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Tri 1 - BioChem > Topic 4 > Flashcards

Topic 4 Flashcards

(54 cards)

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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

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A

breaking of bonds with H2O

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

23
Q

lyase

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A

breaking of bonds w/o H2O

e.g. fumarate –> L-malate

24
Q

isomerase

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A

transfer of groups to form isomeric forms

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

25
ligase
formation of bonds by condensation coupled to cleavage of ATP or similar coenzymes e.g. bicarbonate + pyruvate = oxaloacetate
26
substrate
binds to a specific active substrate-binding site on an enzyme
27
enzyme + substrate
must be complementary with their geometry, stereospecificity, and charge distribution
28
E + S binding
non-covalent forces such as: van der Waals H-bonding hydrophobic forces
29
lock and key model
E + S ES EP E + P
30
E + S interaction
increase reaction rates reaction equilibrium unaffected may form transient covalent bonds may transiently transfer group from S --> E
31
energy barriers
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
Gibbs free energy
energy content in a system that can be converted to do work at a constant temperature and pressure
33
activation energy
difference between ground state and the transition state
34
role of enzymes
increase rate of chemical rx by decreasing activation energy | rx rates enhanced by increasing temp, pressure and catalyst
35
non-covalent reactions in enzymes
generate binding energy; used to build catalytic power
36
catalytic strategies
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
effects of [S]
gradual increase in [S] increases reaction velocity (V0) until E is saturated. Vmax is reached at highest [S]
38
equilibrium constant | Michaelis constant
E + S ES --k3> P | Km = (k2 + k3)/k1
39
km
is the substrate concentration at 1/2 Vmax
40
Michaelis-Menten equation
V0 = Vmax[S]/(Km +[S])
41
Lineweaver-Burk plot
double reciprocal of Michaelis-Menten | 1/V0 = Km/Vmax[S] + 1/Vmax
42
enzyme activity
concentrations of product forms per unit time
43
specific activity of enzyme
concentrations of product formed per unit time per unit concentration of the enzyme
44
types of reversible inhibition
competitive uncompetitive mixed/noncompetitive
45
competitive inhibition
binds to the enzyme's substrate binding site EI I + E + S ES --> E + P Vmax unchanged Km increases
46
uncompetitive inhibition
``` affects catalytic function, not substrate binding E + S ES --> E + P or E + S ES + I ESI Vmax decreases Km decreases ```
47
noncompetitive (mixed) inhibition
inhibitor binds at separate site, but may bind to either E or ES Vmax decreases Km unchanged
48
irreversible inhibition
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
mechanisms of regulation
``` allosteric negative/positive feedback tissue specific isozymes alteration of active binding sites regulation off enzyme concentration regulation of [S] and [P] ```
50
regulation through conformational changes
allosteric modification, reversible non-covalent, with positive modulator reversible covalent
51
protein-protein interaction
separate regulatory proteins can bind to enzyme and can either stimulate or inhibit Ca2+-calmodulin complex binds to Ca2+-calmodulin-dependent protein kinase
52
irreversible regulation
when peptide segments are removed by proteolytic cleavage, activating the enzyme chymotrypsinogen --> chymotrypsin trypsinogen --> trypsin
53
feedback inhibition
formation of isoleucine from threonine uses 5 enzymes E1-E5. End product inhibits E1.
54
examples of reversible covalent modification
``` 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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