1c Enzymes Flashcards by blaise rod

Biological catalysts; “agents of life”

Enzymes

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Properties of Enzymes:

usually acts on a single substrate

Specificity

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Properties of Enzymes:

10^8 to 10^20 times over uncatalyzed reaction

Catalytic efficiency

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Properties of enzymes:

Mostly reversible, except _________ and __________

decarboxylases, hydrolases

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Each type of enzyme has its own uniquely-shaped _________ ______ which give it specificity.

active site

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Catalysis occurs at the active site.

Active site is composed of
(a) ___________________
(b) ___________________

a. binding site
b. catalytic group

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Attracts and positions the substrate

Binding site

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The reactive side chains of amino acids / cofactors.

They also carry out the bond-breaking/forming reactions involved.

Catalytic group

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Two things that compose an enzyme

protein + non-protein component

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Non-protein group:

Tightly bound organic molecule; permanently associated with the enzyme protein

Prosthetic group

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Non-protein component:

Not tightly bound; transiently associated with the protein

Cofactor

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Metal ion cofactor (Zn, Fe, Cu, Mo)

metal activator

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organic molecule cofactor (NAD+, FAD, FMN, vitamins)

coenzyme

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How many levels are there in the enzyme structure? Enumerate

Four

primary, secondary, tertiary, quaternary

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Enzyme structure level:

Amino acid sequence
(amino end <—-> carboxyl end)

Primary

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Enzyme structure level:

Local structural units (aka amino acids) held by Hydrogen bonds

Secondary

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Enzyme structure level:

Pleated sheet
3D shape of polypeptide (subunit)

Tertiary

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Enzyme structure level:

association of two or more subunits

Quaternary

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Give the equation of enzyme catalysis

E + S => E-S => E + P

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What do enzymes do the barrier of the activation energy

lower

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Is there a difference in free energy between catalyzed and uncatalyzed reactions?

No. They’re the same.

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What are the two models of Enzyme-Substrate Interaction? Differentiate.

Lock-and-Key Model
Induced-Fit Model

In induced-fit model, the active site changes shape.

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What happens to the reaction rate when the enzyme becomes saturated with the substrate?

Becomes independent of substrate concentration

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___________ relationship between reaction velocity (v) and substrate concentration [S]

hyperbolic

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What happens to the reaction rate until the substrate is depleted?

remains relatively constant

What is the equation used for the calculation of the reaction rate?

Michaelis-Menten Equation

Write the equation for the Michaelis-Menten Equation

Vi = Vmax [S] / Km + [S]

What is the variable for the Michaelis-Menten constant? What does it represent?

Km substrate concentration when Vi is half of Vmax

Kinetics of Enzyme-Catalyzed Reaction: Reaction rates depend on what (1), which also depends on what (2)?

1. successful collision between substrate and enzyme molecules 2. concentration

Kinetics of Enzyme-Catalyzed Reaction: Given enough substrate, doubling the enzyme concentration _________ the reaction rate.

doubles

At any given [E], reaction rate reaches a maximum at a certain [S], as the enzyme becomes ___________.

limiting

The [S] required to halve the maximum reaction rate

Km value

Give the enzymes and Km for the following substrates C)2 (three enzymes) Lactose HCO3- O2

CO2 - Carbonic anhydrase - 800 CO2 - PEP carboxylase - 2 CO2 - RuBisCO - 12 Lactose - Beta-galactosidase - 4000 HCO3- - Pyruvate carboxylase - 1000 O2 - RuBisCO - 250

Molecules that prevent enzymes reaching their maximum turnover numbers

Inhibitors

Inhibitors: Inhibitors compete with the substrate for the active site

Active site directed inhibition

Inhibitors: Inhibitors affect the active site shape (allosteric site) by binding to some other parts on the enzyme

Non-active site directed inhibition

Give three environmental factors that affect enzyme activity

Temperature, pH, Salt concentration

How does temperature affect the reaction rate?

Increases kinetic energy which increases successful collision rate

Too high temperatures causes enzyme ____________. Low temperature causes enzyme _____________. This disrupts which enzyme structure level? * loss of active site shape * loss of binding efficiency and activity

denaturation inactivity tertiary

Do all enzymes have the same optimum temperature?

No, because each enzyme has a different protein

Changing pH influences the ionization of the substrate which results in the loss of what? Affects which substrate level?

H-bonding Tertiary

Between charged/uncharged amino or carboxyl group, which requires low optimum pH? high optimum pH?

neutral carboxyl = low op pH uncharged amino group = high op pH

True denaturation only occurs at? Why?

extreme pH. Because in between two extremes, the loss of activity is still reversible

Among pepsin, amylase, and arginase, which has an acidic optimum pH? neutral op pH? basic op pH?

acidic = pepsin neutral = amylase basic = arginase

How does increasing substrate concentration [S] affect reaction rate?

increase in [S] => increased collision rate => increases reaction rate

Enzyme activity is often regulated. Give four ways in which cells can control the flux of metabolites.

1. Gene expression 2. Compartmentation 3. Covalent modification 4. Feedback inhibition

Regulates enzyme activity through the AMOUNT/concentration of enzymes PRESENT in the cell. (presence is determined by the rates of enzyme synthesis and enzyme degradation)

Gene expression

LOCALIZES enzymes with different catalytic properties in the different PARTS of the cell. e.g. enzymes involved in photosynthesis are in the chloroplast; hydrolases are found in vacuoles

Compartmentation

Regulates enzyme activity through PHOSPHORYLATION (phosphorylated form = active non-phosphorylated form = inactive)

Covalent modification

Enzyme activity is regulated by the END PRODUCTS of the metabolic pathways which inhibit the enzymes in the earlier steps

Feedback inhibition

Capacity to do work

energy

give examples for potential vs kinetic energies

potential: chemical kinetic: heat, light

What is the 1st Law of Thermodynamics

Total energy in the universe is constant

What is the 2nd Law of Thermodynamics

Natural tendency of the universe is towards increasing disorder

Total entropy (aka degree of randomness) naturally tends to ___________ Energy naturally converts to _______ organized form

increase less

True or False: In all energy exchanges and conversions, even if no energy leaves or enters the system, the potential energy of the final state will always be less than the potential energy of the initial state.

True

Potential energy: 1) final state < initial state 2) final state > initial state

1) exergonic (releases energy) 2) endergonic (requires energy)

The measurement of disorder or randomness of a system. It is indicated by the letter (S).

entropy

2nd Thermodynamic Law: The universe tends to proceed from a state of _______ energy to a state of _______ energy

higher to lower

Events that can occur without the input of external energy

spontaneous

Total energy CONTENT of the system. It is indicated by the letter (H).

enthalpy

Measure of energy for the performance of work; decides the spontaneity of a process. it is indicated by the letter (G).

Gibbs Free Energy

Give the equation for the Gibbs Free Energy

ΔG = ΔH - TΔS

It is the energy available to do work; f(x) reaction from/towards equilibrium

ΔG, Free energy

ΔG < 0 ΔG > 0

exergonic, spontaneous, towards equilibrium endergonic, non-spontaneous, away from equilibrium

Give example of exergonic process (net release of energy). Give its equation and ΔG value in kcal/mole and kJ/mole.

Respiration C6H12O6 + 6O2 --> 6CO2 + 6HO2 + ATP ΔG = -686 kcal/mole or -2880 kJ/mole

Give example of endergonic process (absorbs energy). Give its equation and ΔG value in kcal/mole and kJ/mole.

Photosynthesis 6CO2 + 6H2O --> (CH2O)n + 6O2 ΔG = +686 kcal/mole or +2880 kJ/mole

ENERGY COUPLING: 1. degradative, oxidative energy yielding, exergonic 2. synthetic, reductive energy utilizing, endergonic

1. Catabolic processes 2. Anabolic processes

Metabolism: What do catabolic pathways do? What do they provide for the cell?

Breaks down complex substrates into simple end products. Provides raw materials and chemical energy

Metabolism: What do anabolic pathways do? What are the requirements? What do they use and where do they it from?

Synthesize complex end products from simple substrates. Require energy. use ATP and NADPH (from catabolic pathways)