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Biochemistry > Conceptual Exam 2 > Flashcards

Conceptual Exam 2 Flashcards

1
Q

Kd equation in terms of vmax and concentration?

A
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2
Q

Low kD equals?

A

high affinity

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3
Q

Free Energy equation?

A
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4
Q

Function of myoglobin?

A

Carries oxygen in muscle cells; binds oxygen very tightly

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4
Q

What is p50?

A

The partial pressure of O_2 that results in 50% of the binding sited of myoglobin being occupied.

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4
Q

How many subunits does myoglobin have?

A

One subunit

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5
Q

Cooperative or uncooperative binding in myoglobin?

A

Uncooperative

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5
Q

What is the function of the distal His?

A

stabilizes O_2 (donates proton)

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6
Q

Does O_2 or CO bind better? Why?

A

The CO bond is a triple bond which is stronger than O_2’s double bond. Greater polarity.

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7
Q

What is the makeup of hemoglobin?

A

single domain heterotetramer (4 subunits to bind to O_2; two alpha, two beta)

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8
Q

Describe T-state’s affinity and kD for O_2?

A

High kD, low affinity

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8
Q

Is hemoglobin binding cooperative or uncooperative?

A

Positively cooperative

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8
Q

What does cooperativity mean?

A

binding to one heme group raises the affinity of other subunits for oxygen

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9
Q

Draw myoglobin’s binding graph.

A
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10
Q

What does binding induce?

A

A conformational; change

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11
Q

Deoxyhemoglobin O_2 or none? Oxyhemoglobin?

A

None bound; O_2 bound

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11
Q

Describe R-state’s affinity and kD for O_2?

A

Low kD, high affinity

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12
Q

What is the O_2 binding curve? Draw it.

A

a visual representation of hemoglobin saturation

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12
Q

What does the transition involve from T-state to R-state?

A

broken ionic/electrostatic interactions

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12
Q

What is a cofactor? Function?

A

One or more inorganic ions or complex molecules called coenzymes; helper molecules for enzymes to assist them with biological functions

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13
Q

What is an enzyme? What does it lower?

A

a biomolecule (protein or RNA) that catalyzes a chemical reaction

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14
Q

What is a prosthetic group?

A

A coenzyme or metal ion that is tightly bound to enzyme

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14
Q

Draw out the reaction coordinate diagram.

A
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15
Q

What is an apoenzyme? Holoenzyme?

A

enzyme without its cofactors; a complete catalytically active enzyme together with its bound cofactors

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16
Q

What is an active site?

A

pocket within enzyme at which substrate binds

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16
Q

What is the substrate?

A

Compound that is acted upon by enzyme

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17
Q

Free GIbbs Energy equation for Keq?

A
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18
Q

What do enzymes do and what is the end result?

A

lower activation energy, making it faster for rxn to occur

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19
Q

Keq is equal to?

A

products/reactants

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19
Q

Relationship of enzymes and transition state? What does this mean?

A

Complementary, active site of enzyme is tailored to stabilize the transition state of the reaction

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20
Q

What remains unchanged in the reaction coordinate diagram?

A

change in G, no altered equilibrium

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20
Q

What do transition state analogs do? What do they compete with?

A

They are molecules designed to mimic the transition state during a reaction; they compete with the substrate for binding at the enzyme’s active site

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21
Q

What are the 5 rate enhancement rules?

A
  1. specificity
  2. covalent catalysis
  3. acid-base catalysis
  4. proximity/orientation
  5. transition state stabilization
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21
Q

Explain acid-base catalysis.

A

Acid or base (other than H+ or OH- that accelerates the reaction)

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22
Q

When is the proton transferred in acid-base catalysis?

A

transition state

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22
Q

Explain covalent catalysis.

A

Characterized by the formation of a covalent bond b/w enzyme and substrate

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23
Q

Good acids/bases?

A

Glu, Asp, Lys, Arg, Cys, His, Ser, Thr, Tyr

24
Q

What does chymotrypsin use?

A

acid/base and covalent catalysis

25
Q

Residues that participate in chymotrypsin and their role?

A

1) Ser 195- nucleophile in active site
2) His 57- base, accepts proton from Ser 195
3) Asp 102- acid, donated proton to amino group and promotes departure

26
Q

What is the experimental determination of enzyme kinetics?

A

measure reaction rates of enzyme under different substrate concentrations

27
Q

What is Michaelis-Menten Equation? identify the components.

A
28
Q

Draw the Lineweaver-Burk graph.

A
28
Q

Draw the Michaelis- Menten equation.

A
29
Q

What is the Lineweaver-Burk Equation?

A
30
Q

What is Km the rate of?

A

breakdown of ES/rate of formation of ES

30
Q

Why are these assumptions helpful?

A

They simplify the mathematics.

31
Q

What are the two assumptions for M-M?

A
  1. Conc of enzyme-substrate complex remains constant over time (steady state/equilibrium)
  2. Reaction is observed at initial phase, where substrate conc is much higher than enzyme conc (initial velocity)
32
Q

What is the turnover number (Kcat)?

A

number of substrate molecules converted to product per enzyme molecule per unit time

32
Q

Identify the equations that differentiate Km from Kd? When are they equivalent?

A

——–, when K_-1 is&raquo_space;»> K_2

33
Q

Draw out the aspartic proteases.

A
33
Q

What is catalytic efficiency?

A

effectiveness of an enzyme in facilitating a reaction

33
Q

What is the Kcat equation?

A
34
Q

What is diffusion in limited catalysis?

A

Enzyme’s catalytic rate approaches max diffusion rate of substrate to enzyme’s active site

34
Q

What is the equation for catalytic efficiency?

A

Kcat/Km; cat/mouse

35
Q

In competitive inhibition, where does the inhibitor bind? Km affect? Vm?

A

active site, Km increases, Vm doesn’t change

35
Q

Draw out a pH activity curve.

A
35
Q

Draw out M-M and Lineweaver graphs for competitive inhibited and uninhibited enzymes.

A
36
Q

Draw out M-M and Lineweaver graphs for uncompetitive inhibited and uninhibited enzymes.

A
36
Q

Where does mixed inhibition bind? Effect of Km and Vmax?

A

binds at site distinct from substrate binding site; can increase or decreae

37
Q

Describe irreversible inhibition. Example?

A

combine with or destroy functional group on enzyme that is essential for activity; penicillin

38
Q

What is the catalytic triad?

A

His 57, Ser 195, Asp 102

38
Q

What do serine proteases do (2)? What do they contain?

A
  1. cleave peptide bonds
  2. conserve 3 degrees structures

Contains catalytic triad

39
Q

Draw out the arrow pushing mechanism for serine protease.

A
39
Q

What does change in color intensity indicate?

A

Changes in absorbance at specific wavelengths can reveal conc of substrate/product over time

39
Q

What does a calorimetric substrate/product allow for?

A

Measurement of enzymatic activity based on changes in color intensity

39
Q

Why is nitrophenolate a useful probe?

A

You can mix with enzyme and watch immediate cleavage reaction.

40
Q

Nitrophenolate mechanism.

A
41
Q

What does Km vs. pH reveal?

A

pH the binding affinity is highest or lowest

41
Q

What is burst kinetics? Draw graph.

A

Initial rapid burst of product formation followed by a slower, steady-state phase; ————

41
Q

What does a crystal structure allow for?

A

Allows visualization of the active site

41
Q

What do pH and activity profiles show?

A

Shows how enzyme activity varies with changing pH levels

41
Q

How are AP and Chymotrypsin mechs different and similar?

A

-different active site residues
-AP used nucleophilic attack of H_2O, chym. uses nucleophilic attack of serine residues
-both enzymes exhibit specificity for cleaving peptide bonds
-both form covalent enzyme-substrate intermediate during catalysis

42
Q

What does Kcat vs. pH reveal?

A

pH at which enzyme achieves max catalytic efficiency

43
Q

high Km equals? low Km?

A

low affinity, high affinity

43
Q

Draw out enolase mechanism.

A
44
Q

What is the purpose of enzyme regulation?

A

respond to changing needs of the cell

44
Q

What is allosteric regulation?

A

molecule binds to allosteric site and causes conformational change that alters enzyme’s activity

44
Q

What is feedback inhibition?

A

end product of metabolic pathway binds to proton inhibits an enzyme earlier in the pathway

45
Q

What is covalent modification?

A

phosphorylation, acetylation, methylation —> alters enzyme activity, stability

45
Q

What element does enolase use? What does it do?

A

Mg2+, stabilizes negative charge

45
Q

What is proteolytic cleavage?

A

some enzymes are inactive and require proteolytic cleavage to become active

45
Q

Draw out the kinetic behavior of allosteric enzyme. Pos and neg.

A
46
Q

What does the hill coefficient measure?

A

cooperativity

46
Q

If N>1, pos or neg cooperativity? End result meaning?

A

positive, means that it enhances binding

46
Q

If n <1, pos or neg? Meaning?

A

Negative, inhibits binding of subsequent molecules

47
Q

Why is the coefficient useful?

A

influences enzyme’s sensitivity to changes in substrate concentration

47
Q

What is feedback inhibition?

A

feedback mechanism to respond to needs of isoleucine

47
Q

What is covalent modification?

A

Phosphorylation (adds phosphate, makes molecule bigger and more negative)

47
Q

What adds phosphate? Removes it?

A

Kinase and phosphatase

47
Q

Mechanism of phosphorylation.

A
47
Q

Draw out the proteolytic cascades for chymotrypsin maturation/blood clotting.

A

Biochemistry (8 decks)

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