Chapter 7 + 8 - Cell Metabolism

Front 1

Velocity is related to ----- concentration via the rate constant (k)
V=k[A]

Back 1

substrate

Front 2

Initial velocity rate (Vo) is defined as increase in product when [P] is ---

Back 2

low/negligible

Front 3

What is the Michaelis-Menten Equation

what does it describe

Back 3

Velocity (Vo) = Vmax x [S] / [S] + Km

describes the variation of enzyme activity as a function of substrate concentration

Front 4

Km, a compilation of rate constants called the Michaelis constant, is unique to each enzyme and is ------of enzyme concentration.

Back 4

independent

Front 5

Vmax is directly ---- on enzyme concentration.

Back 5

dependent

Front 6

The maximal velocity possible, Vmax, can be only attained when?

Back 6

be attained only when all of the enzyme (total enzyme, or ET) is bound to substrate (S).

Front 7

Km is equal to the substrate concentration at which the reaction rate is ---- its maximal value.

what is the equation for Km then?

what does it give us an estimate of?

Back 7

half

Vmax / 2 or (k-1 + k2) / k1

Give us an estimate of how strong the enzyme binds to the substrate

Front 8

at vmax all the enzyme is bound to substrate

so... that mean [ES] = ?

and Vmax = __ [E]t

Back 8

[E]t total enzyme conc


k2

rate of ES--E + P (product formation)

Front 9

At very low substrate concentrations, when [S] is much less than the value of KM, the rate is directly --------- to the substrate concentration, that is, V0 =(Vmax/KM)[S].


At high substrate concentrations, when [S] is much greater than KM, V0 ≈ Vmax ; that is, the rate is maximal, ------ of substrate concentration.

Back 9

proportional, independent

Front 10

The Michaelis–Menten equation can be transformed into one that gives a straight-line plot.

this is known as ...

Back 10

lineweaver burk

Front 11

what is the lineweaver burk equation?
give the x- intercept, y intercept, slope,



what are the x and y values for the plot?

Back 11

the recipricol of the Michaelis equation

so

1/V0 = Km/Vmax x 1/S + 1/Vmax
y = m x + b

-1/Km
1/Vmax
Km/Vmax




x = 1/[S] and y= 1/V0

Front 12

if Km is a small number Then it takes ---- level of [S] to fill the active site and the ES complex is --- (---substrate affinity)

Back 12

low, STRONG, high

Front 13

if Km is a large number

it take --- level of sub to fill active site,
EX complex is ---- which means it has --- substrate affinity

Back 13

high, weak, low

Front 14

what is the turnover number and what does it represent?

Back 14

kcat

the turnover number of an enzyme, which is the number of substrate molecules that an enzyme can convert into product per unit time when the enzyme is fully saturated with substrate�

Front 15

so at vmax, all enzymes are occupied thus [ES] = [E]t

so in relationship to mcat [or k2]

Vmax =?

Back 15

Vmax = k2 x [E]t

so k2 or kcat = Vmac / [E]t

Front 16

what does kcat/km measure?

Back 16

catalytic efficiency

Front 17

at [S] << Km, velocity (V0) =

Back 17

(kcat/ KM) [S][E]t

Front 18

Thus, when [S] << KM, the enzymatic velocity depends on the values of kcat/KM, [S], and [E]T. Under these conditions, kcat/KM is the rate constant for the interaction of S and E. The rate constant kcat/KM is a measure of catalytic efficiency because it takes into account both the rate of catalysis with a partic- ular substrate (kcat) and the strength of the enzyme–substrate interaction (KM

Back 18

`

Front 19

Table 6.3 shows the kcat/KM values for several different substrates of chymotrypsin, a digestive enzyme secreted by the pancreas. Chy- motrypsin clearly has a preference for cleaving next to bulky, ----- side chains

Back 19

hydrophobic

Front 20

What is the difference between sequential reactions and double-displacement reaction>

Back 20

sequentia = all reactants bound to enzyme before product release

dbl displace = product is releace before all reactants are bound to enzyme

Front 21

feedback inhibition?

Back 21

the amount of product formed controls the activity of anzymes in pathway

Front 22

positive feedback loop vs positive regulation?

Back 22

pos feedback is when product increases its own production

positive regulation is when a ligand binds to a reg site of enxyme and increases activity

Front 23

allosteric enzymes have what kind of shape curve

Back 23

S

Front 24

Allosteric enzymes have ----- subunits and active sites

R = --- state which is the --- conformation
T= --- state which is the ----- active conformation but more ----

T/R is the ---- constant known as L0

which state is more common?

the substrate binds to which conformation more easily than the other?

Back 24

multiple

relaxed, active
tense, less, stable

allosteric

T state is more common

substrate binds to R conformation more easily

Front 25

what is the symmetry rule?

Back 25

all subunits are either T or all R

Front 26

In the absence of substrate or signal molecules, R and T are in ----, with T being the more-stable state and thus the more-common state
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Back 26

equilibrium

Front 27

What is the physiological significance of cooperativity, seen as a sigmoidal kinetics?
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Back 27

Cooperativity means that allosteric enzymes display a threshold effect: below a certain substrate concentration, there is little enzyme activity�

However, after the threshold has been reached, enzyme activity increases rapidly. In other words, much like an “on or off ” switch, cooperativity ensures that most of the enzyme is either on (R state) or off (T state).
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Front 28

the binding of S --- T-R equilibrium in favor of --

Back 28

disrupts, R

Front 29

In the allosteric enzyme aspartate transcarbamoylase, shape changes are regulated by two molecules: --- and ---


where --- is an activator

and --- is an inhibitor

Back 29

ATP and CTP

Atp = activator


and CTP = inhibitor

Front 30

ATP is an allosteric activator of aspartate transcarbamoylase because it ------- the R state, making it easier for substrate to bind. As a result, the curve is shifted to the ----, as shown in blue�

Back 30

stabilizes, left

Front 31

Cytidine triphosphate (CTP) stabilizes the --- state of aspartate transcarbamoylase, making it more difficult for substrate binding to convert the enzyme into the --- state. As a result, the curve is shifted to the ----, as shown in red.
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Back 31

T, R, right

Front 32

what is the most common modification used to affect protein function?

Back 32

addition or removal of phosphoric groups

Front 33

what enzym catalyzes the addition of PO3 to serene/threonine/tyrosine?

what removes the PO3 moiety

Back 33

kinase


phosphatase

Front 34

The concept of ligand (substrate) association with proteins is the basis for --- design and the design of ----.
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Back 34

drug, inhibitors`

Front 35

factors that effect enzyme activity

------- pH changes the charge on COO- group to COOH
------- pH makes NH3+ a stable NH2
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Back 35

decreasing

increasing

Front 36

competitive inhibition

reversible or irreversible?

can be overcome by what

Back 36

inhibitor competes substrate for active site

it is reversible

can be overcome by higher sub concentrations



At any given inhibitor concentration, competitive inhibition can be relieved by increasing the substrate concentration. Under these conditions, the substrate “out competes” the inhibitor for the active site.
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Front 37

Some competitive inhibitors are useful drugs. One of the earliest examples was the use of sulfanilamide as an antibiotic. Sulfanilamide is an example of a sulfa drug, a sulfur-containing antibiotic.

Structurally, sulfanilamide mimics -----, a metabolite required by bacteria for the synthesis of --- acid.

Sulfanilamide binds to the enzyme that normally metabolizes ---- and competitively inhibits it, preventing ---- acid synthesis
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Back 37

PABA, folic


PABA, folic

Front 38

competive inhibition continued

and increas in inhibiter concentration leads to ------ in Km

does competitive competition effect Vmax?

Back 38

increase (moresubstrate is need for the same rxn rate)


no

Front 39

in uncompetative inhibition, the inhibitor binds to --- complex to form ---

no product is formed, which ------ Vmax


it also decreases---

Back 39

ES, ESI

it decreases Vmax because ESI complex does not generate product

it decreases Km because less substrate is needed for the same rxn rate

Front 40

in NONcompetitive inhibition

S and I bind ----- to enzyme at different binding sites

this decreases the # of --- enzyme molecules

it---- Vmax why?

it ---- Km why?

Back 40

simultaneously, active

decreases, because ESI complex does not form product

unchanges Km, because it only lowers [E]

A noncompetitive inhibitor acts by decreasing the overall number of active enzyme molecules rather than by diminishing the proportion of enzyme molecules that are bound to substrate.

Front 41

Irreversible inhibitors

what are the four kinds?

Back 41

Group-specific reagents
Affinity labels or substrate analogs
Suicide or mechanism-based inhibitors
Transition state analogs
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Front 42

what do group specific reagents do?


--- inhibits the proteolytic enzyme chymotrypsin by modifying only 1 of the 28 --- residues in the protein at ---- site

Back 42

react with specific R-groups of amino acids

DIPF, serine. active

Front 43

Affinity labels, also called substrate analogs, are molecules that ------- modify active-site residues and are structurally similar to the substrate for an enzyme. They are thus more ----- for an enzyme’s active site than are group-specific reagents.


example: ----- binds at chymotrypsin ---- site and modifies -----residue
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Back 43

covalently, more specific

TPCK, active, histidine

Front 44

suicide inhibitors

---- based inhibitors.

the enzyme thinks suicide inhibitor is the substrate

the inhibitor is then ------ by the enzyme, this forms an -------- which through covalently modifies enzyme thus inactivating it


example?

Back 44

mechanism, processed, intermediate


The antibiotic penicillin is a suicide inhibitor of the enzyme that synthesizes bacterial cell walls. (glycopeptide transpeptidase)

Front 45

Transition state analogs

Potent inhibitors

this inhibitor mimics the ---- state of substrate which binds to the enzyme thus making it unavailable for substrate

Back 45

transition