soil. A person eating about 2.5 cups of vegetables might acquire as much sodium nitrate as if eating 10 hot dogs! However, vegetables contain other compounds including vitamin C that prevent nitrosamine formation.

More research is needed to establish the link between processed meats and cancer. The problem is that with processed meats, there are many vari- ables involved. The link is complex because the smoking process, salt, fat, and chemicals in red meat also have a link to cancer. Additional research is necessary to sort out the variables. Further chemical models, just like the one depicted in our story, need to be developed to tease out these variables.

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summary Chemistry impacts our lives in many ways. Our story showed that the most likely mys- tery killer, a simple chemical, unseen and undetected for over 2,000 years, harmed the health of those villagers in Lin Xian. Chemicals make up our surroundings, including each of our cells. Reviewing the organization of matter: atoms join together to organize and form larger substances, including macromolecules, which comprise living systems. Atoms are mostly empty space, and their electron arrangement determines how they react. Exchanges of energy, through several types of reactions, lead to many new prod- ucts. Complex conditions within organisms are maintained to allow chemicals to work together to perform life’s functions. When macromolecules organize into living systems, each performs a vital role in an organism’s survival.

CheCK oUt

summary: Key points

• Chemistry affects our lives in many ways, from diseases such as esophageal cancer to solutions in medicine and in every day needs.

• Chemicals may be classified into types of matter: atoms, elements, ions, isotopes, molecules, and compounds.

• The atom is mostly empty space, with valence electrons orbiting a central nucleus containing pro- tons and neutrons.

• Atomic mass and atomic number on the Periodic Table of Elements allow the calculation of the sub- atomic particles within atoms and ions.

• There are four types of bonds: covalent, polar covalent, ionic, and hydrogen bonds. • Living systems carry out their processes through chemical reactions that keep pH, water balance,

and the right set of conditions. • Organic molecules make up the backbone of living structures. • Organic molecules build up through dehydration synthesis and break down through hydrolysis. • Research findings make many claims about the role of chemicals in human health and disease, all of

which must be supported by the scientific method.

Figure 2.24 Processed Meats Contain Nitrates as a Preservative. These foods are a part of many of our diets but are linked to a variety of digestive cancers.

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acid activation energy active site adenosine triphosphate (ATP) amino acid anion atherosclerosis atom atomic mass atomic number base carbohydrate cation chemical bond chemistry cohesion covalent bond decomposition reaction dehydration synthesis deoxyribonucleic acid (DNA) disaccharide dissolve electron electronegativity element enzyme fibrous protein functional group globular protein Gold Foil experiment hydrogen bond hydrolysis hydrophilic hydrophobic

ionic bond isotope kinetic energy lipid matter macromolecule molecule monosaccharide neutron nitrogenous base nucleic acid neutral fat octet rule organic chemistry phospholipid pH scale polar covalent bond polyatomic ion polypeptide polysaccharide potential energy protein proton reversible reaction ribonucleic acid (RNA) saturated fat solute solution solvent substrate steroid synthesis reaction triglyceride valence electrons

KEy tErMs

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Multiple Choice Questions

1. What role did scientists suspect nitrates of playing in affecting the health of villag- ers in Lin Xian? a. Nitrates caused higher rates of antioxidants. b. Nitrates caused higher rates of heart disease. c. Nitrates caused higher rates of vitamins A and C. d. Nitrates caused higher rates of esophageal cancer.

2. Helium, a gas in the atmosphere, is: a. unreactive and a compound. b. unreactive and an element. c. reactive and a compound. d. reactive and an element.

3. Which BEST describes protons? a. They are positively charged but without mass. b. They are positively charged and have a mass of 1 amu. c. They are negatively charged but without mass. d. They are negatively charged and have a mass of 1 amu.

4. Rutherford’s Gold Foil experiment shows that all matter is: a. mostly empty space. b. mostly dark matter. c. 50% protons and 50% electrons by mass. d. 99% dark energy.

5. Isotopes of carbon contain differing numbers of: a. protons b. neutrons c. electrons d. both a and b are true

6. Which term best describes the forming of covalent bonds? a. polarity b. sharing c. weak d. heavy

7. Using the Periodic Table of Elements, calculate the number of neutrons in an atom of phosphorous (P), found in large amounts within our cell membranes: a. 15 b. 16 c. 31 d. 46

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70 Unit 1: That’s Life

8. Water loses hydrogen ions in milk, giving it a pH of 6.2. You would classify milk as: a. slightly acidic b. slightly basic c. very acidic d. very basic

9. Which reaction forms large starch granules within potatoes? a. dehydration b. dehydration synthesis c. hydrolysis d. hydrolysis synthesis

10. An experiment shows that coconut oil increases levels of bad cholesterol in humans. Which component of coconut oil is most likely the cause of the increase? a. saturated fats b. monounsaturated fats c. polyunsaturated fats d. both b and c are true

short answer

1. Describe how chemicals in a natural ecosystem, such as a lake or pond, could give diseases to humans.

2. List the following terms, from larger to smaller in size, of the following substances: compound, atom, neutron, molecule, electron and matter.

3. What is the number of neutrons found within an ion of potassium (K+)? Show your work.

4. Compare how ionic, covalent, and polar covalent bonds differ from each other. Be sure to include the following terms in your comparison: electronegativity, polarity, and stability.

5. For question #4 above, list and draw an example of compound formed by each of the bonds described. Include in the picture the electron arrangement around the atoms.

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6. The pH of the stomach of humans is roughly 2–3. What processes enable this low pH to form in stomach? Be sure to include an equation with water as the reactant.

7. ATP plays a major role in life’s processes. Describe how the activities of the single-celled` Amoeba are dependent upon ATP.

8. Why is carbon the backbone of life? Describe the characteristics of carbon that make it our unique building block.

9. Explain the differences between fibrous and globular proteins. Which are important in blood clotting? Why?

10. Maltase is a protein that acts within plants, bacteria, and yeast. Explain the role of maltase in these organisms by: a. classifying maltase as a special type of protein. b. describing how maltase changes the activation energy of a reaction? c. identifying its substrate. d. describing its role in changing its substrate.

Biology and society Corner: Discussion Questions 1. Research and then predict how the role of high-fructose corn syrup within our food

supply will affect human health. Explain how this will impact healthcare, the econ- omy, and overall human impacts on the environment.

2. Isotopes are important chemicals found in nature. Trace the history of the discovery of radioactivity. What role do you think radioactivity will play in forming pub- lic policies and in influencing our role in world politics? Use either Iodine-131 or Radium-226 to frame your thesis.

3. In a democratically elected government, people vote for policy changes through elect- ing their officials. Should governments ban foods using certain chemicals? Nitrates?

4. The European Union (EU) has banned over 1,000 chemicals in cosmetics while we ban only 13 of them. What do you think of the EU’s policy as compared with our more limited ban? Are we justified in allowing more chemicals in cosmetics?

5. PCBs (polychlorinated biphenyls) are an industrial waste product contaminating many areas of the world. Research the effects of PCBs on environmental health of animals within North America. Write a plan to help mitigate the effects of PCBs on water systems within North America.

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Figure – Concept Map of Chapter 2 Big Ideas

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Cover
Ch 1

Chapter 1: Welcome to Biology!��

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Unit 1: That's Life...��

Chapter 2: Chemistry Comes Alive��