A patient with multiple carboxylase deficiency will benefit from a dietary restriction of these amino acids except _____ ? Methionine Isoleucine Threonine Serinem

In the KEGG database, the pathway map for glycolysis/gluconeogenesis indicates that ___ unique enzyme/s can catalyze the conversion of ?-D-glucose to ?-D-glucose-6-phosphate (?-D-glucose-6P).

2

3

4

1

Enzyme A has an optimal pH of 4.5, while enzyme B has an optimal pH of 7.2. If you think about the tertiary structure of these two enzymes in their optimal pH environments, which would you say has the fewest positively charged R groups in the primary amino acid sequence? Group of answer choices: enzyme A ,both enzymes could have equal numbers of positively charged R groups, enzyme B

Upon being secreted from the pancreas, glucagon binds to the receptors on liver cells, which initiates a signaling cascade that regulates glycogen metabolism, glycolysis/gluconeogenesis, and fatty acid metabolism. Explain the following:

1. The metabolic conditions in which glucagon is released from the pancreas

2. How it affects metabolism of glycogen, glucose (glycolysis/gluconeogenesis), and fatty acids

3. Why it makes metabolic sense for glucagon to regulate these pathways in this manner in the liver cells.

1. State whether the following statements are true or false.

2. True or False?
Due to transition state stabilization, the enzyme proline racemase would be predicted to bind to an intermediate with a tetrahedral carbon at the reaction site rather than a trigonal planar carbon.

3. An enzyme is found to produce -OH as a nucleophile from water during the mechanism of the catalyzed reaction. Which would NOT be a good candidate in the enzyme for the molecule primarily responsible for the formation of this -OH?

A) a deprotonated Ser in the active site

B) Zn2+

C) a deprotonated His in the active site

D) a Val in the active site

4. What is the best description of the "oxyanion hole" generated during the mechanism of a serine protease - catalyzed reaction?

A) the oxyanion hole describes the stabilization of the tetrahedral intermediate where H-bonding lowers the energy of the negatively charged oxygen resulting from nucleophilic attack on the carbonyl carbon

B) the oxyanion hole describes the planar enzyme-substrate intermediate formed as the carbonyl double-bond is reformed.

C) the oxyanion hole is generated as a result of deprotonation of the serine by a neighboring histidine, resulting in a negatively charged oxygen nucleophile

D) the oxyanion hole describes the binding pocket for the phenylalanine amino acids that are preferred substrates for the serine proteases

5. Which statement describes a common feature of both the RNase A and Serine Protease mechanisms?

A) Water is protonated by a Histidine to generate an acidic hydronium ion.

B) A deprotonated serine acts as a nucleophile

C) a covalent enzyme-substrate intermediate is formed

D) a Histidine acts as a Bronsted base to remove a proton from an alcohol group.

8.

a. Which experimental technique separates proteins based on their relative physical sizes?

1) Ion-exchange chromatography                                                    4) None of the above

2) Affinity chromatography                                                                        5) More than one of the above        

3) Size-exclusion chromatography

b. One round of the sequencing technique called _________ reveals the identity of the amino acid located at the ____________ of a peptide or protein.

1) Trypsin treatment; N-terminus

2) Edman degradation; N-terminus

3) Edman degradation; C-terminus

4) Sanger’s reagent ; C-terminus                

5) Carboxypeptidase treatment; N-terminus                    

c. The following product was found after one round of Edman degradation.

The sequenced peptide must have which one of the following amino acids somewhere in its sequence?

1) D                                                                             4) Q

2) E                                                                             5) None of the above            

3) N

d. Determine the percentage of V_max that an enzyme-catalyzed reaction’s V would be at the following substrate concentration: [S] = ¼K_M. Round your percentage to 1 decimal place. Please do not enter the “%” sign as part of your answer.

e. Determine the percentage of V_max that an enzyme-catalyzed reaction’s V would be at the following substrate concentration: [S] = 20K_M. Round your percentage to 1 decimal place. Please do not enter the “%” sign as part of your answer.

f. You are trying to purify a mixture of proteins using size-exclusion chromatography. The mixture contains 5 proteins, whose lengths (number of amino acids in their sequence) are shown below:

            Protein 1: 88 residues                                               Protein 4: 120 residues

            Protein 2: 135 residues                                Protein 5: 166 residues

            Protein 3: 148 residues

Assume that each protein’s amino acid residues have an average molecular weight of 110. The pore size in the size-exclusion chromatography column’s beads has a molecular weight cutoff of 15,000, meaning that only proteins with a molecular weight that is less than 15,000 can enter the beads.

Given this information, which one option below lists all the proteins that will elute (exit from) the column quickly? Select the correct answer from the choices shown below, and place your answer on the online answer form.

1) Protein 1, Protein 2 4) Protein 3, Protein 5

2) Protein 3, Protein 4 5) None of the above

3) Protein 2, Protein 3, Protein 5

1. Meat, eggs, and dairy are good sources of protein. When you eat these foods, proteins are digested and absorbed. Follow a protein through the digestion process from the mouth through to the intestines. What enzymes are involved in its digestion? What is the smallest unit that proteins are broken down into? Where are these products absorbed?

2. What are a few things proteins are used for in the body once they’ve been absorbed?

3. Once in the body, amino acids are absorbed by our cells and enter the amino acid pool. From here, a cell will draw from the pool to assemble the proteins it needs at that specific time. What will happen if one or more of the essential amino acids are missing?

4. Describe (in your own words) the four structural levels of a protein.

5. What is the relationship between a protein’s structure and its function? Explain how amino acids side chains impact protein structure and function.

6. DNA guides protein assembly. When there is a mutation in our DNA, the impact on the protein can vary. Explain why some mutations can cause no change to the protein and some can completely disrupt the function of the protein.

7. Your body prefers not to use proteins for energy, but it will as a last resort. Explain how amino acids are broken down to generate ATP in this scenario.

8. What happens to the nitrogen portion of the amino acid?

9. Your doctor measures your nitrogen balance and finds it is negative. What does this mean about how your body is using protein? How can you balance out your nitrogen levels?

10. If you decided to become a vegetarian or vegan, how would you ensure you were eating adequate protein? Think about not just the amount, but also the essential amino acids.

11. The RDA for protein is listed below. Calculate your own personal protein requirements and show your work for full credit. You will need to convert your weight to kg. There are 2.2 lbs in 1 kg.

Ex: a 50 kg adult would need 50 kg*0.8 g/kg = 40 g protein per day

How many lysine residues become aldehydes in the Schiff base crosslink?

How many hydrogen atoms are on a proline nitrogen atom at pH = 7 when the proline nitrogen forms a pepetde bond with another amino acid?

What fraction of the amino acids in the collagen peptide are glycine?

1. The rate of transcription in bacteria is approximately 40-80 nt per second for an actively transcribed gene. The rate of translation in bacteria is approximately 20 amino acids per second.

1. How long will it take to transcribe and translate a protein of 550 amino acids?

2. Considering that a codon consists of three bases, the rates of transcription and translation in bacteria are fairly similar on an amino acid basis. (In other words, of the total time needed to express a gene, about half is transcription and about half is translation.) What might be a consequence if one process occurred more rapidly than the other in bacteria?
3. In eukaryotes, the rates of transcription and translation are not as similar as they appear to be in bacteria, with translation being somewhat slower. What is the reason that the rates of transcription and translation in eukaryotes might not be similar?

Answer only.

1. In the reaction of adding a phosphate group from ATP to glucose, the free energy from hydrolysis of ATP is need to drive the phosphorylation of glucose. The free energy released from the coupled reaction is -4.0 kcal/mol. Which of the following statement is not correct?

a) this reaction does not require any enzyme

b) this reaction does not occur at a detectable rate when the temperature is at -20˚

c) The equilibrium of the reaction is favored to form glucose-6-phosphate

d) At equilibrium the temperature of the reaction mixture is slightly higher than before the reaction occurs

2. Which of the following is NOT a role of the anaplerotic reaction of the intermediates of the citric acid cycle in cancer metabolism?

a) Generation of heme for the synthesis of cytochromes

b) Synthesis of amino acids for making proteins

c) Generation of citrate for fatty acid synthesis

d) Generation of glucose for glycolysis

3. After the hydrolysis of sucrose into individual monosaccharides, what is the change in sweetness?

a) Remain the same

b) Sweeter

c) Less sweet

d) As sweet as lactose

4. What is the free energy released or absorbed if the reaction has a K_eq = 1 at 25˚C

a) 32.3 kJ/mol

b) 0 J/mol

c) -1.44 kJ/mol

d) -2478 J/mol

5. Give that the gas constant is 8.315 Jmol^-1 K^-1, the equilibrium constant corresponding to a free energy of -26.5 kJ per mole at 25 ˚C is:

a) 2.369 x 10¹

b) 2.25 x 10³

c) 2.38 x 10^-5

d) 4.41 x 10⁴

6. why is B-D-glucopyranose the most abundant among all other forms such as the linear form and the furanose forms of glucose?

a) Putting 5 atoms in the furan ring is energetically favorable

b) B-configuration of the hydroxyl group of carbon atom 1 has the least steric hindrance

c) a-configuration of the hydroxyl group of carbon atom 1 has the least steric hindrance

d) Putting 6 atoms in the pyranose ring is energetically unfavorable

7. Which of the following can explain why a soup of 20 different free amino acids coming from the hydrolysis of a pure pyruvate kinase the hydrolysis of a pure pyruvate kinase solution is almost impossible to build up into a functional enzyme by linking these amino acids together by chance?

a) The enthalpy involved is too high to be gained form the environment

b) the temperature is not high enough to allow linking up

c) the decrease in entropy is too high

d) Building up of the enzyme requires a specific template to link up in a specific sequence

8. In the reaction of converting fructose -6- phosphate to fructose 1,6-bisphosphate, which of the following is NOT true?

a) the free energy change is highly negative

b) the concentration of ADP at the equilibrium of the reaction is very low

c) The extra phosphate group on fructose-6-bisphosphate comes from ATP

d) The entropy does not increase after the reaction

9. Which of the following best describes the type of reaction catalyzed by a dehydrogenase?

a) Deprotonation

b) Esterification

C) Hydrolysis

d) Oxidation-reduction

10. Which of the following is NOT a reason why carbon is the most important element in building up of biomolecules

a) Possession of various functional group

b) carbon can form bonds with hydrogen, oxygen and nitrogen atoms

c)carbon can link with other atoms with very strong triple bonds

d) carbon can form bonds with 1 to 4 atoms

11. During tumor growth, which of the following does not happen

a) Induction of hypoxia inducible factor

b) Increase in the levels of glycolytic enzymes

c) Increase in the consumption of glucose

d) Decrease in blood capillary appearing on the tumor

12. Why is the TCA cycle central pathway of metabolism of the cell?

a) It occurs in the center of the cell

b) Its intermediates are commonly used by other metabolic reaction

c) All other metabolic pathways depend upon it

d) None of the above

13. Which of the following signaling pathways does not involve a nucleotide?

a) G protein-coupled receptor

b) Second messenger generated by adenylyl cyclase

c) Receptor tyrosine kinase

d) None of the above

14. The synthesis of heme requires:

a) An amino acid and a product from the citric acid cycle

b) An amino acid and a product from the urea cycle

c) A fatty acid and a product from the urea cycle

d) None of the above

15. Which of the follow descriptions about K_d is correct for binding of O² to the T or R state of hemoglobin?

a) K_d of T state > K_d of R state

a) K_d of T state < K_d of R state

a) K_d of T state = K_d of R state

d) A and B could both be correct

16.Which of the following modifications is normally not present in proteins?

a) Polysaccharide conjugation

b) Lipid conjugation

c) Polyadenylation

d) Phosphorylation