Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of a dehydrogenase?

A. An enzyme that catalyzes the addition of phosphate groups to other molecules

B. An enzyme that catalyzes the rearrangement of bonds within a single molecule

C. An enzyme that catalyzes a change in the position of a specific chemical group within a single molecule

D. An enzyme that catalyzes the oxidation of a molecule by removing a hydride ion

For each of the enzymes listed, write down the information requested:

DNA-dependent DNA polymerase

Type of nucleic acid template:  

Type of nucleic acid produced:

When is enzyme used? Eukaryotic, Prokaryotic and DNA virus DNA replication         

DNA-dependent RNA polymerase

Type of nucleic acid template:

Type of nucleic acid produced:

When is enzyme used? Eukaryotic, Prokaryotic and DNA virus transcription

RNA-dependent RNA polymerase

Type of nucleic acid template:

Type of nucleic acid produced:

When is enzyme used? RNA virus replication

Alternative name for enzyme:

RNA-dependent DNA polymerase

Type of nucleic acid template:

Type of nucleic acid produced:

When is enzyme used? Retrovirus replication

Alternative name for enzyme:

A zinc ion in the active site of an enzyme can speed up the reaction by:

A. Making a bound water molecule a more powerful nucleophile by drawing electron density toward itself and facilitating deprotonation of the water

B. Orienting substrates for reaction

C. Stabilizing an anionic intermediate

D. All of these

E. None of these

The role of serine at the active site of serine proteases is to act as a ___ catalyst, while the histidine residue serves as an ___ catalyst.

A. acid-base, covalent

B. anionic; ionic

C. covalent; acid-base

D. strong; weak

E. weak; strong

The active site of an enzyme is being investigated by mutagenesis to determine the stability of the enzyme conformation following substrate binding. A leucine is replaced by glycine. This change will:

A. Destabilize the enzyme

B. Stabilize the enzyme

C. Have no effect on the enzyme

An enzyme was found that catalyzes the reaction between students, S and academic success, P (for pass); the enzyme was called studyase.

An enzyme assay was run on studyase. 10μg of studyase (molecular weight 20,000D) was placed in a set of test tubes each of which contained 1mL of the substrate student at varying concentrations and the amount of product, academic success (P) was determined.

The following results were determined:

Note 1mM = 1millimole/L = 1μmol/mL

Plot a Lineweaver-Burk plot of 1/V versus 1/S

Determine Vmax and Km for the enzyme studyase.

Calculate Kcat and the catalytic constant (kcat/km) for the enzyme. (find [E]_T as total μmoles/mL)

Another enzyme called partyase was analyzed and when 0.010 μmoles of this enzyme was assayed it was found to have a Vmax of about 50 μmol/mL/sec and a Km of 5 mM. Calculate Kcat and the catalytic constant for this enzyme.

i.Compare the 2 enzymes on the basis of affinity for the binding site and kinetic efficiency.

Why do common folding patterns appear in proteins that exhibit very different primary structures?

The carbonyl and amino groups of the amino-acid residues at the N- and C-termini of proteins form regular patterns of hydrogen bonds that define α-helix and β-sheet shapes.

The carbonyl and amide groups of the polypeptide backbone form regular patterns of hydrogen bonds that define α-helix and β-sheet shapes.

The carbonyl and amino groups of glutamate and glutamine, respectively, form regular patterns of ionic bonds that define α-helix and β-sheet shapes.

The carboxyl and amino groups of the amino-acid residues at the N-and C-termini of proteins form regular patterns of ionic bonds that define α-helix and β-sheet shapes.

The carbonyl and amide groups of the amino-acid sidechains form regular patterns of hydrogen bonds that define α-helix and β-sheet shapes.

Explain why gluconegogenesis, not glycolysis, is the predominant pathway in the hepatocytes of a normal fasting rat.

What is a cofactor? Give one example in the glycolysis pathway where a cofactor is involved.

You want to use PCR to amplify a 1Kb exon of the human autosomal gene phenylalanine hydroxylase (PH) from the genome of a person suffering from the disease phenylketonuria, which is due to this enzyme not functioning.

a) You start with 1 nanogram of genomic DNA in your sample tube. Assuming a human haploid genome is 3 x 109 bp, and each bp has a mass of 660 g/mole, how many moles of haploid genomes are present at the start of your PCR experiment?

b) The PH gene is present in a single copy in the haploid genome. How many template molecules of the PH gene are present at the start of your PCR experiment? (Give your answer in molecules, not moles of molecules.)

c) You set your PCR machine to run for 25 cycles to amplify your 1 kb fragment. Assume every cycle exactly doubles your desired target DNA. At the end of your 25 cycles, how much amplified DNA have you created, in terms of number of molecules AND mass of DNA?