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MC Biochem 1 > Chpt 8 > Flashcards

Chpt 8 Flashcards

1
Q

Enzyme Def

A

a protein or RNA molecule that catalyzes biochemical reactions

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2
Q

Common name convention

A

substrate name+ rxn performed+ -ase suffix

Exceptions
Trypsin and Chymotrypson

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3
Q

7 Classes of enzymes

A

OTH LIL-T; 2-CNP; 4-CNS; 6CONS

EC1-oxidoreductase- catalyzes oxidation/reduction reactions (Dehydrogenase)
EC2-transferase- catalyzes the transfer of C, N, or P containing groups (kinase)
EC3- Hydrolase- catalyzes the cleavage off bonds by addition of water
EC4-Lyase-catalyzes the cleavage of C-C, C-S, and some C-N bonds
EC5-Isomerase- catalyzes the racemization of optical and geometric isomers
EC6-Ligase- catalyzes the formation of bonds to C, O, N, and S coupled to hydrolysis of a High Energy Phosphate
EC7-translocase- catalyzes the moment of a molecules from side 1 of a membrane to side 2 (the other side) of the membrane

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4
Q

Common names for Metabolic Enzymes

A

KIM-DA; TiiO_
Kinase-(transferase)-transfer a phosphate from one molecule (ATP) to another molecule
Isomerase (isomerase)
-converts to another isomer
-changes atom configuration without losing or gaining atoms
Mutase (isomerase)-shifts a phosphate from one carbon to another carbon within the SAME molecule
Dehydrogenase (Oxidoreductase)-involves NADH and FADH; oxidation/reduction reaction
Aldolase-cleves C-C bonds (Reverse Aldol condensation)

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5
Q

Properties of Enzymes (5)

A

1) Active site
- 3D pocket or cleft created by catalytic groups which are amino acids who R groups interact to cause the protein to fold into tertiary structure forming the active site
- specific for particular substrate/reaction
2) Enzyme “Helper” Molecules
- cofactor-inorganic metal ion; dissociable from enzyme: ex: Mg2+ and Fe2+
- coenzyme-organic molecules; dissociable from enzyme: ex: NADH, FADH, NADHP and oxidized forms
- prosthetic group-organic molecules that is covalently bonded to enzyme (can’t dissociate) Ex: Heme
* *prosthetic groups and coenzymes are derivatives of Vitamins
3) Catalytic Efficiency
- increases rate of reaction compared to uncatalyzed
- 100 to 1000 substrates convert to products/sec
- turnover-# of substrate molecules/#of enzymes per sec
4) Regulation- enzymes can be activated or inactivated
5) Compartmentalization- enzymes are localized within particular compartments of a cell

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6
Q

Apoenzyme vs holoenzyme

A

Apoenzyme- Enzyme without helper molecule

Holoenzyme-enzyme with helper molecule

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7
Q

Thermodynamics

A

Total E= Usuable E + Unusable E

H=G+TS–>convert to deltaG=deltaH-TdeltaS

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8
Q

Gibbs Free Energy (G)

A

Negative Delta G
-spontaneous
substrate A is at a higher E than substrate B, thus substrate A must release E-EXERGONIC-release E

Positive Delta G
-nonspontanous, but spontaneous in reverse reaction
substrate A is at lower E than substrate B; thus has to consume energy to go to Higher E-ENDERGONIC-energy consumed

Zero Delta G; equilibrium and any living system equilibrium means death

Considerations of Gibbs free Energy

  • tells us nothing about the rate of rxn instead tells us about spontaneity
  • deltaG=the difference between Reactants E and Products E
  • deltaG=is independent of the path of the reaction
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9
Q

Enzymes

  • equilibrium
  • reaction rate
A

Alter Rate but NOT EQUILIBRIUM

1) Enzymes do not change equilibrium of reaction
- amount of product formed is the same despite presence/absence of enzyme
2) Rate is Significantly different between a enzyme catalyzed reaction and uncatalyzed reaction to reach equilibrium
3) *** Enzymes accelerate the attainment of equilibrium, BUT DO NOT shift their position. The equilibrium position is a function only of the free energy difference between products and reactants

Enzymes accelerate reactions by lowering activation E (G=) by facilitating the formation of transition state

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10
Q

Evidence of ES complex

A

1) Saturation of active site by increasing substrate concentration [S]
- at constant enzyme concentration [E], the velocity increases with increasing substrate concentration [S] until a maximum velocity is reached.
- at maximal velocity all active sites are occupied
- uncatalyzed reactions do not exhibit this effect
2) X-ray crystallography
- X-ray structures show interaction between R groups of amino acids (catalytic group) in the active site and the substrate
3) Spectroscopic Characteristics
- changes in absorbance/fluorescence upon mixing substrate and enzyme

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11
Q

Active Site vs Allosteric Site def

A

Active site-region of the enzyme that binds the substrates and cofactors (if needed)

Allosteric Site-binding site other than active site

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12
Q

Active site characteristics

A

1) 3D crevice
- formed by catalytic groups- the amino acids involved in the active site have R groups that span a vast area of the linear protein and interact with one another to allow the protein to form into tertiary structure and forms active site
2) represents a small part of the total volume of enzyme
- the amino acids not involved in the active site serve as scaffolding
3) Creates UNIQUE MICROENVIROMENT
- water is often excluded (unless it participates in the reaction) creating a non polar enviroment
- Polar amino acid R groups often acquire “special” properties
4) binds substrate to the enzyme by multiple weak attractions due to Van Der Waals forces, Hydrogen Bonding, and Hydrophobic interactions NOT Covalent Bonding
- weak and reversible
5) has specificity of binding dependent on the arrange of atoms-2 TYPES
- lock and key model-active site shape matches the shape of substrate
- induced fit model-shape of active site undergoes conformation change as the substrate binds

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13
Q

Binding energy of enzyme

A

free energy released when the enzyme binds to the substrate

-Most E is released when the transition state is reached

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14
Q

Kinetics and Enzyme kinetics Def

A

Kinetics-the study of the rate of a chemical rxn

Enzyme Kinetics-study of the rate of enzyme catalyzed rxn

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15
Q

Kinetics:

  • What is Rate
  • Rxn order
A

What is Rate?
Rxn= A->P
V= -deltaA/deltaT= deltaP/deltaT
-rate of disappearance of substrate A and rate of appearance of product

Rxn Order
First Order-rates are directly proportional to reactant concentrations
A-> P; V=k[A]

2nd Order-Bimolecular Rxn(takes two molecules)
2A->P; V=k[A]^2 OR A+B-> P; V=k[A][B]
-pseudo first order- where substrate B is in excess conc and substrate A is low conc., the rxn will be first order for

Zero Order
-rate of rxn is independent of reactant concentration

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16
Q

How are reaction rates Studied?

A

ONLY look at initial velocities (Vo) so no product in the tube!
-Measure increase in concentration of Products over time at different substrate concentrations

Vo=deltaP/deltaT

  • where Vo is the number of moles or product formed per second
  • approaches equillibrium
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17
Q

Draw a Michaelis Menten Graph with:

  • Vmax
  • x and y axis labeled
  • Km labeled
A

Hyperbolic curve
X-axis= Substrate Conc [S]
Y axis= Rxn Velocity (Vo)
Vmax/2 on the Y axis and where it lines up on the curve to the x-axis=Km

18
Q

Km

A

is a characteristic of an enzyme and its particular substrate

1) Km is the substrate conc [S} to produce 1/2Vmax
- not affected by enzyme conc
2) ratio of rate constants which shows the strength how tightly the substrate is being bounded by the enzyme (STRENGTH OF ES COMPLEX)
- If K-1>K2, ES complex dissociates into E+S faster than E+P
- small Km=high affinity of enzyme to substrate; very little substrate required to saturate enzyme
- High Km=low affinity of enzyme to substrate;Alot of substrate required to saturate enzyme

19
Q

Vmax

  • def
  • equation
A

Number of substrate molecules converted to product by an enzyme molecule in a time where enzyme is saturated

Vmax=k2[E]t–> K2=Vmax/[E]t= K2=Kcat which is the catalytic rate constant

20
Q

Ethanol Sensitivity

A

Two forms of aldehyde dehydrogenase (oxidation/red)

  • Mitochondrial form-low Km
  • Cytoplasmic Form-High Km

Sensitive people have less active mitochondrial enzyme due to an amino acid substitution

  • thus acetylaldehyde is process only by cytoplasmic enzymes
  • with High Km this enzyme achieves a high rate of catalysis only at high concentration of acetylaldehyde

Symptoms-Facial flushing and tachycardia

21
Q

Factors effecting Reaction Velocity

A

Temperature

  • velocity increases as temperature increases; more substrate molecules have sufficient E to reach transition state
  • decrease of velocity due to denaturation of enzyme

pH

  • affects the protonation of the R groups of amino acids involved in catalysis
  • Excessive pH denatures Enzymes
  • pH optimum varies
22
Q

Catalytic Efficiency

A

Property of Enzymes-increased rate of rxn compared to uncatalyzed

catalytic efficiency=Kcat/Km
-allows comparing enzymes preference for different substrates

When [S]»Km the rate=Vmax thus Kcat=Vmax/[E]t
-this situation not typical under physiological conditions

UNDER PHYSIOLOGICAL CONDITIONS: enzyme active sites are not saturated SO:
-When [S]

23
Q

How efficient can an Enzyme Be?

A

CONTROLLED BY DIFFUSION

Catalytic efficiency (Kcat/Km) cannot exceed the diffusion- controlled encounter of an enzyme and its substrate; Diffusion can be controlled by confining substrate to multi enzyme complex

  • K1, rate constant for formation of ES complex, is limited by diffusion to 10^9 to 10^9/ sM, which is the upper limit of Kcat/Km
  • Enzymes approaching this level achieve kinetic perfection

ENZYME with Kinetic Perfection

  • every Substrate that encounters an Enzyme produces a product
  • Enzyme has Circe forces-which is the attractive forces that entice the substrate to the active site
24
Q

How can Diffusion be controlled?

A

by confining substrate to multi enzyme complex

25
Q

Lineweaver-Burke Plot

Graph characteristics

A 
Double Reciprocal-Linear
x-axis= 1/[S]
Y axis=1/Vo
y=mx+b
m=Km/Vmax
x-int=1/-Km
y-int= 1/Vo
26
Q

Define Inhibitor

A

a substance that can diminish the velocity of an enzyme catalyzed reaction

27
Q

What can inhibit the activity of an enzyme?

A
  • specific small molecules or ions

- Drugs or toxics

28
Q

What are the types of inhibitors?

A

Reversible inhibitor

  • bind weakly (noncovalently) to enzyme
  • dilution of enzyme: Inhibitor Complex results in dissociation of inhibitor and recovery of enzyme activity
    1) Competitive inhibitors
    2) Uncompetitive inhibitors
    3) Noncompetitive inhibitors

Irreversible Inhibitor

  • bind tightly (covalently or noncovalently) to enzyme
  • inhibitors dissociate slowly
29
Q

Competitive Inhibitor

  • Define
  • Graph and effect on Vmax and Km
  • Overall effect
A

Type of Reversible Inhibitor

  • Where the inhibitor binds to same site (active site) as substrate
  • competes for active site; inhibitor is same shape as substrate

GRAPH Slide 68 (chopstick shape when using)

  • Vmax remains the same; reversed by increasing [S]
  • Increase Km; more substrate need to reach 1/2Vmax

Overall Effect-diminishes the rate of catalysis by reducing proportion of enzyme molecules bound to a substrate

30
Q

Drug Example of Competitive Inhibitor

A

Statin Drugs

  • antihyperlipidimic agents; atorvastatin(Lipitor) and simvastatin(Zocor)
  • completely inhibit the first committed step in cholesterol synthesis (HMG- CoA reductase)
  • structural analogs of substrate-inhibits de novo cholesterol synthesis
31
Q

Uncompetitive Inhibitor

  • Define
  • Graph and effect on Vmax and Km
  • Overall effect
A

Type of Reversible Inhibitor

  • inhibitor binds to ES complex
  • substrate has to bind to active site first to form inhibitor binding site where the Inhibitor Binds

Graph SLIDE 71 (two parallel Lines)

  • Vmax decreases; Vmax cannot be attained; and cannot be overcome by addition of more substrate
  • Km decreases; as [I] Increases
32
Q

Noncompetitive Inhibitor

  • Define
  • Graph and effect on Vmax and Km
  • Overall effect
A

Type of Reversible Inhibitor

  • inhibitor binds to different site that substrate (allosteric site)
  • binds to either free E or ES complex
  • *Some form covalent bonds with enzymes
    1) Pb forms covalent bonds with sulfhydryl groups of cysteine
    2) acetylcholinesterase inhibitors-cleaves the neurotransmitter acetylcholine; found in insecticides and nerve gases

Graph Slide 73 (shape of V)

  • decreases Vmax; cannot overcome by increase [S]
  • same Km with or without inhibitor; does not interfere with binding of the substrate
33
Q

Many Drugs Inhibit Enzymes

A

50% of the ten most commonly dispensed drugs in USA act as enzyme inhibitors
1) Penicillin and Amoxicillin
-inhibit bacterial cell wall synthesis
2)Angiotensin-converting enzyme (ACE) inhibitors
-lower BP by blocking the enzyme that cleaves angiotensin I and angiotensin II (potent vasoconstrictor)
Ex:captropril, enalapril, lisinopril

34
Q

Reactions with Multiple Substrates

A

Most reactions contain 2 substrates and 2 products

  • Bimolecular and can be categorized into:
    1) Sequential Reactions
    2) Double Displacement reactions
35
Q

Sequential Reactions

A

All substrates bind to the enzyme before any product is released (Ternary Complex)
Two Types:
Ordered (lactate dehydrogenase)
Random (Creatine Kinase)

36
Q

Ordered Sequential Reactions

A

-coenzyme and substrate bind in specific order (release of products also occurs in specific order)
Ex: Lactate dehydrogenase

Use Cleland diagrams to show

37
Q

Random Sequential Reactions

A

-addition/release of substrates and products is random

Ex: Creatine Kinase

38
Q

Double Displacement

A

(Ping Pong)
-One or more products are released before all substrates bind enzymes
-substituted enzyme intermediate is hallmark of ping pong reactions
Ex: Aspartate Aminotransferase

39
Q

Allosteric Enzymes

A

-Enzymes that do not follow Michaelis Menten Kinetics
-contain multiple substrate/multiple active sites
-Sigmoidal Plot
-Cooperativity
-Regulatory Enzymes
Ex: Hemoglobin

40
Q

Regulation of Enzyme activity During Metabolism

A

Velocity (Vo) of enzymes are responsible to changes in [S]because the intracellular level of many substrates is in the range of the Km
Therefore an increase [S] leads to an increase in Velocity (rate)of the reaction

Allosteric Enzymes may be inhibited or stimulated by binding an effector (also called modifier) which can do either or both:

  • Modify the maximal catalytic activity (Vmax) of the enzyme
  • alter the affinity of the enzyme for its substrate (Km)

Allosteric Enzymes are often regulated by feedback inhibition

  • example of heterotrophic effector-effector is different from substrate
  • example of homographic effector-effector molecule is the substrate

MC Biochem 1 (30 decks)

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