midterm 103

Science as a way of learning: A guide to

the natural world

Chapter 1

BIOL-103 Dr Joelle Nader-Nasr

What is science?

 A collection of knowledge about the natural world

 Is both knowledge and process.

 Collection of isolated facts about the natural world

 Process of discovery to link those facts into coherent understandings of the natural world

 It is based on facts not opinions

 Has limits:

 It describes how the world is but doesn’t make moral judgments

 Doesn’t make aesthetic judgments

 Doesn’t tell you how to use scientific knowledge

BIOL-103 Dr Joelle Nader-Nasr

The scientific method

 Knowledge in Biology is acquired through application of the scientific method

 Make an observation

 Ask a question to explain/understand wat is happening

Do a background research: collect information related to the topic

 Build a hypothesis = a tentative answer to your question

 Run an experiment to test variables

 Collect/record data and analyze graphs, statistical tests …

 Draw a conclusion

BIOL-103 Dr Joelle Nader-Nasr

 It should include:

 Independent variable: variable that the scientist intentionally changes

 Dependent variable: changes when independent variable changes

 Controlled variables: variables that are kept the same

 2 groups minimum

 Experimental group: where conditions are changed

 Control group: is a comparative condition in which no variables are introduced

In an experiment

BIOL-103 Dr Joelle Nader-Nasr

Characteristics of living things: 1. Are composed of one or more cells

2. Possess an inherited information encoded in DNA

3. Maintain homeostasis = constant internal environment

4. Assimilate and use energy

5. Respond to the environment

6. Every organism give rise to offspring = reproduction

7. The genetic composition of a whole species changes over many generations = evolution

8. Organisms become larger with time = growing

BIOL-103 Dr Joelle Nader-Nasr

The hierarchy of life • Atom = Smallest particle of an element that retains the properties of that element

• Molecule = Combination of several atoms

• Cell = smallest unit of life

• Tissue = group of similar cells serving the same function

• Organ = combination of different tissues

• Organ system = several organs working together for a specific function

• Organism = living thing composed of many cells

• Population = organisms from same species living in the same area, capable of interbreeding

• Community = populations of different species interacting together

• Ecosystem = community + non living surroundings

• Biosphere = Part of Earth inhabited by both living and nonliving components

simple

complex BIOL-103 Dr Joelle Nader-Nasr

Categorizing life 3 characteristics

 Cell type

 Prokaryotic = no nucleus

 Eukaryotic = nucleus

 The number of cells in each organism

 One cell = single-celled/unicellular

 Several cells = multicellular

 Energy acquisition

 Autotroph = Photosynthetic organisms : capture sunlight and store it; produce their own food

 Heterotroph = Through ingesting molecules in the bodies of other organisms

BIOL-103 Dr Joelle Nader-Nasr

Fundamental Building Blocks :

Chemistry, Water and pH

Chapter 2

BIOL-103 Dr Joelle Nader-Nasr

 Ionic bonds

 Loss or Gain of electrons ➔ ions

 Oppositely charged ions are attracted to each other

Ex salt (sodium chloride NaCl)

 Covalent bonds

 Sharing electrons

 Polar molecules vs Nonpolar molecules

Ex between hydrogen and oxygen atoms to form water molecules

 Hydrogen bonds

 Between hydrogen of one molecule and the negative end of another polar

molecule

From Atoms to Molecules

BIOL-103 Dr Joelle Nader-Nasr

Water is a very good solvent

Water interacts with other molecules

 Solution = mixture of 2 or more kinds of molecules, atoms or ions that is homogenous throughout.

 Solute = the molecule that is dissolved ex. salt

 Solvent = the liquid dissolving the solute ex. water

 Hydrophilic vs Hydrophobic

 Hydrophilic = water-soluble = water-loving = polar molecules

Ex. Salt, sugar

 Hydrophobic = water-insoluble = water-fearing = nonpolar molecules

Ex. Oil, soap …

Properties of water

BIOL-103 Dr Joelle Nader-Nasr

 Cohesion

 Hydrogen bonds between water molecules

 Ex. Composition of a water drop

 Adhesion

 Water molecules stick to polar or charged surfaces

 Ex. Water drop attached to the tip of a leaf

 Surface tension

 Cohesion of water molecules along a surface

 Ex. Fishing spiders rely on surface tension to move across the surface of

ponds

Properties of water

BIOL-103 Dr Joelle Nader-Nasr

 Water helps maintaining a stable temperature

 High specific heat = the amount of energy needed to increase water temperature

by 1°C

 High heat of vaporization = the amount of energy needed to change water from

liquid to vapor

 Internal temperature : sweating = cooling power with minimum water loss

 Great heat buffer for the Earth

 Oceans absorb heat during the day and release it during the night

 In the desert, heat radiates off the floor but at night it cools down

Properties of water

 Ice is less dense than water

 Freezing ➔ stable hydrogen bonds ➔ molecules arranged in the

space

 Lakes, ponds … freeze from top to bottom

 Insulating layer delaying the freezing of the rest

 Aquatic animals and plants survive under the ice

BIOL-103 Dr Joelle Nader-Nasr

 Solutions where H+ > OH- are acidic

 Acid = substance that yields/releases H + when it dissolves in water

 Solutions where OH- > H+ are basic

 Base = substance that combines/accepts with H + reducing their

number

Acid, Base or Neutral?

 pH 0-6 = acidic (H+ > OH-)

 pH 7 = neutral (H+ = OH-)

 pH 8-14 = basic (OH- > H+)

BIOL-103 Dr Joelle Nader-Nasr

Life’s Components : Biological

Molecules

Chapter 3

BIOL-103 Dr Joelle Nader-Nasr

Organic molecules

Built on a carbon framework

Monomers Polymer

4 groups  Carbohydrates

 Lipids

 Proteins

 Nucleic acids

Dehydration synthesis (-H2O)

Hydrolysis (+H2O)

BIOL-103 Dr Joelle Nader-Nasr

Carbohydrates

 Short-term energy storage

 Water soluble / hydrophilic / polar

 Monomer = monosaccharide ex. glucose

 Polymer = polysaccharide

 Storage ➔ Glycogen (liver and muscles of animals) / starch (plants)

 Structural ➔ Chitin (insects, fungi) / Cellulose (cell wall of plants)

 Examples of food: rice, pasta, bread, chocolate, milk, dairy products, fruits, vegetables…

 Simple carbs/bad carbs

 Simple sugars

 Easily digested

 Quick source of energy

 Spike your blood sugar = craving more

 Usually not accompanied by vitamins, minerals, fiber…

 Complex carbs/good carbs

 Complex sugars

 Slower digestion

 Long lasting energy

 Provide vitamins, minerals and fibers

 Provides a highly efficient source of fuel

 Less oxygen needed to burn compared to proteins and fats

 Keeps the brain and nervous system functioning

 Low blood glucose ➔ lack of concentration, irritability, disorientation…

 Aids the metabolism of fat

 Preserves protein muscle mass

 Consuming adequate carbs spares the body from using proteins as energy

source

Carbohydrates Importance

BIOL-103 Dr Joelle Nader-Nasr

Lipids  Water insoluble / hydrophobic / nonpolar

 Functions:

 Long-term energy storage = Fats and oils (Glycerol + fatty acids)

 Saturated vs unsaturated fatty acids

 Saturated = no double bonds between carbon atoms; animal source;

solid at room temperature ex. Meat, dairy products …

 Unsaturated = double bonds between carbon atoms; plant source;

liquid at room temperature ex. Avocados, nuts, coconut, olives, fish …

 Waterproof coverings = waxes

 Long hydrocarbon chains ➔ hydrophobic

 Hormones = steroids (4 carbon rings + side chain)

 Cholesterol = precursor of other steroids/component of cell membrane

 Component of cellular membranes = phospholipids

 Hydrophilic head (glycerol + phosphate) + hydrophobic tail (2 fatty acids)

BIOL-103 Dr Joelle Nader-Nasr

Proteins  Monomer of proteins = amino acids

 Chain of amino acids = polypeptide

 Long polypeptide with a 3D shape = protein

 20 different amino acids

 11 nonessential produced in the body from other amino acids

 9 essential obtained through the diet exclusively

➔ variety of arrangements = variety of proteins = different functions

Importance

 Component of every cell in your body Ex. Hair and nails

 Producing enzymes, hormones and other body chemicals

 Important building block of bones, muscles, cartilage, skin and blood

 Provides energy in late stages of prolonged exercise

 When muscle glycogen stores fall, amino acids broken down into glucose

= 15% of the energy needed BIOL-103 Dr Joelle Nader-Nasr

Proteins Structure

• Polymer = polypeptide/protein

• Peptide bonds between amino acids

• Primary structure = polypeptide = sequence of amino acids

• Secondary structure = hydrogen interactions between amino acids ➔ folding of the polypeptide

• Tertiary structure = more chemical interactions ➔ folded

polypeptide chain

• Quaternary structure = several polypeptide link together

• Disruption of bonds ➔ denatured proteins • Stomach acid untangles proteins to help in digestion • Alcohol = disinfectant → denaturation bacteria’s proteins

• Cooking eggs, meat

• Instruments sterilized in autoclaves

BIOL-103 Dr Joelle Nader-Nasr

Nucleic acids

 Monomer = nucleotide

 Phosphate group + sugar + nitrogen-containing base

 Functions

 Energy carrier ex. ATP

 Intracellular messenger ex. Cyclic AMP

 Nucleic acids = combination of nucleotides

 Polymer = nucleic acid = DNA/RNA

 Examples of food: anything that was living at a certain moment

DNA RNA

Sugar Deoxyribose Ribose

bases A-T, C-G A-U, C-G

Number of strands 2 (double helix) 1

BIOL-103 Dr Joelle Nader-Nasr

Life’s Home : The Cell

Chapter 4

BIOL-103 Dr Joelle Nader-Nasr

Prokaryotic cells Eukaryotic cells

DNA location

Size

Organization

of organisms

Organelles

Free in the cytoplasm

(“nucleoid” region)

within a nucleus

much smaller much larger

always single-celled often multicellular

one type of organelle many types of organelles

 Three principles:

 All cells arise from pre-existing cells

 Every living organism is made of one or more cells.

 Smallest organisms = single cells

Multicellular organisms = many cells

 All living organisms

 Obtain energy and nutrients

 Synthesize important molecules

 Eliminate waste

The Cell Theory

BIOL-103 Dr Joelle Nader-Nasr

The Eukaryotic Cell

 Main parts of a cell:

 Nucleus = membrane-like compartment that encloses DNA

 Different types of organelles = highly organized structures, internal to a cell, serving some specialized functions

 Cytosol = protein-rich, jelly-like fluid in which the cell’s organelles are immersed

 Cytoskeleton = internal scaffolding consisting of 3 types of protein fibers

 Plasma membrane = flexible, chemically active outer-lining of the cell

BIOL-103 Dr Joelle Nader-Nasr

Organelles

 Nucleus = control center

 Contains DNA and information needed to produce ribosomes

 Ribosomes = Site of protein synthesis

 Free (proteins used in the cell)/attached to RER

 Rough Endoplasmic Reticulum (RER)

 Synthesis and processing of proteins

 Golgi complex/apparatus

 Processing and distribution of proteins

 Lysosome = Cellular recycler

 Breaking down large molecules

 Expel molecules outside the cell

 Fuse with membrane of worn-out organelles

 Mitochondria = powerhouse = Energy production

 Cellular respiration process

 Smooth Endoplasmic Reticulum

 Synthesis of various lipids

 Detoxification of harmful substances

BIOL-103 Dr Joelle Nader-Nasr

Protein production pathway

 In the nucleus, DNA is transcribed into

messenger RNA (mRNA)

 mRNA leaves the nucleus through nuclear

pores and is translated into proteins by ribosomes

1

2

BIOL-103 Dr Joelle Nader-Nasr

Figure 4.8 : Processing ad Routing : The Golgi complex

Protein production pathway

3

BIOL-103 Dr Joelle Nader-Nasr

What is the cytoskeleton?  = web of protein

strands

BIOL-103 Dr Joelle Nader-Nasr

The Plant Cell Central Vacuole

A large organelle that has many storage functions

 Water

 Nutrients

 Waste products → digestive enzymes

 Hydrogen ions ➔ keep pH cytoplasm near-neutral

Chloroplast

Tiny oblong structures

Abundant in cell leaves

Photosynthesis site :

Sunlight+ water + CO2 → sugar + O2

Cell Wall

Mostly composed of cellulose and lignin

Provides the cell with:

 Structural strength

 Limit water absorption

 Protection against outside influences

➔ Rigid inflexible organisms

BIOL-103 Dr Joelle Nader-Nasr

Cell-to-cell communication

 Plant cells

 Plasmodesmata = continuous cytoplasm/communication

 Animal cells

 Gap junctions = form whenever a message needs to be communicated

BIOL-103 Dr Joelle Nader-Nasr

Life’s Border : The Plasma

Membrane

Chapter 5

BIOL-103 Dr Joelle Nader-Nasr

Plasma Membrane  Phospholipid bilayer

1- give the membrane its fluid nature

2- forms a barrier to all but hydrophobic molecules (ex. steroids, fatty acids…) and some small hydrophilic ones

 Cholesterol molecules (throughout plasma membrane)

1. Patching substance ➔ keep small molecules from getting through

2. Optimum level of fluidity (even when temperature changes)

 Glycocalyx

 Extracellular space

 Simple carbohydrate chains attached to proteins or phospholipids

 Roles:

 Actual binding sites

 Adhesion layer between the cells BIOL-103 Dr Joelle Nader-Nasr

Plasma Membrane  Proteins

 Structural support (attachment proteins)

 Attached to cytoskeleton ➔ animal cell shape

 Recognition proteins

 Binding sites = cell identification Ex. Immune system cells, Blood type

 Communication (receptor proteins)

 External receptors for signaling molecules Ex. insulin hormone

 Transport proteins

 Facilitate movement of molecules or ions through the membrane

BIOL-103 Dr Joelle Nader-Nasr

 Diffusion

 Movement of molecules from a region of their higher concentration to a region of their lower concentration

 Concentration gradient

 = highest – lowest concentrations of a solute in a solvent

 To move against concentration gradient ➔ energy must be expended

 Osmosis

 Movement of water across a semipermeable membrane from a region of lower solute concentration to a region of higher solute concentration

Diffusion, Gradients and Osmosis

BIOL-103 Dr Joelle Nader-Nasr

Figure 5-6 :

Osmosis in cells

BIOL-103 Dr Joelle Nader-Nasr

Moving smaller substances in and out Passive transport

 Any movement of ions/molecules across the membrane without expending energy

 Simple diffusion = diffusion through a cell membrane that does not require a special protein channel

Ex. gases exchange (O2, CO2), steroid hormones

 Facilitated diffusion = the passage of materials is aided both by a concentration gradient and by a transport protein

Ex. glucose

 Active transport

 Any movement of ions/molecules across the membrane with expending energy

BIOL-103 Dr Joelle Nader-Nasr

 Exocytosis = moving out of the cell

 Endocytosis = moving into the cell

 Pinocytosis = the movement of relatively large materials into a cell by means of the creation of transport vesicles that are produced through an invagination of the plasma membrane

Receptor-mediated Endocytosis

Cholesterol, Invaders ex. Polio and Flu viruses

 Phagocytosis = cells use pseudopodia or « false feet » to first surround and then engulf whole cells, fragments of them or other large organic materials

Many one-celled creatures take in food

Human immune system cells ingest whole bacteria

Moving big substances in and out

BIOL-103 Dr Joelle Nader-Nasr

Vital Harvest : Deriving

Energy from Food

Chapter 7

Chapter 8

BIOL-103 Dr Joelle Nader-Nasr

Photosynthesis  = process by which certain groups of organisms capture energy from sunlight and convert

this solar energy into chemical energy that is initially stored in a carbohydrate

Accomplished by plants, algae and bacteria

Used by the plant itself or other organisms

Importance

• Use of CO2 ➔ reduce pollution

• Production of O2 • 99% of organisms are aerobic ➔ need oxygen to live

• Source of food

• Transformation of solar energy to chemical energy

• Becomes available for all organisms on earth BIOL-103 Dr Joelle Nader-Nasr

Components  Sunlight

 Leaf

 Stomata = gas exchange

 Mesophyll cells

 Chloroplasts

Thylakoids

 Chlorophyll and other pigments

 Convert solar energy to chemical energy

Stroma = microscopic openings in leaves that allow movement of air and water

BIOL-103 Dr Joelle Nader-Nasr

Summary of Photosynthesis in the Chloroplast (Figure 8.8)

BIOL-103 Dr Joelle Nader-Nasr

Figure 8.6 : The Light Reactions

The Oxygen we breathe

Light reaction  Chlorophyll absorbs sunlight

 Water donates electrons

 Electrons move physically through the system

Stroma

Thylakoi d

To Calvin cycle

BIOL-103 Dr Joelle Nader-Nasr

Photorespiration  Calvin cycle frequently binds with O2

 No CO2 binding ➔ no carbohydrate production ➔ Photorespiration

 Temperature increases :

 Stomata closed to minimize water loss ➔ CO2 kept out

➔ Plants evolved mechanisms to deal with this problem

 Adaptation of many warm-climate plants

Ex. Sugarcane and corn

 C4 plants contain an enzyme in mesophyll cells

 Bind CO2 but not O2

 CO2 is escorted into bundle-sheath cells

 No photorespiration BUT uses more ATP than normal photosynthesis

C4 photosynthesis

BIOL-103 Dr Joelle Nader-Nasr

CAM Plants

 Crassulacean Acid Metabolism = CAM metabolism

 Modified form of photosynthesis

 Used by hot-weather plants

Ex. Cactus, Pineapple, Orchids

 Stomata open only at night

 CO2 is banked

 Sunrise, photosynthesis is completed

Less water loss BUT

More ATP is used

Should bank enough CO2 at night

BIOL-103 Dr Joelle Nader-Nasr

Cellular Respiration

 = process by which organisms burn food to produce energy

BIOL-103 Dr Joelle Nader-Nasr

 Glycolysis = « splitting of sugar »

 In the cytosol

 Glucose (6C) + 2ATP → 2 pyruvates (3C) + 2NADH + 4ATP

 Gain = 2ATP

 Transition step = transforming pyruvate

 Pyruvic acid + Coenzyme A → Acetyl coenzyme A + NADH + CO2

 Krebs cycle

 In the mitochondria

 Producing electrons (NADH-FADH2)

 Gain = 2ATP

 Electron Transport Chain

 In the inner membrane of mitochondria

 Oxygen + Hydrogen → Water

 Oxygen = final electron acceptor

 NADH + FADH2 + O2 + Phosphate → H2O + 32ATP

Cellular Respiration

BIOL-103 Dr Joelle Nader-Nasr

Fermentation  After glycolysis, no Krebs cycle

 Anaerobic respiration

 Recycling energy transfer molecules ➔ NADH must lose added electrons ➔ NAD+ that can be reused

 2 main types :

 Lactate fermentation : animals

 Alcoholic fermentation : yeast to produce ethanol

BIOL-103 Dr Joelle Nader-Nasr

SUMMARY

CO2 = carbon dioxide O2 = oxygen H2O = water NADP+ = electron carrier molecule

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BIOL-103 Dr Joelle Nader-Nasr