Chapter 8

Metabolism: pertains to all chemical reactions and physical workings of the cell; from the Greek term
metaballein.
Anabolism (biosynthesis): any process that results in synthesis of cell molecules and structures.
Catabolism: break the bonds of larger molecules into smaller molecules and often release energy.
Metabolism accomplishes:
Assembles smaller molecules into larger macromolecules needed for the cell; in this process, ATP
(energy) is utilized to form bonds (anabolism).
It degrades macromolecules into smaller molecules, a process that yields energy (catabolism).
It conserves energy in the form of ATP (adenosine triphosphate) or heat.
Enzymes: a special class of macromolecules; a class of catalysts.
Catalyst: chemicals that increase the rate of a chemical reaction without becoming part of the products
or being consumed in the reaction.
Energy of activation (activation energy): the resistance to a reaction which must be overcome for the
reaction to proceed.
Substrates: reactant molecules that can be positioned for various interactions.
Holoenzyme: a conjugated enzyme that is a combination of the protein and one or more cofactors.
Apoenzyme: a protein in a holoenzyme.
Cofactor: organic molecules called coenzymes or inorganic elements (metal ions).
Coenzymes: organic molecules used as cofactors.
Ribozymes: a special class of enzymes that are RNA molecules that catalyze reactions on other RNA.
Active site (catalytic site): there the substrate actually binds; a crevice or groove.
Classification of Enzyme Functions:
Oxidoreductases transfer electrons from one substrate to another, and dehydrogenases transfer a
hydrogen from one compound to another.
Transferases transfer functional groups from one substrate to another.
Hydrolases cleave bonds on molecules with the addition of water.
Lyases add groups to or remove groups from double-bonded substrates.
Isomerases change a substrate into its isomeric form.
Ligases catalyze the formation of bonds with the input of ATP and the removal of water.
Exoenzymes: transported extracellularly, where they break down (hydrolyze) large food molecules or
harmful chemicals.
Endoenzymes: retained intracellularly and function there.
Constitutive enzymes: always present and in relatively constant amounts, regardless of the cellular
environment.
Regulated enzymes: the production of these is either turned on (induced) or turned off (repressed) in
response to changes in concentration of the substrate.
Oxidized: the compound that loses electrons.
Reduced: the compound that receives the electrons.
Labile: chemically unstable.
Denaturation: a process by which the weak bonds that collectively maintain the native shape of the
apoenzyme are broken.
Competitive inhibition: a mimic of the enzyme’s active site binder takes the place of the true substrate
and competes with the natural substrate for that site.
Noncompetitive inhibition: the regulatory molecule does not bind in the same site as the substrate.
Enzyme repression: means to stop further synthesis of an enzyme somewhere along its pathway.
Enzyme induction: enzymes appear (are induced) only when suitable substrates are present; the
synthesis of an enzyme is induced by its substrate.
Exergonic: the reaction releases energy as it goes forward; the energy produced is considered free, as in
available for doing cellular work.
Endergonic: a reaction that requires addition of energy. In cells, exergonic and endergonic reactions are
often coupled so that the energy produced is put directly to use.
Phosphorylate: add an inorganic phosphate; the energy in the electron acceptor can do this to ADP or
some other compound.
Glycolysis: the most common cellular pathway to break down glucose.
Aerobic respiration: a series of reactions (glycolysis, the Krebs2 cycle, and the respiratory chain) that
converts glucose to CO2 and allows the cell to recover significant amounts of energy; relies on free
oxygen as the final acceptor for electrons and hydrogens and produces a relatively large amount of ATP.
Anaerobic respiration: involves the same three pathways as aerobic respiration, but does not use
molecular oxygen as the final acceptor; instead, NO3-, SO4-. And CO32- and other oxidized compounds are
utilized.
Steps in the Krebs Cycle
Oxaloacetic acid (oxaloacetate; 4C) reacts with the acetyl group (2C) on acetyl CoA, thereby forming
citric acid (citrate; 6C) and releasing coenzyme A so it can join with another acetyl group.
Citric acid is converted to isocitric acid (isocitrate; 6C) to prepare this substrate for the decarboxylation
and dehydrogenation of the next step.
Isocitric acid is acted upon by an enzyme complex including NAD or NADP (depending on the organism)
in a reaction that generates NADH or NADPH, splits off a carbon dioxide, and leaves apha-ketoglutaric
acid (alpha-ketoglutarate; 5C).
Alpha-ketoglutaric acid serves as a substate for the last decarboxylation reaction and yet another redox
reaction involving coenzyme A and yielding NADH. The product is the high-energy compound succinyl
CoA (4C).
Succinyl CoA is the source of the one substrate-level phosphorylation in the Krebs cycle. In most
microbes, it proceeds with the formation of GTP, which is readily converted to ATP. The product of this
reaction is succinic acid (succinate; 4C).
Cuccinic acid becomes dehydrogenated, but in this case, the electron and H + acceptor is flavin adenine
dinucleotide (FAD). The enzyme that catalyzes this reaction, succinyl dehydrogenase, is found in the
bacterial cell membrane and mitochondrial cristae of eukaryotic cells. FADH2 then directly enteres the
electron transport system. Fumaric acid (fumarate; 4C) is the product of this reaction.
The addition of water to fumaric acid (called hydration) results in malic acid (malate; 4C). This is one of
the few reaction in respiration that directly incorporate water.
Malic acid is dehydrogenated (with the formation of a final NADH), and oxaloacetic acid is formed. This
step brings the cycle back to its original starting position, where oxaloacetic acid can react with acetyl
coenzyme A.
ATP synthase complex: energy captured by this, stationed along the membrane in close association with
the ETS carriers.
Oxidative phosphorylation: the coupling of ATP synthesis to electron transport.
Chemiosmosis: as the electron transport carriers shuttle electrons, they actively pump hydrogen ion
(protons) into the periplasmic space, or the space between the wall and the cytoplasmic membrane,
depending on whether the bacterium is gram-positive or gram-negative.
Aerobic respiration produces 38 net ATP.
Denitrification: reducing nitrate to nitric oxide (NO), nitrous oxide (N2O), and even nitrogen gas (N2).
Fermentation: the incomplete oxidation of glucose or other carbohydrates in the absence of oxygen.
Alcoholic fermentation: occurs in yeast or bacterial species that have metabolic pathways for converting
pyruvic acid to ethanol; this process involves a decarboxylation of pyruvic acid to acetaldehyde, followed
by a reduction of the acetaldehyde to ethanol.
Acidic fermentation: ferment pyruvate by reducing it to lactic acid.
Mixed acid fermentation: produces a combination of acetic, lactic, succinic, and formic acids, and it
lowers the pH of a medium to about 4.0.
Lipase: enzyme that breaks apart fatty acids joined to glycerol (fats).
Beta oxidation: yields 50 ATPs from a 6-carbon fatty acid compared with 38 for a 6-carbon sugar.
Protease: enzyme that breaks down proteins to their amino acid components.
Deamination: amino groups removed by this reaction, leaving a carbon compound, which is easily
converted to one of several Krebs cycle intermediates.
Amphibolism: the property of a system to integrate catabolic and anabolic pathways to improve cell
efficiency.
Gluconeogenesis: in the event of an inadequate glucose supply, pyruvate serves as the starting point in
glucose synthesis from various metabolic intermediates.
Light-dependent reaction: phase one of photosynthesis; proceeds only in the presence of light.
Light-independent reactions: phase two of photosynthesis; proceeds regardless of the lighting
conditions (light or dark).
Photon (quanta): discrete energy packets that travel in waves.
Chlorophyll: photosynthetic pigment colored green.
Carotenoid: photosynthetic pigment colored yellow, orange, or red.
Phycobilin: photosynthetic pigment colored red or blue-green.
Thylakoid: membrane; a compartment called grana in chloroplasts.
Photolysis: the splitting of water.
Carbon fixation: generates a 6-carbon intermediate compound that immediately splits into two 3-carbon
molecules of 3-phosphoglyceric acid (PGA).
Anoxygenic: non-oxygen-producing.
Chapter 9
Genetics: study of the inheritance, or heredity, of living things.
Heredity: inheritance.
Genome: the sum total of genetic material of an organism.
Genomics: the study of an organism’s entire genome; research in this area has grown exponentially over
the past 10 years, leading to new discoveries about microbial evolution, ecology, and pathogenesis.
Chromosome: discrete cellular structure composed of a neatly packaged DNA molecule.
Gene: in classic genetics, ‘gene’ refers to the fundamental unit of heredity responsible for a given trait in
an organism. In the molecular and biochemical sense, ‘gene’ is a site of the chromosome that provides
information for a certain cell function.
Protein: basic unit of structure composed of amino acids.
Types of Genes:
1. Structural genes that code for proteins
2. Genes that code for RNA machinery used in protein production
3. Regulatory genes that control gene expression
Genotype: the sum of all types of genes that constitute an organism’s distinctive genetic makeup.
Phenotype: the traits created by the expression of the genotype.
Nucleotide: the basic unit of DNA structure.
Composition of a nucleotide: phosphate, deoxyribose sugar, and a nitrogenous base.
Nitrogenous bases: purines and pyrimidines.
DNA pairs:
Purines: Adenine (A) and guanine (G)
Pyrimidines: Thymine (T) and cytosine (C)
A always pairs with T, and G always pairs with C.
Antiparallel: the arrangement of the DNA double helix in which one side of the helix runs in the opposite
direction of the other.
Significance of the DNA Structure:
1. Maintenance of the code during reproduction.
2. Providing variety.
Simplified Version of Replication:
1. Uncoiling the parent DNA molecule
2. Unzipping the hydrogen bonds between the base pairs, thus separating the two strands and
exposing the nucleotide sequence of each strand (which is normally buried in the center of the
helix) to serve as templates
3. Synthesizing two new strands by attachment of the correct complementary nucleotides to each
single-stranded template
Semiconservative replication: semi- meaning half, as in a semicircle, and explains the reliability and
fidelity of replication.
Replication fork: the place in the helix where the strands are unwound and replication is taking place.
Each circular DNA molecule will have two replication forks.
Primer: a length of RNA that is inserted initially during replication before it is replaced by DNA.
Leading strand: the strand of new DNA that is synthesized in a continuous manner in the 5’ to 3’
direction.
Lagging strand: the strand of new DNA that must be synthesized in short segments and later sealed
together to form a strand in the 3’ to 5’ strand.
Okazaki fragments: the short segments of DNA synthesized in a 5’ to 3’ direction, which are then sealed
together to form a 3’ to 5’ strand.
Telomere: the 3’ end of DNA that is not completely copied and erodes with each cell division, and, when
reaching a certain length, trigger cell death (apoptosis).
Transcription: RNA molecules are synthesized using a master code of DNA.
Translation: the information in the RNA is used to produce proteins.
Key Points That Connect DNA and an Organism’s Traits
1. A protein’s primary structure—the order and type of amino acids in the chain—determines its
characteristic shape and function.
2. Proteins ultimately determine phenotype, the expression of all aspects of cell function and
structure. Put more simply, living things are what their proteins makes them. Regulatory RNAs
help determine which proteins are made. Proteomics is the study of an organisms complete set
of expressed proteins.
3. DNA is mainly a blueprint that tells the cell which kinds of proteins and RNAs to make and how
to make them.
How RNA Differs From DNA Structurally
1. It is a single-stranded molecule that exists in helical form. This single strand can assume
secondary and tertiary levels of complexity due to bonds within the molecule, leading to
specialized forms of RNA (tRNA and rRNA).
2. RNA contains uracil (U), instead of thymine, as the complementary base-pairing mate for
adenine. This does not change the inherent DNA code in any way because the uracil still follows
the pairing rules.
3. Although RNA, like DNA, contains a backbone that consists of alternating sugar and phosphate
molecules, the sugar in RNA is ribose rather than deoxyribose.
Messenger RNA (mRNA): a transcript (copy) of a structural gene or genes in the DNA; is synthesized by a
process similar to synthesis of the leading strand during DNA replication.
Codon: a series of triplets that a message of the transcribed strand of DNA is read as.
Transfer RNA (tRNA): is also a copy of a specific region of DNA, uniform in length, 75-95 nucleotides
long, and it contains sequences of bases that form hydrogen bonds with complementary sections of the
same tRNA strand.
Anticodon: an exposed triplet at the bottom loop of a cloverleaf that designates the specificity of the
tTNA and complements mRNA’s codons.
Ribosomal RNA (rRNA): a tight package that composes the bacterial (70s) ribosome (which is also
composed of protein).
RNA polymerase: converts the DNA code to RNA through several stages of transcription.
Template strand: one strand of DNA with contains meaningful instruction for synthesis of a function
polypeptide.
Transcript: the strand of mRNA that was used for transcription.
Codon: three nucleotides that dictate which amino acid is added to the growing peptide chain.
Redundancy: when an amino acid is represented by several codons and allows for the insertion of
correct amino acids even when mistakes occur in the DNA sequence, as they do with regularity.
Wobble: when codons permit some variation or mutation without altering the message.
Start codon: the first three RNA nucleotides that signal the beginning of the message. The start codon is
always AUG.
Stop codon (nonsense codon): one of three codons—UAA, UAG, or UGA—that has no corresponding
tRNA and therefore causes translation to be terminated.
Translocation: the process of shifting the ribosome down the mRNA strand to read new codons.
Posttranslational modifications: alterations to the peptide chain, such as clipping off proteins or joining
other completed proteins.
Chemotherapeutic drug: any chemical used in the treatment, relief, or prophylaxis of a disease.
Prophylaxis: Use of a rug to prevent imminent infection of a person at risk.
Antimicrobial chemotherapy: the use of chemotherapeutic drugs to control infection.
Antimicrobials: all-inclusive term for any antimicrobial drug, regardless of what type of microorganism it
targets.
Antibiotics: substances produced by the natural metabolic processes of some microorganisms—or
created by scientists—that can inhibit or destroy microorganisms.
Semisynthetic drugs: drugs that are chemically modified in the laboratory after being isolated from
natural sources.
Synthetic drugs: drugs produced entirely by chemical reactions within a laboratory setting.
Narrow-spectrum (limited spectrum): antimicrobials effective against a limited array of microbial types
—for example, a drug effective mainly on gram-positive bacteria.
Broad-spectrum (extended spectrum): antimicrobials effective against a wide variety of microbial types
—for example, a drug effective against both gram-positive and gram-negative bacteria.
Kirby-Bauer technique: an agar diffusion test that provides useful data on antimicrobial susceptibility.
Minimum inhibitory concentration (MIC): the smallest concentration (highest dilution) of a drug that
visibly inhibits growth.
Therapeutic index (TI): the ratio of the dose of the drug that is toxic to humans to its minimum effective
(therapeutic) dose.
Selectively toxic: should kill or inhibit microbial cells without simultaneously damaging host tissues.
Penicillinases (beta-lactamases): bacterial enzymes that are capable of destroying the beta-lactam ring
of penicillin.
Parenterally: absorbed by injection into a muscle or a vein.
Bacitracin: a narrow-spectrum antibiotic produced by a strain of the bacterium Bacillus subtilis.
Isoniazid (INH): bactericidal to Mycobacterium tuberculosis by only against growing cells.
Vancomycin: narrow-spectrum antibiotic most effective in treating staphylococcal infections in cases of
penicillin and methicillin resistance or in patients with an allergy to penicillins.
Aminoglycosides: complex compounds exclusively the products of various species of soil actinomycetes
In the genera Streptomyces and Micromonospora.
Tetracyclines: semisynthetic; bind to ribosomes and block protein synthesis; broad-spectrum.
Sulfanomides: synthetic and the very first modern antimicrobial drug.
Fluoroquinolones: high potency and broad spectrum; targets DNA and RNA.
Polymyxins: narrow-spectrum antibiotics with a unique fatty acid component that contributes to their
detergent activity.
Daptomycin: lipopeptide made by Streptomyces; most active against gram-positive bacteria, acting to
disrupt multiple aspects of membrane function.
Quinine: extracted from the bark of the cinchona tree; principle treatment of malaria for hundreds of
years; has been replaced by synthesized quinolones, mainly chloroquine and primaquine, which have
less toxicity to humans.
Acyclovir (Zovirax): synthetic purine compounds that block DNA synthesis in a small group of viruses,
mainlu the herpesviruses; some derivatives of this drug are valganciclovir, famciclovir, and penciclovir.
Interferon (IFN): a glycoprotein produced primarily by fibroblasts and leukocytes in response to various
immune stimuli; antiviral and anticancer properties.
Drug resistance: an adaptive response in which microorganisms begin to tolerate an amount of drug
that would ordinarily be inhibitory.
Resistance (R) factors: occurrence of resistance originating through horizontal transfer from plasmids
during conjugation, transformation, or transduction.
Beta-lactamases: bacterial enzymes that hydrolyze the beta-lactam ring (a critical structure) of
penicillins and cephalosporins, rendering the drugs inactive (two are called penicillinase and
cephalosporinase).
Probiotics: preparations of live microorganisms that are fed to animals and humans to improve the
intestinal biota.
Prebiotics: nutrients that encourage the growth of beneficial microbes in the intestine.