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MCAT > Enzymes and Kinetics > Flashcards

Enzymes and Kinetics Flashcards

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MCAT flashcards
1
Q

histone acetyltransferases:

A

add acetyl groups, makes DNA more accessible for transcription

  • histone deacetyltransferases reduce transcription
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2
Q

Km

A

Km is the concentration of substrate which permits the enzyme to achieve half Vmax.

An enzyme with a high Km has a low affinity for its substrate, and requires a greater concentration of substrate to achieve Vmax.”

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3
Q

Mixed Inhibitors

A

Can bind to free enzyme (no substrate bound) of enzyme-substrate complex

Decreases Vmax

Km depends on binding preference, increases when bound to free enzyme

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4
Q

Proteases

Trypsin

Pepsin

A

Proteases cleave peptide bonds

trypsinogen cleaved by enteropeptidase (activated by CCK) into active form, trypsin

  • ​trypsin: cleaves peptide bonds adjacent to lysine and arginine

Pepsinogen cleaved by stomach acid into pepsin; cleaves bonds between hydrophobic and aromatic aminos

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5
Q

Kinase vs. Phosphorylase

A

Kinase is not involved in breaking bonds in the substrate during the addition of phosphate groups whereas phosphorylase breaks the bond between the substrate and the monomer by adding a phosphate group.

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6
Q

Glycosyltransferases

Glycosidase

A

Glycosyltransferases create new glycosidic bonds

  • glycogen synthase in the liver

Glycosidase enzyme breaks glycosidic bonds via acid-catalyzed hydrolysis reaction

  • Beta-galactosidase hydrolyzes glycosidic bond of lactose to liberate glucose and galactose

**Always involve anomeric carbon (carbonyl carbon) of at least one sugar

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7
Q

peptide hormones

A

Chains of amino acids, large and polar
- Can’t diffuse into cell, must interact via membrane receptors and secondary messengers (QUICK ONSET< SHORT LASTING)

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8
Q

Phospholipids can move horizontally but not vertically

  • need enzymes to catalyze movement:
A

Flippase: moves phospholipids from external side to internal side

Floppase: opposite

Scramblaser: bidirectional

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9
Q

transmembrane ATPases catalyze

A

hydrolysis of ATP

ex. Sodium Potassium pump

Na+K+ ATPase

ex. myosin

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10
Q

Oxidoreductases

A

catalyze oxidation reduction reactions

  • oxidases
  • reductases
  • dehydrogenases
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11
Q

Hydrolases

A

General term that catalyze a hydrolytic cleavage

Hydrolysis is the chemical breakdown of a compound due to reaction with water.

- Nucleases and proteases

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12
Q

Nucleases

A

Break down nucleic acids by hydrolyzing bonds between nucleotides

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13
Q

Synthases

A

Synthesize molecules in anabolic reactions by condensing two smaller molecules together

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14
Q

Isomerases

A

Catalyze the rearrangement of bonds within a single molecule

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15
Q

Polymerases

A

Catalyze polymerization reactions such as the synthesis of DNA and RNA

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16
Q

Phosphatases

A

Catalyze the hydrolytic removal of a phosphate group from a molecule

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17
Q

Thrombin

A

an enzyme in blood plasma which causes the clotting of blood by converting fibrinogen to fibrin.

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18
Q

Lysozyme

A

It functions as an antimicrobial agent by cleaving the peptidoglycan component of bacterial cell walls, which leads to cell death.

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19
Q

Transferases

A

Transfer functional group between molecules

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20
Q

Ribosomal rRNA

A

ribozymal component of ribosomes, catalyzes formation of peptide bonds

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21
Q

Cyclins

A

Present at each stage of cell cycle (specialize), levels are cyclical and spike when its time to use them

when at high levels, bind and activate cyclin dependent kinases which phosphorylate and activate proteins which promote activity of a certain phase

22
Q

Prosthetic Groups

A

Coenzymes tightly or covalently bonded to their enzymes

ex. Heme attached to O2 transporters like hemoglobin or myoglobin

23
Q

Substrate

A

Substance an enzyme acts on

24
Q

Committed step of reaction

A

Energetically unfavorable, highly regulated

25
Q

Orders of reactions

A

Zero order reactions: unaffected by changes in reactant concentrations

  • ex. enzyme catalyzed reactions in which enzyme is saturated.
  • reactant concentrations far exceed available active site

First order: radioactive decay or SN1 reactions, rate only depends on one reactant

Second order: physical collisions between two reactant molecules

26
Q

Rate Law

A

In one step elementary rxns, coefficients of reactants are their orders

Rate= k [A]a[B]b

Multistep: using initial rates, find where conc of [A] changes and the other [B] stays the same

a and b are the rate orders of each reactant

rate1/rate2 = (conc1/conc2)x

Rate of 1 = no change

27
Q

apoenzymes

A

Enzymes without cofactors needed to function properly

28
Q

Zymogen

A

Inactive precursor molecule

29
Q

allosteric regulation

A

allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme’s active site.

30
Q

competitive inhibition

A

Only inhibiton at enzyme active site, only one that inhibits binding of substrate

  • increase Km (lower affinity)
  • no change in Vmax
31
Q

Line weaver burk plots

A

*Y-AXIS moves in OPPOSITE direction (Vmax)

  • if reduced, moves up

X-axis moves in correct direction

32
Q

Noncompetitive inhibition

A

Binds on E-S complex, doesn’t inhibit binding of substrate and therefore doesn’t change Km, (noncompetitive)

  • Decrease in Vmax (for all but competitive, which stays the same)
33
Q

uncompetitive inhibition

A

Binds to ES complex or enzyme and decreases Km

  • Decreases Vmax
34
Q

Enzyme inhibition regular graph

A
35
Q

Restriction enzymes can only recognize

A

Palindromic sequences

36
Q

Isoelectric point

A

pH of a solution at which the net charge of a protein becomes zero.

37
Q

How can enzymes be used to form a single stereoisomer?

A

An enzyme is a chiral catalyst capable of preferentially forming one enantiomer because a lower energy chiral transition state leads to the preferred product

38
Q

What enzyme creates glycosidic bonds, what enzyme breaks them down

A

Glycosyltransferases create new glycosidic bonds

  • glycogen synthase in the liver

Glycosidase enzyme breaks glycosidic bonds via acid-catalyzed hydrolysis reaction

  • Beta-galactosidase hydrolyzes glycosidic bond of lactose to liberate glucose and galactose
39
Q

Lock and Key theory (enzyme and substrate)

A

Fit together with no change in tertiary, quaternary structure

oversimplification

40
Q

Enzyme and substrate “Induced fit” theory

A

More realistic than “lock and key”, enzyme and substrate induce conformational shifts, closer binding

41
Q

Orthosteric regulation

A

Interacts with enzyme at active site

42
Q

Lyases

A

cleave bonds not using hydrolysis (ex. glycolysis)

43
Q

Ligases

A

Catalyzes formation of bonds

44
Q

Feed Forward Regulation

A

Upstream product in higher concentration catalyzes downstream reaction

ex. In glycolysis, pyruvate kinase catalyzes ATP producing rxn, enzyme activated by intermediate fructase 1,6-bisphosphate upstream

45
Q

How to lower Ea

A

Lowering Ea done by deploying catalysts (enzymes)

  • stabilize transition state
  • weaken bonds within reactants
  • changing orientation to elicit effective collisions
  • increasing frequency of collisions
  • donating electron density to reactants

Enzymes don’t affect thermodynamics: Gibbs free energy, enthalpy, entropy

Catalysts not consumed, small amount can greatly affect products

46
Q

Heterogenous vs. Homogenous Catalysis

A

Based on the phase of catalyst compared to phase of reactant species

  • heterogenous catalyst: in different phase than reactants
    • typically catalyst is solid and reactants are liquid/gas

based on surface area of catalyst, grinding it into a powder more efficient

  • homogenous catalyst: same phases
47
Q

Kcat

A

turnover number is defined as the maximum number of chemical conversions of substrate molecules per second that a single active site will execute for a given enzyme concentration

High kcat is efficient

48
Q

Sn1

A

Two steps:

  1. Leaving group leaves, generates carbocation (slow)
    * carbocation formation = rate limiting step

​depends only on concentration of substrate, reaction rxn rate only depends on electrophile

  • Stronger carbocation = better substitution, tertiary over primary and secondary
    2. Nucleophile attacks
  • often molecule of water or alcohol, will become positive
  • next step is to deprotonate

Not stereo sensitive, can attack from front or back –> equal conc of S and R stereoisomers

  • Racemic mixture of products

Rate = k[A]

49
Q

Sn2

A

Nucleophile and electrophile involved in rate-limiting step; rxn rate depends on both their concentrations

  • No carbocation is formed, weaker electrophiles
  • most common substrate is alkyl halide (tert, sec, or primary)

Carbon attached to halogen has partial positive charge

  • Nucleophile must attack opposite (back-side) of leaving group (halogen)
    • both nucleophile and leaving group are electron rich

substrate chirality is inverted (ex. S–> R)

Rate = k[A][B]

50
Q

Nucleophilic addition

A

Begin with nucleophilic attack, but no leaving group

  1. Oxygen protonated
  2. nucleophilic attack
    * in base catalyzed, nucleophile made stronger by deprotonation
  3. deprotonation

Common examples of nucleophiles: water, alcohols, hydrogen cyanide

  • all have a spare electron pair to donate
51
Q

Henderson hasselback equation- used to determine pH of buffer system

A

pH = pKa + log([A-]/[HA])

52
Q

Anomers

If an anomer is an aldose, which carbon differs

Ketose?

A

C1 (where aldehyde is)

C2 (where ketone is)

MCAT (8 decks)

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