MICROBIO CH. 7 & 8 DR. Brookins TCC SOUTHEAST

Major elements in cells

Carbon, oxygen, nitrogen, hydrogen, phosphorus, and sulfur, make up the majority of a cell's dry weight with carbon at 50% oxygen at 20% nitrogen at 14% hydrogen at 8% phosphorus at 3% and sulfur at 1%

Chemical composition of an E. coli cell

About 70% of total weight is water; among organic compounds by dry weight proteins make up about 50% RNA about 20% carbohydrates about 10% lipids about 10% and DNA about 3%

Four basic biological macromolecules

Lipids proteins carbohydrates and nucleic acids

Monosaccharide

A simple sugar

Disaccharide

A carbohydrate formed when two monosaccharides are joined by a dehydration synthesis reaction such as two glucose molecules forming maltose and releasing water

Polysaccharide

A carbohydrate made of many monosaccharides such as starch glycogen cellulose and NAG/NAM

Triglyceride

Composed of a glycerol molecule attached to three fatty acids by a dehydration synthesis reaction providing structure and energy for cells

Phospholipid

A lipid with a hydrophilic head containing glycerol and a phosphate group and two hydrophobic tails made of fatty acid chains (one saturated and one often unsaturated)

Lipid bilayer

Formed when phospholipids arrange in two layers with polar heads facing outward and nonpolar tails facing inward making up cell membranes and the membranes of membranous organelles

Liposome (single-layer lipid sphere)

A sphere formed by a single layer of lipids with polar heads on the outside and nonpolar tails filling the center

Primary protein structure

The linear sequence of amino acids in a protein chain from the N-terminus (free amino group) to the C-terminus (free carboxyl group)

Secondary protein structure

The local folding of a polypeptide chain into helices or sheets such as an alpha helix or beta-pleated sheet

Tertiary protein structure

The three-dimensional folding pattern of a protein due to side chain interactions

Quaternary protein structure

A protein structure consisting of more than one amino acid chain

Essential nutrients

Nutrients the human body cannot synthesize in sufficient quantities to meet physiological needs so they must be obtained from food

Non-essential nutrients

Nutrients the body can synthesize in sufficient quantities for normal functioning

Nitrogen fixation

The process of converting N2 gas into ammonium ions (NH4+) a form that can be used for biosynthesis

Nitrogen-fixing bacteria

Bacteria that convert N2 to NH4+

Nitrifying bacteria

Bacteria that convert NH4+ to NO3-

Denitrifying bacteria

Bacteria that convert NO3- to N2

Rhizobium

A nitrogen-fixing plant symbiont that forms bacteria-filled nodules on plant roots

Alanine

An amino acid with an R group of CH3

Serine

An amino acid with an R group of CH2OH

Lysine

An amino acid with an R group of (CH2)4NH3+

Aspartate

An amino acid with an R group of CH2COO-

Cysteine

An amino acid with an R group of CH2SH

Sulfur (nutritional role)

An essential element used to build protein amino acids such as cysteine and methionine

Phosphorus (nutritional role)

An essential element used to build DNA RNA ATP and membranes (phospholipids) typically obtained as phosphate

Trace elements and vitamins

Inorganic elements required in small amounts such as potassium magnesium calcium iron and B vitamins that often function as enzyme cofactors or coenzymes

Metabolism

The sum of all chemical reactions within a cell including anabolism and catabolism

Catabolism

The breakdown of macromolecules into smaller molecules through oxidative reactions that release energy (exergonic) which is transferred to ATP

Anabolism

The synthesis of macromolecules from smaller subunits through reductive reactions using energy from ATP

Chemical work

Work performed by cells using ATP to build a large molecule

Transport work

Work performed by cells using ATP to pump solutes across a membrane

Mechanical work

Work performed by cells using ATP to move a muscle protein

Photoautotroph

An organism that uses light as an energy source and carbon dioxide as a carbon source such as plants algae and cyanobacteria which use H2O to reduce CO2 and produce O2 as a byproduct

Chemoautotroph

An organism that uses chemical compounds as an energy source and carbon dioxide as a carbon source such as hydrogen sulfur and nitrifying bacteria and some archaea

Photoheterotroph

An organism that uses light as an energy source and organic compounds as a carbon source such as green nonsulfur and purple nonsulfur bacteria and some archaea

Chemoheterotroph

An organism that uses chemical compounds as an energy source and organic compounds as a carbon source obtaining energy through aerobic respiration anaerobic respiration or fermentation

Enzyme

A biological catalyst usually a protein (or sometimes a ribozyme) that lowers the activation energy of a reaction allowing rapid conversion of reactants to products

Ribozyme

An RNA molecule that can act as a biological catalyst

Activation energy

The energy required to initiate a chemical reaction which is lowered by an enzyme

Substrate (enzyme)

The substance an enzyme acts upon which binds to the enzyme's active site

Enzyme-substrate complex

The temporary structure formed when a substrate binds to an enzyme's active site before being converted to products

Active site

The region of an enzyme where a substrate binds and is converted to product

Apoenzyme

The protein portion of an enzyme

Cofactor

An inorganic component such as a metal ion required for some enzymes to function

Coenzyme

An organic cofactor required for some enzymes to function

Holoenzyme

The complete active enzyme formed by an apoenzyme bound to its cofactor or coenzyme

Saturation (enzyme activity)

The point at which increasing substrate concentration no longer increases reaction rate because the active sites on all enzyme molecules are filled reaching the maximum rate of reaction

Denaturation (enzyme)

A loss of enzyme structure and function due to factors such as high temperature or extreme pH

Competitive inhibitor

A molecule that competes with the substrate by binding to an enzyme's active site blocking the substrate from binding

Allosteric site

A site on an enzyme other than the active site where a regulatory molecule can bind

Allosteric inhibition

When an allosteric inhibitor binds the allosteric site distorting the active site so the substrate can no longer bind

Allosteric activation

When an allosteric activator binds the allosteric site changing a distorted active site into a functional shape that allows the substrate to bind

Feedback inhibition

Inhibition of one or more critical enzymes in a pathway by its own end product which regulates the entire pathway with each end product regulating its own branch of the pathway

Lactase

An enzyme (systematic name beta-D-galactosidase) that breaks lactose down into glucose and galactose

Penicillinase

An enzyme (systematic name beta-lactamase) that hydrolyzes the beta-lactam ring of penicillin

DNA polymerase (enzyme table)

An enzyme (systematic name DNA nucleotidyl-transferase) that synthesizes a strand of DNA using the complementary strand as a model

Lactate dehydrogenase

An enzyme that catalyzes the conversion of pyruvic acid to lactic acid

Oxidase

An enzyme (systematic name cytochrome oxidase) that acts on molecular oxygen

ATP (adenosine triphosphate)

A molecule that carries energy that can be transferred to cell processes generated by phosphorylation of ADP

Substrate-level phosphorylation

The direct transfer of a phosphate group from a phosphorylated substrate such as phosphoenolpyruvate to ADP to form ATP

Oxidative phosphorylation

ATP generation that occurs through the electron transport chain using energy from a proton gradient

NAD+ (coenzyme)

An electron-carrier coenzyme that becomes reduced to NADH when it accepts electrons and protons removed from an organic molecule during oxidation

Glycolysis

The most common pathway used to break down glucose yielding 2 pyruvate 2 ATP and 2 NADH from one glucose molecule

Transition reaction

The step that converts pyruvate to acetyl-CoA producing CO2 and NADH also called the intermediate step

Tricarboxylic acid (TCA) cycle

Also called the Krebs or citric acid cycle; the oxidation of acetyl-CoA that produces ATP CO2 NADH and FADH2

Electron transport chain (ETC)

A series of membrane-embedded carriers that pass electrons from NADH and FADH2 pumping H+ ions across the membrane to create a gradient used to generate ATP via oxidative phosphorylation; located in the cytoplasmic membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes

Proton motive force

The electrochemical gradient of protons (H+) generated across a membrane by the electron transport chain that drives ATP synthesis

ATP synthase

An enzyme that uses the flow of H+ ions down their electrochemical gradient to catalyze the conversion of ADP to ATP

Aerobic respiration

Cellular respiration that uses oxygen as the terminal electron acceptor and yields the maximum net amount of ATP (about 36 to 38 ATPs)

Anaerobic respiration

Cellular respiration unique to prokaryotes that uses an electron acceptor other than oxygen such as metals oxidized nitrogen ions or sulfur yielding a variable amount of ATP (about 2 to 36 ATPs)

Fermentation

An anaerobic process that regenerates NAD+ without an electron transport chain yielding a maximum net ATP of 2 (from glycolysis alone) and producing alcohols or acids as end products

Lipase

An enzyme that hydrolyzes triglycerides into glycerol and fatty acids

Protease

An enzyme that breaks down proteins

Deamination

The removal of an amino group from an amino acid with the resulting organic acid converted to pyruvate acetyl-CoA or a TCA cycle intermediate

Pyruvic acid (central metabolite)

A central metabolite formed from sugars amino acids and fat metabolites that strict aerobes and some anaerobes send to the Krebs cycle for processing and energy release while facultative anaerobes convert it into acids or other fermentation products

Geobacter metallireducens (anaerobic respiration)

Transfers electrons from catabolism to iron uranium and other metals using the reaction Fe3+ + e- to Fe2+ and can remediate pollutants and generate electricity in a fuel cell

Pseudomonas aeruginosa (anaerobic respiration)

A soil bacterium and opportunistic pathogen that colonizes the lungs of cystic fibrosis patients and reduces nitrate and nitrous oxide

Desulfovibrio spp. (anaerobic respiration)

Found in soil and marine sediments and capable of degrading pollutants by reducing sulfate to sulfite

Pyrococcus furiosus (anaerobic respiration)

A hyperthermophilic archaeon that grows in marine thermal vents above 100 degrees Celsius by reducing elemental sulfur to hydrogen sulfide

Salmonella enterica (anaerobic respiration)

An enteric pathogen that induces white blood cells to produce tetrathionate by reducing it to thiosulfate

Propionibacterium fermentation

Ferments pyruvic acid to produce CO2 and propionic acid used to make Swiss cheese

Lactic acid fermentation

Carried out by organisms such as Aspergillus Lactobacillus and Streptococcus which ferment pyruvic acid into lactic acid used to make cheddar cheese yogurt and soy sauce

Saccharomyces fermentation

Ferments pyruvic acid into CO2 and ethanol used to make wine and beer

Clostridium fermentation

Ferments pyruvic acid into acetone and isopropanol used to make nail polish remover and rubbing alcohol

Mannitol salt agar (MSA)

A high-salt medium that differentiates gram-positive cocci; fermentation of mannitol produces acid detected by the phenol red pH indicator

PR broth

A broth containing the phenol red pH indicator used to test for fermentation of carbohydrates

MacConkey agar

A medium that tests for fermentation of lactose and differentiates gram-negative bacteria

Gas gangrene

A deep anaerobic wound infection most commonly caused by Clostridium perfringens (80-95% of cases) as well as group A strep and S aureus with symptoms appearing about 12-48 hours after injury including myonecrosis high fever septic shock and odor caused by fermentative products and exotoxins that destroy tissue and impair blood flow; treated with debridement or amputation