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z F1: Phys Chem > Exam 2 > Flashcards

Exam 2 Flashcards

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1
Q

How are enzymes categorized

A

by their 6 major classes

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2
Q

Cofactors

A

small inorganic molecules or inorganic ions bound reversibily

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3
Q

Coenzymes

A

more complex organic or metallo-organic molecules bound reversibly

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4
Q

Prosthetic group

A

anything bound tightly

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5
Q

Apoenzyme + cofactor =

A

holoenzyme

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6
Q

What is the relationship between vitamins and coenzymes

A

vitamins are precursors to enzymes

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7
Q

Bind of enzyme to substrate occurs at the ________ site. This is initially facilitated by multiple ___-_________ interactions

A

active, non-covalent

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8
Q

Enzymes bind to the transition site ______ than either substrates or products

A

better

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9
Q

The _____________ is determined by delta G knot of the reaction

A

equilibrium

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10
Q

delta G knot prime and equilibrium of a reaction are ________________ of the path of the reaction

A

independent

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11
Q

What is induced fit?

A

The enzyme adjusts to fit the substrate when it binds to it

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12
Q

The release of __________ ________ contributes to specificity and catalysts

A

binding energy

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13
Q

Phase (1) is also known at the __________________ of reaction

A

pre ready rate

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14
Q

The broad maximum of the reaction rate at phase (2) is called _____________

A

steady state

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15
Q

What is V0?

A

initial rate of reaction

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16
Q

What is Vmax?

A

the maximum rate of reaction – when the enzyme is saturated with substrate

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17
Q

What is Km?

A

Substrate concentration at which the reaction is 1/2 Vmax

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18
Q

What are the three assumptions of Michaelis-Menten equation

A

-k2 can be neglected
-there are many more molecules of substrate than of enzyme (ES can be neglected)
-very little substrate has been converted to product (P can be neglected)

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19
Q

What is the steady state assumption

A

at steady state, the formation of ES (at rate K1) is equal to its breakdown

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20
Q

Kcat describes the _____ of the reaction

A

speed

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21
Q

Kcat/Km is also known as the

A

specificity constant or substrate preference

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22
Q

If Kcat is increased the reaction is _____
If Kcat is low …

A

faster
lower substrate concentration required (higher affinity)

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23
Q

When V0 = Vmax

A

the plateau at high substrate concentrations

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24
Q

S with E leads to number of encounters per second which determines the _____

A

speed

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25
Q

What does diffusion-controlled mean

A

Determined by the speed at which substrate molecules can diffuse to the enzymes

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26
Q

Increasing the speed of diffusion-controlled reactions is only possible by increasing ______

A

diffusion (Circe effect)

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27
Q

What are the two reactions of ternary complexes

A

random-substrate binding does not matter
ordered-substrate binding matters

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28
Q

Reactions with no ternary complexes

A

one product is released before the 2nd substrate binds
Involve covalent modifications of enzyme
Are always ordered

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29
Q

What are the 4 reversible inhibitors

A

Competitive
Uncompetitive
Non-competitive
Mixed

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30
Q

Competitive Inhibition

A

Y-axis interception
Vmax does not change but Km increases

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31
Q

Methotrexate

A

competitive inhibitor
anti-cancer drug

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32
Q

Uncompetitive Inhibition

A

Inhibitor binds only to ES, but not to free enzyme E
Both Vmax and Km decrease
parallel lines

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33
Q

Non-competitive inhibition

A

Inhibitor binds to both free enzyme E and to ES complex with equal affinity
Vmax decreases, but not Km
x-axis interception

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34
Q

Mixed Inhibition

A

Inhibitor binds to E and ES but with two binding constants
(affinity) are different
Vmax decreases, Km increases or decreases
Intersection above or below x-axis

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35
Q

Group-specific inhibitors

A

React with side chains of certain amino acids in the active site or elsewhere

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36
Q

DIPF

A

modifies critical serine residues in acetylcholinesterase and in protease chymotrypsin
(group-specific inhibitor)

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37
Q

Iodoacetamide

A

reacts with the sulfhydryl group of critical cysteines
(group-specific inhibitor)

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38
Q

Affinity labels

A

React only with active side groups

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39
Q

TPCK

A

Binds to the active site of chymotrypsin and modifies an essential histidine residue
(affinity label)

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40
Q

Suicide Inhibitors

A

metabolized by the enzyme to create an inhibitor that inactivates the enzyme

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41
Q

5-fluorouracil

A

Anti-cancer drug
(suicide inhibitor)

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42
Q

Deprenyl

A

suicide inhibitor of monoamine oxidase
used for Parkinson’s disease

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43
Q

Penicillin

A

Suicide inhibitor of an enzyme that catalyzes a critical step in bacterial cell wall synthesis

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44
Q

General acid/base catalysts

A

an AA side chain donates or accepts a proton which may facilitate the formation of a transition state or a reaction intermediate

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45
Q

Covalent catalysts

A

During the enzymatic reaction, an intermediate becomes covalently attached to the enzyme

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46
Q

Metal Ion catalysts

A

may interact with a transition state and stabilize it
generate nucleophile
orient it in the active site

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47
Q

What are the 6 strategies used by enzymes

A

genreal acid-base catalysts
covalent catalysts
metal ion catalysts
electrostatic catalyst
entropy reduction
straining the substrate

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48
Q

Which of the 6 strategies used by enzymes are usually combined to elucidate an enzyme’s catalytic mechanism

A

all of them

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49
Q

Proteases cleave specific ________ _______ in proteins and have a wide variety of roles in digestion, protein recycling, enzyme activation, virus maturation

A

peptide bonds

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50
Q

What do the different types of proteases depend on

A

whether a critical AA or metal is used in the active site

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51
Q

What are the three serine proteases

A

Chymotrypsin
Trypsin
Elastase

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52
Q

Chymotrypsin

A

-cuts the polypeptide chain next to bulky hydrophobic residues
-pocket is deep and hydrophobic -> bulky AA fit

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53
Q

Trypsin

A

-cuts next to positively charged residues
-negatively charge Asp at bottom of pocket -> attracts positively charged AAs

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54
Q

Elastase

A

-cuts next to small neutral AAs
-small pocket is filled with valine residues -> only small AA will fit

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55
Q

What is the first part of covalent mechanisms

A

Serine OH attacks the carbonyl carbon of the peptide bond
first fragment is released

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56
Q

The negative charge of the short-lived intermediate in covalent first step mechanism causes the intermediate to become

A

unstable and start to decay

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57
Q

The ester bonds in acyl enzyme does what to the product of the first step of covalent mechanism

A

stabilizes it

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58
Q

What is the second part of covalent mechanisms

A

water attacks the acylated enzyme
covalent bond with the enzymes is cleaved
second fragment is released, free enzyme is regenerated

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59
Q

Catalytic triad

A

Serine
Histidine
Aspartate

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60
Q

Cysteine proteases use ______ made more active by histidine

A

Cysteine

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61
Q

Aspartyl proteases use _______ activated by _______

A

Water
Aspartate

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62
Q

Metalloproteases use _____ activated by a _____ and a base

A

Water
Metal

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63
Q

HIV protease is a _________

A

Homodimer

64
Q

Inhibitors have been designed that resemble the __________ __________ of the reaction but cannot be cleaved

A

Tetrahedral Intermediate

65
Q

HIV protease inhibitors mimic the negatively charged _________ of the tetrahedral intermediate

A

Oxygen

66
Q

What are the four principle ways of regulation of enzyme activity

A

allosteric regulation
reversible covalent modification
proteolytic activation
regulation of enzyme levels

67
Q

What regulation pathway is reversible? Which one is irreversible?

A

reversible: covalent modification
irreversible: proteolytic activation

68
Q

Which regulation of enzyme activity pathway is multimeric

A

allosteric regulation

69
Q

Allosteric regulators can be…

A

second messengers (cAMP, Ca2+)
indicators of available metabolic energy (ATP)

70
Q

Which step in an activity pathway is usually regulated

A

the first step

71
Q

What kind of regulators are carbamoyl phosphate ad aspartate

A

homotropic regulators

72
Q

Does the response to substrate concentration sigmoid follow michaelis-menten kinetics

A

no

73
Q

ATPase is a multimeric protein with two _______ ______ and three ________ ________

A

catalytic trimers
regulatory dimers

74
Q

CTP and ATP are _________ regulators

A

Heterotropic

75
Q

Binding if CTP shifts the equilibrium to the __ state

A

T state (less active)

76
Q

Binding of ATP shift equilibrium to the __ state

A

R state (more active)

77
Q

Most common covalent modifications

A

R-OH at Ser, Tyr or Thr residues or of His

78
Q

What does glucagon do to the liver

A

Increase phosphorylation b kinase

79
Q

What does epinephrine (increase ca2+, AMP) do to the muscle

A

Increase phosphorylase b kinase

80
Q

Glycogen phosphorylase is made more active by __________ which is catalyzed by what

A

Phosphorylation
Phosphorylase kinase

81
Q

Phosphorylation can be reversed by what

A

Insulin (decreases glucose levels)
Phosphoprotein phosphatase 1 causes this

82
Q

Two examples of zymogens

A

Insulin
Proteases

83
Q

What are zymogens

A

Inactive substance which is converted into an enzyme when activated by another enzyme

84
Q

How is regulation of glycogen phosphorylase by covalent modifications turned off

A

Destruction of the enzyme/hormone
Specific binding of an inhibitor

85
Q

By making zymogens rather than active enzymes the pancreas protects itself from what

A

Auto digestion

86
Q

What are two examples of proteolytic cascades

A

-Blood clotting factors are activated by a cascade of proteolysjs events
-Complement cascade utilized by the immune system to destroy pathogens consists of a series of proteolytic events

87
Q

How are carbohydrates defined

A

They have the formula Cn(H2O)n

88
Q

How to name basic carbohydrates

A

Number of carbon atoms in the carbohydrate +
“ose”
Ex: triose

89
Q

Difference between aldose and ketose

A

Aldose = aldehyde
Ketose = ketone

90
Q

Difference between D and L amino acids

A

They are chiral centers where D is right and L is left

91
Q

Constitutional isomer

A

Molecules with same formula but connected differently

92
Q

Stereoisomers

A

Molecules with same formula and same connectivity but different 3D arrangement

93
Q

Diastereomers

A

Stereoisomers that are not mirror images of each other they have different physical properties

94
Q

Epimers

A

Stereoisomers that differ at only one chiral center

95
Q

Enantiomers

A

Are mirror images of one another

96
Q

Hemiacetals and hemiketals are produced by being attacked by what molecule

A

Alcohols

97
Q

When linear glucose cyclones what species is formed

A

Hemiacetal carbon (is has two isomers: alpha and beta)

98
Q

Upon cyclization the former carbonyl carbon becomes a new chiral center called the

A

Anomeric Carbon

99
Q

Trans is ____
Cis is ____

A

Trans is alpha
Cis is beta

100
Q

Sugars with free anomeric carbon are ______

A

Reducing (can be oxidized)

101
Q

Which functional group in a sugar is reducing

A

Ester

102
Q

Difference between homo and hetero polysaccharides

A

Homo: one monomer
Hetero: two or more sugars

103
Q

Polysaccharides do not have a defined _________ _________

A

Molecular weight

104
Q

Glycogen and starch are composed of which sugar

A

Homopolysaccharides

105
Q

What are glycosaminoglycans

A

Linear polymers of repeating disaccharide units

106
Q

What are the 4 glycoaminoglycans

A

Hyaluronate (GLcNAc)
Chondroitin 4-sulfate (GalNAc45)
Keratan Sulfate (GlcNAc6s)
Heparin (GlcNS3S6S)

107
Q

Heparin sulfate is heparin like ___________ but attached to ________

A

Polysaccharide
Proteins

108
Q

Why is heparin therapeutic

A

Bind to virus and bacteria and decrease virulence
Form blood vessels

109
Q

Glycoproteins are proteins with small ___________________ attached

A

Oligosaccharides

110
Q

Proteoglycans consist of sulfated ________________ which are attached to a large rod shaped protein

A

Glucoseaminoglycans

111
Q

Syndecans and glypicans

A

syndecans: protein has a single transmembrane domain
Glypicans: protein is anchored to a lipid membrane

112
Q

What part of LPS causes septic shock? Which part determines the serotype

A

Endotoxin
O-specific chain

113
Q

What is the function of hyaluronan in proteoglycan aggregates and what are their functions

A

Hyaluronan and aggrecan form huge noncovalent aggregates
-hold water
-provide lubrication
-low friction
-covers joint surfaces

114
Q

Which membrane proteins mediate the interaction of cells with the extracellular matrix

A

Integrins

115
Q

Which sugar targets proteins to lysosomes

A

mannose 6-phosphate receptor/lectin of the trans Golgi complex binds to the oligosaccharide of lysosomal enzymes, targeting them for transfer into the lysosome

116
Q

What is a key feature of a lipid

A

insoluble in water

117
Q

Which functional groups are part of fatty acids

A

carboxylic acids with hydrocarbon chains

118
Q

Structure of 18:1 cis-9-octadecenoic acid

A

cen = double bond
18 carbons
1 double bond

119
Q

What is an omega three fatty acid

A

3rd carbon from end

120
Q

What are the two essential fatty acids

A

Linoleate and Linolenate

121
Q

What is the effect of chain length and unsaturation on the melting point of fatty acids

A

More double bonds = lower melting point
Longer chain = higher melting point

122
Q

Saturated FA are more _______ and can pack closer

A

linear this leads to a higher melting point

123
Q

What are three triglycerols

A

ester, glycerol, fatty acids

124
Q

Most natural triglycerols are ______, containing different fatty acids

A

mixed

125
Q

Often the fatty acid attached at the what carbon is unsaturated

A

C2

126
Q

In glycerophospholipids, the backbone is what and what is the hydrophilic head joined by

A

glycerol
phosphodiester linkage

127
Q

Glycerophospholipids are both fatty acids, forming hydrophobic tails, are joined to C1 and C2 by what kind of bonds

A

ester bonds

128
Q

Ether lipids are joined by what bonds

A

ether bonds

129
Q

The ______ is particularly rich in plasamalogens

A

heart

130
Q

What is the sphingolipid called with no head group

A

ceramide

131
Q

Sphingolipids can be classified as phospholipids or glycolipids, what are the linakes of each

A

phospholipids: phosphodiester
glycolipids: beta-glycosidic

132
Q

Glycolipids with one uncharged sugar are called

A

cerebroside

133
Q

If 2 or more uncharged sugars are attached, these lipids are called

A

globosides

134
Q

More complex glycolipids with at least one sialic acid are called

A

gangliosides

135
Q

Cholesterol spans only one ________ of a lipid bilayer

A

leaflet

136
Q

Three types of lipids can self-assemble in aqueous solution to form a ______ which can close to form _______. This driving force is caused by what

A

bilayer
vesicle
hydrophobic interactions

137
Q

Micelle = __ fatty acid
Bilayer = __ fatty acid
Lipid Droplet = __ fatty acid

A

1
2
3

138
Q

What are the three types of membrane proteins

A

peripheral, integral, lipid-anchored

139
Q

Proteins and lipids can move _______

A

laterally

140
Q

Proteins can not _______ while lipids use enzymes to _____

A

flip-flop
(flippase-inside, flopade-outside)

141
Q

Lipids are asymmetric what is found on the outside and what is found in the inside

A

outside: sphingomyelin and phosphatidylcholine
inside: phosphatidyl ethanolamine and phosphatidyl serine

142
Q

How are peripheral membrane proteins attached

A

attachment to membrane can be disrupted by concentrated salt solutions, low pH, Ca2+ chelators, or urea

143
Q

Integral membrane protein’s membrane must be dissolved by what

A

detergent or organic solvent

144
Q

Membrane spanning integral proteins are _________ and _______. They can be predicted by plotting the __________ of amino acids

A

alpha-helical and beta-conformation
hydrophobicity (hydropathy plot)

145
Q

What are the three common lipid anchors of proteins found inside, what is the one common lipid anchor found outside

A

inside: palmitoyl group, myristoyl group, farnesyl group
outside: GPI

146
Q

Where are GPI proteins concentrated

A

lipid rafts

147
Q

Lipid rafts play an important role in ________ ___________

A

single transduction

148
Q

Caveolae

A

Inward curved rafts
induced by caveolin
membrane traffic and signaling

149
Q

What is the major differences of gram positive and gram negative

A

positive: 1 membrane, more proteoglycan complex
negative: 2 membrane, LPS

150
Q

What are the special characteristics of transporters

A

sterospecific
saturable (michaelis-menten)
transport rates below the limit of unhindered diffusion

151
Q

What are the 4 classes of transport ATPase

A

P-type
V-type
F-type
ABC-type

152
Q

Which class of transport ATPase has sodium/potassium

A

P-type

153
Q

Which class of transport ATPase has cystic fibrosis chloride channel and MDR

A

ABC-type

154
Q

What are the special characteristics of channels

A

greater rate of diffusion
not saturable
not stereospecific

155
Q

Why can the channel open for K+ instead of Na+ when Na+ is smaller

A

there is minimal energy difference because the K+ shape is the same as the active site making it ideal for it to pass causing an influx of K+

z F1: Phys Chem (4 decks)

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