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Enzymes Flashcards

1
Q

Importance of enzymes

A
  • inheratple disorders due to defficancy (pku) or excessive activity of gene (onka genes overactivity)
  • Important in diagnosing illnesses (heart attack - enzimes leak into blood)
  • drugs exert bilogical effects through interactions with enzymes (asprin, dec. inflamation)
  • used in chemical industry, food procesing, agraculture
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2
Q

Enzymes lower

A

activation energy

Catalyze reactions to high rates (107-1019 times greater)

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3
Q

Activation energy is the

A

ammount of energy required to convert 1 mol of substrait from ground state to transition state (top of hill - unstable)

is overcome with enzymes via an alternate pasthway

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4
Q

Enzymes do not

A

alter the standard free energy of rxm.

dosnt change thermodynamics, only kenetics

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5
Q

Phosphatases

A

Catalyze hydrolytic removal of a phosphate group from a molecule

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6
Q

Kinases

A

Catalyze the addition of phosphate group to molecule

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7
Q

ATPases

A

Hydrolyze ATP. Energy-harnessing ATPase activity as part of their function

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8
Q

GTPases

A

Hydrolyze GTP. Play a role in the regulation of cell processes

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9
Q

Proteases

A

Break down proteins, hydrolyze peptide bonds between amino acids

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10
Q

The active site brings substrates into favorable conformations with

A

several amino acid side chains directly involved in the coordination, making, and breaking of bonds.

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11
Q

the 3-D structure of the reactive center of an enzime is formed by the

A

the folded domains of the protein

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12
Q

The active site of enzymes generate a highly selective environment in which

A

specific chemical reactions occur without generating unwanted side reactions.

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13
Q

Substrate is

A

a reactant that binds to the active site

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14
Q

lock in key

A

complemeary exact fit

both rigid

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15
Q

induced fit

A

some flexability in enzyme shape

adjustments made allow for better fit (enhanced catalisis)

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16
Q

Hexokinase

A

Glucose + ATP (enzime)-> Glucose 6-Phosphate + ADP

Two-domain protein with a central binding cleft for glucose and ATP.

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17
Q

•Upon glucose binding to hexokinase there is an ~____ fold increase in the affinity of the enzyme for ATP.

A

50

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18
Q

(in Hexokinase) Glucose binding induces a significant

A

conformational change in the protein that brings the two opposing domains close together to form a high affinity binding cleft for the phospho-transfer reaction to occur.

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19
Q

strategies of Enzyme Catalysis

Align/Position Reactants to favor that transition state

A
  • fewer conformations to explore
  • Increase efficiency
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20
Q

strategies of Enzyme Catalysis

induced charge state

A

Amino acids in active site interact with reactants via charge, polarity

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21
Q

strategies of Enzyme Catalysis

Deform reactants (or strain)

A

force so that it resembles a transition state

  • Enzyme strains substrate
  • Forcing a transition state, favor reaction
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22
Q

Much of the energy required to lower activation energy is derived from

A

weak, non-covalent interactions between substrate and enzyme

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23
Q

Binding energy

A

energy relased, lowers activation energy

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24
Q

Enzymes are __

work in __

are not __

can be ___

A

are catalysts: Lower activation energy, promote the transition state (ie orient substrates, strain substrates, induce charge, induced fit)

Enzymes are highly specific to reactions they catalyze

Enzymes work in moderate temperatures (ex. body temp if too hot, denature protines)

Enzymes are Not consumed in reactions (more effecient to resuse the enzime)

Enzymes can be regulated

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25
Q

Rate of ES formation =

A

rate of ES breakdown

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26
Q

V0

A

inital velocity of protine formation

27
Q

Enzime same

inc. ___

28
Q

enzime becomes saturated

A

Vmax

no longer increase velocity

29
Q

Km

A

dissocation constant

messure of affiity of an ezyme for substrate

is a substrate concentration when velocity is half of its max

30
Q

lowe Km

A

higher affenity for its substrate

31
Q

higher Km

A

need more substrate to get same rate

32
Q

Compedative inhibitor

A

compeets with substrate for active site

Vmax dosent change (because compedative/both are like/are substrates)

33
Q

Lysozyme is a natural

A

natural antibiiotic

34
Q

Lysozyme catalizes

A

catalizes the cutting of polysaccharide chains in cell walls of bacteria

catalizes a hydrolysis reaction: Adds water to bond between two adjacent sugar groups in polysaccharide chain, causing bond to break.

Reaction is favorable

35
Q

Lysozyme reaction

A
  1. Sugar D is forced into strained conformation (strained catalisis)
  2. Glu35 serves as an acid, donates a H+ to sugar E (acid base catalisis)
  3. Asp52 attacks C1 of Sugar D, transient covalent bonds forms between Asp and Sugar D. (nuc. attack, transient, strong bond formed but must go back)
  4. Hydrolysis of glycosidic bond (sugar-sugar bond)
  5. Glu35 polarizes water molecule, oxygen attacks C1 Carbon atom
  6. Covalent bond broken between Asp and C1 (sugar D)
  7. Hydrolysis completed
  8. Lysozyme returned to initial state (EP formation)
36
Q

Why does activity decrease above and below Ph optium for lysozyme?

A

Because when Ph dec. picks up proton and becomes non ioniced interfering with mechanism

Ph increase glu35 releases proton, interfering with mechanism

37
Q

Allosteric Regulation:

A

Regulatory molecule binds to a regulatory site (not active site) of enzyme.

inhibit or activate enzyme - involves conformation changes

site that can be regulated

38
Q

Irreversible Inhibition:

A

Drug Targets

39
Q

Post translational modifications:

A

Phosphorylation/Dephosphorylation reactions that regulate target proteins.

add and removal of phaspate affects acitivity

covalent motification

40
Q

Proteolytic Processing:

A

Enzyme activation relies on cleavage of one or more peptide bonds

41
Q

Nucleotide Regulation:

A

ATPases and GTPases

42
Q

Most protines are

A

allosteric (enzymes, receptors, structural proteins, motor proteins)

43
Q

Binding at one of the sites causes a

(allosteric regulation)

A

shift from one folded shape to a slightly different folded shape

44
Q

linkage principle of allosteric regulation

A

when one binds it increases the affinity for the scond site (can be + or -)

45
Q

Active site and regulatory site communicate so that

A

catalysis at the active site can be influenced by binding of a regulatory molecule at a separate site.

46
Q

Feedback inhibition (negative feedback) in allosteric regulation

A

product produced late in a reaction pathway inhibits an enzyme that acts earlier in the pathway

47
Q

Allosteric Inhibition of Reaction

A

Presence of either ligand interferes with the binding of the other

ligands prefer differnt conformation (neg. regulation)

48
Q

Allosteric Activation of Reaction

A

favorable - promotes binding of second ligand

Each ligand prefers same protein conformation, so each ligand increases the protein’s affinity for the other.

49
Q

Allosteric regulation of ADP / ATP

A

ATP - inhibitor

ADP - activator

50
Q

Cooperative Allosteric Transition

A

The binding of an oxygen molecule to one binding site increases the affinity for oxygen of the remaining sites.

allows hemoglobin to function

substrate affects all sites

51
Q

Hemoglobin Allosteric Transition

Oxygenation of hemoglobin causes

Hemoglobin alternates between

shows a ___ dissociation curve due to

A

the dimers to slide by each other and rotate 15º

Hemoglobin alternates between the two stable states- T (deoxy) and R (oxy)

Hemoglobin shows a sigmoidal oxygen dissociation curve due to cooperative binding.

52
Q

Asprin

innactivates

A

irreversable inhibitor

the Cyclooxygenase enzyme

  • acts as an acetylating agent where an acetyl group is covalently attached to a serine residue in the enzyme’s active site
  • Cyclooxygenase is required for prostaglandin and thromboxane synthesis. Pain and Inflamation
  • Long term usage blocks the formation of thromboxane in platelets. Used as an anticoagulant in the prevention of heart attack and stroke
53
Q

Curcumin

irreversibly inhibits ___

A

(active ingredient in tumeric)
enzyme Aminopeptidase N (APN), an enzyme that promotes
tumor growth and angiogenesis (blood vessel growth, feeds tummor)

54
Q

Protein phosphorylation is __

Expect it too__

via

A

transfer of terminal phosphate group of ATP to target protein.

1) change enzyme activity (adds a neg charge)
2) Create binding site
3) mask binging site

via protine kinase

55
Q

Protein dephosphorylation

via

A

Removal of phosphate from target protein

protine phosphatase

56
Q

Pyruvate Dehydrogenase

A

Key enzyme in Carbohydrate Metabolism

57
Q

Reversable phosphorlation

2 examples

A

cell signaling - phospated sites/create binging sites

Cyclin-Cdk complexes of cell-cycle control system - phophsatase targest protines involved in different stages

58
Q

Regulation: By Proteolytic Processing

A

Some of enzymes and proteins are synthesized in inactive forms that become active following proteolytic processing and cleavage of the precursors

hormaones are inactive, rly on proteolytic processing in cell where needed

active when and where needed - important so that enzimes (ex. digestive) are not aftivated to early (ex. in the liver)

59
Q

Preproinsulin must be processed into

A

mature insulin through a series of cleavage and folding steps.

60
Q

C-peptide

A

has a much longer half-life in plasma
(~30–35 minutes) than mature insulin
(~5 minutes)
can be used as a diagnositic to determin if someone is still making insulun

61
Q

Enzymes that Couple Energy Transduction to Mechanical Work

A

Mechanical enzimes

ATP binding

hydrolosis

relsease

use all in movement

62
Q

Different Classes of Mechanical Enzymes

A

Membrane transporters
Molecular Motors / Machines (ATPases)

63
Q

GTPase

A

GTP binding protine

neucleotide regulators, molecular switch

ON - GTP bouns

OFF - GDP bound

64
Q

GTPase regulation

A

GEF - guanine exchange factor - conformation change causes gdp to realse for fresh GTP

GAP - GTPase activating protine - inducing hydrolosis of GTP to GDP

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