Biochem test 1

how many reducing ends are in one glycogen molecule?

1

What is the response when an aggrecanase inhibitor is added in addition to IL-2?

Aggrecan degradation is reduced to the background system level

Aggrecan degradation was measured by the release of glycosaminoglycan. What is the rationale for this assay?

Aggrecan is heavily decorated with glycosaminoglycans, and the release of these glycosaminoglycans is a sign of aggrecan degradation

What is the effect of adding IL-2 to the system?

Aggregan degradation is greatly enhanced

Why might glycosaminoglycan release not indicate aggrecan degradation?

Another enzyme might be present that cleaves glycosaminoglycans from aggrecan without degrading aggrecan

Raffinose is composed of __________________. Treatment of Raffinose with alpha-galactosidase produces ______________. Raffinose is ________________ sugar.

D-galactose, D-glucose, and D-fructose D-galactose and sucrose not a reducing

There are two types of nucleic acids, DNA and RNA.Nearly all organisms use DNA, not RNA, as the central repository for genetic information. Choose the statements that best explain this phenomenon.

DNA has double stranded structure that ensures an accurate mechanism of duplication DNA is more resistant against enzymes that degrade nucleic acids

Which statement describes the central dogma of biology?

DNA is transcribed into RNA. RNA is translated into an amino acid sequence.

Replication

DNA to DNA

Transcription

DNA to RNA

Identify the false statement regarding disulfide bridges.

Disulfide bridges are important to primary and tertiary structure, not quaternary

Under normal conditions, the central atom of heme is

Fe2+

BPG binds tighter to ___ which ____ its affinity for O2

HbA lowers

Which statements that best explains the role of BPG in O2 transport from mother to fetus?

HbA-bound O2 will tend to move to HbF because HbF has a lower affinity for BPG, an allosteric inhibitor of O2 binding

Which hemoglobin has a higher affinity for O2 at the tissue pO2 of around 4 kPa?

HbF

The alpha and beta subunits of hemoglobin bear a remarkable structural similarity to myoglobin. However, certain residues that are hydrophilic in myoglobin are hydrophobic in the subunits of hemoglobin. Why might this be the case?

Hydrophobic residues on the surface of hemoglobin subunits interact with similar regions on the other subunits through van der Waals interactions

A solution contains DNA polymerase and the Mg2+ salts of dATP, dGTP, dCTP, and TTP. Identify the reasons why the DNA molecule you selected would lead to DNA synthesis?

It has a primer with a free 3'-OH group It has an available template strand

Poly-L-leucine in an organic solvent such as dioxane is α helical, whereas poly-L-isoleucine is not. Why do these amino acids with the same number and kinds of atoms have different helix-forming tendencies?

L-isoleucine's methyl group sterically interferes with alpha helix formation, whereas L-leucine's methyl group does not interfere

Blood type O

N-acetyl-D-glucosamide D-galactose L-fucose

Blood type B

N-acetyl-D-glucosamide D-galactose L-fucose D-galactose

Blood type A

N-acetyl-D-glucosamide D-galactose L-fucose N-acetyl-D-galactosamide

Suppose myoglobin is prepared with Zn2+ in the place of Fe2+ in the porphyrin. Would you expect this modified myoglobin to bind oxygen?

No, because Zn2+ cannot partially transfer an electron to oxygen to form a complex

Is sucrose a reducing sugar? Why or why not?

No, because both anomeric carbons are involved in the glycosidic linkage.

Does myoglobin exhibit a Bohr effect? Why or why not?

No, because myoglobin does not have a quaternary structure

Consider the difference between nucleosides and nucleotides. Select the true statement.

Nucleosides do not contain a phosphate group

Select the true statements about SDS-PAGE, a method of separating proteins. Assume that SDS-PAGE is performed under reducing conditions.

Proteins are separated in a polyacrylamide gel Protein SDS complexes have similar mass to charge ratios; therefore, separation is by size Smaller proteins migrate faster through the polyacrylamide gel

Translation

RNA to protein

Why is there some aggregan destruction in the control with the passage of time?

Some of the factors contributing to cartilage stabilization in vivo may not be present

Protein disulfide isomerase (PDI) is a protein folding enzyme that catalyzes disulfide-sulfhydryl exchange reactions. Ribonuclease is an enzyme with two beta sheets, three alpha helices, and four disulfide bridges critical to the stability of its structure. PDI rapidly converts inactive, scrambled ribonuclease to enzymatically active ribonuclease. This process is driven by the decrease in free energy as the scrambled conformations are converted into stable, active conformation of the enzyme. In contrast, PDI rapidly inactivates insulin. What does PDI's effect on insulin imply about the structure of insulin?

The active conformation of insulin is not the most thermodynamically preferred form

Select the true statements about protein secondary structure.

The beta pleated sheet is held together by hydrogen bonds between adjacent segments In an alpha helix, the side chains are located outside of the helix The secondary level of protein structure refers to the spatial arrangements of of short segments of the protein

What is the purpose of the control (cartilage incubated with no additions)?

The control provides a baseline of "background" aggrecan degradation inherent in the assay

Why are tyrosine kinases other than BTK present in the eluate?

The kinase inhibitor has low specificity

Arthropods such as lobsters have oxygen carriers quite different from hemoglobin. The oxygen-binding sites do not contain heme but, instead, are based on two copper (Cu) ions. The structural changes that accompany oxygen binding are shown in the reaction diagram. How might these changes be used to facilitate cooperative oxygen binding?

The two copper ions move together upon binding oxygen, and this motion could promote cooperativity

which of these amino acids have R groups with hydrogen bonding potential?

Thr Ser Tyr Glu

Which statements about reducing sugars are true?

a disaccharide with its anomeric carbons joined by the glycosidic linkage cannot be a reducing sugar the oxidation of a reducing sugar can forms a carboxylic acid sugar D-arabinose (an aldose) is a reducing sugar

Which statements about reducing sugars is true?

a disaccharide with its anomeric carbons joined by the glycosidic linkage cannot be a reducing sugar the oxidation of a reducing sugar forms a carboxylic acid sugar D-mannose (an aldose) is a reducing sugar

A solution contains DNA polymerase and the Mg2+ salts of dATP, dGTP, dCTP, and TTP. When added to aliquots of the solution, which DNA molecule would lead to DNA synthesis?

a single stranded closed circle of 1000 nucleotide base paired to a linear strand of 500 nucleotides with a free 3'-OH terminus

Hemoglobin is a protein in red blood cells that binds to oxygen. Which physiological changes that naturally occur in the body reduce hemoglobin's affinity for oxygen?

accumulation of carbon dioxide decrease in pH

Which amino acids would be expected to produce a similar sickling effect if substituted for Val at position 6?

alanine leucine

The glucose units in this polysaccharide are joined only by alpha-1,4-glycosidic bonds

amylose

These two polysaccharides make up starch, the storage form of glucose in plants.

amylose amylopectin

Select the stabilizing factors that hold the two strands of DNA together in a double helix.

base stacking hydrogen bonding hydrophobic interactions

Has the molecular formula of (CH2O)n

carbohydrates

The glucose units in this polysaccharide are joined together by beta-1,4-glycosidic bonds

cellulose

This polysaccharide is the structural component of plant cell walls and cannot be digested by humans

cellulose

the most abundant organic molecule in the biosphere

cellulose

purines

contain four ring nitrogen atoms contain two heterocyclic rings

Pyrimidines

contain one heterocyclic ring contain only two ring nitrogen atoms

In __________, the central atom is displaced 0.4A out of the plane of the porphyrin ring system

deoxyhemoglobin

stereoisomers that are mirror images of each other

enantiomers

monosaccharides that differ at a single asymmetric carbon atom

epimers

Consider the Haworth projections of Beta-L-galactose and Beta-L-glucose. Which terms describe the relationship between those two sugars?

epimers diastereomers

Identify the applications for gel filtration chromatography.

estimation of molecular weights separation of components in a mixture by size

Select the most appropriate technique for separating the digestion products of AVGWRVKS if cleaved by trypsin.

gel-filtration chromatography

This polysaccharide is the storage form of glucose in the human body

glycogen

the storage form of glucose in animals

glycogen

These two branched polysaccharides contain both alpha-1,4 and alpha-1,6-glycosidic bonds

glycogen amylopectin

enzymes that synthesize oligosaccharides

glycosyltransferases

The number of reducing ends in a glycogen molecule is _____________ the number of reducing ends in the molecule.

greater than

The prosthetic group of hemoglobin and myoglobin is

heme

Blood cells from some birds do not contain 2,3-biphosphoglycerate but, instead, contain one of the compounds shown, which plays an analogous functional role. Which compound do you think is most likely to play this role? Why?

inositol pentaphosphate , because of its negative charge

Select the most appropriate technique for separating the digestion products of AVGWRVKS if cleaved by chymotrypsin.

ion-exchange chromatography

Carbohydrate-binding proteins

lectins

What characteristics determine the position of a protein on an IPG strip at the end of isoelectric focusing?

local pH in the medium the pI of the protein

N-acetylgalactosamine is a key component of this glycoprotein

mucoprotein

As we will see in Chapter 21, glycogen is an important fuel storage form that is rapidly mobilized. You would expect most metabolism to take place at the _______________ end of glycogen.

nonreducing

Identify the best description of a heme group.

one of four iron-containing parts of hemoglobin that bind to oxygen molecules

What drives the diffusion of oxygen?

partial pressure of oxygen

Which statements about peptide bonds are true?

peptides are polymers of amino acids a tripeptide contains three amino acid residues

Choose two amino acids that would be reasonable candidates for the pocket-Val 6 interaction.

phenylalanine leucine

The organic ring component of heme is

porphyrin

glycoprotein containing glycosaminoglycans

proteoglycan

Select the amino acids that attach carbohydrates to proteins.

serine threonine asparagine

The central atom has ________bonds: ___________ to nitrogen atoms in the prophyrin, one to a _____________ residue, and one to oxygen.

six four histidine

the storage form of glucose in plants

starch

How does glycosylation influence the specification of blood type?

the absence of a glycosyl unit on the O antigen specifies type O the addition of N-acetylgalactosamine to the O antigen specifies type A the addition of galactose to the O antigen specifies type B

What drives the loading of oxygen onto hemoglobin molecules in the lungs?

the high partial pressure of oxygen in the lungs

Suppose that you want to radioactively label DNA, but not RNA, in dividing and growing bacterial cells. Which radioactive molecule would you add to the culture medium?

titrated thymidine

What are the roles of sodium dodecyl sulfate (SDS) in two-dimensional electrophoresis?

to denature proteins to cause bound proteins to have a large negative charge