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Biochemistry 1 > Enzymes 1 > Flashcards

Enzymes 1 Flashcards

1
Q

What are enzymes ? What are ribozymes

A

Catalyst

A substance which increases the rate of a chemical reaction but remains unchanged at the end of the reaction

  • Enzymes are biological catalysts
  • Most enzymes are proteins (names end with ..ase)
  • But some RNA (ribonucleic acid) molecules also show enzyme activity- ribozymes
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2
Q

What are enzymes essential for? If there is a deficiency of enzyme, what can it lead to? Enzyme defect can be due to? (3)

A

Enzymes essential for

  • Breakdown of nutrients to supply energy & building blocks
  • Assembling building blocks into proteins, nucleic acids, membranes, cells & tissues

Deficiency of enzyme activity can cause disease

Enzyme defects can be due to

üGenetic mutations (eg; phenylketonuria)
üNutritional deficits (eg; beri beri)
üViral or bacterial pathogens (eg; cholera toxin)

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3
Q

•

Testing for enzyme in blood can determine …? What other ways are enzymes used? Give example

A
  • Testing for enzyme activities in blood & tissue fluids can help in diagnosis & prognosis of disease (eg; ALT for hepatitis)
  • Enzyme inhibitors are used as drugs (eg; allopurinol for gout)
  • Enzymes are employed in the synthesis of drugs
  • Enzymes are used as therapeutic agents
  • Rennin (a protease) used in the production of cheese
  • Enzymes used as reagents in specific lab tests for biochemical analytes
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4
Q

•What can free energy change ( delta G) be used to predict? If (G) is negative..? If (G) is positive..?

A
  • Change in free energy during a reaction (DG), can be used to predict the direction of a reaction
  • Eg: A to B and B to A
  • If delta G is negative; net loss of energy, exergonic; reaction goes spontaneously from A to B
  • If delta G is positive; net gain of energy, endergonic; reaction does not go spontaneously from B to A
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5
Q

•DG depend on what? If the reaction goes forward, how is it written compared to backward reaction? When is DG =0? Are reactions with large negative DG reversible? How can a reaction go to completion?

A
  • G depends on the concentration of reactants & products, therefore is variable
  • DG of the forward reaction is equal in magnitude but opposite in sign to the back reaction
  • Eg: if DG (forward) = – 5 kcal/mol; back reaction will have DG = + 5 kcal/mol
  • When the reaction reaches equilibrium, no further net chemical change occurs, DG = 0
  • Reactions with large negative DG are irreversible under physiologic conditions
  • A reaction with +ve DG can be coupled to another reaction with a large –ve DG to make it go to completion (usually coupled ATP hydrolysis which releases energy)
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6
Q

What is the effect of enzyme on activation energy of a reaction?

A

∆G- change in free energy

  • Indicates nothing about the rate of the reaction.
  • No difference in the free energy change of the overall reaction between the catalyzed and uncatalyzed reaction.
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7
Q

How do enzymes work?

What is Ea?

What is the transition state?

How are uncatalyzed reactions in comparison to catalyzed?

A
  • All chemical reactions have an energy barrier separating the reactants & products (Free energy of activation, Ea)
  • Ea – energy difference between that of the reactants and transition state
  • Transition state – a high-energy intermediate that occurs during formation of product
  • Uncatalyzed chemical reactions are slow
  • Molecules must possess enough energy to achieve the transition state
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8
Q

What doe an enzyme do in a reaction?

A

An enzyme

•Does not alter the free energy of reactants or products
•Does not change the equilibrium of the reaction
•Provides an alternate reaction pathway with a lower free energy of activation
•Lowers the free energy of activation – transition state is achieved faster
•Stabilizes the transition state
•Therefore accelerates the rate of reaction

Enzyme catalyzed reactions 103 – 108 times faster than uncatalyzed reactions

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9
Q

What is an enzyme’s active site? What does it contain? How does the enzyme accelerate the product formation?

A
  • A site (a pocket or cleft) in the enzyme where the reaction takes place
  • Contains a.a side chains that create a 3-dimensional surface complementary to the substrate
  • Binds the substrate in a manner resembling the transition state of the molecule
  • Provides catalytic groups that enhance the formation of transition state
  • Stabilizes the substrate in its transition state; accelerates product formation
  • E+S ® ES ® EP ® E + P
  • Substrate binding causes a conformational change in the enzyme ® Induced fit ® Catalysis
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10
Q

What are the types of enzyme specificity? ( 2 groups and 4 sub groups)

A

Enzymes are highly specific interacting with one or a few substrates and catalyzing only one type of reaction

Types of enzyme specificity

1.Reaction specificity

Enzymes are classified into 6 groups based on the type of reaction they catalyze

2. Substrate specificity

** a. absolute specificity**

Some enzymes are absolutely specific for a single substrate

Eg: glucose oxidase acts only on glucose

b. Group specificity

Some enzymes act on a few related susbtrates

Eg: trypsin hydrolyzes peptide bonds formed by lysine and arginine

c. Stereospecificity

Enzymes are specific for the D- & L- isomers

Eg: D- & L- amino acid oxidases

d. Geometric isomer specificity

Enzymes show specificity for cis- or trans- isomers

Eg: fumarase acts on fumarate (trans) but not on maleate (cis)

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11
Q

How are most enzymes named? Give example of substrate name, description of reaction and trival names. How are systematic names given/ by what system? And how are they classified?

A

•Common names
–Most enzymes have suffix –ase attached to
•Substrate’s name Ex: Lactase, amylase, maltase
•Description of the reaction Ex: Lactate dehydrogenase
•Trivial names Ex: Trypsin, pepsin
•Systematic names
–By International Union of Biochemistry and Molecular Biology (IUBMB)
–All enzymes are classified into 6 major classes
–Classes are divided into subclasses and sub subclasses.
–Name of the enzyme consists of names of all the substrates; followed by the description of reaction, to which suffix –ase is added
–Ex: Lactate:NAD+ oxidoreductase
– Unambiguous and informative

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12
Q

Give the six groups of classification of enzymes

A

Based on the type of reaction they catalyze

1.Oxidoreductases

Catalyze oxidation-reduction reactions (eg: lactate dehydrogenase)

2. Transferase

Catalyze transfer of groups containing C-, N- or P- (eg: hexokinase)

3. Hydrolases

Catalyze cleavage of bonds by addition of water (eg: lactase)

4. Lyases

Catalyze cleavage of C-C, C-S & C-N bonds by mechanisms other than hydrolysis (eg: aldolase)

5. Isomerases

Catalyze interconversion of isomers (eg: phosphohexose isomerase)

6. Ligases

Catalyze formation of bonds between two molecules coupled to the hydrolysis of high-energy phosphate (ATP)

(eg: pyruvate carboxylase)

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13
Q

What are cofactors , coenzymes , holoenzymes and apoenzymes? Most of the co enzymes are derived from? What are cosubstrates and prosthethic groups?

A

•Some enzymes require non-protein additional factors for activity
•Holoenzyme (active enzyme) = Apoenzyme (protein part) + non-protein component
non-protein component = Organic-coenzymes +Inorganic- Cofactor (Metal ions)

  • Most of the coenzymes are derived from B-complex vitamins
  • Cosubstrates (transiently associated coenzymes) Eg- NAD+
  • Prosthetic group (permanently associated coenzyme)Eg- FAD
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14
Q

For the following coenzyme name the vitamin it is derived from, the group transferred and dependent enzyme

TPP,FMN, FAD, NAD+,NADP+, LIPOIC ACID, PLP, CoA,FH-4,BIOTIN, COBALAMIN

A
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15
Q

What are the cofactor( metal ion ) for the following enzyme:

Carbonic anhydrase, Alcohol dehydrogenase, Carboxy peptidase

Hexokinase, G-6-phosphatase

Enolase

Phosphogluco mutase, Enolase

Dipeptidase, Superoxide dismutase

Salivary amylase

Tyrosinase, SOD

Cytochrome oxidase, Catalase, Peroxidase

Lipase

Xanthine oxidase

Glutathione peroxidase

A
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16
Q

What is kinetics? What is the rate or velocity of an enzymatic reaction? How is the rate expressed? Name the factors affecting the rate of an enzymatic reaction.

A

•Kinetics is a study of the rate of conversion of reactants to products

Rate or velocity of a enzymatic reaction (v)

  • The number of substrate molecules converted to product per unit time under defined conditions
  • Expressed as mmoles product formed/min
  • International Unit (IU): amount of enzyme that catalyzes conversion of 1 mmole of substrate to product per minute

Factors affecting rate of an enzymatic reaction

a. Temperature
b. pH
c. Substrate concentration

17
Q

Explain how temperature increases the rate of the reaction . What is the optimal temperature for most enzymes? What happens at higher temperatures?

A
  • Velocity of an enzyme-catalyzed reaction inc­ with inc ­ in temperature up to a maximum, and then declines
  • With inc ­ in temperature, ­ inc collision of molecules, more molecules have sufficient energy to pass over the energy barrier
  • Optimum temperature for most enzymes between 35-40°C
  • At higher temperatures (usually above 40°C) most enzymes start losing their native structure (denaturation), reaction velocity slows down
18
Q

At, higher temperaturesm most enzymes become inactive, except which of the following?

A

** (exceptions: enzymes from thermophilic bacteria, eg; Taq polymerase from T. aquaticus, used in PCR)**

19
Q

Explain how pH affect the rate of reaction

A

Concentration of H+ ions influences enzyme activity by

  • Affecting the state of ionization of chemical groups in the enzyme active site & substrate
  • Causing denaturation of enzymes at extremes of pH

Velocity against pH graph: bell-shaped curve

Enzymes vary in their optimum pH preferences

20
Q

How does the effect of substrate concentration affect the rate of reaction

A
  • Rate of an enzyme-catalyzed reaction increases with increase in substrate concentration until a maximal velocity (Vmax) is reached
  • At high substrate concentrations, all available binding sites on the enzyme are saturated with substrate
  • Most enzymes show hyperbolic curve when velocity is plotted against substrate concentration [S] (Michaelis-Menten kinetics)
21
Q

How does the michaelis-Menten kinetics reaction look like?

A
22
Q

Compare first order reaction and zero order reaction

A

First order reaction: when [S] is much less than Km, reaction velocity is directly proportional to substrate concentration

Zero order reaction: When [S] is much greater than Km, reaction velocity independent of substrate concentration

Reaction velocity is directly proportional to enzyme concentration

23
Q

What is Km?

A

Substrate concentration [S] at which vo is half of Vmax

  • Is characteristic of an enzyme for its substrate
  • Reflects the affinity of the enzyme for its substrate
  • Does not vary with enzyme concentration
24
Q

What is the significance of low Km and high Km?

A

Low Km:

  • Reflects a high affinity of enzyme for its substrate
  • Low concentration of substrate is needed to half-saturate the enzyme

High Km:

  • Reflects a low affinity of enzyme for its substrate
  • High concentration of substrate is needed to half-saturate the enzyme
25
Q

Explain glucokinase and hexokinase in terms of which one has the higher km vs. lower km and which one has the higher Vmax vs. lower Vmax. When are they active?

A

Glucokinase and hexokinase

  • Both phosphorylate glucose in glycolysis
  • Glucokinase: higher Km for glucose (10 mmol/L)
  • Hexokinase: lower Km for glucose (0.2 mmol/L)
  • Glucokinase: higher Vmax
  • Hexokinase: lower Vmax
  • Hexokinase active even at low glucose level
  • Glucokinase active after a meal
26
Q

Give the mathematical relationship between the initial reaction velocity (Vo) and [S]

A
27
Q

What is the Lineweaver-Burk plot ? What is the other name for it? What is in the x-axis and y-axis? And what is it used to calculate?

A

MM plot – not easy to determine Vmax accurately

  • Linear form of MM plot; taking reciprocal of MM equation
  • Also called double-reciprocal plot
  • Plots the reciprocals of vo against reciprocals of [S]
  • Used to calculate Km and Vmax accurately & to determine mechanism of action of enzyme inhibitors
28
Q
A

Biochemistry 1 (15 decks)

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