1. Alcohol intake in excess of normal daily caloric requirements results in an increase in?

1. NADH/NAD⁺
2. Thiamin absorption
3. The ability of the liver to synthesize ATP
4. Weight
5. Gluconeogenesis

2. In aqueous solution, amphiphilic lipids such as lecithin:

1. Dissolve well due to the ability of the phosphate group to ionize.
2. Cannot interact with water because as lipids they are predominantly hydrophobic.
3. Can dissociate into a soluble hydrophobic portion and an insoluble hydrophilic portion.
4. Form sheets(micelles) composed of two layers.
5. Dissolve well due to the permanent positive charge on the choline nitrogen

3. Enzyme co-factors ALWAYS

1. Are inorganic molecules
2. Are covalently bound to enzymes
3. Form a complex with the substrate to make it more accessible to the enzyme
4. Maintain the native conformation of the enzyme
5. Provide a reactive group not found in the enzyme but necessary for its activity.

4. Proteolytic activation

1. Occurs at a modulator site that is distinct from the active site
2. Is initiated by an end product acting as a positive modulator
3. Occurs when a peptide segment is removed from a protein
4. Involves transcription of a regulatory protease
5. Produces a regulatory protein which activates the enzym

5. A nutrient known to be essential in ALL human diets is

1. Cholesterol
2. Choline
3. Palmitic acid
4. Sphingomyelin
5. Linoleic acid

Which of the following reactions are catalyzed by kinases:

The herbicide glyphosate kills plants by inhibiting an enzyme needed for synthesis of phenylalanine. Deprived of phenylalanine, the plant cannot make the proteins it needs, and it gradually weakens and dies. Although a small amount of glyphosate is deadly to a plant, its human toxicity is quite low.

(a) Suggest why this powerful herbicide has little effect on humans.

(b) Discuss the chemical properties of Glyphosate as an herbicide.

Peptides hold great potential for the cancer therapy because of their ease of rational design. During your first undergraduate research project, you conducted a screen to find peptides that inhibit proliferation of cancer cells. From a large library of 9-residue-long peptides, you got a hit!

Unfortunately, someone mislabeled the vial containing the active peptide, so now you can’t be sure of its entire sequence.

The 3rd amino acid could be any one of the 20 amino acids!!

           M I   _ S E L F I E

Luckily, you collected information about the net charge of all the peptides in your library as a function of pH

(a) Based on the information below, what is the full sequence of this peptide? (please provide a rationale for your answer)

At pH 3, net charge = +1
At pH 7, net charge = -1
At pH 12, net charge = -2

Peptide Sequence:

(b) Estimate the isoelectic point (pI) of the peptide and show how you determined this value.

Part 8

Choose all that apply. The ability to perform differential gene expression is essential to cells because; (hint: three correct choices)

What is the function of the terminator?

• A. stops metastasis of cancers

• B. stops transcription of a gene

• C. stops DNA replication

• D. stops protein synthesis

By definition, a mutation is;

• A. change in a cell cycle controlling protein

• B. replacement of a nucleotide with another

• C. a permanent change in normal DNA sequence

• D. always a harmful event in a cell

What is the function of rRNAs in protein synthesis?

• A. bring the message from the gene to make proteins

• B. makeup the structure of the ribosome

• C. choose the correct amino acid to be added to the chain

• D. bring amino acids to be added to a growing protein chain

1. Sulfide, Indole, Motility (SIM): Bacteria that have the enzyme tryptophanase, can convert the amino acid tryptophan to indole. Indole reacts with Kovac’s reagent to form a Black Color. T or F

2. GROWTH ON EMB & MAC: Which Observations are INCORRECT?

1. both EMB and MAC contain dyes that inhibits gram-positive bacteria.
2. both EMB and MAC differentiate gram negative organisms based on their ability to ferment lactose
3. both EMB and MAC indicate that the pH becomes basic (alkaline) because of fermentation
4. all the above are incorrect
5. none of the above

3. GROWTH On MSA (7.5% NaCl). Which Observations are CORRECT?
   1.    MSA is selective for Staphylococci
   2. Staphylococci species are Gram +
   3.     MSA is differential based on acid production
   4. Acid production on MSA changes the phenol red (acid indictor) to yellow
   5.    All the above

4. Blood Agar is differential with respect to Hemolysis. Which of the following is CORRECT?
   1. hemolytic enzymes are produced in produced hemolysis
   2. Beta (ß) hemolysis and results in the complete breakdown of the RBCs
   3. Alpha (a) hemolysis Partial destruction of the RBCs leads to a greenish brown color
   4. Gamma(γ)hemolysis causes no damage to the RBCs
   5. all the above are correct

5. Blood Agar Plates have the enzyme catalase. We use blood agar to determine whether an unknown bacterium is catalase positive. T or F

6. Differential and/or Selective Media include EMB, MSA, MAC, Blood Agar Plates, Simmons Citrate & SIM Tubes. Regarding what was observed on these media, which is CORRECT?
   1.     a change in color on any of those media means we are looking at the result of enzyme activity
   2.   acid production, or no -acid production indicate the presence or absence of specific enzymes
   3.     all the above are correct
   4.   none of the above are correct

7. A pH sensitive dye (in media) responds to acid production with a change in color, and
   1. MacConkey (MAC) media turns reddish
   2. Eosin Methylene Blue (EMB) agar media inoculated with Escherichia coli produces a green metallic sheen
   3. Mannitol-salt agar (MSA) turns yellow
   4. all the above
   5. none of the above

8. Page 284 of Benson’s summaries some “characteristics of common Gram-positive and Gram-negative bacterial Species.”. The Table identifies a list of Gram (-) bacteria that are all catalase +. Which of the following makes sense?
   1.    the catalase test can be used to categorize bacteria., i.e. they can be categorized as catalase (+ or -)
   2. the catalase test alone could be used to identify a specific Gram (-) bacteria on that list
   3.   all the above makes sense
   4. none of the above makes sense

1. If we inoculated MSA (which has 7.5% NaCl) with Gram negative bacteria, what would be the result? We would find that the growth of MOST Gram-negative bacteria is inhibited by the 7.5% NaCl. T or F

2. If we inoculated MAC with Staphylococcus aureus, what would be the result?

1. we would observe growth and acid production (fermentation)
2. we would observe growth, but no acid production (fermentation)
3. we would observe no growth
4. none of the above

3. If we inoculated EMB with Staphylococcus aureus, what would be the result?

1. we would observe growth and acid production (fermentation)
2. we would observe growth, but no acid production (fermentation)
3. we would observe no growth
4. none of the above

4. S. aureus is catalase positive, which means 2H₂O+ catalase -> O₂ (gas) + 2H₂     T or F

5. Selective & Differential media have specific carbohydrate substrates. Which is CORRECT?
   1. the carbohydrate substrate in MAC is mannitol
   2. the carbohydrate substrate in EMB is eosin
   3. the carbohydrate substrate in MSA is mannitol
   4.   all the above
   5. None of the above

hi, trying to understand the proccess of crebs cycle..

a. If Isocitrate dehydrogenase is inhibited by axcess of citrate, and alpha ketogluterate by axcess of Suc-CoA, what exactly happeneds with the already made citrate and Suc-CoA? do they go back to being Acetyl coA and Alphaketogluterate respectively (and also become into fatty acids, amino acids and purins)?

b. I also don't get how calcium signals for more production of Acethyl coA? who gets this signal? is that the Icam somthing...?

c. in HIF1 degradation in the proteosome, what exactly pVHL and PHD2 do? like what is done individually and what tougether?

d. does HIF1 stop crebs cycle? I only know it encourages anaerobic respiration.. so what proccess does it stop if so? is directly or indirectly?

e. is there any other important substances in the crebs cycle? i remember something said about Fumarate and Succinate is there something worth remembering?

thanks in advance, I am very very lost and my summery is just confusing me.

schematize the following passage:

Ketogenic diet is well known for rapid weight loss. The diet protocol restricts carbohydrate consumption to 30 gm per day for an 80 kg adult. In order to protect the lean body mass, the protein intake should fall between 1.2-1.7 gm per kg BW per day, less than that may cause a loss of lean muscles. The protein intake should be moderate as an excessive amount of protein is metabolized to convert into amino acids, which are required for gluconeogenesis high-fat diet results in the shift of metabolism, depleted levels of glucose and enhanced oxidation of fatty acids that form ketone bodies to provide energy. The use of electrolytes such as sodium and potassium is highly recommended for maintaining nitrogen balance with the preservation of the fuctional tissue in the body.

Samreen Aziz, and Hina Rehman. “Mechanism and Benefits of Ketogenic Diet for Weight Loss and Health.” Rewal Medical Journal, vol. 44, no. 4, 2019, pp. 880–882., http://www.rmj.org.pk/fulltext/27-1545295565.pdf?1583710925.

“Lactose repressor protein (LacI) utilizes an allosteric mechanism to regulate transcription in E. coli, and the transition between inducer- and operator-bound states has been simulated by targeted molecular dynamics (TMD). The side chains of amino acids 149 and 193 interact and were predicted by TMD simulation to play a critical role in the early stages of the LacI conformational change. D149 contacts IPTG directly, and variations at this site provide the opportunity to dissect its role in inducer binding and signal transduction. Single mutants at D149 or S193 exhibit minimal change in operator binding, and alterations in inducer binding parallel changes in operator release, indicating normal allosteric response. The observation that the double mutant D149A/S193A exhibits wild-type properties excludes the requirement for inter-residue hydrogen bond formation in the allosteric response. The double mutant D149C/S193C purified from cell extracts shows decreased sensitivity to inducer binding, while retaining wild-type binding affinities and kinetic constants for both operator and inducer. By manipulating cysteine oxidation, we show that the more reduced state of D149C/ S193C responds to inducer more similarly to wild-type protein, whereas the more oxidized state displays diminished inducer sensitivity. These features of D149C/S193C indicate that the novel disulfide bond formed in this mutant impedes the allosteric transition, consistent with the role of this

region predicted by TMD simulation. Together, these results establish the requirement for flexibility of spatial relationship between D149 and S193 rather than a specific D149-S193 interaction in the LacI allosteric response to inducer.” Biochemistry 48:4988.

(4 points) What is allosteric regulation?

(4 points) How does the lactose repressor protein (LacI) use an allosteric mechanism to regulate transcription?

(6 points) How do the side chains of amino acids 149 and 193, of the lactose repressor protein, play a role in the LacI conformational change.

(6 points) What would you predict would happen if either amino acid 149 or 193 were mutated?