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Chapter 1 BC > Chap 6 > Flashcards

Chap 6 Flashcards

1
Q

a. Allosteric activators b. Allosteric inhibitors

A

cause the enzyme to bind substrate more readily. cause the enzyme to bind substrate less readily. similar to the binding of O2 to hemoglobin

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2
Q

Proenzyme

A

An inactive, precursor protein (also called zymogen) with an additional peptide attached

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3
Q

Proteins can bind to enzymes which will

A

alter their activity

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4
Q

enzyme cascades, arrangement of enzymes

A

exponentially amplifying the availability/activity of products in the pathway

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5
Q

enzymes composed of different amino acid sequences that catalyze the same reaction.

A

Isoenzymes

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6
Q

why are proteins biocatlyst

A

-increase ran rate -enzymes help ensure metabolites are being transformed to the right molecules - can be turn on and off, capacity for REGULATION -SPECIFICITY - have greater run specify c -performed in mild conditions

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7
Q

ENZYME CATALYZE A RXN BY MAKING AN Environment where the run can occur more rapidly , WHAT IS THIS ENVIORNMENT

A

ACTIVE SITY

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8
Q

ARE ENZYME- SUBSTRATE INTERATIONS STEROSPCIFIC?

A

YES

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9
Q

What factor contribute to sterospecifity?

A

chirality

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10
Q

What are the chirality rules

A

1.prioritize, 2 lowest priority should be projecting away , 3.determine sequence 1-2-3-

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11
Q

molecule being catalyzed is the

A

substrate

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12
Q

the active site is lined with

A

residues that bind to the substrate and catalyze its chem. transformation

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13
Q

Active site residues contribute to substrate__

A

specificity the residues line the ACTIVE SITE and bind to the substrate , causing substrate to chemically TRANSFORM

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14
Q

Km is NOT analogous to ___ in all conditions

A

Kd

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15
Q

ES complex is also known as

A

Michealis Complex

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16
Q

How do substrates chemically transform ?

A

The residues in the active site attach to the substrate and cause the transformation

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17
Q

The bigger the transition state is the

A

SLOWER there run is

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18
Q

When the DeltaG’ is negative is it thermodynamically favorable? is it exergonic or endogenic? will the reactant proceed toward the substrate or the product at this point?

A

DeltaG is negative it IS Thermodynamically favorable -exergonic -Will proceed to PRODUCT formation

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19
Q

Transition state goes forward or backwards?

A

BOTH

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20
Q

Energy barriers are important for

A

The STABILITY of molecules if a substance just spontaneously convert to products you wouldn’t keep molecules ( of lower energy, and readily decay) around for long life would not have been able to develop

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21
Q

Energy actvivation is the energy that has to be overcome in order for the run to proceed from the

A

ground sate (s) to transition state

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22
Q

when the graph goes from high to low it is

A

EXERGONIC

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23
Q

EQUILLIBRIUM FAVORS

A

PRODUCT

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24
Q

RATE IS DEPENDENT ON THE MAGNITUDE OF

A

ACTIVATION ENERGY

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25
Q

THE LARGER THE ACTIVATION ENERGY THE

A

slower the reaction this is the same concept if you think about the fact that Ez energy increases the “hill” meaning that for your to comedown the hill would take much longer in Ea is high because the transitional state will be higher

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26
Q

IF DELTA G10 ( NOT PRIME) IS VERY NEGATIVE EMPLYS THAT THE RATE RXN PROCEEDS IS QUICK

A

NO THE RATE IS DEPENDENT ON ACTIVATION ENERGY. IF THE G(NOT PRIME IS VERY NEG THAT WPULD MEAN THAT EA IS VERY HIGH WHICH INDICATES THAT RXN WOULD ACTUALLY MOVE SLOWER IF GNOTPRIME WAS VERYYY NEGATIVE

27
Q

ACTIVATION ENERGY IS the difference between

A

Energy levels of groud state (sor p) and the Transition stat

28
Q

A large negative deltaGnotprime favors

A

Products formation , rate of rxn is increased by lowing Ea

29
Q

What is the rate limiting step?

A

the step or steps with

HIGHEST activation Energy

30
Q

What are the Reaction Intermediates (transient chemicals formed and then decay ) during transition from substrate to product

A

during trasition from S->P reaction itermedicate formed are ES (enzyme-Substrtae) and EP(Enzyme product)

31
Q

WHAT ARE THE 3 Ways enzymes Lower Activation Energy?

MUST KNOW MEMORIZE!

A
  1. Rearrangement of covalent bonds (make or break)during catalysis. The amino acids side chains on the enzyme located inside active site as residues may transiently (not permanently, short lived) COVALENTLY BOND the substrate and may ACTIVATE it for reaction or a GROUP may be transiently transferred from substrate to the enzyme
  2. Enzymes bringing reactant groups into CLOSE proximity ( nuc close to electro) bring the substrate into the active site, position substrate right in front of nuc-> hitting it and enhancing rxn rate! . o Uncatalyzed bimolecular reactions: 2 free reactants -> single restricted transition state (TS)– nucleophhile (-) attacks electro and removes (R from OR on the electrophile then creating single restricted TS) o Uncatalyzed unimolecular reactions: flexible reactant-> single restricted TS o Uncatalyzed unimolecular reactions: inflexible reactant -> single restricted transition state
  3. Stabalize Tranistion state by forming weak noncovalent interations ( hbonding, ionic, hydrophobic, vanderwalls) BETWEEN THE ENZYME ABD SUBSTRATE, lowers Ea
32
Q

What type of interactions OPTIMIZE for transition state ?

A

WEAK INTERMOLECULAR ( hydrophobic effect, van, hbond, ionic)

noncovalent

33
Q

Enzymes stabalize?

A

tranistion state! they are complementary to transition state

making the substrate BEND

so the substratrate will will not interact to the same degree with any other molecule

34
Q

What is Km

A

Micleis Constant

the SUBSTRATE CONCENTRATION AT which Vois 1/2 Vmaximal

35
Q

What is Vmax , V, and Vo,

1/2 Vmz is

A

Vmax is the point that Vo is NO longer increasing although the substrate IS. Vmax is never reached

Vo is intial Velocity

V is Velocity

1/2Vmax

36
Q

Why do substrate ( S) plateau

A

All substrate is converted to product –SATURATION OF ENZYME

37
Q

Simplest model

A

: E+S > ES >E + P

One reactant , one product NO INHIBITOR

38
Q

Assumptions

A

(S)total=S(free)

becuase the amt of substrate in a solution is way greater than THE AMOUNT BOUND TO AN ENZYME IS SO SMALL( Enzyme-Substrate(-ES) SO THE STOTA IS SAME AS SFREE

SO the SMALLer Km the BETTER IT WORKS WITH THE SMALL ENZYME

39
Q

STEADY STATE ASSUMPTION

A

RATE OF FORMATION=RATE OF LOSS (BREAKDOWN)

Simplest model: E+S > ES >E + P

40
Q

KCAT IS REFERED TO AS

A

TURNOVER NUMBER-the number of substrate molecules that ONE enzyme can convert to product per second at MAX SPeed

Product formation at time

“cats turn over”

41
Q

What is the michaelis constant how is it dervived

A

K2+K-1 is the idsapearence of ES over K1 which is the formation of ES

when K2 is very small you can use kd as substitiute km. When KM is very slow at releasing product –NOT ACCURATE NEVER REALLY DONE

42
Q

The lower the km

A

the greater the affinity

43
Q
A

double km to get Vmax

44
Q

When ONE enzyme has TWO or more substrates

enzyme kinetics help us with order of binind

2 types

A

SEQUENTIAL- TERNARY COMPLEX FORMED

  1. Random Ordering - doesnt matter which one goes on first , ternary complex is formed - produces 2 products
  2. Ordered- Substrate 1 has to go on first in order for substrate 2 to bind then catalysis occurs

PING PONG NO TERNARY COMPLES

Sub 1 binds first , the enzyme (E) uses sub 1 to convert it to product 1 which in the process modifies the enzyme (E1). Then E1 binds to Sub 2 and Then Product 2 is produced

similar to phosphorlyation , phosyrl group is removed then attached

45
Q

What do inhibitors do?

A

Inhibitors are compounds that decrease enzyme activity. These can be defined in 2 classes: Irreversible
inhibitors or reversible inhibitors.

46
Q

Irreversible Inhibitor

example of this

A

SUICIDE-Irreversible inhibitors are inactivators typcailly bind COVALENTLY

PERMINTLY SHUTS OFF ONE ENZYME

ofter POWERFUL TOXINS

47
Q

What is the problem with irreversible inhibitors?

A

The bind to a lot of things making them TOXIC

48
Q

REVERSIBLE INHIBITORS

EXAMPLE

A

FREE TO BOTH BIND to AND DISSOSOCIATE from the enzyme

  • either prevent binding of sub or can bind to ES and prevent rxn

Often look similar to substrtare orproducts – so it can trick enzyme into binding but undergo catalysis

USED AS DRUGS TO SLOW DOWN SPECIFIC ENZYE

can bind to bos ES and free enzyme

49
Q

3 types of inhibition

all reversible

A

Competitive

Noncompetive/mixed

uncompetitive

50
Q

Competitive Inhibition

A

Competes with the substrate for binding/active site which inhibits the enzyme

  • Binds to FREE ENZYME only
  • Km is increased
  • Vmax stays the same
51
Q

Uncompetitive Inhibition

A

Binds at allosteric site ( nonvolaent force) OTHER THAN TH THE ACTIVE SITE , This inhibotor binds ONLY AFTER the substrate has bound. once inhibioter binds it prevent catalysis from happening by way of conformational change

  • Only binds to Enzyme substrate complex
  • Vmax is decreases
  • Km decreases

” when your uncompetitive everything lowers”

52
Q

NONcompetitive Inhibition / MIXED

A

Binds at a site distinct from the substrate active site but it can bind to EITHER OR Free Enzyme

  • Km is Is SAME
  • binds either ES or Free E
  • Vmax is the decreased
53
Q

Chymotrypinsin

A

Chymotrypsin is a Protease that CLEAVES PEPTIDES ON the C-Terminal side of Phe, Tyr, and Trp residues - AROMATIC AA

Enzyme will act in some sort of hydrophobic

54
Q

Catalytic Triad

A

Serine 195 is linked to Histidine 57 and Asparatate in a HYDROGEN Bonding network

55
Q

What is the hydrophobic Pocket

A

Region of CHYMOTRYPSIN enzyme that is specific/complementary to the Aromatic AA (PTT) hydrolyzed on the Cterminal side of AA

56
Q

General BASE Catalysis

A

AMino acid, PRoton, Extracted by WEAK base by groups OTHER than OH from water

ex histidine rips proton off of water leaving me with an O- which is a hot nucleophile

57
Q

Specific Base Catalysis

A

Proton Extraction by a STRONG BASE typically H20

58
Q

When a peptide substance binds the Chymotryoicin

A

a subtle change in conformation compresses the H bond between His abd Asp, resulting in a stronger interation

This increase the pka of His from 7 to 12 allowing HIS To act as a general base ( extractproton by weak base) that can removethe proton from SERINE hydroxl group =making SERINE A BETTER NUCLEOPHILE

59
Q

Nucleophile

example

A

electron rich atoms

ex=O-, S-, Carbanion, uncharged amine groups,imadazole, hydroxide ion

60
Q

Electrophile

examples

A

Electron DEFICIENT atoms

carbon of a carbonyl, protonated imine group at carbon, prton (H+), phosphorus of a ohosphate group

61
Q

Enolase

A
  • DEHYDRATION creates double bond, lo)st H2O
  • DIVALENT CATION PRESENT 2 Mg++ (cofactorare captured which stabalizes substrate and the transition state (metal)– that is why divalent metals are needed
    *
62
Q

Lysozyme

A

Lysozome is an ANTIBACTERIAL ENZYME

hydrolyzes the bond

Cleavage of the cell wall ( peptidoglycan)by lysozyme leads to the LYSIS of bacteria

side note Glutamate facilitates elimation of the hydroxyl group by general base catalysis

63
Q

pH and Enzyme Activity

If the ph rises or decreasees the enzyme activity will?

The presence of pKa

A

If the ph rises or decreasees the enzyme activity will DECREASE

Presence of near by POSITIVIE CHARGES can LOWER pKa

Nearby negative charge can INCREASE pka

-resulting in a shift by several pH units from its value in free AA

Chapter 1 BC (4 decks)

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