Ch. 10 Microbial Metabolism

metabolism

all of the chemical reactions and physical workings of the cell

anabolism

. biosynthesis: synthesis of cell molecules and structures

. requires energy input

catabolism

. breaks the bonds of larger molecules

. releases energy

metabolism functions

. assembles smaller molecules into larger molecules for the cell, using ATP to form bonds (anabolism)

. breaks down macromolecules into smaller molecules, a process that yields energy (catabolism)

. collects and spends energy in the form of ATP or heat

examples of catabolism

. glycolysis

. Kreb’s cycle

. Respiratory chain

. Fermentation

catalysts

speed up the rate of chemical reactions without becoming part of the products or being consumed in the reaction

enzymes

overcome activation energy, allowing reaction to proceed

characteristics of enzymes

. most are made of protein and may require cofactors

. act as organic catalysts to speed up the rate of cellular reactions

. lower the activation energy required for a chemical reaction to proceed

. have unique characteristics such as shape, specificity, and function

. enable metabolic reactions to proceed at a speed compatible with life

. have an active site for substrates

. much larger than substrates

. are not used up permanently or changed by the reaction

. greatly affected by temperature and pH

. can be regulated by feedback and genetic mechanisms

substrates

reactant molecules upon which enzymes act

simple enzymes

consist of protein alone

conjugated enzymes

contain protein and some other nonprotein molecule

holoenzymes

whole enzymes

apoenzyme

. the protein portion of the holoenzyme

. where the substrate bonds

. three-dimensional site where the crevice or groove formed by the way amino-acids are folded

cofactor

. the nonprotein portion of the holoenzyme

. can be organic or inorganic

coenzyme

. organic cofactor

. work with the apoenzyme to to alter the substrate

. remove a chemical group from one substrate and add it to another substrate

. carry and transfer hydrogen atoms, electrons, carbon dioxide, and amino groups

. vitamins are an important component

inorganic cofactor

metal ions

each enzyme has a different…

1. primary structure

2. variation in folding

3. unique active site

metallic cofactors

. iron, copper, magnesium, manganese, zinc, cobalt, selenium, etc.

. assist with precise functions between enzyme and substrate: activate enzymes, help bring the active site and substrate close together, participate directly in chemical reactions

6 classes of enzymes:

1. oxidoreductases

2. transferases

3. hydrolases

4. lyases

5. isomerases

6. ligases

oxidoreductases

transfer electrons from one substrate to another

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 substrates to their isometric form

ligases

catalyze the formation of bonds with the input of ATP and the removal of water

Lactase

hydrolase, breaks down lactose into glucose and galactose

Penicillinase

hydrolase, Hydrolyzes beta-lactam ring

DNA polymerase

transferase; synthesizes a strand of DNA using the complimentary strand as a model

lactate dehydrogenase

oxidoreductase; catalyzes the conversion of pyruvic acid to lactic acid

oxidase

oxidoreductase; catalyzes the reduction of O2 (addition of electrons and hydrogen)

oxidation

loss of electrons (OIL-oxidation involves loss)

reduction

gain of electrons (RIG- reduction involves gain)

coenzyme carriers

NAH and FAD

exoenzymes

. transported extracellularly

. break down large food molecules or harmful chemicals

endoenzymes

. retained intracellularly and function there

. most enzymes of metabolic pathways

constitutive enzymes

always present in relatively constant amounts, regardless of cellular environment

regulated enzymes

. production is turned on (induced) or turned off (repressed) in response to changes in concentration of substrates

pathogens role with enzymes

secrete unique exoenzymes that help them avoid host defenses or promote multiplication in tissues

. some enzymes function as toxins

nonfunctional enzymes

block metabolic reactions and can lead to cell death

competitive inhibition

. a molecule that resembles the substrate (the mimic) occupies the active site. preventing the substrate from binding

. enzyme cannot act on the inhibitor as is shut down

noncompetitive inhibition

. a regulatory molecule binds to the regulatory site and changed the conformation of active site so that substrates cannot enter

enzyme repression

. stops further synthesis of an enzyme somewhere along its pathway

. If the end product of an enzymatic reaction reaches excess, the genetic apparatus for replacing enzymes is suppressed

enzyme induction

enzymes appear only when suitable substrates are present

exergonic reactions

. release energy as they go forward

. energy is available for doing cellular work

endergonic reactions

require the addition of energy to move forward

reduced compounds

have more energy than they did in their oxidized state

dehydrogenation

the removal of hydrogens from a compound during a redox reaction

NAD

. most common electron carrier

. carries hydrogens and a pair of electrons from dehydrogenation reactions

. reduced NAD is presented as NADH+

FAD

. electron carrier

. reduced FAD is presented as FADH+

NADP

NAD phosphate

aerobic respiration

converts: glucose to CO₂

final electron acceptor: oxygen

pathways: glycolysis, the Krebs cycle, and respiratory chain

maximum net yield: 36-38 ATP

anaerobic metabolism

converts: glucose to CO₂

final electron acceptor: NO₃⁻, SO₄²⁻, CO₃²⁻

pathways: glycolysis, the Krebs cycle, the respiratory chain

maximum net yield: 2-36 ATP

. found in Escherichia coli

adenosine triphosphate

. adenine-base pair

. ribose- 5-carbon sugar

. three phosphate groups bound to ribose

. removal of the phosphates releases free energy

substrate-level phosphorylation

generation of ATP through a transfer of a phosphate group from a phosphorylated compound directly to ADP

oxidative phosphorylation

. a series of redox reactions occurring during the final phase of the respiratory pathway

. the coupling of ATP synthesis to electron transport

. each NADH that enters the ETS gives rise to 3 ATP molecules

.

photophosphorylation

ATP formed through a series of sunlight-driven reactions in phototrophs

3 basic catabolic pathways

1. aerobic respiration

2. anaerobic respiration

3. fermentation

glycolysis

. most common pathway used to break down glucose

. glucose is enzymatically converted to pyruvic acid

. may be the first phase of aerobic respiration or the primary metabolic pathway

fermentation

. uses only glycolysis

. oxygen is not required and uses organic compounds as electron acceptors

. the incomplete oxidation of glucose or other carbohydrates in the absence of oxygen

. yields a small amount of ATP

carbohydrates are good fuels because they…

. are readily oxidized

. are good hydrogen and electron donors

The Krebs Cycle

1. Pyruvic acid is converted to acetyl coenzyme A (acetyl CoA) before it enters the Krebs Cycle

2. oxidation reaction releases the first CO₂ molecule

3. a cluster of enzymes and coenzyme A dehydrogenate pyruvic acid to a 2-carbon acetyl group

4. NAD is reduced to NADH

5. NADH formed is shuttled to the electron transport system to produce ATP

. all reactions occur twice for each glucose molecule because two pyruvates are formed during glycolysis

. serves to transfer the energy stored in acetyl CoA to NAD+ and FAD by reducing them

products: reduced NADH and 2 ATP produced through substrate level phosphorylation

The Respiratory Chain (Electron Transport System)

. chain of special redox carriers that receives electrons from NADH

. electrons are passed sequentially from one redox molecule to the next

. flow of electrons allows the active transport of hydrogens outside the cell membrane

. oxygen receives hydrogens and electrons and produces water

sequence of electron carriers in the respiratory chain of most aerobic organisms

1. NADH dehydrogenase

2. flavin mononucleotide (FMN)

3. coenzyme Q

4. cytochrome b

5. cytochrome

6. cytochrome c

7. cytochrome a

ATP synthase

. stationed along the membrane in close association with the ETS carriers

. captures released energy from the ETS carriers

chemiosmosis

. as the electron transport carriers shuttle electrons, hydrogen ions are actively pumped into the space between the cell wall and the cytoplasmic membrane (periplasmic space)

proton motive force

. a concentration gradient of hydrogen ions created by chemiosmosis

. Consists of a difference in charge between the outside of the membrane (+) and the inside (−)
. Separation of charges temporarily stores potential energy
. can only diffuse into the membrane through ATP
synthase, which sets the stage for ATP synthesis
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location of ATP synthesis in eukaryotes

mitochondrial membranes, between the
mitochondrial matrix and the outer intermembrane space

total possible production of ATP from aerobic respiration

. 2 from glycolysis

. 2 from Krebs cycle

. 34 from electron transfer

. energy is used transporting NADH across the mitochondrial membrane during glycolysis

alcoholic fermentation

. occurs in yeasts or bacterial species that have metabolic pathways for converting pyruvic acid to ethanol

. decarboxylation of pyruvic acid to acetaldehyde

. reduction of acetaldehyde to ethanol

. NADH formed during glycolysis is oxidized, regenerating NAD and allowing glycolysis to continue

homolactic fermentation

lactic acid bacteria reduce pyruvate to lactic acid mainly

heterolactic fermentation

glucose is fermented to a mixture of lactic acid, acetic acid, and carbon dioxide

lipases

break apart fatty acids joined to glycerol

beta oxidation

oxidation of fatty acids

proteases

. break down proteins into their amino acid components

. amino groups removed through deamination

. remaining carbon compound can be easily converted to one of several Krebs cycle intermediates