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Tri 1 - BioChem > Topic 4 > Flashcards

Topic 4 Flashcards

1
Q

enzymes

A

biological catalysts
reaction specific
increase rate of biochemical concentrations
decrease activation energy (lower free energy)
remain unchanged
specific for their substrates/products

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2
Q

cofactor

A

metal ions required by enzymes for optimal activity

e.g. Fe2+, Mg2+, Mn2+, Zn2+

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3
Q

coenzyme

A

larger complex organic/metallo-organic molecules
bound to apoprotein covalently or noncovalently
e.g. vitamins

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4
Q

holoenzyme

A

active enzyme
complete catalytic activity
= apoenzyme + bound coenzyme/cofactor

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5
Q

apoenzyme

A

inactive protein part of the enzyme

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6
Q

prosthetic group

A

non-amino acid group covalently bound to enzyme

e.g. carb moiety attached to glycoprotein

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7
Q

apoprotein

A

protein which together with a prosthetic group forms a particular biochemical molecule such as a hormone or enzyme

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8
Q

coenzyme functions

A

group transfer reactions (transient carriers of specific functional groups)
cosubstrate or 2nd substrate

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9
Q

group transfer reactions

A

AF + C = A + FC

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10
Q

cosubstrate

A

chemical changes in coenzymes counter-balance those occurring in the substrate

e. g.
1. redux: one molecule of substrate is oxidized, one molecule of coenzyme is reduced
2. transamination rx: pyridoxal phosphate acts as 2nd substate in two concerted reactions and as a carrier of an amino group between different alpha-keto acids

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11
Q

examples of coenzymes

A 
biotin
panthothenic acid
vitamin B12
riboflavin
niacin/nicotinamide
pyridoxine (B6)
folate
thiamine (B1)
endogenously produces S containing FA
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12
Q

examples of cofactors

A 
Cu2+ (copper)
Fe2+/3+ (iron)
K+ (potassium)
Na+ (sodium)
Mg2+ (magnesium)
Mn2+ (manganese)
Se (selenium)
Zn2+ (zinc)
Mo (molybdenum)
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13
Q

enzyme nomenclature

A

based on chemical reaction type & reaction mechanism
1st part indicates substrate
2nd part indicates type of reaction catalyzed
always ends in -ase

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14
Q

class 1 enzymes

A

oxidoreductases

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15
Q

class 2 enzymes

A

transferases

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16
Q

class 3 enzymes

A

hydrolases

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17
Q

class 4 enzymes

A

lyases

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18
Q

class 5 enzymes

A

isomerases

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19
Q

class 6 enzymes

A

ligases

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20
Q

oxidoreductase

A

catalyze oxidation-reduction reactions
transfer of electrons
aka oxidase, dehydrogenase, reductase, monooxygenase, dioxygenase
e.g. ethanol –> acetaldehyde

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21
Q

transferase

A

group transfer

e.g. glucose –> glucose 6-phosphate

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22
Q

hydrolase

A

breaking of bonds with H2O

e.g. ether, peptide, glycosyl, acid anhydride, C-C, C-halide, P-O-P, etc

23
Q

lyase

A

breaking of bonds w/o H2O

e.g. fumarate –> L-malate

24
Q

isomerase

A

transfer of groups to form isomeric forms

e.g. dihydroxyacetone phosphate –> glyceraldehyde 3-phosphate

25
Q

ligase

A

formation of bonds by condensation coupled to cleavage of ATP or similar coenzymes
e.g. bicarbonate + pyruvate = oxaloacetate

26
Q

substrate

A

binds to a specific active substrate-binding site on an enzyme

27
Q

enzyme + substrate

A

must be complementary with their geometry, stereospecificity, and charge distribution

28
Q

E + S binding

A

non-covalent forces such as:
van der Waals
H-bonding
hydrophobic forces

29
Q

lock and key model

A

E + S ES EP E + P

30
Q

E + S interaction

A

increase reaction rates
reaction equilibrium unaffected
may form transient covalent bonds
may transiently transfer group from S –> E

31
Q

energy barriers

A

energy is needed to align reacting groups
formation of transient unstable charges
bond rearrangement
transformation
must be activated to higher energy levels for reaction

32
Q

Gibbs free energy

A

energy content in a system that can be converted to do work at a constant temperature and pressure

33
Q

activation energy

A

difference between ground state and the transition state

34
Q

role of enzymes

A

increase rate of chemical rx by decreasing activation energy

rx rates enhanced by increasing temp, pressure and catalyst

35
Q

non-covalent reactions in enzymes

A

generate binding energy; used to build catalytic power

36
Q

catalytic strategies

A
  1. proper positioning of functional groups
  2. acid-base catalysis: proton donor/acceptor interacting with substrate
  3. covalent catalysis: transient covalent bond between E + S e.g. vitamins
  4. metal ion catalysis: ionic interaction between E-bound metal ion and S e.g. Mg2+ with ATPase
37
Q

effects of [S]

A

gradual increase in [S] increases reaction velocity (V0) until E is saturated. Vmax is reached at highest [S]

38
Q

equilibrium constant

Michaelis constant

A

E + S ES –k3> P

Km = (k2 + k3)/k1

39
Q

km

A

is the substrate concentration at 1/2 Vmax

40
Q

Michaelis-Menten equation

A

V0 = Vmax[S]/(Km +[S])

41
Q

Lineweaver-Burk plot

A

double reciprocal of Michaelis-Menten

1/V0 = Km/Vmax[S] + 1/Vmax

42
Q

enzyme activity

A

concentrations of product forms per unit time

43
Q

specific activity of enzyme

A

concentrations of product formed per unit time per unit concentration of the enzyme

44
Q

types of reversible inhibition

A

competitive
uncompetitive
mixed/noncompetitive

45
Q

competitive inhibition

A

binds to the enzyme’s substrate binding site
EI I + E + S ES –> E + P
Vmax unchanged
Km increases

46
Q

uncompetitive inhibition

A 
affects catalytic function, not substrate binding 
E + S  ES --> E + P 
or 
E + S  ES + I  ESI
Vmax decreases
Km decreases
47
Q

noncompetitive (mixed) inhibition

A

inhibitor binds at separate site, but may bind to either E or ES
Vmax decreases
Km unchanged

48
Q

irreversible inhibition

A

from covalent linkage with required functional group in the active site or partially pretty stable non-covalent linkage
enzyme becomes completely inactive
e.g. aspirin, lead, calcium, mercury, sulfhydryl groups

49
Q

mechanisms of regulation

A 
allosteric
negative/positive feedback
tissue specific isozymes
alteration of active binding sites
regulation off enzyme concentration
regulation of [S] and [P]
50
Q

regulation through conformational changes

A

allosteric modification, reversible non-covalent, with positive modulator
reversible covalent

51
Q

protein-protein interaction

A

separate regulatory proteins can bind to enzyme and can either stimulate or inhibit
Ca2+-calmodulin complex binds to Ca2+-calmodulin-dependent protein kinase

52
Q

irreversible regulation

A

when peptide segments are removed by proteolytic cleavage, activating the enzyme
chymotrypsinogen –> chymotrypsin
trypsinogen –> trypsin

53
Q

feedback inhibition

A

formation of isoleucine from threonine uses 5 enzymes E1-E5. End product inhibits E1.

54
Q

examples of reversible covalent modification

A 
phosphorylation (tyr, ser, thr, his)
adenyiylation (tyr)
acetylation (lys, amino terminus)
myristoylation (amino terminus)
ubiquitination (lys)
ADP-ribosylation (arg, gln, cys, diphtamide-mod his)
methylation (glu)

Tri 1 - BioChem (6 decks)

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