1. The Da-Da-Da-Dah sound at the beginning of the first movement is called a ______________.

2. The form of the first movement is ___________________ form.

3. The tempo marking for the first movement of Beethoven’s Symphony No 5 is _____________.

4. The main theme of the first movement is punctuated with two __________________ and then followed by a third one before moving to the bridge

5. The _________________ play the bridge theme first in the exposition.

6. The tempo marking for the second movement of the symphony is __________________.

7. The form of the second movement is called ________________________.

8. The tempo marking for the third and fourth movements of the symphony is _______________.

9. The form for the third movement is called _______________________.

10. The form of the fourth movement is called _____________________.

Quaternary Structure

Quaternary structure represents the three-dimensional (3D) structure of one functional protein.

25. The 3D quaternary structure is facilitated by interactions between which portions of the polypeptide chain? (Select one)

1. Backbone atoms

2. Side chains/R groups

26. List the different types of interactions that can occur at the level of quaternary protein structure.

1. Covalent bonds

2. Interactions between individual amino acid R units that are near to each other in the linear

3. sequence

4. interactions of individual amino acid R groups between different chains

5. Individual amino acid R units that are separated from each other by a large distance along the linear sequence of amino acids.

27. How many polypeptide chains are present in the Quaternary structure of a protein?

28. When proteins have multiple polypeptide chains, what are the individual polypeptide chains called?

29. Find an example of a functional protein that is composed of multiple polypeptide chains (other than the example given in class). Provide the name of the protein below.

30. Draw a representation of the protein named above (in question 29). Be sure to decipher the different subunits.

Amino acids are the building blocks of proteins, and can act as both a Brønsted acid and a Brønsted base through intramolecular proton transfer (see Chapter 16, pg. 709 of the textbook). The simplest amino acid known is glycine, NH2CH2CO2H (Ka = 4.5 ×10–3 and Kb = 6.0 ×10–5 ), and it can exist in three forms in equilibrium with one another:

H2N––CH2––COOH +H3N––CH2––COOH +H3N––CH2––COO– H2N––CH2––COO–

Glycine cation zwitterion anion

(a) Write the equilibria corresponding to Ka and Kb of glycine.

(b) Estimate the value of the equilibrium constant, K, for the intramolecular proton transfer to form the zwitterion in glycine: H2N––CH2––COOH (aq) K ? +H3N––CH2––COO– (aq)

(c) If the pH of an aqueous solution containing glycine is 7.2, in what form is glycine most abundant?

Researchers have described the “binary patterning” of polar and nonpolar amino acids in the sequences of proteins. In their code, polar and charged residues like D, N, E, Q, K, H, and R are represented as open circles (○) and nonpolar residues like F, L, I, M, and V as closed circles (●). Thus, a polypeptide with the sequence asp-ile-his-phe-gln would be represented as ○●○●○. Researchers analyzed the binary patterns of isolated secondary structure elements (short pieces) from native proteins. A sequence with the pattern ○●●○○●●○○●●○ forms an amphipathic alpha helix that has a nonpolar face and a polar face. A sequence with the pattern ○●○●○● forms an amphipathic beta strand. Explain these observations by discussing the structures of helices and sheets.

For each question, explain how you got the answer.

Which of the following have a net charge of +2 at pH of 1?

A. Asparagine

B.Arginine

C.Glutamine

D.Lysine

E.More than one of the above

2. A 200-amino acid polythreonine protein would have a net charge of _____ at pH 10.9

A.+200

B.-1

C.0

D.-200

E.+199

3. Which of the following amino acids has a side chain that is neutral at pH10?
A. Lysine

B. Aspartate

C. Histidine

D. Cysteine

E. None of the above

4. The net charge of the tripeptide Asn-Asn-Asn at pH=4.5 will be:

A. +2

B. +1

C. 0

D. -3

E. None of these answers are correct

a) Three nucleotides are inserted into a protein-encoding gene. The insertion occurs such that the mRNA transcript has an additional 3 bases (NOT a stop) right next to the stop codon (on the 5’ side). Which of the following will be the result?

b) Which of the following are consequences of encoding each amino acid using 3 nucleotides in the Genetic Code? (mre than one)

Your project should be on temperature adaptation or thermostability of proteins.

For a temperature adaptation project select an ectothermic organism with sub-species living in different climates. You will then focus on one protein, preferably an enzyme, for which you need to find amino acid sequences (one for each sub-species). You also need at least one crystal structure of this protein with enough sequence similarity to your selected amino acid sequences to make it feasible to create homology models. Finally, you will make comparisons between the structures or homology models while focusing on structural features that promote protein stability.

OR

For a thermostability project select a thermophilic organism (for example a bacterium thriving in a hot spring) and one protein, preferably an enzyme for which a crystal structure is already available. Next, you will need to search for crystal structures and/or amino acid sequences of your selected protein in other non-thermophilic organisms so that you can make comparisons between the crystal structures (or homology models). Aim to identify structural features that promote the thermostability of the protein from the thermophilic organism.

State the parameters of your project:

Species:

Protein(s):

PDB ID:

Confirm that you will have access to protein sequences and at least one protein structure (as a template for homology modeling) so that you can carry out your project. Post the access codes for the sequences and the PDB-ID(s) here:

Make a list of structural features that promote protein stability:

Note: Except the isocitrate dehydrogenase protein.

example like in the below articke

. For each of the restriction enzymes listed below: (i) Approximately how many restriction fragments would result from digestion of the human genome (3 x 109 bases) with the enzyme? (ii) State whether the fragments produced by digestion with each enzyme would have sticky ends with a 5’ overhang, sticky ends with a 3’ overhang, or blunt ends. (The recognition sequence for each enzyme is given in parentheses, where N means any of the four nucleotides. ^ marks the site of cleavage.)

a. EcoRV (GAT^ATC)

b. HpaII (C^CGG)

c. DrdI (GACNNNN^NNGTC)