Biokenetics

Question 1

Properties of Enzymes

Answer 1

Biological catalysts
Highly specific
Extremely fast
Regulated

Question 2

Catalyst

Answer 2

A molecule that accelerates a chemical reaction and is regenerated at the end of the reaction

Question 3

Active Site

Answer 3

Amino acids come together in tertiary structure but not in primary structure. Think 3D space

Question 4

Substrates bind reversibly

Answer 4

Hydrogen bonds
Electrostatic forces: ionic and dipole-dipole
Hydrophobic forces
Numerous weak interactions add up to allow tight binding of substrate to enzyme

Question 5

Activation energy

Answer 5

Minimal energy required for 2 molecules to react
Difference between ground state and activation state
What the enzyme alters
Lower ae means that more molecules have the energy to react at physiological temp

Question 6

Catalytic Strategies of Enzymes

Answer 6

Proximity (all)
Transition state stabilization (all)
Covalent catalysis or nucleophilic catalysis (some)
General acid base catalysis (most)
Metal ion catalysis (some)

Question 7

Chymotrypsin Oxyanion hole

Space in enzyme active site that binds a negatively charged group

Answer 7

Stabilizes transitional state
Between serine’s N and glycine
Tetrahedral has an O- part that goes in the Oxyanion hole and hence t-state is stabilized
H donates proton to amine to facilitate acyl-enzyme formation so H is a general acid which donates a proton
So active site has more interactions with transition state than with substrate

Question 8

Km

Answer 8

Concentration of substrate at which enzyme is working at half it’s max capacity
Measure of affinity of substrate for enzyme
Characteristic for an enzyme for a particular substrate
Independent of [E] or [S] but is dependent on temp and pH
Usually close to physiological substrate conc. This is good for regulation

Question 9

Vmax

KCAT

Answer 9

Vmax: max velocity an enzyme can work at; linearly dependent on [E]
Kcat= vmax/e known as the turnover number, reflecting number of moles of substrate to product per s per mol of enzyme; constant for an enzyme, only changes with pH or temp

Question 10

Apoenzymes
Isoenzymes
Zymogens

Answer 10

Apoenzymes: require cofactors (metals/ions) or coenzymes (small organic molecules derived from vitamins) to work ; without them, they’re inactive.
Isoenzymes: perform same fn in different tissues. Thought to originate from gene duplication and divergence
Zymogens: need to be altered to be activated. Think pepsinogen

Question 11

Regulation of enzyme activity

Answer 11

Compartmentation: cell organelles
Enzyme concentration: Synthesis and degradation
PT modifications
Regulatory proteins: TF, etc.
Inhibitors: feedback inhibitors, enzyme inhibitors, products
Activation: feedback activation

Question 12

Allosteric enzymes

Answer 12

Active site and an allosteric site
All are oligomeric (multiple subunits)
Allosteric molecules don’t resemble substrate molecules
Sigmoidal curves rather than hyperbolic (hyperbolic for enzymes following michaelis-menten kinetics) k0.5 rather than km
2 types of activators/inhibitors: k-type (k0.5 is affected, vmax isn’t) and v-type (k0.5 isn’t affected, vmax is)

Question 13

Enzyme inhibition

Answer 13

2 types:
1) irreversible inhibitors: bind covalently to active site to inhibit activity
2) reversible inhibitors:
A) competitive: bind on active site, change km not vmax
B) noncompetitive: don’t bind on active site (subtle difference between this and allosteric, allosteric is on another domain, noncompetitive isn’t) change vmax, not km