Biochemistry 501 - Chapter 6: Enzymes

The specific site on the enzyme where ____1______ binds and catalysis occurs is called the ___2____ site.

1. substrate 2. active site.

Enzyme regulation

-rate slows down as product accumulates since catalysts do not change equilibrium -availability of substrates and cofactors -genetic controls: a. induction (synthesize more) b. repression (shut down synthesis) -covalent modification -allosteric regulation specialized controls: a. zymogens b. isozymes c. modular proteins

Properties of coenzymes:

-they can serve as intermediate carriers of functional groups -they may contain vitamins as a part of their structure. -they are usually actively involved in the catalytic reaction of the enzyme. -tend to be stable to heat.

Three Types of Reversible Inhibition

1. Competitive Inhibitor 2. Uncompetitive inhibitor 3. Mixed Inhibitor

Protein extracts has the highest specific activity?

200mg protein and 80,000 units of activity

For an enzyme which obeys Michaelis-Menten kinetics, what is the Vmax value if V = 35 umol/min when [S] =Km

70

Prosthetic group

A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein.

holoenzyme

A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions.

Identifying Catalytic Amino Acids

AA with key catalytic functions in the active site can sometimes be identified by determining which residue is covalently linked to an inhibitor after the enzyme is inactivated.

Allosteric Enzyme Characteristics:

Their regulatory effect is by altering conformation and interaction of subunits. Effectors may show stimulatory or inhibitory activity. They have multiple subunits. Binding one subunits impacts binding of substrate to other subunits.

All of the following are properties of a coenzyme except: A. they can serve as intermediate carriers of functional groups B. they may contain vitamins as a part of their structure. C. they are a section of amino acids residues in a protein. D. they are usually actively involved in the catalytic reaction of the enzyme.

They are protein components. They are section of amino acids residues in a protein.

True of enzyme catalysts? A. They can increase equilibrium constant for a given reaction by a thousand fold or more. B. They are generally equally active on D and L isomers of a give substrate. C. To be effective, they must be present at the same concentration as their substrate. D. Their catalytic activity is independent of pH. E. They can increase the reaction rate for a given reaction by a thousand fold or more.

They can increase the reaction rate for a given reaction by a thousand fold or more.

Which of the following is true of enzyme catalysis?

They lower the activation energy for conversion of substrate to product.

Which one of the following statements is true of enzyme catalysts? Question options: A) They increase the stability of the product of a desired reaction by allowing ionizations, resonance and isomerizations not normally available to substrates. B) They lower the activation energy for the conversion of substrate to product. C) They increase the equilibrium constant for a reaction, thus favoring product formation. D) To be effective they must be present at the same concentration as their substrates. E) They bind to substrates, but are never covalently attached to substrate or product.

They lower the activation energy for the conversion of substrate to product.

How do catalysts work to accelerate a chemical equation?

They lower the energy of activation.

A molecule, such as malonate, which noncovalently binds within the active site of succinate dehydrogenase, is an example of an effective competitive inhibitor.

True

Enzymes have no effect on the value of delta G prime but do reduce the value of delta G cross for a reaction

True

Specificity is the ability of an enzyme to discriminate among competing substrates.

True

The Vmax value for an enzyme is dependent on the enzyme concentration.

True

The formation of an intermediate, enzyme-substrate complex is a basic assumption in the Michaelis-Menten model.

True

A small molecule that decreases the activity of an enzyme by binding to a site other than the catalytic site is termed an allosteric inhibitor.

True.

Phosphofructokinase-1 is an enzyme in glycolysis that converts fructose-6-phosphate to fructose-1, 6-biphosphate. ADP binds to this enzyme at the sites other than the active sites and causes the reaction velocity to increase. All of the following would be true of ADP except:

True: ADP is a positive allosteric effector. ADP changes the conformation of the active sites when it binds the enzyme. ADP changes the conformation of all the active sites. ADP is an allosteric activator. FALSE: ADP is a competitive inhibitor.

In competitive inhibition:

Vmax is constant, but KM increases.

In competitive inhibition, increasing concentrations of the inhibitor will have the following effect on the kinetics of the enzyme:

Vmax will stay the same?

allosterism

a change in the activity/conformation of an enzyme/protein resulting from the binding of a compound at a site on the enzyme/protein other than the active binding site

A lyase catalyzes

addition of groups to double bonds

one of the enzymes involved in glycolysis, aldoase, requires Zn 2+ for catalysis. Under conditions of zinc deficiency, when the enzyme may lack zinc, it may be referred to as the:

apoenzyme

Irreversible Inhibition

bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme's activity or form a particularly stable nonequivalent association.

An allosteric interaction between a ligand and a protein is one in which:

binding of a molecule to a binding site affects binding properties of another site on the protein.

Mixed inhibitor

binds at a site distinct from the substrate active site, but it binds to either E or ES. usually affects both Km and Vmax.

IN competitive inhibition, an inhibitor

binds reversibly at the active site.

When an enzyme that follows Michaelis-Menten kinetics is treated with a competitive inhibitor

can be biased to favor the substrate. Km increases Vmax stays the same.

Mechanism-Based Inactivators (MBI)

compound produced by the irreversibly binding of (suicide) inactivator with enzyme.

Important mechanisms of enzyme catalysis include:

covalent catalysis, general acid-base catalysis, metal ion catalysis, a combination of acid-base and covalent catalysis. ALL OF THE ABOVE.

Enzymes catalyze reactions by

decreasing the free energy of activation.

Uncompetitive Inhibitor

defined in terms of one-substrate enzymes. binds at a site distinct from the substrate active site and binds only to the ES complex. Kinetics -Lowers the measured Vmax. -Vmax decreases by a factor of alpha ' Km decreases.

The behavior of allosteric enzymes

depends on the changes in their quaternary structure non binding of substrate or inhibitors.

Enzymes differ from other catalysts in that only enzymes:

display specificity toward a single reactant.

which of the following is true about the role of enzymes in catalyzing chemical reactions?

enhance the rate of reactions.

Enzyme pH

every enzyme has an optimum pH or pH range at which it has maximal activity

Allosteric enzymes usually catalyze several different reactions within a metabolic pathway

false

A transferase catalyzes

group transfer reactions

A plot of activity versus pH for an enzyme that functions in the cytosol of a cell of about 7 would probably:

have the highest activity around a pH of 7.

Because the pKa is near 7, __________ side-chains are often involved in acid-base catalysis

histidine

apoenzyme

the protein portion of an enzyme, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity

The higher the (ΔG‡ ) activation energy

the slower the reaction

NOT a Characteristic of Allosteric Enzyme:

they obey Michaelis-Lenten Kinetics.

An isomerase catalyzes:

transfer of groups within a molecule.

The active site of an enzyme is most complimentary to:

transition state

Allosteric enzymes:

usually have more than one polypeptide chain.

Which is not true? The active site is a region: A) that binds the substrate. B) with unchanging conformation. C) on or near the surface of an enzyme. D) where the transition state complex is formed E) where bonds are formed between the substrate and the R-groups of the protein.

with unchanging conformation

Specific activity is the ability of an enzyme to discriminate among competing substrates.

False

The Vmax value for an enzyme is independent of enzyme concentration.

False

Which of the following are not general characteristics of enzymes? Question options: A) Enzymes usually are substrate specific. B) The catalytic activity of some enzymes can be regulated. C) All enzymes show allosteric properties. D) Enzymes increase reaction rates by lowering the activation energy barrier. E) ES complexes are held together by noncovalent interactions.

All enzymes show allosteric properties.

Which is true about general acid-base catalysis:

Amino acid side chains on enzymes can act as proton donors or acceptors.

Zymogens

Are enzymes synthesized in an inactive form and activated by an irreversible cleavage of a peptide bond.

Which of the designations listed below does not correspond to a major class of enzymes as outlined by the enzyme commission? A. Carboxylases B. Oxidoreductases C. Isomerases D. Transferases E. Hydrolases

Carboxylases

A particular oxidoreductase requires FAD as an essential component for its activity. The complete biological unit required for reaction is called a(n):

Coenzyme?

Competitive Inhibitor

Competes with the substrate for the active site of an enzyme. Many are structurally similar to the substrate and combine to form EI complex, but without leading to catalysis. Ki is the equilibrium constant for inhibitor binding to E. Pg. 207

A molecule, such as diisopropylphophofluoridate, which covalently bind irreversibly within the active site of serine proteases, is an example of an effective competitive inhibitor.

False

Allosteric enzymes always exhibit hyperbolic plots of velocity vs. substrate concentration.

False

Enzymes which conform to Michaelis-Menten kinetics are involved in feedback regulation

False

In allosteric interactions, proteins that consist of a single polypeptide chain form aggregates.

False

A catalyst:

Increases the rate of a chemical reaction

The rate of breakdown of the enzyme-substrate complex can be described by the expression:

K-1 [ES] + K2[ES]

An enzyme has catalytic power because it's transition state:

Requires less activation energy.

The steady state assumption, as applied to enzyme kinetics, implies:

The ES complex is formed and broken down at equivalent rates.

According to the steady-state assumption

The concentration of enzyme-substrate complex remains constant with time.

binding energy

The formation of each weak interaction in the ES complex is accompanied by a small release of free energy. This binding energy is the major source of free energy used by enzymes to lower the activation energies of reactions. It holds the substrate in the proper orientation to react (entropy reduction), it desolvates the substrate (removes water molecules that may be in the way), and it promotes formation of the transition state.

Vmax for an enzyme-catalyzed reaction: A. is twice the rate observed when the concentration of substrate is equal to Km B. Generally increases when pH increases C. is unchanged in the presence of an uncompetitive inhibitor. D. Increases in the presence of a competitive inhibitor. E. is limited only by the amount of substrate supplied

is twice the rate observed when the concentration of substrate is equal to Km

enzymes are potent catalysts because they

lower the activation energy for the reactions they catalyze.

Enzyme pathways

metabolic pathways are necessary since enzymes usually catalyze only one specific reaction.

An enzyme's specificity can be due to:

molecular recognition based on structural complementarity.

An enzyme reaction mechanism may involve: Question options: A) an ionic interaction between a metal ion and substrate. B) a nucleophilic substitution. C) a transfer of a proton in the transition state. D) mediation of electron transfer by a metal ion. E) more than one of the above.

more than one of the above

An enzyme reaction mechanism may involve: A. an ionic interaction between a metal ion and substrate. B. A necleophilic substitution C. A transfer of a proton in the transition state. D. mediation of electron transfer by a metal ion. E. more than one of the above.

more than one of the above.

isozyme

multiple forms of an enzyme that catalyze the same reaction but differ in amino acid sequence, substrate affinity, Vmax and/or regulatory properties

Catalytic power could be defined as the:

rate of the enzyme catalyzed reaction divided by the rate of the uncatalyzed reaction.

Distinctive features of enzymes

regulation catalytic activity specificity

A small decrease in ΔG‡ activation activation energy

results in a huge increase in k (reaction rate)

Suicide inactivators

special class of irreversible inhibitors. relatively unreactive until they bind to the active site of a specific enzyme. Process: 1. Undergoes first few chemical steps of normal enzymatic reaction 2. CHANGE: transformation to normal product is altered 3. Product: converted to a very reactive compound that combines irreversibly with the enzyme. (MBI) Play role in rational drug design

The concept of "induced fit" refers to the fact that:

substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation.

A molecule that binds irreversibly to the active site of an enzyme, inactivating it, is said to be a(n):

suicide inhibitor

specificity

the ability to discriminate between a substrate and a competing molecule.

holoenzyme

the catalytically active complex of an apoenzyme and its prosthetic group

The steady state of an enzyme-catalyzed reaction is reached when:

the concentration of the enzyme-substrate complex is constant over time.

in feedback inhibition

the end product of a pathway inhibits one of the enzymes in the pathway