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Biochemistry > Exam 2 Review > Flashcards

Exam 2 Review Flashcards

1
Q

What is the basic principle of catalysis?

A

Stabilizing transition states

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2
Q

What are the 6 classes of enzymes (based on the reactions they catalyze)?

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lysases
  5. Isomerases
  6. Ligases
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3
Q

What function do oxidoreductases have?

A

They perform redox reactions, which involve the transfer of electrons

Ex: Oxidases, peroxidases, reductases …

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4
Q

What is the characteristic feature of all hydrolases?

A

They all use H20 molecules to assist with the catalysis

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5
Q

What is the difference between a Lyases and a Ligase?

A

Lyases do not need energy, whereas ligases use triphosphate molecules (XTP, i.e. ATP) to help drive the reaction

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6
Q

What group of enzymes does ATP synthase fall into?

A

ATP synthase is a hydrolase because it uses an H20 molecule to help form ATP molecules

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7
Q

What is Gibbs free energy?

A

The energy available to do work (drive chemical reactions)

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8
Q

What is standard free energy?

A

The free energy at specific standard conditions:

25 degrees C, 1atm, pH=7

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9
Q

Do enzymes affect the delta G of a reaction?

A

No, enzymes only change the energy that is required to initiate the conversion of reactants into products (rate of reaction)

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10
Q

What is an exergonic reaction?

A

Exergonic means that the reaction is spontaneous. The reaction proceeds in the direction that leads to a loss of free energy “Downhill”

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11
Q

Can enzymes catalyze nonspontaneous reactions?

A

No. Enzymes do not change delta G, they only change the rate of the reaction

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12
Q

How can you make a nonfavorable reaction happen?

A

You can couple it with a favorable reaction with a larger deltaG

ex: ATP hydrolysis

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13
Q

What does a negative delta G signify?

A

A spontaneous reaction

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14
Q

What is the law of mass action?

A

The equilibriam constant can becalculated in the follwing way:

For Rxn: A + B > C + D

K = [C][D] / [A][B]

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15
Q

What is the relationship between delta Go and K?

A

Go = - R T ln(K)

T = temperature in kelvin

R= 8.314 J/(mol*K)

K = equilibrium constant

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16
Q

How do you calculate the delta G of a reaction in non-equilibrium conditions?

A

ΔG = ΔGo + R*T* ln ( [C] [D] / [A][B] )

where A, B, C, D are the molar concentrations of the products and reactants

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17
Q

Is ΔGo’ positive or negative if there is more products than educts?

A

ΔGo’ is negative

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18
Q

Describe the ΔGo of pacemaker reactions, such as the conversion of ATP to ADP + Pi

A

Pacemaker reactions have very large negative ΔGo’ values

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19
Q

How can the spontaneity of a reaction with a small ΔGo’ be changed?

A

By changing the concentrations of reactants or products

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20
Q

What is activation energy, and how do enzymes affect it?

A

Activation energy is the free energy difference between the substrate and the transition state. Enzymes lower activation energy, allowing more molecules to have enough energy to reach the transition state.

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21
Q

Describe the bonding between substrate and enzyme

A

Multiple weak interactions bind the substrate to the enzyme including: electrostatic forces, H-bonds, and vanderwaals forces

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22
Q

How does the enzyme promote the formation of the transition state?

A

It promotes the substrate(s) to be positioned in favorable orientations, making formation/breaking of appropriate bonds more likely to occur

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23
Q

Why is it not strictly correct to say “a catalyst reduces the activation energy of a reaction”?

A

Catalysts allow a completely different reaction to take place that has the same substrate and produces. This reaction has a lower activation energy than the uncatalyzed reaction

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24
Q

What does the fact that enzymes have a Vmax suggest about how substrates and enzymes interact?

A

The existance of a maximal velocity suggests that substrates and enzymes form discrete ES complexes. The vmax occurs when all enzymes are bound to substrates.

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25
Q

Describe the active site of a typical enzyme

A
  • 3D cleft formed from tertiary protein structure
  • precise arrangement and nature of molecules determine the substrate specificity
  • microenvironment that promotes the reaction
  • small volume relative to entire enzyme
  • mutliple weak interactions form ES
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26
Q

What is the difference between the “lock & key” and “induced fit” models?

A

In the lock and key model, only specific substrates can bind to an enzyme because of their inherent shape

In the induced fit model, the enzymes are flexible and can conform to fit to several differently shaped substrates. (catching a baseball analogy)

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27
Q

What is binding energy?

A

The free energy that is released on binding.

This energy is maximized when the correct substrate binds to an enzyme because it has the maximum possible interactions within the active site.

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28
Q

What metal ion is bound to carbonic anhydrase?

A

Zn2+ is bound to three histidine rings in the interior B-sheets of the carbonic anhydrase enzyme

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29
Q

What is the unit for the rate constant of a first order reaction?

A

1/s

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30
Q

What is the equation for the velocity of a first order reaction?

A

v = k*[A]

where v=velocity

k=rate constant

[A] = concentration of substrate A

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31
Q

What is the equaltion for the velocity of a second order reaction?

A

v = k*[A]*[B]

where k = rate constant

[A], [B] = concentrations of substrates

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32
Q

What is the steady state assumption?

A

The concentrations of intermediates ([ES]) stay the same even if the concentrations of starting materials and products are changing

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33
Q

What quantity is varied in order to measure the initial velocity of an enzyme?

A

[S] is varied while [E] is held constant.

As [S] is increased, Vo increases until it the enzymes are saturated at vmax

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34
Q

What quantity tells us about the formation of the ES complex?

A

Vo: initial velocity

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35
Q

What is Km?

A

Km is the Michaelis constant and equals the substrate concentaration at which the reaction rate is half of its maximal value

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36
Q

When [S] <<< Km, what does Vo equal?

A

Vo = (Vmax/Km) * [S], if [S] <<< Km

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37
Q

When is the reaction velocity substrate dependent?

A

At low substrate concentrations, the velocity curve has a large slope, making it substrate dependent. At high [S] the enzymes saturate and the velocity is independent of [S]

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38
Q

What can k2 also be called?

A

The catalytic constant or turnover number

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39
Q

What is the equation for vmax?

A

Vmax is at high substrate concentrations, so all E will be bound in ES form.

vmax = Kcat * [Et]

where Et is total enzyme concentration

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40
Q

What are the two partial reactions involved in Michaelis-Menten kinetics?

A

1) formation and decay of the enzyme-substrate complex (km)
2) formation of the product (kcat)

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41
Q

What is the Michaelis-Menten equation?

A

v = (kcat*[Et] * [S]) / (km + [S])

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42
Q

What are the axes on a Lineweaver-Burk plot?

A

x-axis: 1/[S]

y-axis: 1/v

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43
Q

What is the significance of the intercepts on a lineweaver-burk plot?

A

The y-intercept = 1/Vmax

The x-intercept = -1/Km

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44
Q

What does the Km value say about the affinity of an enzyme for a substrate?

A

A low Km signifies a high affinity for the substrate

*half of the maximal velocity is reached at a lower [S]

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45
Q

Does lower Km mean a higher vmax?

A

No. Km and Vmax are independent

46
Q

How is the rate constant of an enzyme defined?

A

rate constant = kcat/ Km

47
Q

Can an enzyme have more than one rate constant?

A

Yes. Different an enzyme that binds to different substrates like chymotrypsin has a different rate constant for each ES complex.

48
Q

What are the two types of enzyme reactions with multiple substrates?

A

Sequential and Double Displacement (ping-pong)

49
Q

Explain what happens during a double-displacement “Ping-pong reaction”.

A

A substituted enzyme intermediate is formed when the first substrate interacts with the enzyme.

This Enzyme intermediate is then able to interact with a second substrate to form the product.

It is called ping-pong because the substrates appear to bounce off of the enzyme

50
Q

Explain the binding energy curve of an allosteric enzyme.

A

The binding energy peaks at [A]50, where the velocity is equal to half Vmax

It then decreases as [A] increases

This is due to the cooperative binding. Once one substrate binds, the enzyme changes into a complex that has a higher affinity for the substrate.

51
Q

What are additional factors that affect the activity of an enzyme?

A

pH and temperature change the conformation of an enzyme

these can be used to regulate enzyme activity

52
Q

What is the critical temperature that most enzymes denature at?

A

42 degrees celcius

53
Q

What are isozymes?

A

Enzymes that differ in amino acid sequence, but catalyze the same chemical reaction

They have different Km and Vmax

54
Q

How if the fractional saturation of an enzyme calculated?

fes

A

fes = V/Vmax = [S] / ([S] +Km)

55
Q

Which type of inhibition is characterized by rapid dissociation of the enzyme-inhibitor complex?

A

Reversible inhibition (competitive)

55
Q

Describe competitive inhibition

A

Lowers the rate of catalysis by reducing the proportion of enzyme molecules bound to substrate

Km increases

Vmax is unchanged

Inhibitors can be substrate or transition state analogs

56
Q

How does the slope of the L-B plot change with the addition of a competitive inhibitor?

A

The slope increases and the y intercept (and thus Vmax) stays the same

57
Q

Ibuprophen is an example of which type of inhibitor?

A

Competitive inhibitor

58
Q

Describe uncompetitive inhibition

A

The inhibitor only binds to the ES complex, preventing the S from being released

Km and Vmax are reduced

The L-B plot is shifted left (higher intercepts)

59
Q

Describe noncompetitive inhibition

A

The inhibitor can bind to E or ES

Vmax is reduced, but Km stays the same

60
Q

What are suicide inhibitors?

A

Starts out like competitive inhibition with a substrate analog, but then a covalent bond is formed between the inhibitor and the active site of the enzyme.

This appears like non-competitive inhibition.

Example: Penicillin

61
Q

What are the 4 catalytic strategies?

A
  1. Covalent catalysis
  2. General acid-base catalysis
  3. Catalysis by approximation
  4. Metal Ion catalysis
62
Q

Describe how proteases like chymotrpsin work

A

Proteases use covalent catalysis to destabilizze and break a peptide bond through hydrolysis.

The serine OH group is able to act as a nucleophile and attack the carbonyl of the target peptide bond (Acylation)

Then H2O deacylates the group leaving behind the enzyme and cleaved peptide

63
Q

What is the function of the oxyanion hole?

A

It stabilizes the tetrahedral intermediate during covalent catalysis

64
Q

Compare and contrast the role that Mg2+ plays in ATP hydrolysis to the role it plays in restriction endonucleases

A

Mg2+ plays similar roles in both, but it is included as part of the ATP substrate in ATP hydrolysis, whereas it is part of the restriction endonuclease enzyme itself

65
Q

Describe the power stroke of myosin

A

The hing region of the myosin undergoes a large conformational change which allows for the myosin head to be displaced, thus leading to mechanical contraction

66
Q

What does transcriptional control of enzymes regulate?

A

The number/concentration of enzymes

ex: transcription factors

67
Q

Describe interconversion in terms of enzyme regulation

A

Second messenger systems are used in order to activate/de-activate enzymes

68
Q

Which step of a metabolic pathway do key enzymes catalyze?

A

The slowest step

69
Q

What is a zymogen?

A

An inactive form of an enzyme. This can be cleaved in order to activate it.

70
Q

What is the function of aspartate carbamoyl-transferase (ATCase)?

A

It catalyzes the first step in the syntesis of pyrimidines such as CTP

71
Q

Describe how ATCase is regulated

A

CTP inhibits the enzyme via negative feedback

ATP activates the enzyme

72
Q

Describe the structure of ATCase

A

It is made up of 6 dimers that are arranged into 2 groups of 3 stacked on top of one another. Each dimer has a catalytic and regulator end.

ATP and CTP can both bind to the regulatory subunit

2 conformations: T and R state

73
Q

Describe the T and R states of ATCase

A

The R conformation is more active than the T state

CTP binding favors the T state, and substrate binding favors the R state.

In the R state, the regulatory subunits rotate, moving the catalytic subunits apart

74
Q

Which direction does the binding curve shift in the presence of a negative regulator?

A

The sigmoidal curve is shifted right for negative regulators

Ex: CTP affecting ATCase

75
Q

What is L in the context of allosteric regulators?

A

L is the ratio of molecules in T state to R state

L= T/R

76
Q

Describe the Hill coefficient

A

The hill coefficient is a measure of the cooperativity of oxygen binding

77
Q

Does the conversion of ATP to ADP and Pi have a positive or negative Gibbs Free Energy?

A

Very Negative

-30 kJ/mol

78
Q

What role does the P-loop play for ATP Hydrolysis?

A

The P-loop is lowered and is able to stabilize the ATP within the binding sites

79
Q

Can a monomeric protein display cooperative binding?

A

No. Cooperative modulation is only possible in multimeric protein complexes. When a substrate binds to one subunit, the binding affinity increases for the other subunits

80
Q

What molecule provides the phosphate for phosphorylation reactions?

A

ATP

81
Q

What are the only amino acids that can be phosphorylated?

A

Serine, Threonine and Tyrosice

These amino acids have hydroxyl groups capable of binding covalently to phosphate groups

82
Q

What role do kinases and phosphatases play?

A

Kinases add a phosphate group

Phosphatases remove a phosphate group

83
Q

How is Protein Kinase A regulated?

A

Via covalent modification.

Regulatory chains have a sequence that is a substrate analog which occupies the active site (competitive inhibition)

cAMP can bind to the regulator subunits allowing them to be released from the catalytic subunit leading to activation of PKA

84
Q

Where is inactive PKA found in the cell?

A

inactive PKA is found in the cytosol of the cell

Active PKA enters the nucleus because of a nuclear localization sequence (NLS) which is recognized by nuclear transport proteins

85
Q

What molecule is a general activator for most proteases?

A

Trypsin cleaves many proteases from their zymogen form to the active form

86
Q

What is known as the master regulatory step for proteases?

A

The transmembrane protein enteropeptidase catalyzes the conversion from trypsinogen to trypsin

87
Q

What are the two major parts of the blood clotting cascade?

A

The intrinsic pathway and the extrinsic pathway

88
Q

What molecule is formed via both the intrinsic and extrinsic blood clotting pathways and plays a major role in the formation of clots?

A

Clotting factor Xa allows for the activation of thrombin, which catalyzes the conversion of prothrombin to thrombin

89
Q

What happens in hemophiliacs?

A

They are unable to form blood clots properly, which leads to excessive bleeding. They cannot properly form Factor Xa

90
Q

How is the clotting cascade deactivated?

A

Plasminogen is converted to plasmin which is able to dissolve the fibrin thrombus.

Tissue plasminogen activator (TPA) catalyzes the conversion of plasminogen to plasmin and is located within the fibrin thrombus

91
Q

What molecule is commonly referred to as blood sugar?

A

Glucose

92
Q

What is the major glucose storage molecule and where is it found in the body?

A

Glycogen is found in the liver and muscles

93
Q

What is the glycocalyx?

A

The “sugar forest” on the exterior surface of cell membranes.

Useful for the identification of cells

94
Q

What role do carbohydrates play in terms of hydration of cells?

A

Carbs can bind water to prevent cells from drying out

95
Q

What are isomers?

A

Molecules with the same molecular formula but different structures

96
Q

What are constitutional isomers?

A

They differ in the order of attachment of atoms

ex: aldehydes and ketones

97
Q

What are stereoisomers?

A

Atoms that are connected in the same order but differ in spatial arrangement

98
Q

What are enantiomers?

A

Nonsuperimposable mirro images

ex: D-glyceraldehyde, L-glyceraldehyde

99
Q

What are diastereoisomers?

A

Isomers that are not mirror images

ex: D-altrose and D-glucose

100
Q

What are epimers?

A

Molecules that differ at one of serveral asymmetric carbon atoms

101
Q

What are anomers?

A

Isomers that differ at a new asymmetric carbon atom formed on ring closure

alpha-Glucose and beta-Glucose

the direction of the hydroxy group determines which anomer exists

102
Q

In what form is sucrose found?

A

It is found as a dimer where the anomeric carbons are bound together.

103
Q

What are the differences between Pyranose and Furanose?

A

Pyranoses are 6 membered rings formed from aldehydes. Furanoses are 5 C rings formed from ketones

104
Q

What is the difference between ribose and deoxyribose?

A

Deoxyribose does not have a 2’ hydroxyl group

105
Q

Describe glycosidic bonds

A

Covalent bonds between 2 carbohydrate models.

They can either be O-glycosidic bonds attached to an oxygen or N-glycosidic bonds connected through a N that has replaced an OH group

106
Q

What is advantageous about converting glucose to G6P within the cell?

A

The phosphorylation of glucose maintains the glucose concentration gradients.

Additionally, the phosphate group destabilizes the ring structure which makes it easier to break down in later glycolytic steps

107
Q

What are the structural differences between Glycogen and Starch?

A

Glycogen is a branched glucose polymer found in animal cells. 1-4 glycosidic bonds create the chains, and 1-6 glycosidic bonds create the branches

Starches can be branched or unbranched glucose polymers that are found in plant cells

108
Q

What cells in the body rely exclusively on sugar for energy?

A

Red blood cells and brain cells

109
Q

Describe the structure of cellulose

A

Cellulose is combosed of many chains of glucose connected via 1-4 glycosidic bonds. Hydrogen bonds form between strands to make a highly stable network.

Biochemistry (4 decks)

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