BIOCHEMISTRY REVIEWER

ELASTIN

- Vs collagen: more rubberlike, scant hydroxyproline and hydroxylysine

- Precursor: tropoelastin (binds to fibrillin – functions as a ‘scaffold’)
Lysyl oxidase – oxidatively deaminates lysyl side chains to form allysine residues
- Three allyysyl side chains + one unaltered lysyl side chains -> desmosine cross-links

Role of alpha-1 antitrypsin (AAT)

- Inhibits elastase, an enzyme produced in low quantities by activated and degrading neutrophils
in the lungs, which may cause alveolar wall degradation
- Produced mainly in the liver
- Most common deficiency is caused by replacement of glutamic acid (GAG) to lysine (AAG) in
position 342 of the protein
- Causes emphysema
- Exacerbated by smoking (causes oxidation and thus inactivation of methionine which is required
for binding of AAT to elastase)

ENZYMES

Six major classes:

1. Synthetase – requires ATP
2. Synthase – no ATP required
3. Phosphatase – uses water to remove phosphoryl group
4. Phosphorylase – uses inorganic phosphate to break a bond and produce a phosphorylated
product
5. Dehydrogenase – NAD+/FAD is an electron acceptor in a redox reaction
6. Oxidase – oxygen is the acceptor and oxygen atoms are not incorporated into the substrate
7. Oxygenase – one or two oxygen atoms are incorporated

Terms:
1. Holoenzyme – active enzyme with its nonprotein component
2. Apoenzyme – enzyme without its nonprotein component; inactive
3. Cofactor – if the nonprotein moiety is a metal
4. Coenzyme – if the nonprotein moiety is a small organic molecule; commonly derived from
vitamins
a. Co-substrate – Only transiently associate with the enzyme; dissociate from the enzyme in an
altered state (i.e. NAD+ - contains niacin)
b. Prosthetic group – if permanently associated with the enzyme (i.e. FAD – contains
riboflavin)

Isozyme – tissue-specific forms of an enzyme; catalyze the same reaction but differ in their amino acid
composition (primary structure)
 The lower the free energy of activation, the faster the
reaction rate. Enzymes lower the free energy of activation
by (1) providing an alternate, energetically favorable
reaction pathway and (2) stabilizing the transition state of
this pathway.

Enzymes have no effect on the delta G of a reaction.

Kinases – catalyze phosphorylated reactions using ATP as

the phosphate source (opposite: phosphatase)
Infantile tyrosinemia: treated with Nitisinone which
decreases production of the substrate for hydrolase, thus
reducing the reaction velocity (mechanism: substrate
reduction therapy)

MICHAELIS-MENTEN KINETICS
- Describes how reaction velocity varies with
substrate concentration

E + S <-> ES <-> E + P

Assumptions:
1. [S] >>>> [E]
2. Steady state assumption: concentration of [ES] does not change with time (rate of formation
is equal to the rate of breakdown)
3. At the start of the reaction, the concentration of product is very small and thus the rate of
the back reaction is negligible.
Conclusions:
1. Michaelis constant (Km) – reflects the affinity of an enzyme for its substrate; numerically equal
to the substrate concentration at which the reaction velocity is equal to ½ Vmax; not affected by
enzyme concentration
o Low Km: high affinity
o High KM: low affinity
2. Rate of reaction is directly proportional to enzyme concentration.
3. First order reaction: [S] <<< Km; rxn velocity is thus directly proportional to substrate
concentration
Zero order reaction: [S] >>> Km: rnx velocity is constant and independent of substrate
concentration
INHIBITION OF ENZYME ACTIVITY
1. Competitive inhibition: apparent Km increases
2. Noncompetitive inhibition: decrease in apparent Vmax; Km is not affected

BIOENERGETICS

Enthalpy: measure of the change in heat content of the reactants and products
Entropy: measure of the change in randomness or disorder of the reactants and products

Free energy (G): predicts the direction in which a reaction will proceed; measure of the capacity of a
system to do work as it proceed to equilibrium
∆G: represents the change in free energy at any specified concentration of reactants and products
If negative: reaction is exergonic; reaction will proceed forward
If positive: reaction is endergonic;
0
∆G (standard free energy change): energy change when the reactants and products are at concentration
of 1 mol/L; constant

OXIDATIVE PHOSPHORYLATION: coupling of electron transport with ATP synthesis

Electron transport chain

Two mobile carriers:
1. Coenzyme Q (CoQ): lipid-soluble (accepts e- from several mitochondrial dehydrogenases); links
the flavoprotein dehydrogenases to cytochromes
2. Cytochrome C: protein in the intermembrane space; contains a heme group (porphyrin ring +
iron); iron is reversibly converted to its ferric to ferrous form to facilitate electron transfer;
loosely associated with the outer face of the inner membrane

**No energy is lost and no protons are pumped at Complex II

Complex IV (cytochrome c oxidase): only electron carrier in which the heme iron has an available
coordination site that can react directly with O2; where O2 is reduced to water; contains copper atoms
Complex V: ATP synthase

PRIMARY CoQ DEFICIENCY: will decrease ATP production due to impedance of e- transfer from
complexes I and II; manifests as muscle weakness and exercise intolerance
CYANIDE POISONING: binds and inactivates Complex IV

Site-specific inhibitors: all e- carriers before the block are reduced while those after are oxidized
Reperfusion injury: incomplete reduction of O2 to water (caused by the rapid return of O2) produces
ROS which damage DNA and proteins and cause lipid peroxidation
 ‘antioxidant’ enzymes: superoxide dismutase, catalase, glutathione peroxidase

Electrons are transferred as:

- Hydride ions to NAD+
- Hydrogen atoms to FMN, CoQ, and FAD
- Electrons to cytochromes
Oligomycin: inhibits H+ flux through the Fo domain of ATP synthase

MEMBRANE TRANSPORT SYSTEMS:

Adenine nucleotide antiporter: imports one ADP from the cytosol into the matrix while exporting one
ATP from the matrix into the cytosol
Transporter: moves an inorganic phosphate from the cytosol into mitochondria

Transport of reducing equivalents:

Glycerophosphate shuttle: delivers e- to the ETC via FADH2; results in the synthesis of 2 ATPs
Malate-aspartate shuttle: delivers e- via NADH; 3 ATPs synthesized; more efficient