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Cellular Biochemistry > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

3 ways to increase rate of reaction

A
  1. Increase temperature
  2. Increase substrate concentration
  3. add catalyst
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2
Q

Active site of serine protease

A

His 57- Acid/base catalyst
Ser 195- Nuc
Asp 102- hydrogen bond to stabilize

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3
Q

Chymotrypsin unique in that

A

it acts under mild conditions

Digests broad range of substrates

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4
Q

Oxidoreductases

A

oxidation-reduction reactions

ex: Alcohol Dehydrogenase
GAP dehydrogenase

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5
Q

Transferases

A

Transfer functional Groups

Ex: alanine aminotransferase
Hexokinase

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6
Q

Hydrolases

A

Hydrolysis (cleavage by H2O)

Ex: Chymotrypsin

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7
Q

Lyases

A

Group elimination, double bond formed

ex: pyruvate decarboxylase
Aldolase

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8
Q

Isomerases

A

Isomerization Reactions

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9
Q

Ligases

A

Bond formation coupled with ATP hydrolysis

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10
Q

Multiple enzymes catalyzing the same reaction

A

isozymes

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11
Q

What provides required catalytic groups when enzyme can’t

A

Cofactor

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12
Q

Metal ions

A

Can exist in multiple oxidation states, type of cofactor

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13
Q

Coenzymes

A

may be vitamins

  1. Co-substrates: enter/exit active site like substrate
  2. Prosthetic groups: remains in active site between reactions
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14
Q

Acid-base catalysis example

A

tautomerization of ketone

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15
Q

Acid-base catalysts

A

CLAGHT

Cys, Lys, Asp, Glu, His, Try

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16
Q

Covalent catalysis

A

Covalent bond between catalyst and substrate during transition state formation

Ex: Decarboxylation of acetoactetate (Schiff base), makes acetone

2 part reaction, 2 energy barriers with intermediate

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17
Q

Metal catalysis example

A

acetaldehyde to ethanol

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18
Q

Scissile bond

A

bond cleaved by hydrolysis is positioned near Ser 195 when substrate binds to enzyme

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19
Q

Why enzymes so large if few residues require?

A

Must precisely align active site

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20
Q

Transition state in chymotrypsin

A

low barrier hydrogen bond, transition state stabilized (energy lowered).

Bond between Asp 102 and His 57 becomes shorter as reaction goes on

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21
Q

Catalysis is effected by active site microenvironment. Explain this in hexokinase.

A

Electrostatic catalysis
nonaqueous active site allows more powerful electrostatic interactions between enzyme and substrate than aqueous solution

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22
Q

How are chymotrypsin, trypsin, and elastase evolved?

A

Divergent, common ancestor

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23
Q

How has subtilisin evolved?

A

Convergent: unrelated proteins have similar characteristics

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24
Q

Chymotrypsin preferences

A

cleaves peptide bonds following large hydrophobic residues

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25
Q

Trypsin preference

A

Arginine/Lys - basic residues

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26
Q

Elastase

A

Cleaves peptide bonds following small hydrophobic residues (ex: alanine, glycine, valine)

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27
Q

Controlling activity: Proteolysis

A

Inactive chymotrypsin —trypsin–> pi-C —> delta C —> alpha C

Last 2 steps by chymotrypsinogen
More active confirmation

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28
Q

Controlling activity: inhibitors

A

resemble substrate chemically, partial catalysis, but don’t complete reaction

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29
Q

Suicide inhibitor

A

antithrombin- covalent binding, shut off reaction

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30
Q

The fact that the enzyme physically combines with the substrate is suggested by

A

hyperbolic rather than linear curve

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31
Q

unimolecular

A

first order, depends only on one substrate

k= s^-1

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32
Q

bimolecular

A

second order, depends on 2 reactants

k = M^-1 s^-1

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33
Q

What two things does velocity concentration depend on?

A

substrate concentration and Km

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34
Q

Km- what’s going on and what does it indicate

A

substrate concentration when velocity is half max, indicates dissociation of ES

Shows how efficiently enzyme selects substrate and converts it to product

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35
Q

How do you get a linear Lineweaver-Burk plot

A

[S]&raquo_space;> [E]

ES at steady state

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36
Q

Catalytic efficency

A

kcat/km

high kcat to maximize
Ability to convert substrate to product

units= M^-1 s^-1

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37
Q

kcat/turnover number

A

units = s^-1
Rate constant when enzyme is saturated with substrate
number of catalytic cycles that each active site undergoes per unit time

38
Q

Limits to catalytic power

A
  1. electronic rearrangements during TS
  2. frequency of productive enzyme collision with substrate, max is diffusion-control limit
  3. Enzyme reach perfection when rate is diffusion controlled
39
Q

Multi-substrate reactions

A

Km= each substrate is different. To find it, reaction velocity measured at different concentrations of one substrate while the other substrate is present at saturating concentration

Vmax = maximum reaction velocity when both substrates are present at concentrations that saturate their binding sites on enzyme

40
Q

Random order mechanism

A

doesn’t matter who binds first

41
Q

Ordered mechanism

A

one must bind first

42
Q

ping pong mechanism

A

one binds, product released, then the other can bind

ex: transketolase

43
Q

Multistep reaction

A

Ex: transketolase
intermediate: the 2 carbon fragment removed from F6P remains on enzyme while waiting for substrate

44
Q

nonhyperbolic reactions

A

ex: hemoglobin
Oligomeric protein- cooperative binding, multiple active sites

Use quadratic equation

Allosteric attraction

45
Q

irreversible inhibitor

A

any reagent that covalently modifies an amino acid side chain in a protein

ex: thymidylate synthases

46
Q

Suicide substrate

A

enter enzyme’s active site and begin to react, just as a normal substrate would, but then gets stuck in active site

ex: 5-florouracil

47
Q

Competitive inhibitor

A

Reversible
Substance that directly competes with substrate for binding to enzyme’s active site
Increase Km

ex: succinate dehydrogenase is inhibited by malonate

48
Q

___ occurs when product of reaction occupies the enzyme’s active site, thereby preventing the binding of additional substrate molecules

A

Product inhibition

49
Q

Substrate analogues make good inhibitors, but ____ make even better inhibitors

A

transition state analogs

50
Q

Is rate of product formation = ES disassociation?

A

No, ES complex could be going backwards (k-1)

51
Q

noncompetitive inhibition

A

Km binds to site on enzyme other than active site

Km=0
Kcat/vmax are DECREASED

ex: metal ions

52
Q

Mixed inhibition

A

apparent Km may increase or decrease

Vmax decreases

53
Q

Uncompetitive inhibition

A

multi-substrate reactor. inhibitor binds are one substrate has bound.

Vmax/Km are lowered to same degree, parallel lines

54
Q

Allosteric inhibition in glycolysis: phosphoenolpryruvate.

Why inhibit primary regulatory step in glycolysis.

A

To prevent unneeded energy expression.
If pyruvate accumulates, too much glycolysis, not full use of product.

Feedback inhibitor and Negative effector

55
Q

How does phosphoenolpyruvate inhibit glycolysis?

A

Swaps Arg 162 (+ charge) with Glu 161 (- charge)

F6P (- charge) no longer attracted to a + charge, is repelled instead

56
Q

ADP

A

positive effector
binds to same sight as phosphofructokinase
forces ARG 162 to remain where ti can stabilize F6P binding.

57
Q

4 factors that influence enzymatic activity

A
  1. change in rate of enzyme’s synthesis
  2. change in subcellular location
  3. ionic “signal”- change in pH, release of calcium
  4. covalent modification
58
Q

Most modern drugs are _____. Ideal drugs are

A

inhibitors

high affinity, high selectivity, non-toxic

59
Q

As Km increases

A

affinity of enzyme for substrate decreases

60
Q

During inhibition if vmax isn’t 0 (as in competitive), it

A

Decreases

61
Q

prosthetic group

A

cofactors that never leave molecule

62
Q

What is prosthetic group in hemoglobin?

A

heme- iron in hydrophobic pocket between E and F.

63
Q

6 bonds on iron

A

4 with nitrogen in ring
1 with histidine residue in F helix
1 with oxygen

64
Q

Why must heme be part of a protein to be a good oxygen carrier?

A

by itself, central atom Fe(II) can easily be oxidized to FE(III), which can’t bind O2.

65
Q

Myoglobin and hemoglobin: structural similarities

A

heme group in hydrophobic pocket
His F8 on iron
His E7 H-bond to O2

HOWEVER: primary linear structure different

66
Q

Invariant residues

A

essential for function. If you change them, alter molecule function (similar in myoglobin and alpha/beta subunits)

67
Q

Myoglobin and Hb are homologous proteins meaning

A

common ancestor (oxygen binding proteins)

68
Q

Conservatively substituted residues

A

position under less pressure to maintain particular amino acid, can be substituted by similar amino acid

69
Q

Variable position

A

position that can accommodate variety of residues, none critical for structure/function

70
Q

Deoxy

A 
Large cavity
T 
P. ring is bowed 
low O2 affinity 
Heme Fe has 5 ligands

Histidine residue on beta between proline and threonine residues on alpha

71
Q

Oxy

A 
small cavity
R
heme group planar
high O2 affinity 
Heme Fe has 6 ligands

Histidine residue on beta between threonine residues on alpha

72
Q

Bohr Effect

A

reduction of hemoglobin’s O2 binding affinity when pH DECREASES ( [H+] increases)

73
Q

BPG

A

stabilizes deoxy confirmation of hemoglobin to unload oxygen. Without, hemoglobin would bind too tightly.

5- charges that interact with + charge on hemoglobin
only binds to central cavity in T state

74
Q

Fetus: H21 —> Serine, so…

A

+ charge that interacts with BPG is gone

reduces fetal binding, helps transfer O2 from maternal circulation to fetus

75
Q

Microfilament functions

A 
support PM
determines cell shape
structural support
cell movement 
tensile strength
76
Q

Actin polymer

A

polymerized is F-actin
+ end grows faster
ATP is - end
G-actin is globular

77
Q

Prevent actin growth

A

adding capping protein.

78
Q

Microtubule functions

A

reinforce cytoskeleton
construct cilia/flagella
align and separate chromosomes, form spindle apparatus

79
Q

Microtubules structure

A

Binds to GTP/GDP
1 nucleotide binding site/tubulin subunit
Alpha GTP binding site buried in interface while beta exposed, GTP hydrolyzed, but resulting GDP remains bound and can’t diffuse

80
Q

Single strand microtubule called

A

protofilament

81
Q

Positive end of microtubule called

A

beta (alpha is negative, often anchored)

82
Q

Paciltaxel

A

binds to beta tubulin

blocks depolymerization, stabilizes

83
Q

Colchicine

A

destabilizes protofilament, interferes with side/side interactions.
Binds at interface between alpha/beta dimer
shut off cell division

84
Q

Intermediation filaments: Keratin

A

coil-coiled.
dimer of alpha helices.
1/4th residues hydrophobic and holds coil together
7 residue repeat units

85
Q

Keratin tetramers are antiparallel staggering held together by

A

cystine residues

86
Q

Intermediate filaments: Collagen

A

Triple helix
every 3rd is glycine –> secondary structures
30% proline/hydroxyproline
Gly-Pro-Hyp triplet (left- more stable)

3 polypeptides in right hand triplet, stabilized by H bonding.

Staggered parallel

87
Q

Where is collagen assembled?

Collagen is modified/cross linked by…

A

Endoplasmic Reticulum

covalent modifications

88
Q

Myosin

A

microfilaments
change triggered by hydrolysis of ATP bound to head
unidirectional
alpha helix lever

89
Q

Kinesin

A

microtubules
moves toward + end
unidirectional

90
Q

Why is kinesin, unlike myosin, processive or highly processive?

A

kinesin constantly holds microtubules, many cycles of ATP hydrolysis and kinesin advancement occur before the motor dissociates from its microtubule tract.

Myosin dissociates after 1 stroke.

Cellular Biochemistry (15 decks)

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