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Lecture prepared by Mindy Miller-Kittrell, University of Tennessee, Knoxville

M I C R O B I O L O G Y WITH DISEASES BY TAXONOMY, THIRD EDITION

Chapter 2

The Chemistry of Microbiology

Learning some basic concepts of chemistry will enable us to understand fully the variety of interactions between microorganisms and their environments, including, humans, animals and plants.

Atoms and atomic structure

Matter – anything that takes up space and has mass

Atoms – the smallest chemical units of matter

Electrons – negatively charged subatomic particles circling a nucleus

Nucleus – structure containing neutrons and protons

Bohr model of atomic structure

Figure 2.1

Atoms and atomic Structure

Atoms and atomic structure (continued)

Neutrons – uncharged particles

Protons – positively charged particles

Element – composed of a single type of atom

Atomic number – equal to the number of protons in the nucleus

Atomic mass (atomic weight) – sum of masses of protons, neutrons, and electrons

Isotopes

Every atom of an element has the same number of protons, but atoms of a given element can differ in the number of neutrons in their nuclei

Atoms that differ in the number of neutrons in their nuclei are isotopes. Examples are the three naturally occurring isotopes of Carbon

Carbon-12 (12C) has 6 protons and 6 neutrons

Carbon-13 (13C) has 6 protons and 7 neutrons

Carbon-14 (14C) has 6 protons and 8 neutrons

Stable isotopes (equal ratio of protons and neutrons)

Unstable isotopes (un-equal ratio of protons and neutrons). Unstable isotopes release energy during radioactive decay

Isotopes that undergo radioactive decay are radioactive isotopes

Radioactive isotopes play important roles in microbiological research, medical diagnosis, treatment of disease and sterilization of medical equipment and medical supplies/materials

Isotopes of carbon

Figure 2.2

Atom and atomic structure

Electron configurations

Only the electrons of atoms interact, so they determine atom’s chemical behavior

Electrons occupy electron shells or form clouds in an atom

Each electron shell can hold only a certain, maximum number of electrons (e.g., the first shell can accommodate a maximum of 2 electrons and the second no more than 8 electrons (more on this, please refer to periodic table, Fig. 2.4 page 29 in text)

Valence electrons – electrons in the outermost shell that interact with other atoms

Electron configurations

Figure 2.3

Bohr diagrams of the first 20 elements

Figure 2.4

Chemical Bonds

Chemical bonds

Chemical bonds – atoms combine by sharing or transferring valence electrons

Outer electron shells (valence shells) are stable when they contain eight electrons (except for the first electron shell, which is stable with only two electrons)

When an atom’s outer shells are not filled with 8 electrons, they either have room for more electrons to gain or have extra electrons to lose or are stable when outer electron shells contain eight electrons

Atoms’ outer most electrons are valence electrons and outer most shell of an atom is valence shell

An atom’s valence is its combining capacity and is positive if its valence shell has “extra” electrons to give up, and negative if its valence shell has spaces to fill in (e.g., Calcium with 2 electrons in its valence shell has a valence of +2, whereas Oxygen atom with 2 spaces to fill in its valence shell, has a valence of -2)

Molecule – two or more atoms held together by chemical bonds

Compound – a molecule composed of more than one element

Chemical Bonds

Chemical bonds (continued)

There are three principal types of chemical bonds (plus hydrogen bonds–weak forces that combine with polar covalent bonds)

Covalent bond – sharing of a pair of electrons by two atoms (when more than a pair of electrons are involved, double or triple covalent bonds are formed)

Electro-negativity – attraction of an atom for electrons. The more electronegative an atom, the greater the pull its nucleus exerts on electrons

Elements with more protons in their atoms exert a greater pull on electrons

Elements with increased distance between the nucleus and the valence shell have decreased electro-negativity

Chemical Bonds

Nonpolar covalent bonds

Atoms with similar electro-negativities share electrons equally

Shared electrons spend equal amount of time around each nucleus

No poles exist and the bond between is a non-polar covalent bond

Example: carbon atoms form four non-polar covalent bonds with one another and with many other types of atoms forming very large chains of many organic compounds

Organic compounds: compounds that contain carbon and hydrogen atoms (e. g. proteins and carbohydrates)

Molecules formed by covalent bonds: Hydrogen and oxygen

Figure 2.5a-b

Molecules formed by covalent bonds: Methane and formaldehyde

Figure 2.5c-d

Electronegativity values of selected elements

Figure 2.6

Chemical Bonds

Polar covalent bonds

Unequal sharing of electrons due to significantly different electronegativities (e. g. molecule of water)

Oxygen being more electronegative than hydrogen, electrons spend more time near the oxygen nucleus (partial negative charge, δ-) than the hydrogen nuclei (partial positive charge, δ+)

Thus, the bonds between oxygen atom and two hydrogen atoms are called polar, because they have opposite electrical charges

Most important polar covalent bonds for life processes are those that involve hydrogen because they allow hydrogen bonding to occur

Example of polar covalent bonds: Water molecule with 2 polar covalent bonds

Polar covalent bonding in a water molecule

Figure 2.7

Chemical Bonds

Ionic bonds

Occur when two atoms with vastly different electronegativities come together (e.g., sodium and chlorine ions)

Atom or group of atoms that have either a full negative charge or a full positive charge is called an ion

Positively charged ions are called cation, whereas negatively charged ions are called anion

Cations and anions attract each other and form ionic bonds (no electrons shared, but opposite electrical charges attract each other)

Typically form crystalline ionic compounds known as salts (e.g., sodium chloride and potassium chloride)

When cations and anions dissociate (ionize) from one another and surrounded by water molecules (or are hydrated), they are called electrolytes because they can conduct electricity through the solution

Electrolytes are important in biological/chemical processes - stabilize a variety of compounds, act like electron carriers and allow electron gradients to exist within cells

Interaction of sodium and chlorine to form an ionic bond

Figure 2.8

Dissociation of NaCl in water

Figure 2.9

Chemical Bonds

Hydrogen bonds

Hydrogen bond - Weak forces that combine with polar covalent bonds

Electrical attraction between partially charged hydrogen atom (H+) and a full or partially negative charge on either a different region of the same molecule or another molecule

Hydrogen bonds can be likened to week ionic bonds but are weaker than covalent and ionic bonds but essential for biological processes (for life)

The cumulative effect of weak hydrogen bonds is to stabilize 3-D shapes of large molecules (e.g., DNA)

Because hydrogen bonds are weak, they can be overcome when necessary (e.g., separation of DNA complementary halves during DNA replication)

Hydrogen bonds

Figure 2.10

Chemical Bonds

Table 2.2

Chemical Reactions

Chemical reactions

The making or breaking of chemical bonds

Involve reactants and products (e.g., atoms, ions, molecules)

Reactants and products may have different physical and chemical properties (e.g., hydrogen and oxygen gases react and form water)

The number and types of atoms never changes in a chemical reaction (atoms are neither destroyed nor created, only rearranged)

Biochemistry (biochemical reactions) involves chemical reactions of living things

Three categories of chemical reactions: synthesis, decomposition, and exchange reactions

Chemical Reactions

Synthesis reactions

Involve the formation of larger, more complex molecules. Example: synthesis of glucose by green plants and algae:

6H2O + 6CO2 ↔ C6H12O6 (Glucose) + 6O2

Require energy to break bonds in reactants and to form new bonds to make products (endothermic reactions)

Most common type of synthesis reaction is dehydration synthesis- an important synthesis reaction in which 2 smaller molecules are joined together by a covalent bond to form water molecule (H+ ion from one reactant combines with OH- ion from another reactant to form H2O)

All synthesis reactions in an organism are called anabolism

Dehydration synthesis

Figure 2.11a

Chemical Reactions

Decomposition reactions

Break bonds within larger molecules to form smaller atoms, ions and molecules. Example: aerobic decomposition of glucose to form CO2 and H2O:

C6H12O6 (Glucose) + 6O2 → 6H2O + 6CO2

Decomposition reactions release energy (exothermic reaction)

Hydrolysis: a common type of decomposition reaction in which ionic components of water (H+ and -OH) are added to products

All the decomposition reactions in an organism are called catabolism

Synthesis and decomposition reactions are often reversible in living things

Hydrolysis

Figure 2.11b

Chemical Reactions

Exchange reactions

Have similar features to both synthesis and decomposition reactions

Involve breaking and forming covalent bonds, and involve endothermic and exothermic steps

Involve atoms moving from one molecule to another

A + BC → AB + C or

AB + CD → AD + BC

An important exchange reaction within organisms is the phosphorylation of glucose:

Glucose + Adenosine triphosphate (ATP) → Glucose phosphate + adenosine diphosphate (ADP)

Sum of all chemical reactions in an organisms is called metabolism

Water, Acids, Bases, and Salts

Characteristics of water

Living things depend on organic compounds (those that contain carbon and hydrogen) to survive and reproduce

Also require a variety of inorganic chemicals (lack carbon but contain substances including water, oxygen molecules, metal ions, and many acids, bases and salts) to survive and reproduce.

Water is the:

Most abundant substance in organisms (50-90% of their body mass)

Most of its special characteristics are due to two polar covalent bonds

Cohesive nature of water molecules (tend to stick to one another by hydrogen bonding) – Biologically, creates surface tension, a thin layer on the surface of cells through which dissolved materials are transported into and out of the cell

Characteristics of Water

Characteristics of water (continued)

Excellent solvent - it dissolves salts and other electrically charged molecules because it is attracted to both positive and negative charges

Remains liquid across wide range of temperatures

Can absorb significant amounts of energy without changing temperature; when heated evaporates and molecules take away absorbed energy with them

Participates in many chemical reactions within cells, both as reactants in hydrolysis and as products of hydration synthesis

The cohesiveness of water

Figure 2.12

Water, Acids, Bases, and Salts

Acids and bases

Dissociated by water into component of cations and anions

Acid – dissociates into one or more H+ and one or more anions

Acids can be inorganic molecules (e. g. sulfuric acid, hydrochloric acid) or organic molecules (e. g. amino acids and nucleic acids)

Base – a molecule that binds with H+ when dissolved into water

Some bases (e.g., sodium hydroxide) dissociate into cations and OH- anions which then combine with H+ to form water molecules

Water, Acids, Bases, and Salts

Acids and bases (continued)

Metabolism requires relatively constant balance of acids and bases

When acidity changes (deviation concentration of either hydrogen ions or hydroxyl ions) too far from normal, metabolism stops

Concentration of H+ in solution is expressed using the logarithmic pH (potential hydrogen) scale

Most organisms contain natural buffers such as proteins that prevent drastic changes in internal pH

Microbiological culture media contain pH buffers (e.g. KH2PO4) that prevent a shift in pH as a result of metabolic activity of growing microorganisms

KH2PO4 exists either as a weak acid or a weak base, depending on the pH of its environment

Under acidic conditions, it is a base and combines with H+ neutralizing the acidic environment

In alkaline conditions, KH2PO4 acts as an acid, releasing hydrogen ions

Dissociation of acids and bases

Figure 2.13

The pH scale

Figure 2.14

Water, Acids, Bases, and Salts

Salts

Compounds that dissociate in water into cations and anions other than H+ and OH-

Acids (H+) and hydroxyl (OH-) yielding bases neutralize each other during exchange reactions and form salt and water

Cations and anions of salts are electrolytes

A cell uses electrolytes to:

Create electrical differences between its inside and outside

Transfer electrons from one location to another

Form important components of many enzymes

Organic Macromolecules

Organic macromolecules

Contain carbon and hydrogen atoms

Are larger and much more complex than inorganic molecules, forming branched chains, un-branched chains, and rings - the basic frameworks of organic molecules

Most common elements in organic compounds are: Carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur

Atoms often appear in certain common arrangements called functional groups

Amino functional group (- NH2) - is found in all amino acids and

Hydroxyl functional group (-OH) - is common to all alcohols

Organic Macromolecules

Organic macromolecules (continued)

Macromolecules – large molecules used by all organisms

Lipids

Carbohydrates

Proteins

Nucleic acids

Monomers – basic building blocks of macromolecules

Polymers: monomers of macromolecules joined together in chains

Organic Macromolecules

Lipids

Not composed of monomers, but are all hydrophobic (insoluble in water)

Four groups: Fats, Phospholipids, Waxes and Steroids

Composed of almost entirely of carbon and hydrogen atoms linked by non-polar covalent bonds

Non-polar bonds have no attraction to the polar bonds of water molecules, i.e., polar water molecules are attracted to each other and exclude the non-polar lipid molecules

Organic Macromolecules

Fats

Made in organisms by dehydration synthesis reaction that form esters between three chain-like fatty acids and alcohol called glycerol

Also called triglycerides-contain three fatty acid molecules linked to a molecule of glycerol

Saturated fatty acids: when every carbon atoms are linked solely by single bonds, with the exception of the terminal ones, covalently linked to two hydrogen atoms (e.g. stearic acid and palmitic acid)

Unsaturated fatty acids: contain at least one double bond between adjacent carbon atoms, and one carbon atom bound to only a single hydrogen atom (e.g., oleic acid)

Polyunsaturated fatty acids: presence of several double bonds between adjacent carbons atoms in a fat molecule (linoleic acid)

Saturated fats (those found in animals) are usually solid at room temperature because their fatty acids can pack close together

Unsaturated fatty acids are bent at every double bond, cannot pack tightly and remain liquid at room temperature (e.g., unsaturated or polyunsaturated fats of most plants)

The primary role of fats in organisms is to store energy in their carbon-carbon covalent bonds

Fats (triglycerides)

Figure 2.15

Organic Macromolecules

Phospholipids

Similar to fats, but contain two fatty acid chains and the third carbon atom of glycerol is linked to a phosphate (PO4) functional group instead of to a fatty acid

The phospholipid “head” is polar and thus is hydrophilic (attracted to water and soluble in water) and the “tail”portion of the molecule is non-polar and is thus hydrophobic (insoluble in water)

Phospholipid bilayers make up the outer membranes of all cells, as well as the internal membranes of plant, fungal and animal cells.

Phospholipids

Figure 2.16

Organic Macromolecules

Steroids

Consist of four rings (containing five or six carbon atoms) that are linked to one another and attached to various side chains and functional groups

Steroids play many roles in human metabolism acting as hormones

Cholesterol is an essential part of the phospholipids bilayer membrane surrounding all animal cells

Sterols, steroids with – OH functional group make membranes fluid and flexible at low temperatures and without them, membranes of cells would become stiff and inflexible in the cold

Steroids

Figure 2.17

Organic Macromolecules

Waxes

Contain one long-chain fatty acid covalently linked to long-chain alcohol by ester bond

Completely insoluble in water

Lack hydrophilic head

Organic Macromolecules

Carbohydrates

Organic molecules composed of atoms of carbon, hydrogen, and oxygen

Most carbohydrates contain an equal number of oxygen and carbon atoms and twice as many as hydrogen atoms as carbon atoms

(CH2O)n, where n indicates the number of CH2O units

Carbohydrates play many important roles in organisms:

Large carbohydrate molecule - long-term storage of chemical energy (e. g. starch and glycogen)

Small carbohydrate molecule - ready energy source (e.g. glucose)

Part of backbones of nucleic acids (RNA and DNA)

Routinely converted into amino acids

Polymers of carbohydrates form cell wall of fungi, algae, plants and prokaryotes

Are involved in intracellular interactions between animal cells (cell surface receptors)

Organic Macromolecules

Types of carbohydrates

Monosaccharides

The simplest carbohydrates (sugars) are monosaccharides

Names are formed from a prefix indicating the number of carbon atoms and the suffix – ose: Example, pentoses and hexoses are sugars with 5 and 6 carbon atoms respectively

Deoxyribose (sugar component of DNA) is a pentose; fructose and glucose are hexoses

Monosaccharides may exist as linear molecules but due to energy dynamics they usually take cyclic forms (e.g., alpha and beta configurations of glucose)

Monosaccharides

Figure 2.18

Organic Macromolecules

Disaccharides

Two monosaccharide molecules link together to form a disaccharide molecule by dehydration synthesis reaction

The linkage of two hexoses, e.g., glucose and fructose forms sucrose (table sugar)

Other examples of disaccharides are maltose (malt sugar) and lactose (milk sugar)

Broken into their monosaccharide components via hydrolysis reaction

Disaccharides

Figure 2.19

Organic Macromolecules

Polysaccharides

Polymers of thousands of monosaccharides covalently linked together in dehydration synthesis reaction

Diverse in monomer configuration (alpha or beta) and shapes (branched or unbranched)

Examples of polysaccharides are: cellulose (constituent of cell wall of plants and algae), amylose (storage starch compound in plants), amylopectin (plant starch) and glycogen (storage molecule in animal liver and muscle cells)

Bacterial cell walls are composed of peptidoglycan (polysaccharide plus amino acids). Lipopolysaccharides (cell wall components of Gram negative bacteria) are formed from polysaccharides and lipids

Polysaccharides

Figure 2.20

Organic Macromolecules

Proteins

Most complex organic compounds, composed mostly of carbon, hydrogen, oxygen, nitrogen, and sulfur

Proteins perform many functions in cells including:

Structure: structural components in cell walls, in membranes and within cells and structural material in hair, nail, skin and muscle

Transportation: certain proteins act as channels and “pumps” that move substances into or out of cells

Enzymatic catalysis - catalysts (typically proteins) that enhance speed of chemical reactions in cells are called enzymes

Regulation - some proteins regulate cell function by stimulating or hindering either the action of other proteins or the expression of genes (e.g., hormones are regulatory proteins)

Defense and offense - Antibodies and complements (proteins) defend our body against microorganisms

Organic Macromolecules

Amino acids

The monomers that make up proteins (protein polymers)

Contain a basic amino group (-NH2), an acidic carboxyl group (-COOH) and a hydrogen atom, all attached to the same carbon atom

Hundreds of amino acids, but most organisms use only 21 amino acids to in the synthesis of proteins

Side groups affect how amino acids interact with one another and how protein interacts with other molecules

A covalent bond (Peptide bond) is formed between two amino acids by dehydration synthesis reaction

A molecule composed of two amino acids linked together by single peptide bond is dipeptide and long chains of amino acids are called polypeptides

Amino acids

Figure 2.21

Organic Macromolecules

Protein structure

Un-branched polypeptides composed of hundreds of amino acids linked together in specific patterns as determined by genes

Every protein has at least 3 levels of structure and some proteins have 4 levels

Primary structure: the sequence of amino acid; sequence vary widely in length; a change in a single amino acid can drastically affect a protein’s overall structure and function

Secondary structure: polypeptide chains of proteins fold into coils (α-helices) or structures called β–pleated sheets as a result of ionic and hydrogen bonding and hydrophobic and hydrophilic characteristics of the proteins

Tertiary structure: protein polypeptides further fold into more complex three- dimensional shapes that are not repetitive like α-helices or β–pleated sheets

Protein structure (continued)

Quaternary structure: some proteins are composed of two or more peptide chains linked together by disulfide bridges or other bonds

Protein structure is directly related to its function; anything that interrupts shape (amino acid substitution, physical and chemical factors such as heat, change in pH and salt concentrations) severely disrupt protein function

The temporary or permanently disruption of structure and function of proteins is called denaturation

Stereoisomers

Figure 2.22

Linkage of amino acids by peptide bonds

Figure 2.23

Levels of protein structure

Figure 2.24

Organic Macromolecules

Nucleic acids and nucleotides

DNA and RNA vital as genetic material of organisms

RNA acting as an enzyme, binds amino acids to form polypeptides

Both are DNA and RNA are un-branched macromolecular polymers that differ primarily in the structures of their monomers

Organic Macromolecules

Nucleic acids and nucleotides

The monomers that make up nucleic acids (nucleotides) are composed of three parts:

A phosphate (PO42-)

A pentose sugar either deoxyribose or ribose

One of five cyclic (ring-shaped) nitrogenous bases

Adenine (A)

Guanine (G)

Cytosine (C)

Thymine (T)

Uracil (U)

Adenine and guanine are double-ringed molecules called purines, whereas cytosine, thymine and uracil are single-ringed and are called pyrymidines.

DNA contains A, G, C and T bases, whereas RNA contains A, G, C and U bases.

Nucleotides

Figure 2.25

Organic Macromolecules

Nucleic acids structure

Nucleic acids are polymers composed of nucleotides linked by covalent bonds between the phosphate of one nucleotide and the sugar of the next

The linear spines of nucleotides is composed of alternating sugars and phosphates, with bases extending from it

Three H bonds form between C and G in DNA and U and A in RNA

Two H bonds form between T and A in DNA or between U and A in RNA

DNA is a double-stranded molecule in most cells and viruses

The two strands of DNA are complementary to one another and also anti-parallel. One strand runs from the 3’ (3 prime) end to 5’ (5 prime) end and its complement runs in the opposite direction from its 5’ end to its 3’ end

General nucleic acid structure

Figure 2.26

Organic Macromolecules

Nucleic acids function

DNA is the genetic material of all organisms and many viruses

Carries instructions for the synthesis of RNA molecules and proteins in all organism

By controlling the synthesis of enzymes and regulatory proteins, DNA controls the synthesis of all other molecules in an organism

Genetic instructions are carried in the sequence of nucleotides of nucleic acid

Cells replicate their DNA molecules and pass copies to their progenies, making sure that each has the instruction necessary for life

Ribonucleic acids play several roles in the synthesis of proteins, including catalyzing the synthesis of proteins

RNA molecules also function as structural components of ribosomes and in place of DNA as the genome (genetic material) of RNA viruses

Organic Macromolecules

Adenosine triphosphate (ATP)

Phosphate - a highly reactive functional group in nucleotides

Forms covalent bonds with other phosphates to make di-phosphates and triphosphates

Molecules made from ribosome nucleotides (AMP, ADP and ATP) are important in many metabolic reactions

ATP is the principal, short-term and renewable energy supply of cells

When the high energy bonds (phosphate-phosphate bond) of ATP are broken, energy is released and ATP is converted to ADP

Energy from ATP is used for life activities such as synthesis reaction, locomotion, and transportation of substances into and out of cells

Adenosine triphosphate (ATP)

Figure 2.27