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