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biochem 410 and 411 > 410 exam 3 > Flashcards

410 exam 3 Flashcards

1
Q

transition state analogues

A
  • chemically and structurally similar to the transition state
  • bind more strongly than substrate or competitive inhibitors
  • the tighter an enzyme binds to t.s., the higher the rate of catalyzed reaction
  • the more t.s. –> less side effects
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2
Q

3 types of transition state analogues

A
  1. statins (cholesterol-lowering drugs that inhibit HMG-CoA reductace ex: lipitor)
  2. protease inhibitors (AIDS drugs, HIV-1 inhibitors ex: squinavir)
  3. viral neuraminidase inhibitor- treats influenza by inhibiting the neuramidase rxn (essential for viral respiration ex: tamiflu)
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3
Q

specific vs. general acid-base catalysis

A

specific- H+ or -OH diffusing in from solutions
general- proton transferred in transition state
* acid: proton transfer lowers free energy of t.s.
* base: proton abstraction lowers free energy of t.s.

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4
Q

RNase A Acid-Base Catalysis

A
  • digestive enzyme secreted by pancreas
  • hydrolyzes RNA to its component nucleotides
  • 2 residues: His 12 (base) and His 119 (acid)
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5
Q

Metalloenzymes

A
  • tightly bound metal cofactors
  • Fe 2+, Fe 3+, Cu2+, Zn 2+, Mn 2+, Co2+
  • bind to substrates for orientation, mediate redox rxns by changing oxidation state, and stabilize/shield negative charges
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6
Q

Metal activated enzymes

A
  • only loosely bind the metal ions
  • Na+, K+, Mg 2+, Ca 2+
  • structural role
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7
Q

where do Trypsin, Chymotrypsin, and Elastase cleave?

A

Trypsin: Lys, Arg
Chymotrypsin: Tyr, Phe, Trp
Elastase: Ala, Gly

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8
Q

catalytic triad

A

active sites composed of His, Asp, Ser

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9
Q

what stabilizes transition state ?

A
  • oxyanion hole (amide groups)
  • Ser 195 and Gly 193 provide primary stabilization of tetrahedral oxyanion
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10
Q

oxyanion hole

A
  • carbonyl oxygen moves deeper into active site due to conformational changes
  • preferential binding of t.s. (tetrahedral intermediate) –> enhanced rates
  • lowers t.s. free energy for formation of tetrahedral intermediate
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11
Q

aspartic proteases

A
  • acid-base mechanism
  • has 2 active site aspartic acid residues (catalytic dyad)
  • active at acidic pHs
  • a-b: extraction of 2 protons leads to Nu attack
  • c-d: Asp 32 extracts proton; Asp 215 donates proton
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12
Q

HIV-1 protease

A
  • aspartic protease
  • cleave yields active products
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13
Q

protease inhibitors

A
  • transition state analogs (enzyme inhibitors)
  • older meds targeted reverse transcriptase
  • newer meds target HIV protease and mimic a T.S.
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14
Q

what are the 2 ways to regulate enzyme activity

A

1) availability of enzyme
2) control of enzyme activity

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15
Q

zymogens

A
  • inactive precursor of a proteolytic enzyme
  • aka proenzyme
  • made and activated in different places
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16
Q

digestive enzymes

A

made as proenzymes so dont destroy tissues

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17
Q

enteropeptidase

A

cleaves digestive system enzymes at specific peptide bonds (autocatalytic process)

18
Q

proteolytic cleavage

A

produces the active enzyme

19
Q

protein hormones

A

can also be synthesized in inactive form and later activated

20
Q

4 ways to regulate enzyme activity

A

1) synthesis/degradation
2) proteolysis
3) allosteric regulation
4) covalent modification (global signal)

21
Q

allosteric effectors

A
  • binds to “other site” (allosteric) and regulate their catalytic activity (S-> P)
  • dont need to have structural similarity to substrates or products
    • effectors shift equilibrium to R state
    • effectors shift equilibrium to T state
22
Q

allosteric enzymes

A
  • give multiple subunits -> multiple binding sites
  • hill coefficient x=x 1
  • have 2 sites: active (for substrate) and allosteric
23
Q

example of feedback inhibition pathway

A

Aspartate Transcarbamoylase (ATCase)

24
Q

ATCase

A
  • hexameric (6 subunits; dimer of trimers)
  • each monomer has a catalytic enzyme positively affected by ATP and negatively affected by CTP
  • substrate binding sites change after allosteric binds
  • sigmodial shape (T–>R)
25
Q

ATCase activator

A

ATP –> shift left –> Km decrease –> increase affinity for aspartate

26
Q

ATCase inhibitor

A

CTP –> shifts right –> Km increases –> lower affinity for aspartate

aka negative allosteric inhibitor

27
Q

kinase vs phosphatase

A

kinase- adds phosphate group
phosphatase- removes phosphate group

28
Q

cAMP-dependent protein kinase

aka protein kinase A

A
  • aka protein kinase A
  • R2C2 tetramer
  • 2R bind cAMP –> release R subunits from C subunit –> C subunits activate as monomers
29
Q

covalent modification

A
  • substrate and allosteric react in non-covalent way
  • enzyme activity controlled with covalent modification
  • ex: dephosphorylation at -OH of Ser, Thr, Tyr
30
Q

glycogen phosphorylase

A
  • activity regulated by allosteric control and covalent modification (controlled both locally and globally)
  • feedback inhibitor= ATP
  • positive effector= AMP
  • phosphorylation of Ser14 activates enzyme
31
Q

isozymes definition

A
  • enzymes that have similar but not identical amino acid sequence
  • degrade glycogen
  • each will catalyze the same biochemical rxn
  • different Km and Vmax values
  • use different effects and coenzymes to regulate
32
Q

isozymes examples

A

1) glycogen phosphorylase- 3 isozymes (different affinities for glycogen and phosphate substrates and different allosteric effectors depending on location in body)
2) hexokinase- muscle tissue (catalyzes 1st step in glycolysis)
3) glucokinase- liver, brain, pancreas, maintains blood glucose levels (catalyzes 1st step in glycolysis but lower affinity for glucose than hexokinase)

33
Q

setereoisomers vs epimers

A

seteroisomers- mirror images
epimers- sterohcemically differs by 1 carbon

34
Q

Triose phosphate isomerase

A
  • responsible for interconversions
  • catalyzes isomerization of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate
  • catalyically perfect enzyme (Kcat/Km)
  • rate of rxn between E & S is diffusion controlled (P occurs as quickly as E & S collide)
35
Q

what do aldohexose and ketohexose sugars perfer as ring?

A

aldohexose- pyran (6-membered)
ketohexose- furan (5-membered)

36
Q

anomeric carbon

A

carbonyl carbon used for cyclic formation

37
Q

anomers

A

carbs that differ in configuraion only at their anomeric carbons

38
Q

where can glycosidic bond be found in RNA?

A

between base and sugar

39
Q

glycosydic bond

A
  • between anomeric C and -OR group
  • links monosaccharides to form polysaccharides
  • form glycoside (where -OH of anomeric C is replaced by -OR)
40
Q
A

biochem 410 and 411 (4 decks)

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