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biochem > exam 2 > Flashcards

exam 2 Flashcards

1
Q

enzyme

A

biological catalyst

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2
Q

with the exception of some RNAs,

A

enzymes are proteins

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3
Q

reaction rate is increased/decreased by enzymes?

A

increased up to 10^20 fold

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4
Q

most enzymes are so specific they..

A

catalyze reactions of only 1 stereoisomer of a given substrate

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5
Q

what can also catalyze a reaction?

A

temperature and it increases rate

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6
Q

activation energy

A

delta G with the temp sign and the lil cross thing

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7
Q

delta G is lowered/increased by

A

enzymes

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8
Q

in an enzyme catalyzed reaction…

A

enzyme binds substrate (S) which is the reactant

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9
Q

after enzyme binds substrate,

A

ES complex is formed

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10
Q

after ES complex forms,

A

transition-state species forms

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11
Q

after transition-state species is formed,

A

product is released from enzyme

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12
Q

substrate binds to the

A

active site

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13
Q

the active site is where a

A

small portion of enzyme where the substrate binds

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14
Q

active site is bound by what kind of forces?

A

non-covalent forces (so that easy separation can occur)

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15
Q

the delta G of a rxn doesn’t tell us..

A

anything about the rate at which a reaction will occur

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16
Q

what does delta G tell us?

A

if a reaction will proceed and release energy

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17
Q

rate of rxn usually expressed in terms of

A

delta in reaction or delta in product in a given time

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18
Q

rxn rate at low substrate…

A

slow rxn rate

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19
Q

substrate increases…

A

initial rate of rxn increases

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20
Q

what happens to enzyme binding sites when substrate becomes larger?

A

enzyme binding sites become filled to limit of Vmax (max rate of rxn)

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21
Q

beyond this limit, the enzyme is…

A

saturated with substrate and the reaction rate ceases to increase

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22
Q

Vo =

A

initial velocity (product formed/time)

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23
Q

S =

A

substrate concentration

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24
Q

as more substrate is added, rxn rate…

A

increases

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25
Q

at higher substrate, rxn rate changes…

A

very little

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26
Q

max rxn rate is reached when..

A

enzyme is saturated with substrate

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27
Q

Vmax =

A

maximum velocity

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28
Q

Km is also known as…

A

Michaelis-Menten constant

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29
Q

Km =

A

substrate concentration when Vo is 1/2 Vmax

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30
Q

Km is substrate that

A

leads to half-maximal velocity

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31
Q

when substrate gets large, Vmax is the…

A

max velocity

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32
Q

Km (Michaelis-Menten constant) is the..

A

dissociation constant for ES complex

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33
Q

a small Km indicates…

A

high enzyme/substrate affinity, meaning Vmax will be reached more quickly at lower S

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34
Q

from a hyperbolic curve, Vmax is…

A
  • difficult to determine
  • hyperbolic curve can be transformed into a straight line by taking the reciprocal of each variable
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35
Q

Michaelis-Menten

A

V = Vmax [S] / Km + [S]

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36
Q

lineweaver-burk plot

A

1/V = Km / Vmax x 1/[S] + 1/Vmax

in simpler words… y = m times x + b

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37
Q

plot of 1/V vs 1/[S] will give a straight line with

A

slope of Km/Vmax, y intercept of 1/Vmax, x intercept of -1/Km (absolute values)

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38
Q

rxn rate is also dependent on…

A

[S] at low concentration

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39
Q

reaction also reaches max velocity..

A

at high [S]

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40
Q

allosteric enzymes have a….

A

sigmoidal shape

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41
Q

allosteric behavior manifests as..

A

subtle changes at one site of enzyme affects substrate binding
allosteric enzymes are always multi-subunit

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42
Q

example of allosteric enzymes

A

oxygen binding of hemoglobin
multimeric
each chain has 1 heme group that can bind O2 (hemoglobin can bind up to 4 O2)

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43
Q

O2 binding curve for myoglobin is a…

A

hyberbolic curve

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44
Q

O2 binding curve for hemoglobin is…

A

sigmoidal (allosteric!!!!!)

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45
Q

O2 binding to myoglobin shows

A

steady rise until complete saturation

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46
Q

O2 binding to hemoglobin indicates

A

binding of 1st O2 which helps binding of next O2 (allosteric effect)

positive cooperativity

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47
Q

enzyme inhibition

A

competitive inhibitor and noncompetitive inhibitor

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48
Q

competitive inhibitor binds to the

A

active (catalytic) site and blocks access to it by substrate

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49
Q

noncompetitive inhibitor

A
  • binds to a site other than the active site
  • inhibits the enzyme by changing its conformation
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50
Q

competitive inhibitor is comprised of

A
  • substrate competing with inhibitor for the active site
  • more substrate needed to ‘outcompete’ inhibitor
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51
Q

changes in competitive inhibition variables

A

slope and x-int change, y doesn’t
y int –> Vmax doesn’t change
x int –> Km does change (apparent Km)

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52
Q

in competitive inhibition, inhibitor is directly…

A
  • competing with the substrate active sites on enzymes
  • apparent Km increases (you will need more substrate to get the same 1/2 Vmax)
  • vmax doesn’t change
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53
Q

in noncompetitive inhibition, the inhibitor does not…

A
  • interfere with binding of substrate to the active site, Km is unchanged
  • increasing [S] can’t overcome noncompetitive inhibition
54
Q

noncompetitive inhibition variables

A

slope and y-int change, x-int does not change

Vmax changes (apparent Vmax)
Km does not change

55
Q

in noncompetitive inhibition, inhibitor does not bind..

A

the active site, binds allosterically

substrate cannot win binding race (rxn will not occur as fast as it could - apparent Vmax decreases)

56
Q

in noncompetitive inhibition, the overall rxn will..

A

not occur as fast as it could ; Vmax decreases

57
Q

allosteric enzymes are..

A

an oligomer whose bio activity is affected by other substances binding to it

58
Q

substances binding to allosteric enzyme can..

A

change the enzyme’s activity by altering the conformations of the quaternary structure

59
Q

allosteric effector is a…

A

subtance that modifies the behavior of an allosteric enzyme

60
Q

components of allosteric effectors…

A

allosteric activator and allosteric inhibitor

61
Q

allosteric inhibitor means that..

A

the formation of product inhibits its continued production (aka feedback inhibition or end-product inhibition)

62
Q

allosteric enzymes are single or multi subunit?

A

multi-subunit ; meaning multiple conformations of the enzyme exist

63
Q

allosteric effector is..

A

a substance that modifies the quarternary structure of an allosteric enzyme (can be homotropic or heterotropic)

64
Q

models for allosteric enzyme behavior

A

concerted model or sequential model

65
Q

concerted model

A

enzyme has two conformations

66
Q

conformations of the concerted model

A

R (relaxed) - binds substrate tightly (active form)
T (tight) - binds substrate less tightly (inactive)

67
Q

when there’s no substrate in the concerted model, most enzyme molecules are in the…

A

T (inactive) form

68
Q

in the presence of substrate in the concerted model,

A

equilibrium shifts T form to R form
- inactive to active
- simultaneous

69
Q

changing from T to R and vice versa, all subunits change…

A

conformation simultaneously in the concerted model

70
Q

allosteric activator binds and stabilizes…

A

R form (active)

71
Q

allosteric inhibitor binds and stabilizes…

A

T form (inactive)

72
Q

sequential model’s main features are the

A
  • binding of substrate induces conformational change from T to R form
  • change in conformation is induced by the fit of substrate to enzyme (induced-fit model)
  • REPRESENTS cooperativity
73
Q

in the sequential model…

A
  • R form is favored by the allosteric activator
  • T form is favored by allosteric inhibitor
74
Q

main difference between concerted and sequential models

A

concerted - all subunits change simultaneously
sequential - subunits change in sequence (not at the same time)

75
Q

allosterism and pharmaceuticals

A
  • beta blockers
  • binds to beta-adrenergic receptors
  • used to treat chance of 2nd heart attack
76
Q

another example of allosterism and pharmaceuticals…

A

valium
- binds to allosteric site on GABA receptors
- leads to CNS depressant effects

77
Q

control of enzyme activity

A

side chain (-OH groups) of serine, threonine, tyrosine can form phosphate esters

the phosphorylation by ATP converts inactive precursor into active enzymes

78
Q

phosphorylation - protein kinases are…

A

proteins that catalyze phosphorylation rxns

79
Q

other ways to control enzymes (way 1)

A

zymogen - inactive precursor of an enzyme
- cleavage of one or more covalent bonds transforms it into an active enzyme

80
Q

2nd way to control enzymes

A

chymotrypsinogen
- synthesized and stored in the pancreas
- when secreted into the small intestine, the digestive enzyme trypsin cleaves it to give pi-chymotrypsin

81
Q

chymotrypsin is..

A

alpha-chymotrypsin is enzymatically active bc of its tertiary structure
- was inactive b/c of its tertiary structure

82
Q

common types of catalytic mechanism

A

general acid base catalysis
lewis acid/base rxns

83
Q

coenzyme is…

A

a nonprotein substance bound covalently or non-covalently to an enzyme
- takes part in an enzymatic rxn and is regenerated for further rxn
- organic compounds, many of which are vitamins or are metabolically related to vitaminds

84
Q

cofactors are…

A

metal ions that behave as coordination compounds (Zn2+, Fe2+)

85
Q

coenzyme (NAD+)

A

nicotinamide adenine dinucleotide (NAD+) is used in many redox rxns (precursor is niacin - B3)
- redox rxns provide energy

86
Q

coenzymes (NADH)

A

NADH is formed from the reduction of NAD+, a two-electron oxidizing agent

87
Q

lipids are organic compounds that are….

A

insoluble in water and are nonpolar

have SOME ampipathic qualities

88
Q

open chain forms (fatty acids)

A

triacylglycerols
phosphoacylglycerols
sphingolipids
glycolipids
lipid-soluble vitamins
prostaglandins
leukotrienes, and thromboxanes

89
Q

cyclic forms of lipids - sterols

A

cholesterol
steroid hormones
bile salts

90
Q

fatty acids qualities

A
  • unbranched-chain carboxylic acids
  • length of chain plays a role in chemical character
  • most commonly 12 - 20 carbons
  • usually even #s of carbons
  • C=C is UNSATURATED
  • C-C is SATURATED
91
Q

most unsaturated fatty acids have a (x) isomer

A

cis

92
Q

unsaturated fatty acids have a (x) melting point than their saturated counterparts

A

lower (greater degree of unsaturation, lower melting point)
- think: oils

93
Q

triglycerides are..

A
  • an ester of glycerol w/ 3 fatty acid chains
  • more energy per gram than carbs or proteins
  • can be saturated or unsaturated
94
Q

trans-fatty acids are made from…

A

hydrogenation process makes trans bonds
- trans fat leads to heart disease
- high LDL = not good

95
Q

phospholipids are…

A

one alcohol group of glycerol esterified by a phosphoric acid

rather than by a carboxylic acid

96
Q

phospholipids are found in

A

biological membranes
- can be saturated or unsaturated fatty acid chains

97
Q

lipid bilayer is found in the

A

biological membrane

98
Q

the lipid bilayer is made of

A

predominantly phospholipids

polar head groups get in contact w/ water

nonpolar tails buried within (hydrophobic)

can be rigid (lots of saturated fatty acids) or fluid (lots of unsaturated FA)

99
Q

membrane layers

A

both layers contain mixtures of lipids
- asymmetric (compositions on inside/outside of lipid bilayer can be different)
- exterior usually has more bulky lipids

100
Q

unsaturated FA in membranes put…

A

a kink in chain
- causes disorder in packing
- disorder increases fluidity

101
Q

cholesterol prevents…

A

extremes in temperature in membrane
- stabilizes extended chain conformations in FA (hydrophobic interactions)
- reduces fluidity on inside

102
Q

cholesterol also disrupts..

A

the tight packing of phospholipids so FA chains can’t come together
- increases fluidity outside cell

103
Q

fluid mosaic model

A

lateral motion of various components in membrane that exist side-by-side as separate entities

(lipid bilayer w/ proteins, glycolipids, glycoproteins, sterols)

104
Q

membrane proteins

A

peripheral proteins (electrostatic interactions)

integral proteins (hydrophobic interactions)

105
Q

membrane protein functions

A
  • transport substances across membranes
  • act as receptor sites
  • sites of enzyme catalysis
106
Q

glycoproteins on cell surface are involved in

A
  • cell identification
  • receptor sites
  • immune function
107
Q

glycolipids are important for

A
  • membranes
  • brain
  • nervous systems
108
Q

gangliosides are glycolipids with…

A

complex carbohydrate moiety that contains more than 3 sugars

109
Q

membrane is selectively…

A

permeable

110
Q

types of transport

A

passive & active

111
Q

active transport requires…

A

energy

112
Q

passive transport doesn’t…

A

require energy
- moves down a concentration gradient

113
Q

simple diffusion is..

A

passive
- movement of a molecules across membrane from higher to lower concentration

114
Q

facilitated diffusion is…

A

passive

uses a carrier protein or channel protein

115
Q

active transport is linked to…

A

hydrolysis of ATP or any other high-energy molecule

116
Q

membrane receptors are responsible for…

A

the binding of a biologically active substance to a receptor initiates an action within the cell

117
Q

types of lipoproteins

A

low density lipoprotein (LDL)
high density lipoprotein (HDL)

118
Q

LDLs are…

A
  • LDLs carry cholesterol and phosphoglycerides along w/ protein in blood
  • excess of cholesterol inhibits synthesis of LDL receptor which keeps cholesterol in blood
119
Q

HDL transports…

A

cholesterol back to liver

120
Q

vitamins are separated by

A

lipid soluble and water soluble

121
Q

vitamin A

A

site of primary photochemical reaction in vision
- often found in cell membrane
- vitamin A (retinol) occurs only in the animal world

122
Q

vitamin D regulates

A

calcium and phosphorus metabolism

123
Q

vitamin E

A

serves as an antioxidant

may be necessary for reproduction in humans and rats

124
Q

vitamin K

A

important for blood clotting

125
Q

vitamin A is found in the…

A

plant world as a group of pigments called carotenes
- enzyme catalyzed cleavage of beta-carotene followed by reduction gives 2 molecules of vitamin A

126
Q

vitamin A’s active molecule is…

A

retinal
- helps to form visual pigment rhodopsin

127
Q

vitamin D is mostly found in the

A

circulatory system

128
Q

vitamin E is often found in the

A

cell membrane

129
Q

reducing agent

A

electron donor

130
Q

oxidizing agent

A

electron acceptor

biochem (11 decks)

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