You wish to determine the sequence of a polypeptide that has the following amino acid composition: Ala: 1 Arg: 4 Asn: 2 Asp: 3 Cys: 4 Gly: 3 Gln: 1 Glu: 4 His: 1 Lys :1 Met: 1 Phe: 1 Pro: 2 Ser: 4 Tyr: 2 Trp: 1 What is the maximum number of peptides you can expect if you cleave the polypeptide with: A) Trypsin B) Chymotrypsin C) CNBr D) There are no free sulfhydryl groups in the peptide. How many disulfide bonds do you expect to find? E) How many different possible arrangements of disulfide bonds are possible in this peptide?

19.A mutation that changes an amino acid-coding codon to a stop codon is classified as:

A – Silent

B – Missense

C – Nonsense

D – Neutral

20.Spontaneous mutations can arise from:

A – All answers are correct

B – A base gets damaged

C – DNA polymerase inserts an incorrect nucleotide

D – A loop occurs during replication

21.DNA Repair Systems:

A – Counteract spontaneous and induced mutations

B – Counteract induced mutations only

C – Counteract amino acid changes introduced by mutations

D – Prevent DNA damage

22.Which of the following general mechanisms appear to be involved in the formation of cancer cells?

A – Genomic instability, DNA repair failure, chromatin modifications

B – RNA failure, DNA phosphorylation, phosphorylation of adenyl cyclase

C – Transdetermination, mutation, allosteric interactions

D – Inversions, operon formation, methylation

23.Mutations in the ras gene family induce normal cells to proceed into the replication cycle. This convert the ras gene from a ____ gene to a ____ gene.                                         

A – Mutant; oncogene

B – Proto -oncogene; oncogene

C – Tumor suppressor; proto-oncogene

D – Oncogene; proto-oncogene

24.What is a potential carcinogen?

A – Any substance that damages DNA

B – Any pollutant

C – Any toxic chemical

D – Any chemical

Question 2

Tyrosine is a triprotic amino acid with pKa of 2.17, 9.19, and 10.47 The first proton is removed

from the carboxylic acid ( –COOH), the second from the protonated amine group (–NH3

+) . The

third, with a pKa of 10.47, is the phenolic proton (–OH) on the aromatic ring.

Tyrosine

a) What is the structure of the most protonated form of tyrosine in aqueous solution?

! "#$%!*!'(!)!

b) Write the three acid dissociation equilibria with the correct charge (use Tyr as shorthand

for the part of the molecule excluding the acidic protons, i.e. Tyr(charge), HTyr(charge),

H2Tyr(charge), H3Tyr(charge)).

c) Suppose we titrate a 0.100 M solution of tyrosine hydrochloride salt (often written

Tyr!HCl) with a 0.100 M solution of a strong base (NaOH). Calculate pH at the

following points:

i. initially,

ii. half way to the first,

iii. at the first,

iv. half way to the second,

v. at the second, and

vi. half way to the third equivalence points

d) Using your results calculated in (c) sketch an accurate titration curve.

e) Based on your sketch, identify which equivalence point(s) can be used to identify end

point with an indicator dye.

f) For part (e), indicate what the pKa (or range) of indicator dye should be to minimize

determinate titration error.

g) Write the general expressions for the mass balance and the charge balance for part (c).

Enzymes Kinetics:
The following kinetic data were obtained for an enzyme in the absence of inhibitor (1), and in the presence of two

different inhibitors (2) and (3) at 5 mM concentration. Assume [Etotal] is the same in each experiment.

a. From a double-reciprocal plot of the data, Determine Vmax and Km.

b. Determine the type of inhibition that has occurred in 2 and 3.

NO GRAPHS FROM EXCEL PLEASE

Consider the following data for an enzyme catalyzed hydrolysis reaction in the presence and absence of inhibitor I:

[Substrate] M                                    v_o (µmol/min)                    v_oI (µmol/min)

6x10^-6 20.8 4.2

1x10^-5                                                    29                                                           5.8

2x10^-5                                                    45                                                           9

6x10^-5                                                    67.6                                                        13.6

1.8x10^-4                                                87                                                           16.2  

Use the above data, do the following:

a. Generate Lineweaver-Burk plots of the data.

b. Explain the significance of the x-interecpt, y-intercept, and the slope.

c.   Identify the type of inhibition.

You digest a plasmid with a restriction enzyme that recognizes a single site on the plasmid. When you perform gel electrophoresis on the digestion product, you quickly realize that there are two bands; one at the expected size and one near the well. Which of the following best explains the outcome?

a.DNA was trapped in the agarose gel
b.Some plasmids were not digested
c.The presence of the chromosomal DNA
d.The some plasmids ligated together

In order to learn more about the PAH enzyme, it was necessary to purify it. PAH has been isolated from both rats and humans. In the rat, three isozymes of PAH have been identified in the liver. Their molecular weights are identical, but their charges are different, as demonstrated by isoelectric focusing. The pI values are 5.2, 5.3 and 5.6. DEAE-cellulose (anion exchange) chromatography was one of the steps in the purification procedure of the enzymes. Predict the order of elution of these isozymes from the DEAE-cellulose column. What pH buffer would you choose in running the column? ?

Give an example of an enzyme

Give a type of reaction

Name a pathway for each coenzyme/cofactor

For each:

Fe2+: found in Mb/Hb

Mg2+: stabilizes negative charges on ADP/ATP

Biotin: 1-C (carboxy) carrier

NAD+/NADH & FAD(H2): electron carriers (how many electrons?)

TPP: 2-C (acetaldehyde) carrier

Lipoate: acyl/acetyl group and electron carrier

Coenzyme A: acyl/acetyl carrier with thiol group

Please explain if you can:

In which of the following is the enzyme properly paired with its allosteric inhibitor?

Multiple answers: You can select more than one option

A- hexokinase: glucose-6-phosphate

B- phosphofructokinase: fructose 2 6-bisphosphate

C- pyruvate kinase: alanine

D- glucokinase: glucose-6-phosphate

(I know it is not B, and I know it is definetly A so far. However, I am unsure about the other two. Please provide an explanation if possible.)

Describe the range of techniques that can be used to monitor human gene expression. Compare high-resolution techniques, used to analyze individual genes and high-throughput techniques that analyze all human genes. (MIn 2 and a half pages)