chp 9-11 biochem

How is the kinase cascade activated?

-hormones that bind to membrane receptors. This activates adenylate cylase, which causes the formation of cAMP The cAMP activates a allosteric enzyme, protein kinase A, which then phosphorylates various target proteins.

Blood clotting cascades are controlled by A)zymogen activation. B)phosphorylation. C)allosteric activation. D)All of the above. E)None of the above.

A

Glycoforms refers to A)a single protein type that can have forms that vary in glycosylation. B)glycoproteins from the same gene family. C)a common core of sugars that can be found on many different proteins. D)all of the above. E)none of the above.

A

Many allosteric enzymes have two types of subunits, termed A)catalytic and regulatory. B)regulatory and allosteric. C)allosteric and regulatory. D)All of the above. E)None of the above.

A

The regulatory effects of substrates on allosteric enzymes are referred to as _____ effects. A)homotropic B)heterotropic C)allotropic D)All of the above.E)None of the above.

A

The relaxed form of an allosteric enzyme has _____ affinity for the substrates. A) higher B) equal C) lower D) no E) None of the above.

A

Phosphorylation is an extremely effective tool for catalytic control. Explain the reasons.

A phosphoryl group adds negative charges, allowing new electrostatic interactions and new hydrogen-bond formation. The free energy charge of phosphorylation is large, which can affect the conformational equilibrium of different states. Using ATP means that the reaction is linked to the energy status of the cell. Phosphorylation is rapid and reversible and can result in amplified effects. These factors affect structural, thermodynamic, regulatory, and kinetic properties. Section: 10.3

_____ is the most common donor molecule in phosphorylation reactions catalyzed by protein kinases.

ATP Section:

The nutritional storage form(s) of glucose in plants are.

Amylose and amylopectin.

What are zymogens?

An inactive enzyme precursor

Changes in ATCase conformation were detected by crystallizing the enzyme in the presence of PALA (N-(phosphonacetyl)-L-aspartate). What is PALA? A)a radioactive tag that binds to the subunits B)a bi-substrate analog that resembles the catalytic transition-state intermediate C)a fluorescent substrate analog D)All of the above. E)None of the above.

B

How is trypsin activity turned off? A)by dephosphorylation B)by binding an inhibitor protein C)by a second cleavage D)All of the above. E)None of the above.

B

Multifunctional protein kinases A)carry out phosphorylation as well as sulfation reactions. B)can modify several different targets. C)conserve energy in the form of ATP from the degradation of proteins. D)All of the above. E)None of the above.

B

What linkages occur in the cellulose?

Beta-1, 4.

How is specificity determined by chymotrypsin?

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

How does a genetic mutation account for some of the different human blood types?

Blood type is determined by specific glycosyltransferases that add the end sugar to the glycoproteins found on red blood cells. Three different types of glycosyltransferase genes can be inherited, and each individual receives one from each parent. Two different forms result in the A and B blood types. A mutation in a third type results in a truncated product that is not active.

Compare the structures of amylopectin and amylose.

Both are homopolymers of glucose. Amylose consists of unbranched a-1,4 linkages of glucose. Amylopectin is a branched structure, and contains both a-1,4 linkages and a-1,6 linkages, with the a-1,6 branches occurring about once every 30 glucose residues.

How is the clotting cascade initiated?

Both intrinsic (damaged surface) and extrinsic (trauma) pathways can induce the cascade. The initial steps differ, but lead to a final, common path to form the fibrin clot. Section

Fructose can cyclize to form

Both pyranose and furanose ring forms.

The processes of N-linked and O-linked glycosylation

Both take place in the Golgi apparatus

A regulatory mechanism that is NOT readily reversible: A)phosphorylation B)allosteric control C)proteolytic cleavage D)All of the above.E)None of the above.

C

An aldehyde and alcohol can react to form a A)hemiaketal. B)hemiketal. C)hemiacetal. D)All of the above. E)None of the above.

C

Fructose can cyclize to (a) A)pyranose ring. B)furanose ring. C)both pyranose and furanose ring forms. D)All of the above. E)None of the above.

C

How do some viruses gain entry into specific cells? A)by attaching to ion channels B)by cleaving the glycosidic bonds and altering protein shapes C)by binding to glycoproteins on the cell surface that are unique to specific cells D)All of the above. E)None of the above.

C

The common activator of the pancreatic zymogens is A)trypsinogen. B)chymotrypsin. C)trypsin. D)elastase. E)None of the above.

C

How is chymotrypsinogen activated? A)cleavage between an Arg and Ile by chymotrypsin B)cAMP binding, followed by cleavage by elastase C)cleavage between an Arg and Ile by trypsin D)All of the above. E)None of the above.

C Sectio

Sucrose is a glycoside of which of the following structures? A. 4-D-glucose-a-D-galactopyranoside. B. 4-D-glucose-

C. a-D-glucopyranosido-

Why is covalent modification advantageous when compared to proteolytic activation?

Covalent modification is usually a reversible process.

How is DIFP able to inactivate chymotrypsin?

Covalently modifies Serine-195 because it is in an environment which gives it a higher than normal reactivity to DIFP

A)contain distinct regulatory sites and have multiple functional sites. B)display cooperativity. C)always consist of several identical subunits. D)a and bE)a, b, and c

D

Examples of covalent modification include A)phosphorylation and dephosphorylation. B)acetylation. C)ubiquination. D)All of the above. E)a and b only

D

Glycoproteins are normally A)found on membranes. B)secreted as extracellular proteins. C)found inside organelles. D)a and b. E)All of the above.

D

Which amino acid residue side chains is/are phosphorylated by protein kinases?A) serine B) tyrosine C) threonine D) All of the above. E) a and c only

D

At what sites in a cell are proteins glycosylated? A)ribosome B)endoplasmic reticulum C)Golgi complex D)b and c E)a, b, and c

D Section: 11.3

Carbohydrates are A)polyhydroxy aldehydes. B)polyhydroxy ketones. C)polyhydroxy acids. D)polyhydroxy alcohols. E)a and b.

E

The most common strategy(ies) for enzymatic regulation: A)multiple enzyme forms B)allosteric control C)reversible covalent modification D)proteolytic activation E)All of the above.

E

Which of the following is an example of a zymogen?A)pepsinogen B)procarboxypeptidse C)T-form of ACTaseD)All of the above. E)a and b

E

Which of the following is correct concerning the adaptor molecule tRNA? A. tRNA contains an anticodon sequence that serves as the template recognition site. B. The amino acid is attached to the 5' end of tRNA. C. tRNA contains a poly(A) tail at the 3' end. D. tRNA serves as the gene in some viruses. E. None of the above.

E. None of the above.

D-glucose and D-galactose are

Epimers.

Give several examples of enzymes and proteins that are activated by proteolytic activation.

Examples include digestive enzymes (trypsin), hormones (insulin), clotting enzymes (fibrinogen), developmental process proteins (collagen), and apoptosis proteins (caspases).

_____ This is a test solution used to identify reducing and nonreducing sugars.

Fehling

Hydrolysis of Maltose by the enzyme Maltase yields:

Glucose only

_____ This is an example of a glycosaminoglycan.

Heparin

What are the effects of molecules other than substrate on allosteric enzymes called?

Heterotropic effects

What is the final step in the clotting pathway?

In the final step, fibrinogen, which contains six chains of three subunit types, is altered. Thrombin cleaves four of the chains, resulting in the formation of fibrin monomers. These monomers spontaneously assemble into the fibrin array. The clot is stabilized by cross-links between the amino acids catalyzed by transglutaminase.

Enzymes that catalyze the same reaction but differ in amino acid sequence are called

Isozymes

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

Isozymes or Isoenzymes Section

Why are certain forms of lactate dehydrogenase used as heart attack indicators?

LDH is a tetramer, made of M and H isozyme subunits. The M tetramer functions in an anaerobic environment and is primarily found in skeletal tissue, whereas the H tetramer, found primarily in the heart, functions optimally in an aerobic environment. An excess of the H type in serum indicates that a heart attack occurred.

_____ is a galactose joined to a glucose by a

Lactose

Do allosteric enzymes follow traditional Michaelis-Menten kinetics? Draw a graph of rate relative to substrate concentration for ATCase and compare it to Michaelis-Menten enzyme.

No, ATCase displays different kinetics. A plot of rate versus substrate concentration is a sigmoidal curve, as opposed to the simple hyperbolic curve obtained by enzymes displaying Michaelis-Menten kinetics.

Where does cleavage of the scissile bond by chymotrypsin occur?

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

Which amino acid residue side chains are phosphorylated by protein kinases?

Ser, Tyr, Thr.

Which of the following amino acids is important in the active site of chymotrypsin and trypsin?

Ser.

To which amino acid residues in glycoproteins are the sugars commonly linked?

Serine, Threonine, and Asparagine

The naturally occurring fruit sugar D-fructose has a specific rotation of -88.5

Structural relationship to D-glyceraldehyde.

Which of the following is a non-reducing sugar?

Sucrose.

_____ The less active conformational form of an allosteric enzyme.

T-state

How is the D or L configuration determined?

The D or L designation is determined by the asymmetric carbon farthest from the ketone or aldehyde group, and is related to the glyceraldehyde D and L structures.

How does the sequential model differ from the concerted model for allosteric enzymes?

The concerted model does not allow for anything other than an

A heterotropic effector that activates an enzyme will have what effect on the sigmoidal kinetic plot (V vs. [S])?

The curve will shift to the left.

Individuals in a royal family suffered from hemophilia and often died early from bleeding. What is the cause of this disease? How is it treated?

The disease in the royal family was caused by faulty factor VIII of the intrinsic pathway. It is treated by the addition of supplemental protein, originally isolated from serum, but now a recombinant product. Section: 10.4 and Figure 10.26

What is the function of aspartate transcarbamoylase?

The enzyme catalyzes the first step in the synthesis of pyrimidines. It condenses carbamoyl phosphate and aspartate to form N-carbamoylaspartate and inorganic phosphate.

You have isolated a new protease that cleaves peptide bonds following Asp and Glu. Based on its inactivation by DIFP, you suspect that it may utilize a mechanism similar to chymotrypsin. The difference in specificity might be explained by

The presence of a positively charged residue in the S1 binding pocket.

Why was it surprising to find that CTP inhibits ATCase?

The substrates for ATCase are carbamoyl phosphate and aspartate. These molecules do not resemble CTP. Thus, it was clear that the CTP must not bind to the active site, but to a distinct regulatory site.

What is the dual action of thrombin?

Thrombin catalyzes the hydrolysis of fibrinogen to form active fibrin. But it also has a role in shutting down the cascade by regulating protein C, a protease that digests other clotting enzymes Va and VIIIa.

What protein is administered after heart attacks to increase survival odds, and what is the biochemistry involved?

Tissue-type plasminogen activator, or TPA. TPA leads to the dissolution of blood clots so that blood flow through the blocked coronary artery can be restored. TPA activates plasminogen that is bound to the fibrin clot to active plasmin, which then hydrolyzes the fibrin of the clot.

_____ Molecule to which most sugars are attached prior to transfer.

UDP

Maltose is composed of two molecules of glucose linked together by _____ glycosidic bond.

a-1,4

In N-linked glycoproteins, the carbohydrate portion is attached to a(n)_____ residue in the protein.

asparagine

Protein kinase A is activated by binding _____ to specific sites on the regulatory subunit.

c-AMP

In C-type lectins, a _____ acts as a bridge between the carbohydrate and the protein.

calcium ion :

_____ This is the most abundant organic molecule in the biosphere.

cellulose

p-Hydroxymercuribenzoate reacts with crucial _____ residues in ATCase.

cysteine

A _____ is a stereoisomer that is not a mirror image.

diastereoisomer

A _____ is formed when two monosaccharides are linked together via a glycosidic bond.

disaccharide

_____ These are stereoisomers that are mirror images of each other.

enantiomers

_____ These monosaccharides differ at a single asymmetric carbon.

epimers

_____ The name for the regulatory mechanism in which the final product inhibits activity of the first step.

feedback inhibition

A _____ is a five-membered ring formed from a monosaccharide.

furanose

_____ The storage form of glucose in animals.

glycogen

_____ These are the enzymes that synthesize oligosaccharides.

glycosyltransferases

_____ A type of regulator of an allosteric enzyme that is not a substrate.

heterotropic

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

homotropic

_____ Multiple forms of homologous enzymes found within an organism.

isozymes

Blood serum analysis of _____ isozymes is used in the diagnosis of a myocardial infarction.

lactate dehydrogenase or LDH

_____ These proteins bind to specific carbohydrate structures.

lectins

Histones are acetylated at specific _____ residues.

lysine Section: 10.3

_____ This class of compounds has the molecular formula of (CH2O)n.

monosaccharides

_____ Enzymes activated by proteolytic cleavage.

phosphoserine

_____ The enzymes that catalyze protein phosphorylation.

protein kinases

Removal of protein phosphates is catalyzed by _____.

protein phosphatases

Aspartyl transcarbamylase catalyzes the first step in the synthesis of _____.

pyrimidines

_____ The shape of the kinetic plot of an enzyme that exhibits cooperative binding.

sigmoidal

Protein kinases add phosphoryl groups to serine, threonine, and _____ residues in target proteins.

tyrosine

_____ Vitamin required for the clotting pathway.

vitamin K

_____ Modified amino acid found in prothrombin, necessary for activation.

y-carboxyglutamate

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

zymogen Section