1. The carboxylic acid group of an amino acid has a pKa of approximately 2. However, carboxylic acids like benzoic acid and acetic acid have pKas in the range of 4-5 pKa units. Explain why the carboxylic acid of an amino acid is more acidic.

2. Consider the amino acid arginine: a. At physiological pH (pH = 7.4), what is the predominant form in solution? b. What percent of the carboxylic acid group is ionized at this pH? c. What percent of the amino group is ionized at this pH?

How do Hemogloblin's amino acids dictate the structure & function of the protein? (using binding/active sites, polar/non-polar residues & catalytic mechanisms)

How proteins bind ligands (specific examples/explaining of IMFs)? supply specific amino acids or prosthetic groups and demonstrating how they could interact with a ligand?

The arrangement of the peptide bonds in a polypeptide can havve a strong effect on the dipole moment in the secindary structure.

a. since the peptide bonds are the main contributors in the alpha helix, what is the direction of the dipole?

b. would Glu or Asp amino acid at the N terminus matter for the stability of an alpha helix segment? why or why not? (hint: think about electrostatic stabilization)

c. are there any amino acids that would stabilize an alpha helix if they were placed at the C terminus? what are they and why would they matter?

d. H bonds also have a dipole moment, but they have a lesser contribution to the alpha helix dipole moment than do the peptide bonds. why would that be?

e. draw the arrangement of the backbone atoms for an anti-parallel beta sheet-two strands of 4 amino acids long each and indicate the dipole moments of the peptide binds. will an anti-parallel beta sheet have a dipole moment: why or why not?

f. draw the arrangement of the backbone atoms for a parallel beta sheet-two strands of 4 amino acids long each and indicate the dipole moments of the peptide bonds. will an parallel beta sheet have a dipole moment: why or why not?

g. will H-bonds contribute to a dipole moment in an anti-parallel or parallel beta sheets? why or why not?

You wish to make a buffer with a pH of 11.

A) Which of the following amino acids would you use to make your buffer: glutamine, aspartate, histidine, or tyrosine?

B) Why would your chosen amino acid be better than the others?

C) Start with 0.02M of the base form of your amino acid and calculate the concentration of the acidic form needed to have your buffer at the desire pH of 11. Show your work.

​​​​​​​Mass spectrometry is a very accurate means of determining the mass and sequence of peptides, however some inconsistencies occur due to incomplete reactions and similar structures.

a. Name two amino acids whose mass can’t be distinguished by mass spectrometry.

b. If a bond between Ser and Val is not hydrolyzed, what amino acid could be mistakenly identified?

c. If a bond between two Gly residues is not hydrolyzed, what amino acid could be mistakenly identified?

 Describe the relationship between functional groups and macromolecules.  Compare and contrast different types of isomeric compounds.  List the different kinds of biological macromolecules.  What is the special type of reaction that they all have in common to put them together? What about to breaks them apart?  Understand the relationship between amino acid sequence and their three-dimensional structure.  Know what makes the 20 different amino acids. Know the general structure of an amino acid.

26. a. (7 pts) Match elements of a eukaryotic gene shown above, with correct statement.

1. Eukaryotic Gene ____                                A. Composed of RNA

2. Exon   ____                                                 B. Composed of DNA

3. Intron    ____                                                C. RNA Polymerase binds here for transcription initiation

4. Promoter    _____                                         D. Binding site for protein which is an activator of transcription                                                   

5. Translation initiation site   ____                    E. Three nucleotides which code for one amino acid

6. Codon ____                                                  F. Non coding region of gene; removed after transcription

7. Enhancer _____                                           G. Contains an ATG codon

                                                                          H. Segment of gene which codes for segment of encoded protein

b. (3 pts) Choose three of the above elements which are also present in a prokaryotic gene:

Element 1 ____          Element 2 ____     Element 3 ____

27. (2 pts) Place the following steps in cloning human insulin DNA into bacteria in correct order:

1. Use transformation to deliver new recombinant DNA to bacterial cells

2. Use restriction enzyme from step 3 to cut bacterial plasmid. Then add cut human insulin cDNA

3. Cut human insulin cDNA at each end with restriction enzyme

4. Convert human insulin mRNA to human insulin cDNA using the enzyme reverse transcriptase

5. Allow the enzyme DNA ligase to seal the new gene in to the vector (bacterial plasmid)

6. Allow bacterial cells to replicate and produce insulin.

a. 4, 3, 2, 5, 6, 1        b. 3, 2, 4, 5, 6, 1       c. 2, 3, 4, 5, 1, 6        d. 1, 3, 2, 4, 5, 6        e. 4, 3, 2, 5,1, 6   

28. (2 pts) Blue/White screening is used to screen bacterial colonies in gene cloning methods. Which bacterial colony is selected for expression of a gene?

a. A white colony. These bacteria do not have Ampicillin resistance.

b. A blue colony. These bacteria express the foreign gene inserted into the plasmid.

c. A white colony. These bacteria do not express the LacZ gene.

d. A blue colony. These bacteria do not express the LacZ gene.

Compare glycolysis with gluconeogenesis: location, common enzymes, explain how the same enzyme can be used in both pathways, describe which steps of the two pathways require different enzymes and explain why, describe in detail how the liver regulates the two pathways.