Which single category of gene function has the most representation in both bacterial and eukaryotic genomes?

Which list of elements below is present in all biomolecules in plants?

Case Study 2: Bill (please answer question 2 and 5 only)

Bill is 52 and has been previously diagnosed with Type 2 Diabetes Mellitus. He admits that he often does not take his medications which are metformin and glyburide.

1. What types of medications are metformin and glyburide? Briefly describe their general mechanisms as well as their potential side effects/drug-nutrient interactions

Bill has come into hospital because he has been diagnosed with HHS. Hyperosmolar hyperglycemic state/ syndrome (HHS) is when a diabetes patient has an abnormally high plasma glucose level (greater than 30 mmol/L) due to inadequate amounts of insulin to maintain normoglycemia. HHS is very common amongst T2DM older adults, and symptoms tend to include dehydration due to reduced thirst recognition—this causes older adults to be slightly confused. This happens when T2DM is uncontrolled for a long time. Symptoms may include poluyuria and polydipsia. Patients must be hospitalized.

The treatment of HHS consists of correction of the dehydration with intravenous fluids, reduction of the blood sugar levels with insulin, and management of any other underlying conditions that might have precipitated the condition

In hospital insulin therapy is started for Bill.

2. Outline the basic principles for Bill’s nutrition therapy to assist in control of his DM.

Bill’s measurements and typical daily diet is recorded as follows:

Weight: 97.3 kg; Height: 175

Daily Diet:

BF: 2 crumpets, 1 tbspn each of honey and cream cheese, diet cola

MT: 1 coffee scroll, 1 coffee with milk, no sugar

Lunch: Fast-food roll from subway (full size), 9 Chips

Dinner: 1 breast grilled chicken/beef, 1 cup salad, 1 potato/rice

Supper: 4 biscuits and a hot chocolate made with full cream milk

3. Assess Bill’s weight and BMI. What would be a healthy weight range for Bill?

4. Determine Bill’s energy and protein requirements for weight maintenance. What energy and protein intakes would you recommend to assist with weight loss?

5. Prioritize two nutrition problems and discuss how you would implement solutions to these. What foods would you change? Write out some daily food choices

You are given a sample containing two proteins in phosphate-buffered saline: Protein A (pI value 8.4) and Protein B (pI value 7.0).

You wish to separate this protein mixture by ion-exchange and have available a column of CM­Sephadex. To carry out the procedure, you have prepared an appropriate MES buffer (50 mM, pH 6.0, with 20 mM NaC1). We will call this Buffer M.

(i) Suggest a preparatory procedure and materials needed to change the phosphate buffer of the protein sample with the MES buffer (Buffer M) required for ion-exchange.

(ii)Once the proteins are introduced into Buffer M, comment on the overall charge states for each of Protein A and Protein B.

(iii)The column of CM-Sephadex is equilibrated with Buffer M. What is the overall charge state of the matrix under these buffer conditions?

(iv)The protein mixture is now introduced to the column. Describe the process of adsorption that will occur. Which of the two proteins, Protein A or Protein B, will experience strongest adsorption under these conditions? Justify your answer.

(v) What should be done next to effect the best separation of Protein A and Protein B from the matrix? Give a full molecular description of events.

(vi) Consider a different separation procedure in which a different buffer choice was made to carry out the separation on CM-Sephadex. In this second scenario, Buffer T, containing 50 mM Tris buffer, pH 7.5 with 50 mM NaC1 was used for starting conditions. Outline how a separation of Protein A and Protein B can still be effected in Buffer T utilizing CM-Sephadex matrix. Explain the order of elution that would occur for each of the Protein A and Protein B species with your new procedure.

(vii) Comment on whether it would be possible to separate Protein A from Protein B again using Buffer T, but with a different column chemistry, one containing Mono-Q matrix.

6. (4pts) Indicate if you “AGREE” or DISAGREE” with the following statements. Explain your reasoning.

A) (1pt) ATP hydrolysis is necessary for actin treadmilling. (4 sentence max)

B) (1pt) Late endosomes are converted to mature lysosomes by an increase in their internal pH. (4 sentence max)

C) (1pt) Lysosomal membranes contain a proton pump that utilizes the energy of ATP hydrolysis to pump protons out of the lysosome, thereby maintaining the lumen at a low pH. (4 sentence max)

D) (1pt) If cells were treated with a weak base which neutralizes the pH of organelles, it is expected that M6P receptors would accumulate in the Golgi due to the M6P receptors inability to bind lysosomal enzymes. (4 sentence max)

Which of the following is the source of new, novel alleles in a population?

A) mutation

B) crossing over in meiosis

C) gene flow

D) mitosis

What does it mean for a population to be in Hardy-Weinberg equilibrium?

Multiple Choice

• There are no changes in gene frequencies from one generation to the next.

• Natural selection is occuring and selecting a particular phenotype in the population.

• Evolution is occurring in the population.

• Allele frequencies in the population are occurring over time.

In a sample population of people, 36% have the recessive trait of "free" earlobes (q2). What is the frequency of the dominant allele for attached earlobes, p?

Multiple Choice

• 0.40

• 0.64

• 0.10

• 0.24

Global regulators are proteins that can repress or activate the expression of large numbers of genes in an organism. A recent report describes structural studies on the anti-repressor AbbA from the bacterium Bacillus subtilis [Tucker et aL, J. Mol. Biol. (2014)]. This protein has the ability to bind to a second protein, a global repressor named AbrB.

These researchers first characterized their recombinant version of AbbA, a 65-residue protein prepared in E.coli cells.

(Qa).During the isolation and purification of AbbA, samples were monitored using a combination of SDS-PAGE gels, Bradford and BCA assays. Identify the general chemical properties utilized for protein measurements by 1. Bradford and 2. BCA assays.In each case, comment on the effectiveness of the particular assay for monitoring protein concentration.

(Qb).What specific information is obtained for a protein sample from an SDS-PAGE gel that cannot be obtained from the Bradford or BCA procedures?

2. (3pts) You are studying a single-pass transmembrane protein which is destined to the plasma membrane. The protein has a lysine amino acid which flanks the N-terminal side of the transmembrane domain and a glutamic acid amino acid which flanks the C-terminal side of the transmembrane domain. Both the N-terminus and the Cterminus of the protein carries amino acid sequences that can by glycosylated.

A) (0.5pt) When the protein reaches the plasma membrane, will the N-terminus or the C-terminus point to the extracellular side?

B) (0.5pt) When the protein reaches the plasma membrane, will the N-terminus or the C-terminus be glycosylated?

C) (0.5pt) In a mutant protein, the flanking “K” and “E” amino acids are switched with each other. After the protein is transported to the plasma membrane, will the Nterminus or the C-terminus point to the cytosolic side?

D) (0.5pt) When the protein is glycosylated in the ER, will the glycosylation occur in the lumen side or cytosolic side of the protein?

E) (1pt) How does glycosylation contribute to proper protein folding and quality control in the ER? (5 sentence max)

Copy of

Among the four available choices, which one best describes the following statement:

chemical modifications on the tails of histones determine whether chromatin is open (decondensed) or closed

When comparing replication and transcription, pick the best answer that describes this property:

in eukaryotes, the new strands are modified by addition of a string of A nucleotides