CHM 20EXAM 3 – REVIEWName Ms Dang

  1. Indicate whether each of the following is D-glyceraldehyde or L-Glyceraldehyde, assuming that the horizontal bonds point toward you and the vertical bonds point way from you
  1. What sugar is the C-3 epimer of D-xylose? C-5 of Dallose?

D-Ribose and L - Talose

  1. What other monosaccharide is reduced only to the alditol obtained from the reduction of D-Galactose?
  1. Identify the following sugars:

An aldopentose that is not D-arabinose forms D-arabinitol when it is reduced with NaBH4

D-lyxose

A ketose, when reduced with NaBH4, forms D-altritol and D-allitol

D-psicose

  1. The reaction of D-ribose with one equivalent of methanol plus HCl forms four products. Give the structures of the products and their names
  1. What is the main structural difference between

Amylose and cellulose?

Amylose has -1,4’-glycosidic linkage, whereas cellulose has β-1,4’-glycosidic linkage

Amylopectin and glycogen

Glycogen and amylopectin have the same kind of linages, but glycogen has a higher frequency of -1,6’-glycosidic linkages

  1. People with type O blood can donate blood to anyone, but they cannot receive blood from everyone. From whom can they not receive blood?

People with type O blood can receive blood only from other people with Type O Blood, because Type A, B, and AB blood have sugar components that Type O blood does not have

  1. Draw the form in which each of the following amino acids predominately exists at physiological pH (7.3)
  1. Aspartic acidb.Glutaminec. arginine
  1. Draw the structural formula of the tripeptide met-ser-cys
  1. Draw the different ionic structure of this tripeptide at pH 2.0, 10.0.
  1. What kinds of changes are necessary to transform a protein having a predominantly -helical structure into one having a β-pleated sheet structure?

Both the α-helix and the β-pleated sheet are examples of secondary structure. Thesestructures are held together by hydrogen bonding between the amide carbonyl and theamide hydrogens. To change from one to the other, the protein must become denaturedso that the hydrogen bonds are disrupted. The protein will then exist in a random coilstate and may then form a new secondary structure as new hydrogen bonds are formedwithin a chain or between chains.

  1. How would a protein that resides in the interior of a membrane fold, compared with the water-soluble protein?

It would fold so that its nonpolar residues are on the outside of the protein in tact with the nonpolar membrane and its polar residues are on the inside of the protein

  1. Explain why the following are not found in-helix: two adjacent glutamates, two adjacent aspartates, or a glutamate adjacent to an aspartate

In each case, the two adjacent amino acids each have a negative charge. Two adjacent side chains will be close to one another if they are in the helix, so they will repel each other if they have the same charge

  1. Why does the body need so many different enzymes?

There are thousands of different kinds of biochemicals in an organism and thousands of

reactions are required to synthesize and degrade the compounds. The mild conditions

inside the cell are not conducive to fast reaction rates so each reaction requires an enzyme

for catalysis under physiological conditions.

  1. Monoamine oxidases are important enzyme in brain chemistry. Judging from the name, which of the following would be suitable substrate for this class of enzyme

Substrates for the monoamine oxidases usually have only one amino group. Therefore,

based only on the name of the enzymes, both (a) and (b) should be active substrates.

Compound (c) contains a nitro group, not an amino group. In actuality, the monoamine

oxidases also prefer primary and secondary amines and aromatic compounds as

substrates, so it is expected that (a) is the best substrate.

  1. What term do we use to refer to (a) the protein portion and (b) the organic molecule portion?

a) The protein portion of the enzyme is called the apoenzyme.

(b) The organic molecule portion is called a coenzyme.

  1. At a very concentration of a certain substrate, we find that, when the substrate concentration doubles, the rate of the enzyme-catalyzed reaction also doubles. Would you expect the same finding at a very high substrate concentration? Explain

At very low concentrations of substrate, the rate of an enzyme-catalyzed reaction increases in a linear fashion with increasing substrate concentrations. At higher concentrations of substrate, the active sites of the enzyme molecules become saturated

  1. The hydrolysis of glycogen to yield glucose is catalyzed by the enzyme phospharylase. Caffeine, which is not a carbohydrate and not a substrate for the enzyme, inhibits phosphorylase. What kind of regulatory mechanism is at work?

At first, one might expect the inhibition of phosphorylase action by caffeine to be a case of traditional noncompetitive inhibition because the inhibitor apparently does not bind at the active site. However, glycogen phosphorylase is known to be an allosteric enzyme and the classical terms competitive and noncompetitive are not used to define inhibition. The term negative modulator is used to define the action of caffeine on the allosteric enzyme, phosphorylase.

  1. Which LDH isozyme is monitored in the case of a heart attack?

Lactate dehydrogenase, which is tetrameric, has two different kinds of subunits called H and M. Thus, LDH exists as isoenzymes (isozymes). The subunit that dominates in heart cells is the H type. Therefore, the isoform, H4, is monitored in the diagnosis of a heart attack.

  1. Explain why transition-state analogs are potent inhibitors?

A transition state analog is a molecule that has a shape that fits the active site of an enzyme almost perfectly. However, being an analog and not the real transition state, no reaction is catalyzed. Therefore, the transition state analog acts as an inhibitor, and its perfect fit makes it a potent one.

  1. Can the product of a reaction that is part of a sequence act as an inhibitor for another reaction in the sequence? Explain

The regulation process described in the problem is called feedback inhibition and is a common mechanism for controlling metabolic reactions. Consider the reaction sequence:

A B C D E F

The letters refer to metabolites or intermediates that are produced in the pathway to synthesize compound F. In feedback inhibition, compound F acts as an inhibitor for the enzyme that converts A to B. This type of inhibition becomes important when enough F has been produced for the cell.

  1. Draw the following nucleotides
  1. Deoxycytidine-3’-monophosphoate (dCMP)b.Deoxythymine-5’-triphosphate (dTTP)

c.Uracil-5’-diphosphate (UDP)

  1. RNA and DNA refer to nucleic acids. Which part of the molecule is acidic?

The name nucleic acid comes from the fact that the nucleosides are linked by phosphate

groups, which are the dissociated form of phosphoric acid.

  1. What type of bond connects the base to the ribose in GTP?

The bond that connects the base to the ribose in GTP is a β-N-glycosidic bond

  1. What are the higher order structures of DNA that eventually make up a chromosome?

DNA is wound around histones, collectively forming nucleosomes that are further wound

into solenoids, loops, and bands.

  1. Draw the structure of adenine and thymine, and show with a diagram the two hydrogen bonds that stabilize C-G pairing in nucleic acids
  1. When cytosine is deaminated, uracil if formed. Uracil is a naturally occurring base. Why would the cell use base excision repair to remove it?

Deamination of the base cytosine transforms it to uracil which creates a mismatch. What

was a C-G pair now becomes a U-G mismatched pair that must be removed by BER.

  1. What 12-nucleotide primer would you use in the PCR technique when you want to amplify a gene whose end is as follows: 3’TACCGTCATCCGGTG5’

The 12-nucleotide primer to use is: 5’ATGGCAGTAGGC3’.

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