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BMSC 200 > Chapter 6 > Flashcards

Chapter 6 Flashcards

1
Q

what were biochemical rxns originally believed to be

A

inseparable from life

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2
Q

what is vitalism

A

its the belief that living things are the fundamentally different from non-living things; that they contain some non-physical element and are governed by different principles that inanimate objects

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3
Q

what did eduard buchner demonstrate

A

that dead yeast still convert sugars into alcohol, indicating the reactions of life were separate from life

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4
Q

where is the word enzyme from

A

from greek it means “in yeast”

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5
Q

although the protein factor of some enzymes is fully active, other enzymes require…

A

cofactors or co enzymes for activity

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6
Q

what are co factors

A

in organic ions (Mg 2+, Fe2+, etc…)

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7
Q

what are co enzymes

A

complex organic molecules (vitamins)

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8
Q

what is a prosthetic group

A

a co enzyme or co factor that is tightly associated with the enzyme

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9
Q

different enzymes that use the same enzymes…

A

usually preform similar types of reactions

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10
Q

apoenzyme + cofactor/co enzyme =

A

holoenzyme (biologically active from)

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11
Q

why do we need to take vitamans

A

because its a molecule required by the body that cant be produced by the body

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12
Q

what do catalysts do

A

-lower the amount of energy required for a reaction to proceed
-speed up attainment of equilibrium, but do not change equilibrium
-are unchanged by the reaction; recycled to participate in another reaction

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13
Q

enzymes dont make a impossible reaction possible they…

A

take a already possible reaction and make it faster

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14
Q

how does catalyst compair to enzymes interms of speed

A

enzymes are often much faster than chemical catalysts, some approaching catalytic perfection

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15
Q

how does catalyst compair to enzymes interms of conditions

A

many chemical catalysts that require extremes of temperature, pressure and pH while enzymes function under physiological conditions

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16
Q

how does catalyst compare to enzymes interms of specificity

A

enzymes have a higher degree of specificity (incuding steriospecificity) than most chemical catalysts. this includes specificity for what they act apon and what they produce

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17
Q

how does catalyst compare to enzymes interms of regulation

A

unlike chemical catalyst many enzymes are responsiveness to the dynamic needs of the cell and organism

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18
Q

what is a anabolic reaction

A

building stuff up

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19
Q

what is a catabolic reaction

A

breaking stuff down

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20
Q

what enzymes are more spicific? ones that preform anabolic or catabolic reactions

A

enzymes preforming anabolic rxns

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21
Q

what is a substrate, product and active site

A

-substrate is the molecule acted upon by the enzyme
-product is the molecule produced by the enzyme
-active site is the portion of enzyme responsible for binding the substrate to formation of an enzyme-substrate complex

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22
Q

enzymes convert substrates into products but also…

A

convert products into substrates

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23
Q

what is the active site of an enzyme

A

3D cleft formed from the different parts of the polypeptide chain

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24
Q

how much of the enzyme does the active site represent

A

just a small portion

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25
Q

active sites are unique…

A

microenvironments

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26
Q

how are substrates bound to enzymes

A

by multiple weak interactions

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27
Q

what does the specificity of substrate binding depend on

A

the precisely defined arrangement of atoms in the active site

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28
Q

can enzymes and their active sited be flexible

A

yes

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29
Q

what can substrate binding cause

A

induced fit or conformational selection

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30
Q

why is hand in glove analogy better then lock in key analogy for enzyme specificity

A

because when you put ur hand in glove it canges the conformation and it is a perfect fit

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31
Q

when is a reaction spontanious

A

only when the delta G is negative

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32
Q

what is a spontaneous reaction

A

when a reaction will proceed with out the input of energy and the reaction releases energy (exergonic)

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33
Q

what if a reaction cannot take place spontaneously

A

then the delta G is positive and in imput of free energy is required to drive such reactions (endergonic)

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34
Q

what is the delta G at equilibrium

A

in a system at equilibrium there is no net charge in the concentrations of the products and reactants and the delta G is at 0

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35
Q

what does the delta G of a reaction dependent on

A

only on the free energy of the product minus the free energy of the reactants. The delta G of a reaction is independedt of the steps of the transformation

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36
Q

how come the delta G doesnt tell us anything on the rate of the reaction

A

because a negative delta G indicates that a reaction can take place spontaneously but does not signify weather or not it will proceed at a perceptible rate

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37
Q

what does the activation energy between substrate and product determine

A

the rate at which equilibrium is reached

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38
Q

what do enzymes do between substrate and product

A

they provide a lower-energy pathway between the substrate and the product, lowering the activation energy

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39
Q

what is the relationship between the rate of a reaction and activation energy

A

it is inverse and exponential

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40
Q

what determines the equilibrium of the reaction

A

the difference between S and P

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41
Q

do enzymes influence the difference in free energy

A

no, there for they dont influence the equlibrium

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42
Q

what two ways can enzyme forces lower activation energy

A

catalytic capabilities of enzymes results from both

-chemical effects (1 acid/base catalyst, 2 covalent catalyst)

-binding effects (1 substrate binding, 2 transition state stabilization)

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43
Q

what does the binding of substrate in the active site provide

A

specificity and catalytic power

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44
Q

how much can catalytic mechanisms limited to binding properties increase reaction rates

A

by over 10,000-fold

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45
Q

is there a overlap between substrate binding and transition state binding

A

yes there is a conceptual overlap

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46
Q

what do we need for an enzyme in terms of specificity

A

-must be complementary enough for the substrate to ensure specificity (meaning one substrate and one substrate only)
-at the same time it needs to be different enough from the substrate to promote change within the substrate

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47
Q

how do substrates binding promote reactions

A

by
-reducing entropy (decreased freedom of motion of two molecules in solution)

-alignment of reactive functional groups of the enzyme with the substrate

-desolvation of the substrate (demoval of water molecules) to expose reactive groups

-distortion of substrates

-induced fit of the enzyme in response to substrate binding

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48
Q

where is there an increased interaction of the enzyme and substraight

A

in the transition state

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49
Q

essence of a catalyst is stabilization of…

A

the transition state

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50
Q

how is the active site complementary to the transition state

A

in shape and chemical character

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51
Q

how much tighter may a enzyme bind to their transition states then their substraights

A

10^10-10^15 times more tightly

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52
Q

what are transition state analogs

A

they are stable compounds that resemble unstable transition states

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53
Q

are transition states of enzymes stable

A

no

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54
Q

what do transition state analogs have the potential for

A

therapeutic applications as competitive inhibitors

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55
Q

what are competitive inhibitors

A

they are molecules that bind to the active site of an enzyme, they tend to resemble the substrate molecule

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56
Q

how can transition state analogs prevent substrate binding

A

because they can bind the active site of a target enzyme site with high affinity

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57
Q

why is it better to design drug molecules that represent the transition state

A

-because itll bind to enzyme with much higher affinity
-youll have to use less drug molecule into the pacient
-the less you put in the lower probability itll react with something else causing some type of side effect
-cheaper

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58
Q

what are some ways that pathogens are interacting with hosts

A

in very complex ways for example:
rabies, spread from saliva to blood, host wants to spread to next victim, would do this by causing the victim to want to bite

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59
Q

what kind of side chains does the active site often contain

A

chemically reactive side chains such as Asp, Glu, His, Cys, Tyr, Lys, Arg, and Ser

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60
Q

what are two commonly observed mechanisms of chemical catalyst

A

acid/base catalyst
covalent catalyst

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61
Q

what is acid base catalysis reaction acceleration achieved by

A

catalytic transfer of a proton

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62
Q

in acid base catalyst the side chains can act as either… or…

A

bases (acceptors) or acids (donors)

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63
Q

histidine is often involved with…

A

with a pKa near physiological pH is often involved in acid/base catalysis

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64
Q

what is the pKa of a functional group influenced by

A

chemical microenvironment

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65
Q

what makes functional groups more suitable for acid base catalyst

A

functional groups from amino acids can have different pKas within the active site which makes them more suitable for acid/base reactions

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66
Q

covalent catalyst often involves two steps what are they

A

the first which forms a covalent linkage to the enzyme, the second to regenerate the free enzyme

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67
Q

what is kinetics

A

the study of the velocity of reactions

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68
Q

how is the velocity of a reaction quantified as

A

the change in concentration of product overtime V=delta [P]/delta t

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69
Q

what units in enzyme kinetics measured in

A

inits of concentration over time, for example mmoles/sec or moles/min

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70
Q

as enzymes are proteins any variable that influences protein structure…

A

my influence enzymatic activity

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71
Q

what is the activity of enzymes sensitive to

A

pH and tempature

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72
Q

what is enzyme velocity influenced by

A

enzyme and substrate concentration

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73
Q

for kinetics what relationship are we most interested in

A

the relationship between velocity and substrate concentration

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74
Q

when would you need induction of expression

A

at times of increases biological activity

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75
Q

what happens if there is an access of enzymes around

A

they can be targeted for distruction

76
Q

velocity is defined as change in product concentration over time. when is it necessary to measure product

A

it is necessary to measure product formation before equilibrium is reached

77
Q

what is initial velocity (Vo)

A

the velocity at the beginning of an enzyme catalyzed reaction, prior to product accumulation

78
Q

what does K1 and K-1 represent

A

rapid, non-covalent interactions between enzyme and substrate

79
Q

what is K2

A

its rate constant of formation of product from ES

80
Q

why can you measure kinetics at equilibrium

A

because there is no change in conc of products overtime

81
Q

how do you calculate initial velocity (Vo)

A

Vo=[ES]K2

82
Q

how do you calculate the velocity of a reaction

A

V=delta[R]/delta t=[ES]K2

83
Q

what happens when E+S interact (for a reaction)

A

E+S (K1–> or <–K-1)ES (–>K2) E+P

84
Q

when a system is trying to reach eq what kind of reactions are happening

A

it is all about converting substrate into product with very little back reaction (<–)

85
Q

what is the steady assumption

A

E+S (K1–> or <–K-1)ES (K2–> or <–K-2) E+P

86
Q

what does the steady state assumption mathematically state

A

[E][S]K1=[ES]k-1+[ES]k2

87
Q

in deriving the michaelis and menton equation what assumption did they work from

A

that the rate of formation of the ES complex was equal to the rate of its break down

88
Q

what is the rate of formation of the ES complex

A

[E][S]k1

89
Q

what is the rate of break down of the ES complex

A

[ES]k-1 + [ES]k2

90
Q

what does the michaelis-menten equation describe

A

the relationship between substrate concentration and initial velocity

91
Q

what is the Michaelis-menten equation

A

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

92
Q

the more substrate you present to a enzyme…

A

the faster it can use to product but it levels off

93
Q

what is the Km on a Michaelis-menten plot

A

it is the concentration of substrate required to reach 1/2 Vmax

94
Q

what is Kmax on a Michaelis-menten plot

A

it is the maximun velocity of the enzyme

95
Q

when does velocity become independent of substrate concentration

A

at Vmax

96
Q

the lower the km…

A

the higher the affinity of that particular enzyme for that particular substrate

97
Q

what is 1/2 Vmax not…

A

1/2 the Vmax
not a measure of velocity

98
Q

what is 1/2 Vmax a measure of

A

substrate concentration

99
Q

what does the ES complex depend on

A

the conc of the enzyme, substrate and the K1 rate constant

100
Q

for many enzymes Km provides an accurate approximation of…

A

the in vivo substrate concentration

101
Q

if the Km provides a accurate approximation of the in vivo substrate what does this say

A

that most enzymes are usually functioning at about half there max velocity

102
Q

when [S]<Km…

A

enzymes are highly sensitive to changes in substrate concentration but have very little activity

103
Q

when [S]>Km…

A

enzymes have high activity but are insensitive to changes in substrate concentration

104
Q

when [S]=Km…

A

enzymes has significant activity and is responsive to changes in substrate concentration

105
Q

michaelis-menten sample question 1: what is the velocity of a reaction when substrate concentration is = to Km

A

step 1: pick values of Km and [S] that are consistent with the question here we can say Km and [S] are = to 2 mM

step 2: substitute these vales into the equation Vo=VmaxX(2mM)/2mM+2mM

step 3: express the velocity as a fraction of Vmax
Vo=2Vmax/4 Vo=1Vmax/2

106
Q

michaelis-menten sample question 2: what is the velocity of a reaction when substrate concentration is double Km

A

step 1: pick values of Km and [S] that are consistent with the question here we can say Km is = to 2 mM and [S] is = to 4 mM

step 2: substitute these vales into the equation Vo=Vmax X 4mM / 2mM + 4mM

step 3: express the velocity as a fraction of Vmax
Vo=4Vmax/6 Vo=2Vmax/3

107
Q

michaelis-menten sample question 3: what is the velocity of a reaction when substrate concentration is 1/3 of Km

A

step 1: pick values of Km and [S] that are consistent with the question here we can say Km 3mM and [S] is = to 1 mM

step 2: substitute these vales into the equation Vo=Vmax X (1mM) / 3mM + 1mM

step 3: express the velocity as a fraction of Vmax
Vo=1Vmax/4

108
Q

how does lineweaver-burke compare to the michaelis-manten

A

lineweaver-burk plots are more precise method of analysis of kenetic data

109
Q

what is a lineweaver-burke

A

-describes the relationship between [S] and V0
-double-reciprocal plot of 1/Vo vs 1/[S]
-used to determine Vmax and Km

110
Q

what is the enzyme turn over number

A

-also called Kcat
-equals the number of molecules of substrate converted to product per unit time under saturating conditions

111
Q

how do you calculate the enzyme turnover number

A

Vmax / [Et]

112
Q

what is a enzyme inhibitor

A

a compound that binds to an enzyme to interfere with activity

113
Q

what do enzyme inhibitors prevent

A

the formation of ES or the breakdown to E and P

114
Q

how do reversible inhibitors bind to the enzyme

A

by non covalent interactions

115
Q

what are the classes of reversible enzyme inhibitors with different mechanisms and kinetic consequences

A

-competitive
-uncompetitive
-noncompetitive

116
Q

what do competitive inhibitors resemble and how do they function

A

the substrate and compete with the substrate for binding of the active site

117
Q

competitive inhibitors only bind…

A

free enzymes

118
Q

how can the effects of competitive inhibitors be over come

A

with an access of substrate (washing out)

119
Q

how does a competitive inhibitor compare to substrate with no inhibitor present

A

Vmax is the same but apparent Km is increased

120
Q

uncompetitive inhibitors bind only to…

A

the ES complex

121
Q

how is Vmax decrease for uncompetitive inhibitors

A

by the conversion of ES to ESI which cannot form product

122
Q

what do uncompetitive inhibitors reduce

A

[ES]

123
Q

in uncompetitive inhibitors what happens as E binds to S to replenish ES

A

this apparent increase in affinity of the E for S causes a decrease in Km

124
Q

what is round up

A

a uncompetitive inhibitor of a plant enzyme involved in amino acid metabolism

125
Q

increased affinity of an enzyme would…. the Km

A

Shift a decrease in Km

126
Q

what do uncompetitive inhibitors do to Vmax

A

decrease Vmax of an enzyme (so passes through graph at a higher point)

127
Q

what do non competitive inhibitors bind to

A

E and ES (bind a site distinct from active site)

128
Q

how do noncompetitive inhibitors effect Vmax and Km

A

Vmax is decrease with no change in Km

129
Q

non competitive inhibitors dont influence S binding therefor…

A

there is no change in Km

130
Q

what do non competitive inhibitors essentially do

A

essentially they reduce the number if active enzyme molecules

131
Q

what does serine proteases serve as

A

it serves as digestive enzymes,
including trypsin, chymotrypsin, and elastase, that cleave peptide bonds in protein substrated

132
Q

what does the members of the serine protease family share

A

simular sequences of active site residues

133
Q

where are members of protease family synthesized and stored

A

they are synthesized and stored in the pancreas as inactive zymogens to prevent damage to cellular proteins

134
Q

when and how are inactive zymogens activated

A

at the appropriate time by selective proteolysis

135
Q

what kind of catalytic mechanism occurs with serine proteases

A

catalytic mechanism contains elements of both covalent and acid-base catalysis

136
Q

serine proteases have unique specificities that reflect…

A

unique substrate binding pockets

137
Q

what does thrombin cleave

A

Arg-Gly bonds

138
Q

what does trypsin cleave by

A

Lys and Arg

139
Q

what does Chymotrypsin cleave by

A

Phe, Tyr or Met

140
Q

what does Elastase cleave by

A

Gly and Ala

141
Q

what does papain cleave

A

it cuts all peptide bonds

142
Q

what does serine proteases have a conserved catalytic mechanism based on

A

a catalytic triad of residues (Asp, His, Ser)

143
Q

what does His act to do in serine proteases catalytic mechanism

A

acts to accept and donate a proton at each of the two stages of the reaction mechanism (acid base catalyst)

144
Q

what does Asp act to do in serine proteases catalytic mechanism

A

it stabilizes the positively-charges His to facilitate serine ionization

145
Q

what does Ser act to do in serine proteases catalytic mechanism

A

it attacks the carbonyl group of the peptide bond to be cleaved (covalent catalysis)

146
Q

out of the serine protases catalytic triad of residues (Asp, His, Ser) which one is the least important

A

Asp

147
Q

what is phase 1 of the chymotrypsin mechanism

A

step 1: (acid/base) His acts as base to extract proton from hydroxyl of Ser. This activates the oxygen of the hydroxyl group

step 2: (covalent) formation of a covalent linkagefrom the hydroxyl group of the Ser to the carbonyl carbon of the peptide bond to be cleaved in the substrate

step 3: (acid/base) His acts as an acid to donate a proton to the amine group of peptide bond to be cleaved, this cuts the substrate peptide into two pieces

148
Q

what is phase 2 of the chymotrypsin mechanism

A

step 1: (acid/base) His acts as a bas to extract a proton from a water molecule activating the oxygen of this molecule

step 2: (covalent) activated water molecule attacks the point of covalent linkage between enzyme and substrate

step 3: (acid/base) His acts as an acid to donate a proton to reform the hydroxyl group of Ser

149
Q

what are some ways you can tell the different phases of the chymotrypsin mechanism

A

-if polypep chain is still in one piece its phase 1 if in two phases its in phase 2

-differs in where His gets/donates its protons. in phase 1 it gets a proton from ser in phase 2 it gets a proton from h2o molec

-phase 1 it donates it onto the peptide bond phase 2 it donates it onto the peptide bond phase 2 it donates it onto the hydroxyl group of ser

150
Q

how can the activity of an enzyme be regulated by

A

controlling the amount of the enzyme (long term) or by the activity of a constant quality of the enzyme (short term)

151
Q

what can regulate the enzyme availability

A

location, rates of synthesis and degridation

152
Q

what can regulate the enzyme activity

A

a) covalent modifacation
-phosphorolation, methylation, glyosylation etc

b) non-covalent modification (allosteric)
-allosteric regulation

153
Q

enzymatic reactions are often controlled through _______ by the final product of the pathway

A

negative feedback inhibition

154
Q

what often inhibits the enzyme and what step is it

A

the final product often inhibits the enzyme catalyzing the first unique and committed step

155
Q

in regulation of enzymatic activity what does inhibiting the the first unique and committed step prevent

A

regulation at this step conserves material and energy and prevents accumulation of intermediates

156
Q

in points of regulation describe the roles of steps A(e1)B(e2)C(e3)D(e4)E(e5)F

A

-F is the end product it is needed in limited amounts and cannot be stores
-A is valuable and showed to be conserved unless F is needed
-BCD and E have no biological roles other then as an intermediate in production of F

157
Q

how does the negative feed back in a branched pathway often occur

A

by the final product of each branch acting to inhibit the enzyme catalyzing the first unique and committed step of the branch

158
Q

what happens in regulation when two pathways cooperate to form a single product

A

-the final product can inhibit the first unique step of each branch
-the molecules preceding the merger can inhibit the first step if their branch as well as activating the first step if the opposing branch

159
Q

what do allostaric enzymes do

A

they serve as information sensors to coordinate cellular metabolism

160
Q

how are allosteric regulated

A

-interactions with metabolic intermediates

-allosteric modulators that bind non-covalently at sites other then the active site

161
Q

what structures are allosteric usally

A

usually examples of quantinary structures

162
Q

what kind of reactions do allosteric enzymes catalyze

A

branch point reactions

163
Q

because allosteric enzymes reactions are slow this represents…

A

rate limiting steps of the pathway

164
Q

allosteric enzymes do not obey _____, instead they have ______ curves

A

michaelis-menten kinetics, sigmoidal curves

165
Q

allosteric enzymes transition from a…….within a ……….

A

less active state to a more active state, narrow range if substrate concentration

166
Q

the activity of allosteric enzymes is more sensitive to changes in….

A

substraite concentration near the Km than are the michaelis-manten enzymes of the same Vmax

167
Q

decribe the sensitivity in allosteric enzymes called threshold effect

A

below a certain substrate concentration there is little enzyme activity; after the threshold has been reached the enzyme activity increases rapidly (on/off)

168
Q

what does PFK1 catalyze (phosphofructokinase)

A

an early step of glycolysis

169
Q

what is an inhibitor and activator of phosphofructokinase

A

phosphoenolpyruvate (PEP) is an intermediate near the end of the pathway. it is an allosteric inhibitor of PFK1

ADP is an allosteric activator of PFK1

170
Q

what happens when ratio [PEP]/[ADP] is high

A

PFK1 is inhibited

171
Q

what happens when [PEP]/[ADP] is low

A

PFK1 is activated and glycolysis produces more ATP from ADP

172
Q

alostaric inhibitors are rate….

A

limiting steps

173
Q

the activity of PFK1 is responsive yo the concentration of…

A

substrate as well as the allosteric activators and limitors

174
Q

even at levels of substrate the activity of the enzyme can be through changes…

A

in levels of the allosteric modulators

175
Q

many enzymes are regulated through…

A

covalent linkages of a modifying group to change some aspect of the proteins behavior such as activity

176
Q

the most common post translation modifacation is…

A

through phosphoralation

177
Q

is enzyme regulation by covalent modifacation reversable

A

yes they are usually reversable with one enzyme catalyzing the addition of the group and another enzyme catalyzing the its removal

178
Q

what adds phosphoryl groups and what removes them

A

kinase adds phosphoryl and phosphates removes them

179
Q

what two enzymes are responsible for the production and utilization of glycogen

A

-glycogen synthase (anabolic) which catalyzes production of glycogen from glucose

glycogen phosphorylase (catabolic) which catalyzes the breakdown if glycogen into glucose

180
Q

what is it called if you had both anabolic and catabolic reactions occurring at the same time

A

its called futile cycling

181
Q

how do you avoid futile cycling

A

through reciprocal regulation ensuring that only anabolic or catabolic is happening at any given time

182
Q

what happens to glycogen phosphorylase and glycogen synthase in response to hormones released when your scared or hungry

A

both enzymes are phosphoralated. which activates the catabolic enzyme and inactivates the anabolic enzymes

183
Q

in glycogen metabolism what reaction if favored when in the fed state and un fed/scared state

A

unfed/scared: glycogen into glucose
fed state: storage og glucose within glycogen

184
Q

what happens in response to glycogen phosphorylase and glycogen synthase when hormones released when the body has been fed in glycogen metabolism

A

both enzymes are unphosphorylated

185
Q

in glycogen metabolism when unphosphoralated the anabolic enzyme is____and the catabolic enzyme is____

A

active, unactive

BMSC 200 (10 decks)

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