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Biochem 6200 > Lecture 3 Enzymes Ning > Flashcards

Lecture 3 Enzymes Ning Flashcards

1
Q

Enzymes

A

Catalyze thermodynamically possible biological reactions. Not changed by reaction or used up, doesn’t change reaction position or equilibrium, act by forming a transient complex with reactant, stabilizing transition state. Have optimum temp and pH.

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2
Q

Enzymes vs inorganic catalysts

A

Accelerate reactions in higher degree, higher specificity, more sensitive to temp and pH (enzymes made of proteins).

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3
Q

Most enzymes are optimum at

A

37 degC, pH 7. Enzymes will denature above 45-50 degC

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4
Q

Ex of prosthetic group

A

metalloenzymes have firmly bound metal ions at active site (copper, zinc, iron, cobalt). Vitamins are critical

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5
Q

Holoenzymes/complex

A

Protein and nonprotein parts

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6
Q

Apoenzyme

A

Protein part of holoenzyme

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7
Q

Cofactor

A

Nonprotein part of holoenzyme

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8
Q

Prosthetic group

A

Small inorganic molecule or atom usually. Tightly bound to apoenzyme typically.

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9
Q

Coenzyme

A

Large organic molecule loosely bound to apoenzyme. Act as group transfer reagents. Hydrogen, electrons or groups of atoms can be transferred. Metabolite coenzymes or vitamin-derived coenzymes.

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10
Q

Metabolite coenzymes

A

Synthesized from common metabolites.

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11
Q

Vitamin-derived coenzymes

A

Derivatives of vitamins.

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12
Q

Vitamins

A

Cannot be synthesized by animals, must be obtained via diet.

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13
Q

TPP

A

derivative of thiamine (vit B12). Participates in reactions of Oxidative decarboxylation, Transketo-lase enzyme reactions don’t worry about structure Coenzyme example

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14
Q

Pyridoxal Phosphate

A

PLP is derived from Vit B6 family of vitamins
PLP is a coenzyme for enzymes catalyzing reactions involving amino acid metabolism (isomerizations, decarboxylations, transamination). All of these - helping transfer a specific group from one molecule to another.

Coenzyme example

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15
Q

Oxidoreductases

A

Ared + Box→Aox + Bred, enzyme: Dehydrogenases, peroxidases, oxidases
Catalyze oxidation/reduction reactions.

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16
Q

Transferases

A

A-B + C→A + B-C, enzyme - Hexokinase, transaminases

Catalyze group transfer reactions - some amino acids formed this way.

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17
Q

Hydrolases

A

A-B + H2O→A-H + B-OH, enzyme = Alkaline phosphatase, trypsin

Catalyze hydrolysis reactions where water is the accepter of the transferred group.

esterases peptidases glycosidases

Pyrophosphate to 2 phosphate groups via phosphatase.

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18
Q

4. Lyases (synthases)

A

X-A-B-Y→A = B + XY, enzyme = fumarase, dehydratases

Catalyze lysis of a substrate, generating a double bond in a nonhydrolytic, nonoxidative elimination

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19
Q

5. Isomerases

A

A ⇌ isoA, enzyme =Triose phosphate isomerase, phosphogluco-mutase

Catalyze isomerization reactions

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20
Q

Ligases (synthetases)

A

A + B + ATP→A-B + ADP + Pi enzyme = Pyruvate carboxylase, DNA ligases

Catalyze ligation, or joining of two substrates
Require chemical energy (e.g. ATP)

Glutamine synthetase is an example.

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21
Q

Common names

A

-ase to end of substrate, don’t describe chemistry of reaction

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22
Q

Trivial names

A

Don’t give info about enzyme, substrate or product

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23
Q

Enzyme classification number

A 
EC: 2.3.4.2
First digit refers to a class of enzyme, second -to a subclass, third – to a subsubclass, and fourth means the ordinal number of enzyme in subsubclass
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24
Q

Active site

A

Specific region in the enzyme to which substrate molecule is bound (substrate is usually pretty small).

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25
Q

Characteristics of active site

A

Specificity (absolute, relative (group), stereospecificity), small 3D region of protein (only 3-5 AAs interact), Binds substrates through multiple weak interactions (noncovalent bonds), there are contact and catalytic regions in the active site.

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26
Q

Fischer theory

A

The enzyme active site (lock) is able to accept only a specific type of substrate (key)

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27
Q

Absolute Specificity

A

One enzyme one substrate

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28
Q

Relative specificity

A

one enzyme acts on different substrates which have the same bond type (example: pepsin splits different proteins)

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29
Q

Stereospecificity

A

Some enzymes can catalyze the transformation only substrates which are in certain geometrical configuration, cis- or trans. Don’t worry about when an enzyme is absolute or relative. Just another way to describe it.

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30
Q

Enzymatic activity def.

A

One international unit (IU) of enzyme catalyzes conversion of 1 µmol of substrate to product per minute

The specific activity of an enzyme is a measure of the number of IU/mg protein

31
Q

Rate of catalysis

A

At a fixed enzyme concentration [E], the initial velocity Vo is almost linearly proportional to substrate concentration [S] when [S] is small but is nearly independent of [S] when [S] is large. Rate rises linearly as [S] increases and then levels off at high [S] (saturated)

32
Q

ES complex

A

Intermediate enzyme-substrate complex

33
Q

Km

A

Michaelis constant - Km = 1/2Vmax. When Km is small, increase in substrate results in low increase in rate.

34
Q

Vo

A

initial velocity caused by substrate concentration, [S];
=Vmax[S]/(Km+[S])

35
Q

Vmax

A

Max velocity - plateau at top of graph

36
Q

Higher E concentration in fixed saturated S

A

greater initial reaction rate

37
Q

Enzyme inhibitors

A

metabolites, substrate analogs, toxins, drugs, metal complexes, binds to an enzyme and prevents the formation of ES complex or breakdown of it to E + P

38
Q

Reversible inhibitors

A

Three basic types of reversible inhibition: Competitive, Uncompetitive, Noncompetitive – after combining with enzyme (EI complex is formed) can rapidly dissociate
Enzyme is inactive only when bound to inhibitor

EI complex is held together by weak, noncovalent interaction

39
Q

Competitive inhibition

A

•Inhibitor has a structure similar to the substrate thus can bind to the same active site, higher concentration of substrate can kick it out.

40
Q

Ex of comp. inhibition

A

Benzamidine competes with arginine for binding to trypsin

41
Q

Noncompetitive inhibition

A
  • Binds to an enzyme site different from the active site
  • Inhibitor and substrate can bind enzyme at the same time

*Can help reaction, not just hurt it.

•Cannot be overcome by increasing the substrate concentration

42
Q

Uncompetitive inhibition

A

Uncompetitive inhibitors bind to ES not to free E

This type of inhibition usually only occurs in multisubstrate reactions

43
Q

Irreversible inhibitors

A

very slow dissociation of EI complex

Tightly bound through covalent or noncovalent interactions

3 types: group-specific reagents

  • substrate analogs
  • suicide inhibitors
44
Q

Group specific reagents

A

–react with specific R groups of amino acids

DIPF is an example.

45
Q

Substrate analogs

A

structurally similar to the substrate for the enzyme

-covalently modify active site residues

46
Q

Suicide inhibitors

A

Inhibitor binds as a substrate and is initially processed by the normal catalytic mechanism
•It then generates a chemically reactive intermediate that inactivates the enzyme through covalent modification

•Suicide because enzyme participates in its own irreversible inhibition (makes product that kills it).

47
Q

Regulation of enzyme activity

A

4 main methods: allosteric control, reversible covalent modification, isozymes, proteolytic activation.

48
Q

Allosteric enzymes

A

have a second regulatory site distinct from active site. Have quarternary structure. Noncompetitively inhibited enzymes are this.

49
Q

Allosteric modulator

A

Allosteric modulators bind noncovalently to allosteric site and regulate enzyme activity via conformational changes. Two types of modulators–positive and negative.

50
Q

Negative modulator

A

Bind to active site and inhibit enzyme action. Usually end product feeds back to stop reaction.

51
Q

End-product inhibition

A

exactly what it sounds like.

52
Q

Positive modulator

A

Binds to allosteric site and stimulates activity, usually rxn substrate.

53
Q

Isoenzymes/isozymes

A

Multiple forms of an enzyme which differ in amino acid sequence but catalyze the same reaction. kinetics,
regulatory properties,
the form of coenzyme they prefer and
distribution in cell and tissues

Isoenzymes are coded by different genes

Lactate dehydrogenase is a key example.

Isoenzymes are important for diagnosis of different diseases - acute myocardial infarction (large amount of LDH in heart, not elsewhere - opposite for hepatitis in liver).

54
Q

Lactate dehydrogenase

A

5 Isozymes of LDH:
Lactate to pyruvate (NAD+ goes to NADH)
H4 – heart -highest affinity best in aerobic environment
HM3
H2M2
H3M
M4 – liver, muscle -lowest affinity best in anaerobic environment

55
Q

Zymogens

A

Inactive precursors to enzymes - activated by proteolytic cleavage.

56
Q

Proteolytic cleavage

A

Proteolytic activation only occurs once in the life of an enzyme molecule, Examples of specific proteolysis

•Digestive enzymes
–Synthesized as zymogens in stomach and pancreas

•Blood clotting enzymes
–Cascade of proteolytic activations

•Protein hormones
–Proinsulin to insulin by removal of a peptide

57
Q

Multienzyme complexes

A

different enzymes that catalyze sequential reactions in the same pathway are bound together. Usually created when one enzyme that cuts others is cut.

58
Q

Multifunctional enzymes

A

different activities may be found on a single, multifunctional polypeptide chain

59
Q

Metabolite channeling

A

“channeling” of reactants between active sites. Occurs when the product of one reaction is transferred directly to the next active site without entering the bulk solvent. Can greatly increase rate of a reactions
Channeling is possible in multienzyme complexes and multifunctional enzymes

60
Q

pH sensitivity of enzymes results from

A

The effect of pH on the ionic charge of amino acid side chains of enzymes.

61
Q

Pepsin

A

Stomach, optimum pH is around 2

62
Q

metalloenzymes

A

have firmly bound metal ions at active site (copper, zinc, iron, cobalt).

63
Q

Group transfer reagents

A

transfer hydrogens, electrons, groups of atoms

64
Q

Lactate dehydrogenase

A

Oxidizes lactate to pyruvate, reduces NAD+ to NADH.

65
Q

Pyruvate decarboxylases

A

Lyase - converts pyruvate + H+ to acetaldehyde and CO2

66
Q

Lysozyme

A

Active area has 6 AA residues which are far apart in sequence.

67
Q

Active site functional groups

A

-OH, -NH, -COO to name a few. Bind through weak interactions (noncovalent).

68
Q

Salt bridge

A
  • to + interaction
69
Q

Hydrophobic pocket

A

Exactly what it sounds like

70
Q

Small hydrophobic pocket

A

Exactly what it sounds like - built around target size.

71
Q

Hexokinase, Glucokinase

A

Add phosphate group to glucose. Glucokinase is much faster, Km is much larger.

72
Q

Penicillin

A

Competitive inhibition. Enzyme that links bacterial cell walls caught up with penicillin. Not a bacteriocidal drug, just prevents bacterial growth.

73
Q

Phosphorylation

A

Covalently add phosphate group to enzyme, you can make it more or less active.

74
Q

Proenzyme

A

Enzyme activated by cuts. Can lead to cascade by activating other enzymes.

Biochem 6200 (18 decks)

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