Microbio Chapter 10: Introduction to Metabolism

Metabolism

total of all chemical reactions in the cell

What is metabolism divided into

Catabolism and Anabolism

Calorie (cal)

energy needed to raise 1g of water up 1 C

Joules (J)

1 cal = 4.184 J

Kilocalorie (kcal)

1000 calories

Exergonic reactions

standard free energy change is negative

reaction proceeds spontaneously

Endergonic reactions

standard free energy change is positive

reaction is not spontaneous

GTP is used in

protein synthesis

CTP is used in

Lipid synthesis

UTP is used in

peptidoglycan synthesis

ATP has a high…

phosphate transfer potential which means that it donates a phosphoryl group

What is substrate level phosphorylation (SLP)

Process in which ATP is made from ADP by adding a phosphoryl group

What happens during Redox

electrons move from a donor to an acceptor

Oxidized reaction…

loses electrons

Reduced reaction…

gains electrons

Standard redox potential (E’0)

• measures the tendency of the donor to lose electrons

  • more negative = better donor

  • more positive = better acceptor

• measured in volts

Redox Rules

1. reduced member of the pair that is more negative donates electrons to the oxidized member of the more positive pair

   1. difference in redox potential the greater amount of energy available

Substance being oxidized

electron donor / reducing agent / reductant

Substance being reduced

electron acceptor / oxidizing agent / oxidant

Nernst equation

DG⁰’    = -n F DE’₀

Faraday’s constant (F)

23 kcal/volt

96.5 kJ/volt

ETC

• First electron carrier = most negative E’0

• ETC is found

  • Eukaryotes: inner mitochondria or chloroplast

  • Prokaryotes: cell membrane

• As e- pass from one carrier to next, a small amount of energy is released at each step

NADH and NADPH

two electrons and one protons

FAD and FMN

two electrons and two protons

flavoproteins

CoQ/ubiquinone

two electrons and two protons

lipid

lipophilic, embedded in the membrane itself

Nonheme iron-rulfur proteins

one electron at a time

ferredoxin

iron is not part of a heme group

What do enzymes do

carry out reactions at physiological conditions

• speed up the rate

  • by lowering activation energy

• do not alter the equilibrium

• includes catalysts

What kind of bonds do enzymes use

noncovalent bonds

Lyase

breaks covalent bonds without using water or redox

Ligase

joins two molecules together via covalent bonds

• uses ATP

Isomerase

rearranges bonds of a molecule

Transferase

transfers a functional group from one molecule to another

Hydrolase

breaks covalent bonds using water

Oxidoreductase

transfers electrons from one molecule to another

Enzmyes are composed of

polypeptide(s) (apoenzyme) and nonprotein components (cofactor) forming the haloenzyme

Cofactors

• non protein component

• prosthetic group

  • covalently binds

• coenzyme

  • loosely attached

    • can attach/deattach to activate/deactivate the enzyme

How do enzymes lower the activation energy

• increasing [substrate]

• orienting substrates properly

• induced fit model

  • ex. hexokinase

What increases reaction rate

increased [substrate]

• can reach saturation

How can enzyme activity change

• [substrate] (Km)

  • low value = high affinity

• pH + temperature

  • beyond optimal range and it will denature

Competitive Inhibitors

competes for the same binding site

• ex. Sulfa drugs and PABA

Noncompetitive Inhibitors

binds to the allosteric site that inhibits the reaction

• changes the shape of the site

  • substrate still binds

Ribozyme

catalytic RNA molecules

• peptide bond formation

  • translation

• self-splicing

  • post-transcription

• self-replication

  • supports RNA World hypothesis

• RNase P

  • processes tRNA precursors by cleaving 5’ leader sequence

What are the mechanisms of regulating metabolism

• Metabolic channeling (compartmentalization)

  • allows for simultaneous but separate operation and regulation of similar pathways

• gene expression

  • transcriptional and translational

• post translational

  • irreversible

    • ex. cleavage of a protein

  • reversible

    • ex. allosteric regulation + covalent modifications

Allosteric effector

binds noncovalently and changes the shape of the enzyme

Positive effector

• alters active site to allow substrate to bind

  • increases enzyme activity

Negative effector

• prevents substrate from binding

• decreases enzyme activity

Covalent modifications of enzymes

addition or removal of a chemical group

• phosphoryl, methyl, adenylyl

Pacemaker enzyme

• catalyzes the rate limiting step of a pathyway

• first enzyme

• may be catalyzed by several isoenzymes

Isoenzymes

different forms of the same enzyme that catalyze the same reaction

• allows for the pathway to slow down if the product is in excess

What can end-products regulate

• its own branch

• initial pacemaker enzyme

What is the holoenzyme

the complete, active form of an enzyme

What is a holoenzyme composed of

• apoenzyme: polypeptide(s)

  • inactive protein part

• cofactor: non-protein component

  • helps enzyme to function

Catabolism

• fueling reactions

• energy-conserving reactions

• provide reducing power

• generate precursors

Anabolism

• synthesis of complex organic molecules

  • requires energy

ADP

beta phosphate

AMP

alpha phosphate

ATP

gamma phosphate

Lowest to highest phosphate transfer potential

• G1P

• G6P

• ATP → ADP

• ATP → AMP

• 1,3-BPG

• PEP

Steps in an Enzyme-Catalyzed Reaction

1. substrate binds to enzyme active site

2. formation of transition-state complex

3. activation energy lowered

4. product released

What does catabolism use as an electron carrier

NAD+/NADH and FAD/FADH2

What does anabolism use as an electron carrier

NADP+/NADPH