Which of the following amino acids exists predominantly as a zwitterion? The terminal amino group, terminal carboxyl group, and side chain pKa values can be found in Table 3.1 (Any pKa table).

Read each question carefully. Write your response in the space provided for each part of each question. Answers must be written out in paragraph form. Outlines, bulleted lists, or diagrams alone are not acceptable and will not be scored.

Enolase is an enzyme that catalyzes one reaction in glycolysis in all organisms that carry out this process. The amino acid sequence of enolase is similar but not identical in the organisms. Researchers purified enolase from  Saccharomyces cerevisiae, a single-celled eukaryotic yeast that grows best at  37°C, and from  Chloroflexus  aurantiacus, a bacterium that grows best at the much higher temperature of  55°C. The researchers compared the activity of purified enolase from the two organisms by measuring the rate of the reaction in the presence of varying concentrations of substrate and a constant amount of each enzyme at both  37°C and  55°C.

(a) Depending on the organism, the optimal  pH for enolase to catalyze its reaction is between  6.5 and  8.0.  Describe how a  pH below or above this range is likely to affect enolase and its catalytic ability.

(b)  Identify the appropriate negative control the researchers most likely used when measuring the reaction rate in the presence of each organism’s enolase.

(c) The researchers predict that for any particular concentration of substrate, the  C. aurantiacus enolase-catalyzed reaction is more rapid at  55°C than at  37°C. Provide reasoning to  justify the researchers’ prediction.

Yeast cells need to convert all sugars to glucose before they can perform glycolysis. Some carbohydrates need to be prepared in longer metabolic pathways than others. Write a prediction about the efficiency of respiration for each of the three food sources given the properties listed below. (Note: an equal mass of sugar was used in each case)

Glucose, Sucrose, Maltose

1. Glucose is ready for glycolysis.
2. Maltose is a disaccharide made from two glucose monomers. The glycosidic bond between the monosaccharides must be hydrolyzed before glycolysis can begin.
3. Sucrose is a disaccharide made from one glucose and one fructose. First, the glycosidic bond between the monosaccharides must be hydrolyzed, then the fructose must be converted to glucose by another enzyme.

Methionine is one of the two amino acids that is specified only by a codon. How do prokaryotes use this single codon to specify the initiator residue of a polypeptide and the internal methionine residues in a polypeptide chain?

Which of the following amino acids has a side chain that can serve as a hydrogen bond donor (but not acceptor) in its predominant form at pH 7?

What metabolic pathways provide molecules from which plants, microbes and mammals make amino acids? List, and name a few of the most important metabolites that provide those carbon parts.

1.) TRUE/FALSE: Most naturally occurring fatty acids have an odd number of carbon atoms. The pathway for catabolism of fatty acids is referred to as the ?-oxidation pathway, because oxidation occurs at the ?-carbon (C-3). The fatty acids can be oxidized by ?-oxidation and converted into acetyl-CoA.

(a) Compare similarity and difference between fats and carbohydrates as they can both function as fuel storage

(b)Explain how glycerol hydrolyzed from triacylglycerols can be oxidized and enter glycolysis (how many steps reactions, what are those products? Etc.).

(c)For oxidation of palmitoyl-CoA, how many total acetyl-CoA, NADH, and FADH2 are produced?

) What are the functions of protein degradation? (2 pts)

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    ii) What are amino acid or other sequence aspects that appear to correlate with the half-lives of proteins? (2 pts)

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    iii) Then discuss the following:

                a. What are the steps/characteristics of lysosome centered protein degradation? Discuss any specificities and give an example of at least one protein which is cleared via the lysosomal degradation. (3 pts)

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                b. What are the steps in the proteasome centered protein degradation via ubiquitination? Include the labeling with ubiquitin and the steps in proteasome and post proteasome processing. Discuss any specificities and give an example of at least one protein which is degraded via ubiquitination and the proteasome. (4 pts)

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    iv) Protein degradation may also be a way of regulating enzyme activities. What is an example of regulation of a key enzyme of a pathway where a product or effector regulates enzyme activity by increasing or decreasing the rate of degradation of the enzyme protein? (1 pt)

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5. There are some differences in the way unsaturated fatty acids are catabolized versus standard beta oxidation. What would be the products of the complete oxidation of the cis fatty acid 15:1^D9 ? Show your work by including full reactions, names of enzymes and cofactors required for the steps necessary for the catabolism of the given fatty acid. However, if you are just repeating rounds of fatty acid oxidation, you may just state that in a manner similar to what you see in your text on page 677. Be sure to make this specific to the complete catabolism of cis 15:1^D9.

A protein chemist told a molecular geneticist that he had found a new mutant hemoglobin in which aspartate replaced lysine. The molecular geneticist expressed surprise and sent his friend scurrying back to the laboratory. (a) Why did the molecular geneticist doubt the reported amino acid substitution? (b) Which amino acid substitutions would have been more palatable to the molecular geneticist?

Answer everything but please focus on part b. I do not understand how to identify the amino acids that would’ve made for better substitutions.