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Biochem > Lecture 7 Information > Flashcards

Lecture 7 Information Flashcards

1
Q

How do enzymes with more than 1 substrate bind them?

A

Can form a tertiary complex to bind both at the same time

Can interact with multiple substrates in an ordered manner (interact with one substrate before the other)

Can interact with multiple substrates in a ping pong manner (one is converted to product then the other is converted to product)

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2
Q

Binding affinity for more than 1 substrate

A

Enzymes will have a different binding affinity (Km) for each substrate they bind

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3
Q

2 main classes of enzyme inhibition

A

Reversible interaction

Irreversible interaction

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4
Q

Competitive inhibition

A

a type of reversible inhibition

inhibitor binds at the active site and forms EI complex

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5
Q

Kinetic effects of competitive inhibition

A

Vmax stays the same because you can flood the system with a high amount of substrate

Apparent Km increases

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6
Q

Uncompetitive inhibition

A

a type of reversible inhibition

inhibitor binds to the ES complex apart from the active site

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7
Q

Kinetic effects of uncompetitive inhibition

A

Vmax decreases

Apparent Km decreases

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8
Q

Mixed inhibition

A

a type of reversible inhibition

inhibitor binds to free enzyme or ES complex

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9
Q

Noncompetitive inhibition

A

a special type of mixed inhibition

the affinity of the inhibitor to bind to the free enzyme or to the ES complex is equal

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10
Q

Kinetic effects of noncompetitive inhibition

A

Vmax decreases

Apparent Km stays the same

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11
Q

Irreversible inhibition

A

bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme’s activity

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12
Q

Example of irreversible inhibition

A

penicillin binds irreversibly to transpeptidase to prevent bacterial cell wall from being generated

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13
Q

Transition-state analogs

A

A type of irreversible inhibition that uses weak interactions

Creates a better transition state with more weak interactions that prevents the substrate from binding

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14
Q

Suicide inactivators

A

combines irreversibly to the enzyme through covalent interactions

hijack the normal enzyme reaction mechanism

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15
Q

Regulatory enzymes

A

exhibit increased or decreased catalytic activity in response to certain signals

they regulate and they also are regulated

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16
Q

Allosteric enzymes

A

function through reversible, non-covalent binding of regulatory components

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17
Q

Allosteric modulators/effectors

A

noncovalently bind to allosteric enzymes to either inhibitory or stimulatory regulate

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18
Q

Different ways to regulate enzymes

A

1) Allosteric enzymes
2) Covalent modification
3) Separate regulatory proteins
4) Proteolytic cleavage

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19
Q

Proteolytic cleavage

A

activates enzymes through removing peptide segments

this is irreversible unlike allosteric regulation

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20
Q

How do allosteric modulators work cooperatively?

A

conformational changes induced by one or more modulators interconvert more-active and less-active forms of the enzyme

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21
Q

Homotrophic enzyme

A

the modulator is the substrate and the active site is the regulatory site

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22
Q

Feedback inhibition

A

type of inhibition where the final product comes back to the first enzyme in a product and binds to it

binds to the first enzyme to save energy/materials

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23
Q

Heterotophic enzyme

A

the modulator is a molecule other than the substrate and the active site is not the regulatory site

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24
Q

Are enzymes turned completely off or on?

A

No! This is rare. Most are turned up or turned down in levels

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25
Q

Are regulatory sites specific?

A

yes, each regulatory site is specific for its modulator

26
Q

How are allosteric modulators different from inhibitors?

A

Inhibitors do not necessarily mediate conformational changes between active and inactivate enzymes

27
Q

Shape of allosteric enzymes on Michaelis-menten plot

A

Sigmoidal shape which reflects cooperative binding between multiple subunits

28
Q

What do we call the Km of allosteric enzymes?

A

K(0.5)

have to do this since it doesn’t follow normal hyperbolic shape

represents substrate concentration giving half-maximal velocity

29
Q

Covalent modifications of enzymes

A

examples: methylation, ribosylation, acetylation, adenylation, ubiquitin tag, phosphylation

30
Q

Ubiquitin

A

entire protein that is covalently added to enzyme to tag it for destruction by a proteasome

31
Q

Kinases

A

take a phosphate group (often from ATP) and use it to add phosphoryl groups to specific amino acids

32
Q

What amino acids do kinases add to?

A

Ser, Thr, Tyr or sometimes His

33
Q

How can phosphorylation effect an enzyme

A

can turn off an enzyme through the repulsion of negatively charged groups

can turn on an enzyme through the attraction of positively charged and H-bonds

34
Q

Tyrosine kinases

A

important in cell signaling and associated with the cell membrane

often inactive, but when you bind a ligand the two subunits of the kinase come together

now, this kinase is activated and auto-phosphorylates more tyrosine kinases

now there are all these kinases that can turn on more enzymes

35
Q

protein phosphatases

A

removes phosphoryl groups from same target proteins

36
Q

When glycogen is phosphorylated what happens?

A

it releases a glucose-1 phosphate that can be used by the bloodstream

this transformation is catalyzed by glycogen phosphorylase

37
Q

Is glycogen phosphorylase a kinase?

A

No

because it does not use ATP or any other nucleotide triphosphate to transfer phosphoryl group

38
Q

Phosphorylase a

A

more active form of glycogen phosphorylase

39
Q

Phosphorylase b

A

less active form of glycogen phosphorylase

40
Q

Phosphorylase phosphatase

A

removes phosphoryl groups from phosphorylase a to make the enzyme less active in b form

41
Q

Phosphorylase kinase

A

adds ATP to phosphorylase b to make the enzyme more active in a form

42
Q

How is glycogen breakdown regulated?

A

by various ratios of phosphorylase a and phosphorylase b

43
Q

Consensus sequences

A

common structual motifs where Ser Thr or Tyr residues are found to phosphorylate

44
Q

Zymogen

A

inactive precursor that is cleaved to form an active enzyme

this is irreversible activation

proteases like chymotrypsin, trypsin, and pepsin have zymogen precursors to not destroy proteins within the cell

name does not apply to all precursors

45
Q

What are most inactive precursors generally called?

A

proproteins or proenzymes

46
Q

Proteolytic cleavage

A

changes zymogen to active chymotrypsin and trypsin enzymes

47
Q

How do we regulate proteases once they are turned on?

A

Need another protein to interact with them

regulated through protein-protein interactions

48
Q

Trypsin

A

cleaves after positive charges

breaks down proteins in the gut

49
Q

Chymotrypsin

A

cleaves after aromatic rings

50
Q

Glucagon

A

hormone that stimulates the process of glycogen breaking down into glucose 1-phosphate

51
Q

Insulin

A

hormone that inactivates the process of glycogen breaking down into glucose 1-phosphate

decreases blood-sugar levels

52
Q

Size of allosteric enzymes

A

typically bigger enzymes with more than one polypeptide chain

53
Q

What are the zymogen’s called?

A

ex: trypsinogen is the inactive form of trypsin

54
Q

Why are certain enzymes kept a low pH even when the cell is at a neutral pH? Like lysozomes?

A

So if the lysosome breaks open, the enzymes will have little activity in the neutral pH

55
Q

ATCase

A

has homotrophic and heterotrophic regulation

ATCase has a sigmoidal curve cause has cooperative binding

56
Q

Why does phosphatase not generate ATP when it removes phosphoryl?

A

requires too much energy

just cleaves a Pi

57
Q

PKA

A

protein kinase a

sticks a phosphate onto inactive form of phosphorylase kinase to activate it

58
Q

Hyperglycmic

A

too high blood-sugar levels

pancreas picks up on this signal and triggers insulin to drop glucose

59
Q

Hypoglycmic

A

too low blood-sugar levels

pancreas picks up on this signal and triggers increase of glucose released (glucagon)

60
Q

What does glucagon do?

A

inceases cAMP which activates PKA

PKA then activates phosphorylase kinase which can then change phosphorylase b to phosphorylase a

Biochem (20 decks)

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