Biochemistry Ch 9-11

recognition sequence

A specific sequence of nucleotides at which a restriction enzyme cleaves a DNA molecule

CTP is a(n) _____ inhibitor of ATCase because it binds to a site distinct from the active site at which substrate binds.

Allosteric

Monosaccharaides that have the same molecular formula but differ in the order of attachment of atoms are called:

Constitutional Isomers

_____ are enzymes that differ in amino acid sequence yet catalyze the same reaction.

Isozymes

What metal ion is frequently found in enzyme active sites that act on phosphate-containing substrates?

Mg2+

_____ sugars attach at _____, while O-linked sugars attach at _____.

N-linked; Asn; Ser or Thr

Binding of a water molecule to the zinc ion induces:

a lowered pKa for water, which leads to formation of a zinc bound hydroxide ion.

How is specificity determined by chymotrypsin?

binding of the proper amino acid into a deep pocket on the enzyme

Multifunctional protein kinases:

can modify several different targets.

Blood clotting cascades are controlled MOSTLY by:

zymogen activation.

(5 points) Molecule AE is and allosteric effector of an enzyme. In its presence, the curve of enzyme activity versus substrate concentration is shifted to the left. Which of the following is TRUE?

AE increases the affinity of the enzyme for its substrate.

In phosphorylations, the phosphoryl group usually originates from _____ and is MOST often linked to _____.

ATP; Thr or Ser

Hydrolysis of a peptide substrate by chymotrypsin takes place in two phases: _____ to form the _____, followed by _____ to regenerate the enzyme.

Acylation; acyl-enzyme intermediate; deacylation

Monosaccharide can be modified through the addition of a(n) _____forming a(n) _____.

Alcohol; glycosidic bond

Metal ion catalysis is facilitated by any of several mechanisms, including:

All of the answers are correct

Which of the following amino acids is LEAST likely to be mutated in the HIV protease active site?

Asp

In chymotrypsin, the catalytic triad is made up of which tree amino acids?

Asp, His, Ser

catalytic triad

Asp-His-Ser

Which of the following explains why sucrose is NOT a reducing sugar?

Both anomeric carbons are involved in the glycosidic bond.

If a sample of glycogen was treated with dimethyl sulfate and then completely hydrolyzed to break all glycosidic bonds, which of the following structures represent the glucose residues found at the branch points of the glycogen molecule?

CH2OH

Which of the following polysaccharides are NOT connected by a-glycosidic linkages?

Cellulose

Which of the following is paired with a proper description?

D-fructose: a ketohexose

Which of the following compounds does NOT correctly match the name with the molecular formula?

D-fructose; C6H10O6

chromogenic substrate

For chymotrypsin, such a ____ is N-acetyl-L-phenylanine p-nitrophenly ester

The optimum pH for aspartate transcarbamoylase activity is about 6.5. Which of the following amino acids is MOST likely found in the active site of the enzyme and thus responsible for this pH optimum?

His

What amino acid serves as the "buffer" in the active site of carbonic anhydrase?

His

Which amino acids in chymotrypsin are found in the active site and are participants in substrate cleavage?

His, Ser, Asp

Which of the following is a characteristic of glycogen?

It contains both a-1,4-glycosidic bonds and a-1,6-glycosidic bonds.

a-D-fructofuranose forms when a(n) and a(n) _____react to form a cyclic sugar.

Ketone; Alcohol

The enzymes catalyzing phosphorylation reactions of proteins are called protein:

Kinases

Which two amino acids are involved in formation of the crosslinks that convert a soft clot to a mature clot?

Lys and Gln

For each restriction endonuclease, the host cell produces a corresponding _____. These pairs of enzymes are referred to as restriction-modification systems.

Methylase

Which of the following is NOT a common covalent modification used to alter the activity of a protein?

Methylation

Which of the following describes the relationship between D-glucose and D-galactose?

One is an epimer of the other

Which of the following structures is isomeric at C-2 and C-4 with glucose?

One with 3 OH on the left side in a row

Which of the following is NOT true of restriction endonucleases?

Restriction endonucleases prevent viral DNA from entering the bacterial cell.

Elastase is specifically inhibited by the aldehyde derivative shown below. Which of the following active site residues is MOST likely to form a covalent bond and what type of bond is formed?

Ser, hemiacetal

Why does a plot of ATCase activity (v) versus aspartate concentration (S) yield a sigmoidal curve?

The binding of substrate to one active site in ATCase increase the likelihood that substrate will bind to additional active sites.

Peptide hydrolysis by chymotrypsin involves several steps. Which of the following occurs FIRST in the mechanism?

The oxygen atom of Ser makes a nucelophilic attack on the carbonyl carbon of the target peptide bond.

(5 points) Which of the following is TRUE of the reaction catalyzed by restriction endonucleases?

The reaction produces DNA strands with a free 3'-hydroxyl group and a 5'-phosphoryl group

Which of the following occurs when cAMP levels are elevated?

The regulatory subunit of PKA dissociates from the catalytic subunit resulting in an active kinase.

What is the evidence that ATCase has distinct regulatory and catalytic sites?

The subunits can be readily separated by ion-exchange chromatography following treatment with mercurial because they differ markedly in charge. The larger subunit has catalytic activity but does not display sigmoidal kinetics. In addition, reconstitution of the enzyme results in its having the same allosteric and kinetic properties as those of the native enzyme.

If an influenza virus is designed that contains normally active hemagglutinin but inactive neuraminidase, which of the following would be TRUE?

The virus could attach to the target cell, penetrate the membrane, and replicate, but new viral particles would not be released.

In addition to water, the metal in carbonic anhydrase is coordinated to:

Three His residues

Which of the following is an important step in clot formation?

Upon cleavage with thrombin the exposed ends or "knobs" of the a subunits fit into the holes on the y subunits of another monomer to form a protofibril.

Carbonic anhydrases are a class of _____ that catalyze _____.

Zinc-containing enzymes; the conversion of CO2 into HCO3-

metal ion catalysis

a metal ion may facilitate the formation of nucleophiles such as hydroxide ion by direct coordination

general acid-base catalysis

a molecule other that water plays the role of a proton donor or acceptor

Glycoform refers to:

a single protein type that can have forms that differ only in their glycosylation.

Changes in ATCase conformation were detected by crystallizing the enzyme in the presence of PALA (N-(phosphonacetyl)-L-aspartate). What is PALA?

a substrate analog that resembles the transition state

cooperativity

activity at one function site affects the activity of others

The nutritional storage form(s) of glucose in plants is/are:

amylose and amylopectin.

protease inhibitor

an antiviral used for HIV and Hepatitis C that blocks the enzyme responsible for viral replication

The bond between a glycoprotein and a carbohydrate is made to which atom of a monosaccharide?

anomeric carbon

Which of the following contains α-1,6-glycosidic bonds?

both amylopectin and glycogen

Which of the following is NOT a way in which enzymes stabilize a transition state

causing the temperature of the environment to increase

Which of the following is among the MOST abundant organic molecules in the biosphere?

cellulose

covalent modification

changing enzyme shape by phosphorylation/dephosphorylation

Multifunctional kinases phosphorylate proteins by recognizing related sequences called:

consensus sequences.

Myosins function to:

couple ATP hydrolysis to large conformational changes.

Type II restriction enzymes cut:

double-stranded DNA, forming a 5' phosphoryl group and a 3' hydroxyl group on each strand.

homotropic effect

effects of substrates on allosteric enzymes

ATPase

enzyme that causes ATP molecules to release the energy stored in their terminal phosphate bonds

isozyme

enzymes that differ in amino acid sequence yet catalyze the same reaction

What type of enzyme synthesizes oligosaccharides?

glycosyltransferase

An aldehyde and alcohol can react to form a:

hemiacetal

The relaxed form of an allosteric enzyme has _____ affinity for the substrates than the tense form.

higher

The regulatory effects of substrates on allosteric enzymes are referred to as _____ effects.

homotropic

P-loop

it interacts with phosphorylation groups on the bound nucleotide

sequential model

ligand binding can induce a change of conformation in an individual subunit

What is the result from treatment of carbonic anhydrase with EDTA?

loss of Zn2+ from the active site

concerted model

model in which the overall assembly of hemoglobin can only be in two forms, R and T

Which of the following terms describes a class of compounds with the molecular formula (CH2O)n?

monosaccharides

For a dimeric enzyme with two identical active sites, if the binding of substrate to one active site decreases the substrate affinity of the other active site, what sort of activity is observed?

negative cooperativity

Where does cleavage of the scissile bond by chymotrypsin occur?

on the C-terminal side of a Phe or Trp residue

If the following oligosaccharide were treated with β-galactosidase, what would be the resulting products?

one monosaccharide and one trisaccharide

Which of the following is an example of a zymogen?

pepsinogen and procarboxypeptidase

Removal of protein phosphates is catalyzed by protein:

phosphatase

Which type of enzymes specifically catalyzes protein phosphorylation?

protein kinases

A regulatory mechanism that is NOT readily reversible is

proteolytic cleavage

Sugars are commonly linked to which amino acid residues in glycoproteins?

serine, threonine, and asparagine

What shape is seen in the kinetic plot of an enzyme that exhibits cooperative binding?

sigmoidal

allosteric (regulatory) site

site district from the active site at which substrate binds. CTP is an example

Which of the following techniques allows investigators to test the role of individual amino acids in the determination of enzyme structure/function relationships, even if the investigated amino acid is not present in the active site?

site-directed mutagenesis

oxyanion hole

stabilizes a tetrahedral intermediate that arises during serine protease catalysis

chemical modification reaction

suggests that this unusually reactive serine residue plays a central role in the catalytic mechanism of chymotrypsin

covalent catalysis

the active site contains a reactive group, usually a powerful nucleophile, that becomes temporarily covalently attached to a part of the substrate in the course of catalysis

induced fit

the binding energy can also promote structural changes in both the enzyme and the substrate that facilitate catalysis

heterotrophic effect

the effects of non substrate molecules on allosteric enzymes (such as those of CTP and ATP on ATCase)

binding energy

the free energy released in the formation of a large number of weak interactions between the enzyme and the substrate

methylases

the host DNA is methylated on specific adenine bases within host recognition sequences by other enzymes called

restriction-modification system

the host cell produces a corresponding methyl's that marks the host DNA at the appropriate methylation site

Which of the following serves as the nucleophile in the reaction catalyzed by protein kinase?

the hydroxyl of Ser

feedback (end-product) inhibition

the inhibition of an enzyme by the end product of the pathway. The inhibition of ATCase by CTP is an example

horizontal gene transfer

the passing of pieces of DNA(such as plasmids) between species that provide a selective advantage in a particular environment

catalysis by approximation

the reaction rate may be considerably enhanced by bringing the two substrates together along a single binding surface on an enzyme

proton shuttle

transfers protons to buffers

A chymotrypsin mutant was constructed with Ser 189, which is in the bottom of the substrate-specificity pocket, changed to Asp. Of the following proteases, which would have a substrate specificity most similar to this mutant chymotrypsin?

trypsin

Which of the following enzymes would MOST likely be inhibited by the molecule shown below?

trypsin

in-line displacement

when a reaction takes place by inverting the stereochemistry of certain groups within the line