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    chymotrypsin catalyzes the hydrolysis of a peptide bond and is therefore categorized as a _____.

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    93cards Chemistry

    Introduction To Biochemistry

    How does a catalyst increase the rate of a reaction?

    It allows reacting molecules to more easily form the transition state.

    Chymotrypsin catalyzes the hydrolysis of a peptide bond and is therefore categorized as a........

    hydrolase

    Which of the following amino acids would be most likely found in the active site of an enzyme that uses acid-base catalysis?

    His

    In an enzyme mechanism that generates a negative charge in the transition state which would be most effective to have in the active site of the enzyme

    Transition metal cation

    If the Asp in the chymotrypsin active site was mutated to another amino acid, which of the following would be considered an invisible mutation in that it is least likely to impact the function of the enzyme? (Asp--> Asn, Glu, His, Ser, or Lys?)

    Asp --> Glu

    Chymotrypsin catalyzes the hydrolysis of peptide binds adjacent to _________ residues In a peptide

    Nonpolar

    Chymotrypsin has a large specificity pocket to bind the aromatic amino acids while elastase has a very small specificity pocket meant to bind Ala or Gly. Which of the following amino acid substitutions changes the specificity pocket of chymotrypsin to that of elastase?

    Gly --> Val

    Zymogens are not enzymatically active because

    their active sites are distorted.

    In order to catalyze reactions, enzymes frequently require additional substances in their active site. What is the name for this family of substances?

    cofactors

    The difference in free energy between the substrate and product of a reaction catalyzed by Enzyme A is negative and small. What conclusions can be drawn about this reaction?

    The reaction is spontaneous and its speed is unknown from these data.

    In studying the structure of a new enzyme, you find that side chains of Phe, Leu, and Ile are directed into the active site: Which of the following can logically be proposed on the basis of this observation?

    Some groups on the substrate are likely to be hydrophobic.

    A reversible inhibitor that binds to a site other than the active site regardless of whether or not the substrate is bound is a...

    noncompetitive inhibitor

    Reversible inhibitor that only affects multisubstrate enzymes and binds to the enzyme only after one substrate has bound is a

    Uncompetitive

    what is a "suicide inhibitor"

    one that forms a covalent bond to active site

    why does Phosphorylation cause a change in the shape of the enzyme

    because a phosphate group is bigger and more negatively charged than a hydroxyl group

    Which of the following does NOT alter enzyme activity in a cell by changing the exact geometry of the active site?

    A. Allostery.

    B. Competitive inhibition.

    C. Phosphorylation.

    D. Increased gene expression.

    B and D.

    competitive inhibition and increased gene expression do NOT alter the geometry of the active site

    A molecule decreases the activity of an enzyme by binding to a site other than the active site is called

    Allosteric inhibitor

    Which of the following features in a Lineweaver-Burk plot is altered by a competitive inhibitor in an enzyme-catalyzed reaction?

    Shape of the plot

    Intercept on the x-axis

    Intercept on the y-axis

    Intercept on the 1/Vo axis

    Intercept on the y-axis which is the 1/Vo axis

    intercept on the x-axis

    The presence of an uncompetitive inhibitor in an enzyme-catalyzed reaction will alter which of the following in a Lineweaver-Burk plot?

    Intercept on the y-axis

    The intercept on both axes

    Shape of the plot

    Intercept on the x-axis

    Slope of the plot

    The intercept on both axes

    For an enzyme that displays Michaelis-Menten kinetics, what is the effect of a competitive inhibitor on ?

    km increases

    For an enzyme that displays Michaelis-Menten kinetics, what is the effect of a competitive inhibitor on ?

    stays same

    If an inhibitor binds irreversibly to an enzyme the inhibitor is called an

    Inactivator

    An inhibitor that binds to the active site only in the absence of the substrate and in a reversible fashion is an _____.

    competitive inhibitor

    What does the K I for a competitive inhibitor mean?

    lower K I values mean tighter binding to the enzyme

    Which inhibition can be reversed by addition of more substrate

    Competitive

    Which of the following statements regarding allosteric enzymes is true?

    they are always oligomeric

    they are generally found at regulatory sites in metabolic pathways

    they are subject to regulation by both positive and negative effectors

    a plot of velocity versus [substrate] often yields a sigmoidal curve

    all of the above all of the above

    Chymotrypsin catalyzes the hydrolysis of peptide binds adjacent to _________ residues In a peptide

    Nonpolar

    Which protein in the blood is responsible for converting fibrinogen to fibrin?

    thrombin

    Conversion of factor X to Xa represents_____ form of activation

    And binding of anti thrombin to thrombin represents _____ form of inhibition

    Irreversible Reversible

    Which of the following is a feature of protease inhibitor specific for trypsin? contains a positive charge to mimic the charge of the substrate

    Source : www.chegg.com

    biochemistry exam 2 Flashcards

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    serine, histidine, aspartic acid

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    The chymotrypsin/trypsin family of proteases has which combination of amino acids in the active site

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    suicide substrates

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    Some irreversible inhibitors are called _____ because they bind to the active site of the enzyme and begin

    the catalytic process, just like a normal substrate.

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    1/45 Created by longhorn512

    Terms in this set (45)

    serine, histidine, aspartic acid

    The chymotrypsin/trypsin family of proteases has which combination of amino acids in the active site

    suicide substrates

    Some irreversible inhibitors are called _____ because they bind to the active site of the enzyme and begin

    the catalytic process, just like a normal substrate.

    second messenger

    A small molecule produced inside a cell in response to a hormone binding to its receptor is called a(n)

    _____. His

    Which of the following amino acids would be most likely found in the active site of an enzyme that uses

    acid-base catalysis?

    all of the above

    Which of the following types of enzyme-catalyzed reactions follows non-Michaelis-Menten kinetics?

    it has no effect

    How does a catalyst affect the overall ΔG of an endergonic reaction?

    hydrolase

    Chymotrypsin catalyzes the hydrolysis of a peptide bond and is therefore categorized as a _____.

    K+ efflux

    After depolarization of a nerve cell, what event restores the resting potential? (Efflux is movement out of

    the cell and influx is movement into the cell.)

    covalent attachment of a phosphate group to increase or decrease activity

    Which of the following represents a rapid and reversible mechanism to alter the activity of an enzyme?

    GTP; α

    Activation of a G protein in response to hormone binding requires binding of _____ to the _____ subunit.

    the transition state

    The highest point in a reaction coordinate diagram represents _____.

    insulin

    The _____ receptor is a receptor tyrosine kinase

    B and D

    Which of the following residues would you expect in the membrane spanning portion of an integral

    membrane protein? cholesterol

    The most notable difference between _____ and other lipids is the presence of four fused rings.

    no

    Is it necessary to know [E]T in order to determine Vmax?

    hormone response elements

    The complex formed between a lipid hormone and its receptor binds to _____ which are specific DNA

    sequences

    GTPase activity of the alpha subunit

    What limits the signaling activity of a G protein once it has been stimulated by an epinephrine binding

    receptor?

    transition metal cation

    In an enzyme mechanism that generates a negative charge in the transition state, which of the following

    would be most effective to have in the active site of the enzyme?

    passive transport; active transport

    The movement of glucose into a cell when blood sugar is high is accomplished by _____. The movement of

    K+ against its concentration gradient is accomplished by _____.

    trimeric; β-barrels

    All known porins are _____ proteins composed of _____.

    hydrogen bonding between the enzyme and the anion from the carbonyl oxygen

    In the chymotrypsin mechanism, what is used to stabilize the negative charge on the carbonyl oxygen of

    the transition state?

    proteins that are mobile only in a small area are sequestered by proteins attached to the cytoskeleton

    Which of the following aspects of membrane protein movement is explained by the fluid mosaic model?

    Secondary active transport

    Kidney cells include two antiport proteins, a H+/Na+ exchanger and a Cl-/HCO3- exchanger. What is the

    source of free energy that drives the transmembrane movement of all these ions?

    remain the same

    If the enzyme concentration for a biochemical reaction is increased 100-fold, the equilibrium constant for

    the reaction will symporter

    What is a transporter that moves two different molecules or ions in the same direction?

    higher at the hoof

    Membrane lipids in tissue samples obtained from different parts of the leg of a reindeer in the Arctic show

    different fatty acid compositions. Would the proportion of unsaturated fatty acyl chains be higher at the

    top of the leg or at the hoof?

    methyl

    Which of these amino acid groups would NOT make a good nucleophilic catalyst?

    general base then general acid

    During the first half of the chymotrypsin mechanism where the acyl-enzyme intermediate is formed, what

    role does His play? active transport

    A molecule moves across a membrane from a lower to a higher concentration with the aid of a membrane

    protein. This process is known as:

    only on the extracellular side of the membrane

    The carbohydrate portion of a membrane spanning glycoprotein is found _____.

    acidic amino acid

    A pH/rate curve with an inflection point at pH~4 suggests the involvement of a(n) ________ in the

    catalytic step. 20%

    What percentage of Vmax is obtained when the substrate is present at 1/4 of the KM?

    6.5

    What is the ratio [Na+]in/[Na+]out created by depolarization in a nerve cell if the final potential is +50 mV

    Source : quizlet.com

    Protein Function

    We have seen that each type of protein consists of a precise sequence of amino acids that allows it to fold up into a particular three-dimensional shape, or conformation. But proteins are not rigid lumps of material. They can have precisely engineered moving parts whose mechanical actions are coupled to chemical events. It is this coupling of chemistry and movement that gives proteins the extraordinary capabilities that underlie the dynamic processes in living cells.

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    Molecular Biology of the Cell. 4th edition.

    Show details

    Protein Function

    We have seen that each type of protein consists of a precise sequence of amino acids that allows it to fold up into a particular three-dimensional shape, or conformation. But proteins are not rigid lumps of material. They can have precisely engineered moving parts whose mechanical actions are coupled to chemical events. It is this coupling of chemistry and movement that gives proteins the extraordinary capabilities that underlie the dynamic processes in living cells.

    In this section, we explain how proteins bind to other selected molecules and how their activity depends on such binding. We show that the ability to bind to other molecules enables proteins to act as catalysts, signal receptors, switches, motors, or tiny pumps. The examples we discuss in this chapter by no means exhaust the vast functional repertoire of proteins. However, the specialized functions of many of the proteins you will encounter elsewhere in this book are based on similar principles.

    Go to:

    All Proteins Bind to Other Molecules

    The biological properties of a protein molecule depend on its physical interaction with other molecules. Thus, antibodies attach to viruses or bacteria to mark them for destruction, the enzyme hexokinase binds glucose and ATP so as to catalyze a reaction between them, actin molecules bind to each other to assemble into actin filaments, and so on. Indeed, all proteins stick, or , to other molecules. In some cases, this binding is very tight; in others, it is weak and short-lived. But the binding always shows great , in the sense that each protein molecule can usually bind just one or a few molecules out of the many thousands of different types it encounters. The substance that is bound by the protein—no matter whether it is an ion, a small molecule, or a macromolecule— is referred to as a ligand for that protein (from the Latin word , meaning “to bind”).

    The ability of a protein to bind selectively and with high affinity to a ligand depends on the formation of a set of weak, noncovalent bonds—hydrogen bonds, ionic bonds, and van der Waals attractions—plus favorable hydrophobic interactions (see Panel 2-3, pp. 114–115). Because each individual bond is weak, an effective binding interaction requires that many weak bonds be formed simultaneously. This is possible only if the surface contours of the ligand molecule fit very closely to the protein, matching it like a hand in a glove (Figure 3-37).

    Figure 3-37

    The selective binding of a protein to another molecule. Many weak bonds are needed to enable a protein to bind tightly to a second molecule, which is called a for the protein A ligand must therefore fit precisely into a protein’s binding (more...)

    The region of a protein that associates with a ligand, known as the ligand’s usually consists of a cavity in the protein surface formed by a particular arrangement of amino acids. These amino acids can belong to different portions of the polypeptide chain that are brought together when the protein folds (Figure 3-38). Separate regions of the protein surface generally provide binding sites for different ligands, allowing the protein’s activity to be regulated, as we shall see later. And other parts of the protein can serve as a handle to place the protein in a particular location in the cell—an example is the SH2 domain discussed previously, which is often used to move a protein containing it to sites in the plasma membrane in response to particular signals.

    Figure 3-38

    The binding site of a protein. (A) The folding of the polypeptide chain typically creates a crevice or cavity on the protein surface. This crevice contains a set of amino acid side chains disposed in such a way that they can make noncovalent bonds only (more...)

    Although the atoms buried in the interior of the protein have no direct contact with the ligand, they provide an essential scaffold that gives the surface its contours and chemical properties. Even small changes to the amino acids in the interior of a protein molecule can change its three-dimensional shape enough to destroy a binding site on the surface.

    Go to:

    The Details of a Protein’s Conformation Determine Its Chemistry

    Proteins have impressive chemical capabilities because the neighboring chemical groups on their surface often interact in ways that enhance the chemical reactivity of amino acid side chains. These interactions fall into two main categories.

    First, neighboring parts of the polypeptide chain may interact in a way that restricts the access of water molecules to a ligand binding site. Because water molecules tend to form hydrogen bonds, they can compete with ligands for sites on the protein surface. The tightness of hydrogen bonds (and ionic interactions) between proteins and their ligands is therefore greatly increased if water molecules are excluded. Initially, it is hard to imagine a mechanism that would exclude a molecule as small as water from a protein surface without affecting the access of the ligand itself. Because of the strong tendency of water molecules to form water–water hydrogen bonds, however, water molecules exist in a large hydrogen-bonded network (see Panel 2-2, pp. 112–113). In effect, a ligand binding site can be kept dry because it is energetically unfavorable for individual water molecules to break away from this network, as they must do to reach into a crevice on a protein’s surface.

    Source : www.ncbi.nlm.nih.gov

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