Biochem I

EcoRV cleaves cognate DNA with a specificity approximately ___ times that of non cognate DNA

1,000,000

what is the composition of fetal hemoglobin

2 alpha chains and 2 gamma chains

restriction endonucleases cut DNA at specific sites. how many different patterns can be formed by a 4-base sequence combination of any 4 bases

256

myosins hydrolyze ___ in a controlled manner and use the free energy of hydrolysis to promote conformational changes within myosin itself

ATP

kinetic studies on myosin, in the presence and absence of divalent cations, show that ___ is the true substrate for this enzyme

ATP-Mg2+

which amino acids in chymotrypsin are found in the active site and participate in substrate cleavage

Asp 102-His 57-Ser 195

which of the following represents the most predominant form for the transfer of carbon dioxide in the blood

HCO₃⁻

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

Mg2+

what structures found in proteins are named for the fact that they interact with phosphoryl groups

P-loop

2,3-bisphosphoglycerate binds only to the ___ form of hemoglobin

T

the less active conformational form of an allosteric enzyme is called the

T-state

what metal ion is required by carbonic anhydrase for activity

Zn2+

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

if you cared out site-directed mutagenesis of subtilisin, changing Ser 221 to isoleucine, what would you expect?

a small change in Km and a large change in kcat

changes in ATCase conformation were detected by crystallizing the enzyme in the presence of PALA. what is PALA?

a substrate analog that resembles the transition state

what do trypsin, subtilisin, and elastase have in common

all contain a catalytic triad at the active site

a zymogen/proenzyme is

an inactive precursor of an enzyme that is activated by a proteolytic cleavage

in trypsin, the specificity pocket contains a/an ___ residues that binds to the positive charge of the K or R residue of the substrate

aspartate, Asp

how is specificity determined by chymotrypsin

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

2,3-bisphosphoglycerate

binds in the central cavity in the T-form of hemoglobin and binds to positively charged groups on the beta subunits

the effect of pH on oxygen-binding of hemoglobin is referred to as the

bohr effect

how is trypsin activity turned off

by binding an inhibitor protein

protein kinase A is activated by the binding of ___ to specific sites on the regulatory subunit

cAMP

multifunctional protein kinases

can modify several different targets

what is formed when carbon dioxide reacts with the amino terminal group of deoxyhemoglobin

carbamate

which of the following is the immediate product of the reaction between carbon dioxide and water

carbonic acid

the catalytic mechanism of carbonic anhydrase, in which the substrate are simply oriented to stabilize the transition state, is called ___

catalysis by approximation

many allosteric enzymes have two types of subunits, termed

catalytic and regulatory

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

causing the temperature of the environment to increase

convergent evolution is attributed to similarities found between

chymotrypsin and subtilisin

how is chymotrypsinogen activated

cleavage between an Arg and Ile by trypsin

which of the following is correct concerning fetal hemoglobin

composed of 2 alpha and 2 gamma subunits

multifunctional kinases phosphorylate proteins by recognizing related sequences called

consensus sequences

what type of binding is indicated by a sigmoidal-shaped binding curve

cooperative

myosins function to

couple ATP hydrolysis to large conformational changes

in proteases such as papain, a ___ residue is activated by H-bonding to a histidine residue

cysteine

p-hydroxymercuribenzoate displaces Zn2+ from binding to crucial ___ residues in ATCase

cysteine

as the partial pressure of carbon dioxide increases, the affinity of oxygen binding to hemoglobin ___

decreases

the binding of 2,3-bisphosphoglycerate to hemoglobin ___ (increases, decreases) its affinity of oxygen binding

decreases

type II restriction enzymes cut

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

which of the following is the most crucial pathway for blood clotting

extrinsic pathway

what regulatory mechanism relies on inhibition of the first step of the pathway by the final product of the pathway

feedback inhibition

under normal conditions, the heme iron in myoglobin and hemoglobin is in the ___ oxidation state

ferrous, Fe2+

which modified amino acid is found in prothrombin that allows for Ca2+ binding

gamma-carboxyglutamate

which of the following is correct concerning myoglobin

globin chain contains an extensive alpha-helix structure, iron of the heme group is in the Fe2+ oxidation state, diameter of the iron ion decreases upon binding to oxygen, and its function is oxygen storage in muscle

the ability of myoglobin to bind oxygen depends on the presence of a bound prosthetic group called

heme

which of the following is correct concerning the differences between hemoglobin and myoglobin

hemoglobin exhibits cooperative binding of O2 while myoglobin does not

the relaxed form of an allosteric enzyme has ___ affinity for the substrates than the tense form

higher

another reason why hemoglobin is sensitive to changes in pH is that the T-state of hemoglobin is stabilized by a salt bridge between beta-1 Asp 94 and the C-terminal ___ of the beta-1 chain

histidine

in hemoglobin, the iron of the heme is bonded to the four nitrogens of porphyrin and to the proximal ___ of the globin chain

histidine residue

the reaction center of most carbonic anhydrase is a zinc ion bound to water and ___ residues of the enzyme

histidine, His

the effects of substrates on allosteric enzymes are referred to as ___ effects

homotropic

what type of reaction is catalyzed by proteases

hydrolysis

the ___ pathway is activated by exposure of anionic surfaces on ruptured endothelial cells

intrinsic

what term describes multiple forms of homologous enzymes found within an organism

isozymes

blood serum analysis of ___ isozymes is used in the diagnosis of myocardial infarction

lactate dehydrogenase

one type of hemophilia is due to

loss of the gene for the anti hemophilic factor

which of the following describes the bohr effect

lowering the pH and increasing the concentration of HCO₃⁻ results in the release of O2 from oxyhemoglobin

histones are acetylated at specific ___ residues

lysine

what modification is made to DNA that protects the host DNA from cleavage by host restriction endonucleases

methylation

what oxidized heme protein does not reversibly bind oxygen

metmyoglobin

what are the most common strategies for enzymatic regulation

multiple enzyme forms, allosteric control, reversible covalent modification, proteolytic activation

isozymes are

multiple forms of homologous enzymes within the same organism that catalyze the same reaction but with different kinetic properties

what molecule stores oxygen in muscle cells

myoglobin

allosteric proteins

often display cooperativity

where does cleavage of the scissile bond by chymotrypsin occur

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

in chymotrypsin, the tetrahedral intermediate transition state is stabilized by a structural feature referred to as the ___ hole

oxyanion

enzymes that temporarily undergo covalent catalysis as part of its mechanism

papain, chymotrypsin, caspase, elastase

why is the HbS mutation so prevalent in Africa and other tropical regions

people with sickle cell trait are resistant to malaria, increasing the prevalence of the HbS allele

which of the following is an example of a zymogen

pepsinogen and procarboxypeptidase

what process converts chymotrypsinogen to chymotrypsin

peptide bond cleavage

removal of protein phosphates is catalyzed by protein

phosphatase

examples of covalent modifications include

phosphorylation, dephosphorylation, acetylation, ubiquitination

which type of enzymes specifically catalyzes protein phosphorylation

protein kinases

a regulatory mechanism that is NOT readily reversible is

proteolytic cleavage

what is the organic portion of the heme group in hemoglobin

protoporphyrin

aspartyl transcarbmylase catalyzes the first step in the synthesis of

pyrimidines

what is the bohr effect

regulation of hemoglobin binding by hydrogen ions and carbon dioxide

homotropic effects

regulatory effects of substrates on allosteric enzymes

the T-state structure of deoxyhemoglovin is stabilized through ___ interactions between the carbamates and positively charged amino acids at the interface between alpha-beta dimers

salt bridge

hemoglobin binding of oxygen is best described as

sequential model

what condition results from a single point mutation of the hemoglobin beta chain, producing the HbS variant

sickle cell anemia

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

sigmoidal

what technique 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

effective protease inhibitors are often ___ for one enzyme

specific

carbonic anhydrases are necessary because

spontaneous hydration and dehydration of CO2 are rapid, but not at speeds necessary for biochemical processes, and hydration and dehydration of carbon dioxide are sometimes coupled to other biochemical processes

metal ion catalysis is facilitated by any of several mechanisms, including

stabilizing negative charges on an intermediate, promoting formation of nucleophiles, and metals binding directly to substrates

what type of assay allows analysis of an enzyme catalyzed reaction in milliseconds

stopped-flow

the mechanism of chymotrypsin involves the formation of an unstable ___ -shaped intermediate that is stabilized by the oxyanion hole

tetrahedral

which of the following is a genetic disease that results from a decreased production of one of the subunits of hemoglobin

thalassemia

which of the following is NOT correct concerning myoglobin

the heme group is bound to the globin chain by two disulfide bonds to cysteine residues

what factor(s) influence(s) the binding of oxygen to myoglobin

the partial pressure of oxygen, PO2

the structure of normal adult hemoglobin can be described as a tetramer composed of

two alpha-beta dimers

what type of symmetry is created by inverted repeats in double stranded DNA

two fold rotational

protein kinases add phosphoryl groups to serine, threonine, and ___ residues in target proteins

tyrosine

in normal adult hemoglobin, HbA, the beta-6 position is a glutamate residue, whereas in sickle-cell hemoglobin, HbS, it is a ___ residue

valine

what molecule is required for the proper production of prothrombin

vitamin K

the metal ion most commonly found at the active site of metalloproteases is

zinc

blood clotting cascades are controlled mostly by

zymogen activation

what term describes enzymes that are activated by proteolytic cleavage

zymogens