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Biochemistry > Lecture 9-10: Theisen > Flashcards

Lecture 9-10: Theisen Flashcards

1
Q

Oxioreductases

A

Transfer electrons from a donor to an acceptor

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2
Q

Transferases

A

Transfer a functional group between molecules

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3
Q

Isomerases

A

Rearrange/isomerize molecule

Intramolecular

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4
Q

Lyases

A

“Synthases” add or remove atoms to or from a double bond (from water, ammonia, CO2)

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5
Q

Ligases

A

Synthetases-form bonds w/ hydrolysis of ATP

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6
Q

Hydrolases

A

Cleave bonds via the addition of water-hydrolysis

Transfers functional groups to water

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7
Q

Catalysts

A

Increasing the rate of chemical reactions

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8
Q

How do enzymes affect energy of activation?

A

By forming an enzyme-substrate complex—lowering the energy of activation

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9
Q

Enzymes get substrates to their:

A

Transition state

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10
Q

Uncatalyzed rate w/ carbonic anhydrase

A

Significantly slower [ 10-1 vs 10^6] -1,000,000 X / sec

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11
Q

Sir Archibald Edward Garrod

A

1st making connection btw disease and fundamental errors in biochem. Rxn’s. [alkaptonuria] coined the term inborn errors of metabolism

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12
Q

2 Reaction drivers:

A

Mass action [Le Chatelier’s Principle]

Coupled reactions [input of energy]

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13
Q

MAss action / Le Chatelier’s

A

Increase in [ ] of products= more reactants
Increase [ ] of reactants = more products

Opposite direction from adjustment made

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14
Q

Coupled reactions [input of energy]

A

Coupling rxn’s is possible if they share a common intermediate

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15
Q

What increases rxn velocity?

A

Enzymes

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16
Q

What indicates whether the rxn will proceed w/ or w/o input of energy? Spontaneous

A

Gibbs free energy deltaG

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17
Q

What Gibbs energy is favored?

A

Negative

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18
Q

Oxidation-reduction reactions

A

Electron donor will reduce the electron acceptor (reducing and oxidizing agents)

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19
Q

Acid-base rxn’s

A

Weak acid dissociates in water==releases proton and conjugate base

Weak base combines w/ protons in water. Forming its conjugate acid

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20
Q

Characteristic of enzymes r/t specificity

A

3D structure and active site.

Specificity of binding depends on the precisely defined arrangement of atoms in the active site.

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21
Q

Where does substrate bind to enzyme?

A

Active site

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22
Q

Enzyme substrate complex formation: 2 types

A

Lock n key and induced fit

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23
Q

Example of enzyme specificity:

A

proteases cleave peptides btw carboxyl and amino group.

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24
Q

What limits the reaction rate?

A

Substrate occupying all the available catalytic sites of enzymes

Increasing substrate [ ], reaction rates hit a Vmax.

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25
Q

What evidence shows ES complex formed??

A

X-Ray crystallography. Cytochrome P450 is bound to its substrate camphor- surrounded by residues of the active site and a heme cofactor

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26
Q

What is the enzyme active site

A

3D cleft or crevice formed from the residues of various protein regions an occupies call total volume

Contains a unique microenvironment, usually void of water, and controls the proper shape, pH and polarity for substrate binding and chemical reactivity

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27
Q

First law thermodynamics

A

Conservation of energy. Can’t be created or destroyed

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28
Q

Transition state

A

Defined as intermediate structure that is not the substrate and not yet the product—-

Unstable and highest free energy

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29
Q

Gibbs free energy of activation

A

The difference in free energy of the transition state and the substrate —-this can be lowered by enzymes

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30
Q

Chymotrypsin

A

Consists of 3 chains. Side chains of the catalytic triad. There are also 2 interstrand and 2 intra strand disulfide linkage.

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31
Q

Active AA in Chymotrypsin

A

Serine- if it is mutated the enzyme will not function.

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32
Q

What is the catalytic triad function in Chymotrypsin

A

Converts serine 195 into a potent nucelophile.

Peptide hydrolysis

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33
Q

Mechanism of peptide hydrolysis

A

Covalent and Acid-base catalysis.

His-57 positions side chain of Ser-195 and to polarize its hydroxyl group so that it is poised for deprotonation. His-57 accepts the proton from Ser-195 hydroxyl group [this is an example of acting as a general base catalyst]

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34
Q

His 57 acts as what type of catalyst in Chymotrypsin

A

General base catalyst

This is because it accepts the H from the OH grp from serine 195

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35
Q

Chymotrypsin active site hydrophobic or hydrophilic?

A

Hydrophobic

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36
Q

Cofactor

A

Small molecule that contributes to the chemical reaction of the enzyme

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37
Q

Apoenzyme

A

Enzyme w/o its cofactor….inactive…Similar to a guitar capo…inactive strings

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38
Q

Haloenzyme

A

Cofactor bound and catalytically active.

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39
Q

Are metal cofactors positively or negatively charged?

A

Positive

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40
Q

How do metal cofactors function:

A

Stable coordination of active site groups-contribute to chemical reactivity

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41
Q

Example of metal cofactor:

A

Zinc activates H2O to form OH nucelophile. 2Histidine-Zn+2-OH2-> 2His-Zn+2-OH-

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42
Q

Coenzymes

A

are small organic molecules- often derived from vitamins

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43
Q

Prosthetic group

A

Cofactor tightly bound to enzyme

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44
Q

Cofactor vs. coenzyme

A

Cofactors are metals; coenzymes are organic [vitamin] based. Coenzymes are cofactors

45
Q

Need to know ex of coenzyme

A

Tetrahydrofolate (THF)-folate

Source of one-carbon groups for enzymes that transfer them btw molecules.

Vitamin-derived and assists thymidylate synthetase

46
Q

Thiamine pyrophosphate is derived from

A

Thiamine (vitB-1) transfers 2 carbon groups

47
Q

Pyridoxal phosphate derived from

A

Pyridoxine (VIT B6)

Transfers amino and carbonyl groups

48
Q

NAD+ and NADP+

A

Derived from Niacin VIT B-3.

Transfers electrons

49
Q

Ex of disease d.t coenzymes:

A

Scurvy [lack of VIT C which is cofactor for Lysyl hydroxylase- for collagen assembly-gum and skin disease]

Ariboflavinosis [riboflavin B2-reduced glutathione Reductase activity -Req’s FAD] lesion in mouth corners/lips

50
Q

NAD+ is an ex of

A

Oxioreductase . (Binding site of a Dehydrogenase)

It is cofactor that binds active site in well-defined arrangement for substrate activation

51
Q

Alcohol dehydragenase components function:

A

NAD is coenzyme
Zn is cofactor -stabilizes coordination of charge residues in a specific arrangement for catalysis……
Acetaldehyde is substrate or product.
NADH is applied electron transfer

52
Q

Overall function of alcohol dehydrogenase

A

NAD+ is reduced to NADH in the conversion of ethanol to acetaldehyde

53
Q

Fumarase is in what class of enzymes

A

Hydrates the double bond of Fumarate to malate to make a single bond

Since it removes a bond from fumarate it is a Lyase

54
Q

chymotrpysin is in which enzyme class?

A

It is involved in peptide hydrolysis- therefore it is a hydrolases

55
Q

Reductant

A

H or electron donor

56
Q

Oxidant

A

H or electron acceptor

57
Q

Reducing agent

A

Gets oxidized

58
Q

Oxidizing agent

A

Gets reduced

59
Q

Function of alcohol dehydrogenase

A

Convert alcohol to aldehydes or ketones w/ the reduction of NAD+ (cofactor) to NADH…..

NADH oxidized the ethanol to aldehyde/ketone…oxioreductase

60
Q

Ex of transferase

A

Kinase: receives functional group from donor-> gives functional group to substrate…

Functional group is phosphate
donor group could be ATP

61
Q

Kinase receptors

A

Phosphorylate proteins and themselves- transferases—-important in signaling

62
Q

Which enzyme class transfers functional groups to water?

A

Hydrolases—–hydrolysis

63
Q

What is ex of hydrolase that cleaves disaccharide to monosaccharide?

A

Lactase—via hydrolysis

64
Q

Can add or remove groups to form double bonds WITHOUT WATER

A

Lyases

65
Q

Ex of Lyase in glycolysis

A

Aldolase: F-1,6-BP-> DHAP + GAP

66
Q

Enzyme class that creates products which are isomers of the substrate

A

Isomerases

67
Q

Ex of isomerases:

A

Triose phosphate isomerases

Intra molecular oxidation-reduction: DHAP-> G-3P

68
Q

Enzyme that uses ATP to covalently bind DNA

A

DNA ligase- forms covalent phosphodiester bonds btw nucleotides

69
Q

Enzyme kinetics

A

Study of biochemical reactions that’re catalyzed by enzymes…focusing on reaction rates

70
Q

How to determine michalis mention and line weaver burk graph?

A

From exp. data only

71
Q

Rate of reaction formula

A

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

72
Q

Assumptions of steady-state kinetics

A

1- ES is in rapid equilibrium
2-Rate of ES formation = rate of ES breakdown
3-[S]»>[E], S is essentially constant
4- initial velocity is measured at time 0

73
Q

A short description of steady state kinetics:

A

Affinities

74
Q

Km

A

Substrate [ ] producing 1/2 Vmax for catalyzed reaction

75
Q

Vmax

A

Maximum velocity at which enzyme is saturated w/ substrate

76
Q

Michaelis-Menten formula

A

Vo= Vmax X ([S]/ [S] + Km)

77
Q

Line weaver-burk:

A

Reciprocal of michaelis-menten

78
Q

Y intercept of line weaver burk

A

1/ Vmax

79
Q

Slope of line weaver burk

A

Km / Vmax

80
Q

X-int of line weaver burk

A

-1 / Km

81
Q

Arginine-tRNA synthetase composed of 3 substrate w/ 3 different Km. Why?

A

Arginine-3
tRNA-0.4
ATP-300

ATP is limiting b/c it is most inefficient substrate. tRNA is lowest Km=most efficient therefore, largest Km=limiting substrate because it must reach 300 for all 3 to function

82
Q

Bisubstrate reactions

A

Start w/ 2 substrates and end w. 2 products. Most biochemical rxn’s and mostly transfer functional group from one substrate to another

83
Q

2 types of bisubstrate reaction

A

Sequential rxn’s

Double displacemnent (ping pong)

84
Q

Sequential reactions:

A

All substrates bind to the enzyme before any product is released…ex: NADH + pyruvate= lactate + NAD+

85
Q

Double-displacement (Ping pong) reactions

A

One of the products is released before a second rxn occurs; one product must come off before the rxn can move to next rxn. Ex:Aspartate to OAA/ K-KG, Glutamate

86
Q

Can you apply michaelis menten to allosteric enzymes?

A

NO!…this has a sigmoidal curve. MM kinetics has hyperbolic curve

87
Q

3 types of enzyme inhibition

A

Competitive, noncompetitive and uncompetitive

88
Q

Example of an enzyme inhibitor commonly prescribed by MD

A

Methotrexate—looks much like dihydrofolate but binds 100 fold more tightly

Aspirin—blocks 1st step of prostaglandin synthesis (COX-2 inhibitor)

89
Q

Reversible inhibiton

A

Binding to enzymes w/ non-covalent interactions: H bonds, hydrophobic interactions, and ionic bonds…do not undergo chem rxn’s and can be easily removed by dilution/dialysis

90
Q

Irreversible inhibition

A

Covalently modifies an enzyme; irreversible. Specifically alter the active site of the protein. EX: FFR-CK covalently binds to active site serine in plasmin.

91
Q

What does the kinetics reveal of an irreversible inhibited enzyme?

A

Vmax is lowered- d/t less functional enzymes

Km is unchanged- less enzymes doesn’t change the functioning ones Km

92
Q

Enzyme inactivation

A

If continues will eventually lead to 0 Vmax…thus, Vmax decreases, but Km doesn’t change…the enzymes are just rendered ineffective by the inactivation-irreversible inhibition

93
Q

3 types of reversible inhibition?

A

Competitive, uncompetitive, and noncompetitive

94
Q

Competitive inhibition

A

Inhibitors that compete w/ substrates for the active site of the enzyme. Increases Km

95
Q

Uncompetitive inhibition

A

Inhibition that does not affect the formation of the ES complex but inhibits the enzyme at site other than the active site (allosteric binding site). Since binds to EScomplex… Km and Vmax affected

96
Q

Noncompetitive inhibiton

A

Inhibitors that can bind w/ both the enzyme and ES complex. Since it is not inhibiting enzyme function, it only affect Vmax(decreases).

97
Q

V max and Km for Competitive inhibition:

A

Vmax unchanged; Km increased

Vmax doesn’t change b/c enzymes still functioning.
Km increases b/c decreased Km would be MORE efficient. When there are 2 competing for the same enzyme…the efficiency will suffer.

98
Q

V max and Km for Uncompetitive inhibition

A

Vmax decreases; Km decreases

Vmax decreases b/c enzymes are beginning to be unable to function.
Km decreases b/c uncompetitive binds to ES complexes…thus Enzyme and substrate have been inactivated.

99
Q

V max and Km for NONcompetitive inhibition

A

Vmax decreased; Km unchanged

Vmax is decreased b/c the inhibitor lowers the [] of functional enzyme

Km is unchanged because there is still enzyme that is functional in sol’n

100
Q

pH and activity

A

Sigmoidal curve w/ low Kcat @ 6 and higher point @ 9 pH…pH affects shape and function of proteins(denaturation @ low pH)—this changes function b/c shape changes effect substrate binding and activity

101
Q

Pepsin vs. trypsin in pH

A

Pepsin optimally functions at low pH(2) in stomach

Trypsin is further down GI tract and functions optimally at higher pH [8]

Resembles a bell curve….this can be done for temperature too.

102
Q

The jist of inhibiton for these lectures: 2 things:

A 
Covalent modification (irreversible-signaling) 
vs. 
allosteric inhibiton (Enzyme-substrate-reversible)
103
Q

Common covalent modification:

A

phosphorylation

104
Q

What part of the enzyme dictates specificity

A

Active site

105
Q

Enzyme inactivation: irreversible inhibition

A

Vmax decreased; Km unchanged

Vmax decreased=less functionality enzyme
Km = the functional enzyme that is still available Km doesn’t change

106
Q

Can bind w/ Enzyme and ES complex:

A

Noncompetitive inhibition

107
Q

Inhibition that doesn’t affect the formation of the ES complex but inhibits the enzyme at a site other than their active site. Only binds to ES complex.

A

Uncompetitive inhibiton

108
Q

Inhibitors that compete w/ substances for the active site of the enzyme.

A

Competitive inhibition

109
Q

What is ATCase ‘s substrate?

A

Aspartate

Biochemistry (13 decks)

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