(This is BIOchemistry)

A patient who is diabetic decides to go on the beef jerky diet. She eats almost nothing other than beef jerky and similar dried meat products. She does drink plenty of water and gets vitamin supplements. Describe how her body reacts to the diet. Be sure to list any concerns you might have about the diet and the person's health. (This problem relates to chapters 22, Biosynthesis of amino acids, nucleotides, and related molecules; and chapter 23, hormonal regulation and integration of mammalian metabolism, from the Lehninger Biochemistry textbook).

What’s wrong with this?

1. During the fasting phase, the central nervous system is using glucose and amino acids for energy.

2. The chief substrate for gluconeogenesis during the fasting state is ketones.

3. Liver glycogen is highest during the starvation state.

4. Large amounts of ketones in the blood indicates metabolism of glucose.

5. The red blood cells need to always use glucose for energy because they do not contain a nucleus.

6. Red blood cells always make ATP via aerobic metabolism

7. Insulin levels are likely to be high during the postabsorptive phase.

8. The chief substrate for gluconeogenesis during the fasting state is glycerol from fat mobilization.

9. The largest loss of urinary nitrogen is associated with the post-absorption phase.

10. NADPH + H needed for fatty acid synthesis in the starvation phase.

11. The TCA cycle can best be described as catabolic.

12. Ketones are made from glucose.

13. During the starvation phase the primary substrate for gluconeogenesis is acetyl CoA.

14. The most gluconeogenic amino acid is leucine.

1) What is the shortest possible length of an mRNA molecule that corresponds to a polypeptide 10 amino acids long? For your answer just give me the number. E.g., "12" or "120." (Ignore the 5' cap and poly-A tail.)

2) How can the deletion of one nucleotide result in a longer polypeptide being made? Write out 2 examples of mRNA sequence (before and after the mutation) and its corresponding amino acid sequence (before and after the mutation) to show how this could happen.

3)In the metabolic pathway above, paraoxon is the most toxic compound. What change would likely lead to the greatest build-up of paraoxon in the body?

Group of answer choices

a) decrease in the amount of diethylphosphate and p-nitrophenol in the body.

b) nonsense mutation near the beginning of the gene that codes for cytochrome P450.

c) silent mutation in the gene that codes for paraoxonase.  

d) severe change in the shape of the active site of paraoxonase.

1. Two reactions involving L-amino acids and the values of their respective free-energy changes are as follows:

            Glutamate + pyruvate « a-ketoglutarate + alanine

                                                DG°‘ = -2.4 kcal/mol

            Glutamate + oxaloacetate « a-ketoglutarate + aspartate

                                                DG°‘ = -11.5 kcal/mol

            a) Write the overall reaction for production of alanine and oxaloacetate from aspartate and pyruvate.

            b) Show that under standard conditions the net formation of alanine and oxaloacetate from aspartate and pyruvate is thermodynamically unfavorable.

            c) Suppose that at 25 °C, the molar concentrations of reactants and products are as follows:

            [pyruvate] = [aspartate] = 10 ^-2 M

            [alanine] = 10^-4 M

            [oxaloacetate] = 10^-5 M

Is the spontaneous synthesis of alanine and oxaloacetate possible under these conditions?

Bacteria can carry out gluconeogenesis using components of the citric acid cycle or amino acids, but unlike mammals, they can generate glucose from acetate via the glyoxylate pathway. Because bacteria have no organelles, the enzymes of the citric acid cycle and the glyoxylate pathway are not compartmentalized. (a) Why is regulation of the glyoxylate pathway necessary in bacteria? (b) Studies show that bacterial isocitrate lyase is allosterically inhibited by high concentrations of phosphoenolpyruvate. Would you expect to see the inhibition of isocitrate lyase when bacteria are utilizing glucose as a sole carbon source? Why? (c) Would you expect the glyoxylate pathway to be more active than the citric acid cycle when bacteria are growing on acetate? Why? (d) Would you expect to find glucose-6-phosphatase in bacteria?

10.During protein degradation, a polypeptide chain is broken down into individual amino acids. Which of the following is false about this process?

a.It is an exergonic reaction.

b.The products have lower disorder than the reactants.

C.The products have lower free energy than the reactants

D.It is a catabolic process.

E.It is catalyzed by enzymes.

12.You quantitatively determine that an enzyme-catalyzed reaction has a ΔG of -8 kcal/mol. If you half the amount of enzyme in the reaction, what will be the ΔG of this reaction?

A.16 kcal/mol

B. -4 kcal/mol

C. 0 kcal/mol

D. 8 kcal/mol

E. -8 kcal/mol

18. Hemoglobin is a protein responsible for transporting oxygen in the blood of vertebrates. Carbon dioxide binds to hemoglobin at a distinct site from where oxygen binds. However, CO2 binding causes a conformational change in hemoglobin that decreases the protein’s binding affinity for O2. What kind of interaction does this describe?

A. catalyzed interaction

B. covalent binding

C. competitive interaction

D. irreversible interaction

E. allosteric interaction

19. Which of the following states the relevance of the first law of thermodynamics to biology?

A. Photosynthetic organisms produce energy in sugars from sunlight.

B. The total energy taken in by an organism must be greater than the total energy stored or released by the organism.

C. Living organisms must increase the entropy of their surroundings.

D. Energy is destroyed as glucose is broken down during cellular respiration.

E. Energy can be freely transformed among different forms as long as the total energy is conserved.

22. An artificial liposome (ie, a test-tube created vesicle), whose membrane contains no proteins and whose interior is filled with water is dropped into a beaker of 0.03 M sucrose solution (Note: Sucrose is a disaccharide). Which best describes what will quickly happen?

A. Sucrose will diffuse into the liposome.

B. The liposome will shrink as water leaves this vesicle.

C. Since there are no membrane proteins, nothing will cross the membrane.

D. Water will diffuse into the liposome, causing it to burst.

E. Sucrose will diffuse out of the liposome.

Prokaryotic DNA Pol III cannot catalyze nick translation. Why? a. It lacks 3'-5' exonuclease activity b. It lacks 5'-3' exonuclease activity c. It lacks 3'-5' endonuclease activity e. It lacks 5'-3' endonuclease activity e. none of the above

Which of the following enzyme activity enables DNA Pol I to edit its mistakes? a. 3'-5' exonuclease activity b. 5'-3' exonuclease activity c. 3'-5' endonuclease activity d. 5'-3' endonuclease activity e. none of the above

How is mRNA translated? a. 5' 3' direction b. 3' 5' direction c. amino-to-carboxyl direction d. carboxyl-to-amino direction e. none of the above

Which of the following processes is not a part of gene expression? a. replication b. transcription c. processing of mRNA d. translation e. none of the above

Suppose that you are studying a positive inducible operon. TrcA is constitutively expressed and encodes an activator protein that can bind to fumarate, which acts as an inducer. The operon consists of three structural genes, TrcW, TrcX, TrcY that are transcribed upon activation of TrcA. Which of the following statements represents an observation you are likely to make in the course of your studies?

a. Expression of TrcA was turned off after addition of fumarate

b. None of the statements are likely to be observed in the study of this operon

c. Protein levels of TrcX were increased following addition of fumarate

d. Absence of fumarate resulted in activation of TrcA

e. Expression of TrcY, which processes fumarate into another form, resulted in enhanced expression of the operon

Polynucleotide phosphorylase was absolutely critical in helping scientists answer which research question?

a. Which part of a tRNA constitutes the anticodon sequence?

b. Which aminoacyl-tRNA synthetases coded for each amino acid?

c. Which amino acids are specified by codons consisting of one nucleotide?

d. Which proteins can bind to which DNA domains?Which aminoacyl-tRNA synthetases coded for each amino acid?

e. Which nucleotide sequences were critical for ribosome binding

Like all viral pathogens, severe acute respiratory syndrome coronavirus 2, or SARS-CoV 2, requires a cell surface receptor in order to invade a given host cell. For SARS-CoV 2, this receptor is actually the enzyme Angiotensin Converting Enzyme 2, or ACE2. ACE2 is responsible for downregulation of the Renin-Angiotensin-Aldosterone System by deactivation of Angiotensin II. Explain the RAAS in detail, including the roles played by kidneys and the lungs, and then explain what effects using recombinant human ACE2, or rhACE2, to treat acute respiratory distress syndrome could have on blood pressure.

The enzyme enolase catalyzes the following reaction in the glycolysis pathway (Chapter 14):

2-phosphoglycerate ® phosphoenolpyruvate + H₂O

Dehydration of 2-phosphoglycerate (2PG) results in phosphoenolpyruvate (PEP), which is a high-energy phosphate donor that can be used to phosphorylate ADP to make ATP. Thus, this is an important reaction to set up the final step of the pathway.

Balantidiasis is a disease caused by the ciliated protozoan, Balantidium coli. As it is a eukaryote, antibiotics against bacteria will not affect it. Your research group has recently found that members of the Balantidium genus possess an unusual form of enolase, which may allow you to develop an inhibitor that would affect it (and not the enolase in human cells). You have cloned the gene for the enolase from Balantidium coli, and expressed it in E. coli (which is a bacterium) and then purified the enzyme. You call this BcEno, to distinguish it from the other types of enolase. The polypeptide is predicted to be 32 kDa in size, and protein behaves as a homodimer with 2 active sites in each dimer. It requires Mg²⁺ for activity and is inhibited by EDTA, a chelator of divalent cations.

1. You perform a kinetic analysis on the enzyme by measuring the rate of catalysis in the presence of increasing amounts of 2PG. You initiate each reaction by adding 5 µL of a solution of 0.1 µg/mL enzyme to each assay tube, which already contains buffer and various amounts of 2PG in a total volume of 95 µL. After each reaction has proceeded for 30 seconds, during which time it should still be in the initial phase, you terminate it by adding 10 µL of 1 M EDTA. You then quantify the amount of PEP.

From these data, calculate k_cat and K_m of BcENO for 2PG:

k_cat =

K_m =

What is its specificity constant for 2PG?

Comment on the efficiency of this enzyme – is it “catalytically perfect”

2. The most promising molecule produced by your synthesis team is code-named BCEI-17. You repeat the assays exactly as in part (a), except that the tubes also contain BCEI-17. Here is the relevant data:

What sort of inhibitor is BCEI-17: competitive, uncompetitive, or mixed?

What is the K_I and/or K_I' of BCEI-17?