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Biochemistry > Coenzymes, Inhibitors and Allostery and Enzyme Complexes > Flashcards

Coenzymes, Inhibitors and Allostery and Enzyme Complexes Flashcards

1
Q

What is an enzyme?

A

A biological catalyst that speeds up a chemical reaction without undergoing any change by itself.

Speeds up rxn by lowering the activation energy

Generally made up of a protein part (apoenzyme) and a non-protein part (cofactor)

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2
Q

Cofactors/Coenzymes

A

Bind in the active site to help the bonding of the substrate and enzyme to function best!

Assist in stabilizing the TS dagger

Can ferry around electrons to next enzyme in pathway

Cofactors are inorganic (metals like Zinc or Iron) while coenzymes are organic (vitamins)

May be temporary or permanent

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3
Q

Prosthetic groups

A

Similar to coenzyme/cofactor but is tightly COVALENTLY bonded to enzyme; assists in stabilizing TS dagger; can deliver product to next enzyme, but only by handing it off DIRECTLY

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4
Q

Inhibitors

A

Reversible or nonreversible, depending on how they are bonded

Competitive (sit in the active site, blocking substrate from being able to bind) or non-competitive (bind someone other than the active site, known as the allosteric site; changes the enzyme shape so substrate cannot bind).

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5
Q

Prosthetic Group vs Coenzyme/Cofactor

A
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6
Q

Coenzyme vs Cofactor

A
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7
Q

Cofactors, coenzymes and prosthetic groups are required to:

A
  • Support redox rxns
  • Chaperone electrons from one pathway to another
  • Carry acyl groups from one pathway to another
  • Catalyze rxns that AA side chains cannot
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8
Q

D, E and H side chains CANNOT make a change in oxidation-reduction state more probable because…

A

they are charged AAs

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9
Q

B1

A

THIAMINE; Water soluble; formation of coenzyme thiamine pyrophosphate (TPP)

**Works with Lopoic acid to OXIDIZE acetyl groups **

Prosthetic group

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10
Q

B2

A

RIBOFLAVIN; Water soluble; formation of coenzymes FMN/FAD/FADH

FAD+/FADH2 catalyzes 2-electron redox rxns!

Prosthetic group

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11
Q

B3

A

NIACIN; Water soluble; formation of coenzymes NAD/NADP

NAD+/NADH2 are REDOX COFACTORS; can carry 2 electrons

Co-enzyme

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12
Q

B5

A

PANTOTHENIC ACID; Water soluble; formation of coenzyme A (CoA)

CoA carries ACYL GROUPS (-CO2-); part of LIGASES

Coenzyme

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13
Q

B6

A

PYRIDOXINE; Water soluble; formation of coenzyme pyridoxal phosphate (PLP);

PLP Catalyzes isomerases, ligase, and transferase rxns of AAs. AA METABOLISM DEPENDENT ON PLP

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14
Q

An enzyme involved in transfer of electrons is an…

A

oxido-reductase

therefore the two electron-carriers, Riboflavin and Niacin can change the oxido-reduction state

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15
Q

K

A

UBIQUINONE; formation of coenzyme Q10 (CoQ10);

Redox co-factor; carrier of 1 or 2-electrons

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16
Q

Lipoic Acid

A

We make; 2-electron redox and acetyl transfer -SH prosthetic group

17
Q

Fe, S Clusters

A

We make;
Catalyze 1 or more electron transfers

18
Q

Heterotropic vs Homotropic

A

Homotropic = ligand IS the substrate
Heterotropic = ligand is DIFFERENT from the susbtrate

19
Q

Positive HETEROtropic

A

Stabilizes high affinity (low Km) state, making enzyme with QUATERNARY structure MORE responsive to changes in [S]

20
Q

Negative HETEROtropic

A

Stabilizes low affinity (high Km) state, making enzyme with quaternary structure LESS ersponsive to changes in [S]

21
Q

Competitive inhibition

A

A ligand that COMPETES with substrate for binding at the ACTIVE SITE; apparent Km INCREASED

22
Q

Uncompetitive inhibition

A

A ligand that binds to ES resulting in a DECREASE in apparent Km and DECREASE in apparent Kcat

23
Q

Non-competitive inhibition

A

A ligand that binds to E AND ES resulting in a DECREASE in experimental Kcat

24
Q

Allostery

A

A conformational behavior reflected by the behavior “v” vs “s” data of an enzyme that is composed of 2+ subunits, independently folded protein units that associate via non-covalent interactions AND the hydrophobic effect

QUATERNARY STRUCTURE!

25
Q

POSITIVE Cooperativity

A

the allosteric behavior that is represented by an apparent INCREASE in affinity for S as [S] increases

makes “v” MORE responsive to changes in [S]

26
Q

NEGATIVE Cooperativity

A

the allosteric behavior that is represented by an apparent DECREASE in affinity for S or kcat as [S] increases

makes “v” LESS responsive to changes in [S]

27
Q

Feed-back Modulation

A

What a product down-stream in a metabolic pathway does to alter the substrate flux through an enzyme upstream in the pathway

Most common effect is to INHIBIT by a NEGATIVE COOPERATIVITY MECHANISM

28
Q

Monomeric Enzymes

A

Composed of single protein subunit; regulated by ligand binding at substrate binding site;

Results in competitive, non-competitive or uncompetitive inhibition = ALL LEAD TO DECREASE IN VELOCITY AT GIVEN S

29
Q

Quaaternary Enzymes

A

Composed of multiple subunits; regulated by cooperative substrate binding; cooperative behavior modulated by hetero-ligand that shifts them to positive/negative modulation

Results in being MORE SENSITIVE to changes in S aka MORE RESPONSIVE to their ligand

30
Q

Initial Velocity

A

The experimental velocity (rate) of P formation at beginning of rxn, when [S] hasn’t decreased and [P] ~ 0

31
Q

Steady-state

A

The period of the rxn when [ES] (and all other forms of the enzyme) is costant (steady). If [ES] doesn’t change, velocity doesn’t change since V=kcat[ES], the enzyme RATE EQUATION

32
Q

Michaelis-Menten-Henri Eq.

A

the rate equation for an enzyme catalyzed rxn

33
Q

Michaelis Complex

A

the complex of E with substrates (e.g. ES)

34
Q

Michaelis Constant

A

Km, number which is given by the [S] that supports 1/2 of the enzyme rxns max velocity

35
Q

Fractional Velocity/Fractional Saturation

A

the concept that the measured “V” is a reflection of the fraction of E that is “IN” ES

36
Q

Catalytic rate constant

A

kcat, the value that represents the probability of ES being on the ES dagger rung of the Boltzmann ladder

37
Q

The enzyme efficiency or catalyst number

A

Kcat/Km, value that represents the probability of S being on the ES dagger rung

Biochemistry (3 decks)

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