CH 10: Micro Exam 3

metabolism two parts

catabolism and anabolism

steps of enzyme catalyzed reaction

1. substrate binds to enzyme active site

2. formation of transition state complex

3. activation energy lowered

4. product released

metabolism simple definition

total of all chemical reactions in the cell

catabolism 4 parts

fueling reactions

energy conserving reactions

provide reducing power

generate precursors

anabolism 2 parts

the synthesis of complex organic molecules

requires energy

does microbe metabolism cover all major nutritional cycles

yes, there are representatives in all five major nutritional cycles (C, N, P, S, H2O)

how many steps of the N cycle is done by microbes

4 are solely done by microbes

4 include microbes

calorie (cal)

energy needed to raise 1 gram of water 1°C

joules (J)

1 cal of heat is equivalent to 4.1840 J of work

exergonic reactions

ΔG° is negative, faster, releases energy

reaction proceeds spontaneously

endergonic reactions

ΔG° is positive, slower, requires energy

reaction does not proceed spontaneously and will favor reactants

role of ATP in metabolism

endergonic reactions coupled w ATP breakdown (ATP → ADP + Pi) will favor products; or a coupling agent that links energy releasing reactions w/ energy requiring

• composed of two high energy bonds

ATP, GTP, CTP, UTP

• adenosine 5’-triphosphate (ATP): primary energy currency

• guanosine 5’-triphosphate (GTP): energy for protein synthesis

• cytidine 5’-triphosphate (CTP): RNA synthesis, lipid synthesis

• uridine 5’-triphosphate (UTP): RNA synthesis, peptidoglycan synthesis

which triphosphate has a high phosphate transfer potential

ATP; it donates a phosphoryl group

low to high energy phosphate transfer potential

1. glycerol 1-phosphate

2. glucose 6-phosphate

3. ATP → ADP

4. ATP → AMP

5. 1,3-biphosphoglycerate

6. phosphoenolpyruvate

substrate level phosphorylation (SLP)

direct production of ATP by transferring a phosphate group from a high energy organic molecule to ADP (ADP + high energy substrate = ATP); also synthesis of high energy phosphate bonds through rxn of inorganic phosphate w/ an activated organic substrate

• does not need O

• does not need ETC

• does not need proton gradient

redox

• oxidizing reaction and reducing reaction

• acceptor and donor are a conjugate redox pair

  • oxidized form + e- → reduced form

standard redox potential (E’_°)

• in volts (V)

• more negative E_° means a better e- donor

• more positive E_° means a better e- acceptor

two rules of redox pairs

1. reduced member that is more negative donates e- to oxidized member that is more positive

2. the greater the difference (ΔE’_°) the greater the energy available (ΔG°’)

comparing two redox pairs

1. pick two pairs

   1. NAD⁺ + 2H⁺ + 2e- → NADH + H⁺ (-0.32 V)

   2. ½ O2 + 2H⁺ + 2e- → H2O (+0.82 V)

2. rule #1: NADH donates to O2

   1. picture**

3. rule #2: ΔE’_° = (E’_° of oxidized) - (E’_° of reduced)

substance being oxidized

electron donor/ reducing agent/ reductant

substance being reduced

electron acceptor/ oxidizing agent/ oxidant

calculating ΔG°’

ΔG°’ = -n F ΔE’_° = -(2 equiv of e-) (23 kcal/volt equiv) (ΔE’_°)

most negative E’_°

first e- carrier

where is the ETC found

mitochondria or chloroplast in eukaryotes and cell membrane of prokaryotes

main e- carriers of ETC

• NADH and NADPH

• FAD and FMN

• CoQ / Ubiquinone

• Cytochromes

• Nonheme iron-sulfur proteins

NADH and NADPH carrier

two e- and one proton

FAD and FMN carrier

two e- and two protons; flavoproteins

CoQ / Ubiquinone carrier

two e- and two protons; lipids

Cytochromes carrier

one e- at a time; iron is part of a heme group

Nonheme iron-sulfur protein carrier

one e- at a time; ferredoxin; iron is not part of a heme group

biochem pathways

• pathways: linear, cyclic, branching

• substrate, intermediate, end product

• pathway overlap: complex network, dynamic pathways (monitor changes in metabolite levels)

enzyme overview

proteins that carry out reactions at physiological conditions and speed up rate without altering the equilibrium; catalysts

lyase

dissociates molecules, breaks covalent bonds w/o using water, oxidation, or reduction

A → B + C

ligase

joins two molecules together, forms covalent bonds between two molecules

A + B → AB

isomerase

rearranges bonds of a molecule, a reactant forms one of its isomers

A → B

transferase

transfers a functional group from one molecule to another

A + BX → AX + B

hydrolase

uses water to cleave a molecule, breaks covalent bonds with water

A + H2O → B + C

oxidoreductase

transfers electrons from one molecule to another, alters oxidation state of reactants

A + B: → A: + B

enzyme composition

• one or more polypeptides

• holoenzyme: one or more polypeptides (apoenzyme) and nonprotein components (cofactor- either prosthetic group (tight) or coenzyme (loose))

mechanism of enzyme reactions

transition state complex, activation energy (Ea), and enzyme speeding up reaction by lowering E_a

how do enzymes lower E_a

• increasing concentrations of substances at active or catalytic site

• orienting substrates properly

• induced fit model for enzyme substrate interaction

enzyme activity changes due to what

• substrate concentration (K_m)

• pH

• temperature

• denaturation

saturation

happens when reaction rate increases as the [substrate] increases

enzyme inhibition

• competitive: blocks substrate binding

• noncompetitive: substrate binds but is blocked by inhibitor at allosteric site

ribozymes

• RNA

• catalyze peptide bond formation

• self-splicing

• involved in self-replication

regulation of metabolism general

metabolism must be regulated to maintain homeostasis and prevent waste

• conservation of energy and materials

• maintenance of metabolic balance

3 major mechanisms for regulating metabolism

• metabolic channeling

• gene expression- transcription and translation

• post-translation- irreversible and reversible

allosteric regulation

reversible process, uses allosteric effectors on regulatory sites (positive or negative), most are regulatory enzymes, use non covalent bonds, form of post translational regulation

allosteric inhibition

inhibitor binds to allosteric site on enzyme causing a conformational change to block substrate binding

allosteric activation

activator binds to allosteric site on enzyme changing an altered active site to allow substrate binding

covalent modification of enzymes

reversible; addition or removal of a chemical group

• phosphorylation (by kinase and phosphatase)

• methylation

• ubiquitination

• glycosylation

• adenylylation

feedback / end-product inhibition

end-product: single end product inhibits first enzyme in biosynthetic pathway

feedback: multiple end products each inhibit different enzyme in branched pathway

pacemaker enzyme

controls overall rate of pathway, not always first enzyme

ex. phosphofructokinase (PFK1) irreversible step in glycolysis

isoenzymes

look different than pacemaker enzymes but do the same thing (controls overall rate of pathway)

ex. lactate dehydrogenase’s (LDH) 5 isoenzymes in different tissues