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Biochemistry > Exam 4 > Flashcards

Exam 4 Flashcards

1
Q

Metabolic pathways are constructed from several different individual chemical reactions. For a metabolic pathway to occur, it must satisfy two criteria:

A
  1. the individual reactions must be specific
    1. convert a specific substrate to a specific product
  2. the enite set of individual reactions that make up a pathway must have an overall negative free energy change (deltaG)
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2
Q

FAD

A
  • flavin adenine dinucleotides
  • the second electron relay molecule in fuel oxidation
  • oxidized = FAD
  • reduced = FADH2
  • can accept two electron and two hydrogens
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3
Q

What does KM value describe?

A
  • describes the affinity of an enzyme for a substrate
    • High = weak substrate binding
    • Low = strong substrate binding
  • for most enzymes, value ranges from 10-1 to 10-7M
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4
Q

Addition or removal of functional groups

A

addition of functional groups to double bonds or their removal to form double bonds

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5
Q

NADH

A
  • nicotinamide adenine diculeotide (NAD)
  • major carrier of electrons in the oxidation of fuels
  • during oxidation, oxidized NAD+ accepts a hydride (hydrogen plus two electrions) to form NADH
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6
Q

Define Uncompetitive Inhibition

A
  • an inhibitor that binds to the enzyme only after the substrate is bound
    • binding site for inhibitor is formed only when substrate is bound
    • inhibitor binds ot a site other than the active site
    • cannot overcom uncompetitibe inhibition simply by adding more substrate
  • bind only to ES complex to form ESI
    • ESI complex cannot form product resulting in lower Vmax
    • lowers KM
      • b/c it depletes ES
  • to maintain equilibrium, E binds more S at lower concentrations
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7
Q

Substrate A can be broken down to products B and C with an overall free energy change of +21 kJ/mol. Substrate B can then be broken down to product D with an overall free energy change of -34 kJ/mol. What is the overall free energy change from A being converte to products C and D.

A

The overall reaction of A being converted to products C and D has a thermodynamically favorable free energy change of -13 kJ/mol

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8
Q

What is Feedback Inhibition?

A
  • a cellular control mechanism in which an enzyme that catalyzes the production of a particular substance in the cell is suppressed when that substance has accummulated to a certian level thus balancing the amount provided with the amount needed
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9
Q

What is Catalytic Efficiency?

A
  • kcat / KM
  • an enzyme that binds substrate tightly and rapidly turns substrate to product is a highly efficient enzyme
  • an ensyme that binds substrate loosely and slowly turns substrate to product is not an efficient enzyme
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10
Q

What is Steady-State Assumption?

A
  • once a reaction has started, the concentration of ES remains constant
    • ES is being converted to product
    • ES is converting back to free enzyme and substrate
  • allows for the derivation of the Michaelis-Menten equation (pg 231-232)
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11
Q

What are the two classes of Multiple Substrate Reactions?

A

Sequential

Double-Displacement

reactions involving two substrates and two products

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12
Q

What is Metabolism?

A
  • series of chemical reactions that begin with a particular molecule and convert it into some other molecule or molecules in a carefully designed and highly regulated fashion
  • refers to the complex network of how molecules are both synthesized and degraded
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13
Q

Activated carriers of electrons for fuel oxidation

A
  • these molecules relay electron during fuel oxidation
    • molecules are pyridine nucleotides and flavins
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14
Q

True or False

The more reduced a carbon compound is, the smaller its potential to generate free energy via oxidation

A

False

The more reduced (more energy) a carbon compound is, the greater its potential to generate free energy via oxidation

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15
Q

Define Rate Constant (k)

A
  • describes velocity
  • states how fast something progresses
  • rate constant k is directly related to the concentration of A

V = k[A]

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16
Q

Define Affinity-Label Inhibitors

A
  • a type of irreversible inhibitor
  • inhibitors that are structurally similar to the natural substrate and covalently bind to the active site
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17
Q

Why do we measure the rate (V0) at very early times near time zero in kinetics?

A
  • looking at only the forward reaction (substrate to product) and not the reverse reaction (product back to substrate)
  • measure early when the rate is at its highest prior to reaching equilibrium
  • often times the product can inhibit the enzyme (product inhibition) which slows the rate
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18
Q

What is the Citric Acid Cycle?

A
  • one of the 2 pathways that acetyl is shuttled through in Stage 3
  • the acetyl group is oxiized to CO2
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19
Q

Activated carriers of electrons for fuel oxidation

A
  • these molecules receive electrons during oxidation and relay them on to other molecules (oxygen) to make ATP
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20
Q

Define Kinetics

A
  • study of the rates of chemical reactions
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21
Q

What are the promary sources of ATP production?

A

oxidation of molecules such as glucose and lipids via catabolism

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22
Q

What are the two types of Metabolism?

A

Catabolism

Anabolism

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23
Q

There is a equation that was used prior to the Michaelis-Menten Equation. Write out that equation.

A
  • Lineweaver-Burk (Double Reciprocal) Plot
    • gives a straight line
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24
Q

Fill in Blank

As higher amounts of product is formed per time (V) is _________ as higher concentrations of substate are added

A

increasing

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25
Q

Ligation requiring ATP clevage

A

formation of covalent bonds

carbon carbon bonds

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26
Q

If you measure V0 at different substrate concentrations you get a graph. Draw this graph with appropiate units.

A
  • Rate (V0) will increase until it levels off at high substrate concentrations
    • all enzyme has been saturated with substrate
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27
Q

Explain the 3 stages of energy production

A

Stage 1

  • fuel molecules such as fats, sugars, and proteins are digested and broken down into smaller components
  • small components are absorbed by the intestine and transported to cells
  • no ATP is produced at this stage

Stage 2

  • small molecules are further converted to a few simple compounds, the most common being a two carbon acetyl group linked to coenzyme A
  • a small amount of ATP is produced during this process

Stage 3

  • ATP is generated from the comlete oxidation of Acetyl CoA
    • Acetyl is shuttled through two pathways
      • Citric Acid (Krebs, or TCA)
      • Oxidative Phosphorylation
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28
Q

What is the equation that Rate decribes?

A

V= -deltaA/deltaT

(negative due to it being a forward reaction; positive if it’s a reverse reaction)

where A is products and T is time

as A decreases P will increase so…

V= deltaP/deltaT

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29
Q

What does a high KM and a low kcat describe?

A

An enzyme that binds substrate loosely and slowly turns substrate to product is not an efficienct enzyme

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30
Q

True or False

A reaction can only proceed (is spontaneous) if it has an overall positive free energy change

A

False

A reaction is spontaneous if it has an overall negative free energy change

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31
Q

What kind of reaction is the following?

Aspartate Aminotransferase

A
  • double displacement reaction
  • transfers an amino group from aspartate to alpha-ketoglutarate
    • oxaloacetate must release from the enzyme before alpha-ketoglutarate can bind
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32
Q

Activated carriers of two-carbon fragments

A
  • activated and transport molecules needed to make ATP
33
Q

Define Noncompetitive Inhibition

A
  • a type of reversible inhibition
  • when an inhibitor ans substrate can bind the enzyme simultaneously
    • substrate and inhibitor bind to two different sites on the ensyme
    • differs from uncompetive inhibition in that the inhibitor can bind both free enzyme and ES complex
    • cannot be overcome by adding more substrate
  • lowers Vmax
  • does not alter KM
34
Q

Define Irreversible Inhibitors

A
  • molecules that form covalent bonds with the enzyme and do not dissociate
    • 4 types
      • group-specific
      • affinity labels
      • suicide inhibitors
      • transition-state analogs
35
Q

True of False

The hydrolysis and removal of phosphates from ATP is a highly exergonic process

A

True

a lot of free energy is released

2 Forms

ADP + Pi = -30.5 kJ/mol (2 phosphates remain)

AMP + PPi = -45.6 kJ/mol (1 phospate remain)

36
Q

Define Reversible Inhibitors

A
  • molecules that bind non-covalently to the enzyme and can freely dissociate
    • 3 types
      • competitive, uncompetitive, and noncompetitive
37
Q

Hydrolytic

A

Cleavage of bonds by the addition of water

38
Q

What are Double-Displacement Reactions?

A
  • one or more products must be released before all substrates can bind the enzyme
    • results in a substituted enzyme intermediate, where the enzyme is temporarily modified
  • substrates and products bounce on and off like ping pong balls
39
Q

Draw a plot for Allosteric Enzymes

A
  • allosteric enzymes do not show hyperbolic plots but show sigmoidal behavior
    • require more complex kinetic models to interpret
40
Q

Define Transition-State Analogs

A
  • a type of irreversible inhibitor
  • inhibitors that are designed to look like the transition state
  • enzymes are designed to release maximal binding energy during binding of the transition state
  • highly potent inhibitors b/c they maximize binding with the enzyme
41
Q

Define Competitive Inhibition

A
  • type of reversible inhibitor
  • an inhibitor binds to the same site as the actual substrate
  • an enzyme can bind to either a substrate to form ES or an inhibitor to form EI but it cannot bind to both (for an ESI complex)
  • can increase KM but do not alter Vmax
42
Q

What happens in Sequential reactions?

A

all substrates must bind to the enzyme before a product can be made

43
Q

What are the two types of Sequential Reactions?

A
  • ordered
    • the substrates will bind to the enzyme in a specific order
  • random
    • the substrates can bind randomly ( in no particular order) to the enzyme
44
Q

Group Transfer

A

Transfer of a functional group from one molecule to another

45
Q

True or False

Thermodynamically unfavorable reactions are made favorable by the input of free energy from ATP hydrolysis

A

True

this is controlled by enzymes

46
Q

What is a proton gradient?

A
  • protons are pumped out of the mitochondial membrane (yellow cartoon) to generate an electrochemical gradient
  • gradient is used by an ATP synthase (purple cartoon)
  • ATP synthase pumps protons back in and uses the free energy of this reaction to generate ATP from ADP and P​i
47
Q

What is the most efficient way that aerobic organism regenerate ATP?

A

Via the oxidation of fuels (photosynthesis in plants)

48
Q

How do I get rid of Competitive Inhibition?

A
  • can be relieved by increasing the concentration of substrate
    • more substrate wil outcompete the inhibitor
    • competitive inhibitors increase KM but do not alter Vmax
49
Q

What is Oxidative Phosphorylation?

A
  • one of the 2 pathways acetyl is shuttled through in Stage 3
  • 4 pairs of electrons (8 total) generated in the citric acid cycle are used to make a proton gradient that shuttles electrons to O2 and generates ATP
50
Q

What are the two types of Enzyme Inhibition?

A

Reversible Inhibitors

Irreversible Inhibitors

51
Q

What kind of reaction is the following?

Lactate Dehydrogenase

A
  • ordered sequential reaction
  • electrons are transferred from NADH to reduce pyruvate to lactate
    • NADH binds first, then pyruvate
    • lactate is released first, then NAD+
52
Q

What kind of buffer conditions change kinetic parameters?

A
  • temperature
    • enzymes become faster as the temp is increased but can unfold if temp is too high
  • ionic strength
    • adding more salt could weaken electrostatic interactions with a substrate
  • pH
    • enzymes can lose activity if certain amino acids are not properly protonated or deprotonated
53
Q

Leonor Michaelis and Maud Menten developed a model that describes the behavior of the rate of enzymes. What is this model?

A

Where:

  • E = enzyme (kept at a constant concentration)
  • S = substrate
  • ES = enzyme substrate complex
  • P = product
  • k1 = forward rate constant for formation of ES
  • k-1 = reverse rate constant for decomposition of ES back to E + S
  • k2 = forward rate constant for conversion of ES to P

Since we measure early near time zero, we do not worry about conversion of P back to S (k-2)

54
Q

What kind of reaction is the following?

Creatine Kinase

A
  • random sequential reaction
  • transfers phosphate from ATP to creatine to form phosphocreatine and ADP
  • substrates and products bind and release randomly
55
Q

Isomerization

A

Rearrangement of atoms to form isomers

56
Q

Your experiment shows your Vmax to be 44 micromolar per second. What is your turnover number given that you have 100nM enzyme in the assay?

A

440 s-1

57
Q

Define Group-Specific Inhibitors

A
  • a type of irreversible inhibitor
  • they form covalent bonds with specific amino acids
    • ex) DIPE reacts specifically with chemically reactibe serine residues
      • helpful when trying to locate active site of amino acids
58
Q

What does a low KM and a high kcat describe?

A

An enzyme that binds substrate tightly and rapidly turns substrate to product is a highly efficient enzyme

59
Q

What are some advantages of being able to inhibit enzyme activity?

A
  • ensymes that are part of metabolic pathways are inhibited when the pathway needs to be shut down
  • inhibitors are used as drugs to treat infections
    • they target an essential enzyme from a pathogen
  • inhibitors allow us to study enzyme mechanisms
60
Q

True or False

Inhibitors can not alter KM or Vmax

A

False

Inhibitos can alter them individually or both

61
Q

Activated carriers of two carbon fragments

A
  • these molecules shuttle two carbon groups (acetyl) to where they will be used in metabolism
  • most common is coenzyme A (CoA) which forms a thioester bond with the 2 carbon fragments
62
Q

How fast can an enzyme work?

A
  • the rate of an enzyme cannot be faster than the rate of diffusional control
    • means that an enzyme rate is restricted by how often it encounters a substrate in solution
    • limits enzyme to a maximum kcat/KM of 108 - 109 M-1s-1
    • enzymes that can do this are said to have catalytic perfection
      • every encounter with a substrate is productive and leads to product
63
Q

What does Vmax reveal?

A
  • reveals the turnover number of an enzyme
    • how fast it converts substrate to product
  • when Vmax is reached, this means that all enzyme is in ES complex
  • Vmax = k2*Etotal​
    • k2 is also called kcat
      • the turnover number and is what is reported in literature
64
Q

True or False

Fuel molecules such as glucose and lipids are complex, but the oxidation of these molecules occur one carbon at a time

A

True

These molecules get broken down into smaller fragments that are then oxidized to produce energy

65
Q

What are the 5 Metabolic Principles?

A
  1. fuels are degraded and large molecules are synthesized, by a series of linked chemical reactions called metabolic pathways
  2. Adenosine triphosphate ATP is the metabolic energy source common to all life forms
  3. the oxidation of carbon fuels powers the formation of ATP
  4. although there are many metabolic pathways, they share a limited number of types of reactions and intermediates
  5. metabolism is highly regulated
66
Q

NADP(H)

A
  • nicotinamide adenine dinucleotide phosphate
  • a major carrier of electrons that are donated to molecules during reductive biosynthesis
  • differs from NADH in that is has a phosphate group attached to the 2’ carbon of the ribose sugar
  • oxidized = NADP+
  • reduced = NADPH
67
Q

Define Catabolism

A
  • a type of metabolism
  • breakdown of fules to make useful cellular energy (ATP)

Fuel (carbohydrates, lipids) → CO2 + H2O + useful energy

68
Q

True or False

Inhibitors can have different affinities for enzymes

A

True

some inhibitos are potent (strong binding) while some are weak inhibitors

69
Q

Define Anabolism

A
  • a type of metabolism
  • use useful energy (ATP) to make complex molecules from simple precursors

useful energy + simple precursors → complex molecules

70
Q

What are the units for velocity?

A

change in concentration over time

M/s

71
Q

Oxidation - Reduction

A

electron transfer

72
Q

What is First Order Reaction?

A
  • when the reaction only depends on the concentration of A

A →P

V = k[A]

73
Q

Define Suicide Inhibitors

A
  • highly specific irreversible inhibitors
  • inhibitor binds to active site as a substrate and is initially processed by the normal catalytic mechanism
    • catalysis generates a reactive intermediate that then inactivates the enzyme
74
Q

Define Enzyme Kinetics

A
  • study of the rates of enzyme-catalyzed chemical reactions
    • allows us to understant how efficiently an enzyme functions
75
Q

Draw the Lineweaver-Burk Plot

A
76
Q

What is the Michaelis-Menten Equation?

Write out the equation with corresponding graph

A

Where:

V0 = initial velocity V0 = (Vmax[S]) / (KM + [S])

Vmax = maximal velocity

[S] = substrate concentration

KM = Michaelis constant

  • substrate concentration that results in 1/2 maximal velocity
77
Q

What are Allosteric Enzymes?

A
  • do not behave Michaelis-Menten kinetics
  • can be positively or negatively regulated by molecules other than their substrates
  • molecules will bind to places other than the active site to cause a conformational change
  • results in cooperativity
    • the binding of one substrate facilitates the binding of another substrate at a second active site
78
Q

Activated carriers for reductive biosynthesis

A
  • donate electrons to molecules to reduce them
79
Q

What is Second Order Reaction?

A
  • when two substrates are involved in a reaction

V = k[A]2

units for k is 1/Ms

A + B → P

Biochemistry (5 decks)

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