Common structural elements in proteins such as α-helices or β-sheets are characterized by uniformly repeating, energetically favorable main chain conformations which additionally exhibit a completely saturated hydrogen-bonding network of the main chain NH and CO groups. Although polyproline or polyglycine type II helices (PPII or PGII ) are frequently found in proteins, they are not considered as equivalent secondary structure elements. Which of the following statements are correct about PP and PGs.

A. PGII -like helices form hexagonal bundles which appear to fulfill the criterion of a (largely) saturated hydrogen-bonding network of the main-chain groups

B. main chain NH and CO groups of the central PGII -helix are saturated by either intra- or intermolecular hydrogen-bonds, resulting in a self-contained hydrogen-bonding network

C. The formation of the right-handed PPI helix is possible only with proline residues because of the required cis conformation. 

D. PPII helices seem to be stabilized by main chain-water hydrogen bonds (in the absence of main chain- main chain H-bonds), and tend to have a regular pattern of hydrogen bonds with water. After this, it is not surprising, that PPII helices are found mostly on the protein surface.

#Question id: 2831

#Unit 2. Cellular Organization

Specific DNA control elements in promoters can

a. interact with general transcription factors.

b. interact with repressor proteins.                 

c. interact with activator proteins.

d. remain unavailable because of condensed chromatin. 

#Question id: 2832

#Unit 2. Cellular Organization

Reporter genes are used to

a. express enzymes that are not easily assayed in cell extracts.

b. express enzymes that are easily assayed in cell extracts.

c. characterize DNA control elements.                     

d. characterize reporter plasmids.

#Question id: 2835

#Unit 2. Cellular Organization

An enhancer

a. can be located upstream of a promoter.

b. can be located downstream of a promoter.

c. can be located a variable distance from the promoter.

d. is always located within 1 kb of the promoter.

e. can be cell-type-specific.

#Question id: 2836

#Unit 2. Cellular Organization

#Question id: 2837

#Unit 2. Cellular Organization

#Question id: 2838

#Unit 2. Cellular Organization

You want to study the potential interaction between nucleosome-bound DNA and a specific histone deacetylase. You decide to perform an electrophoretic mobility shift assay (EMSA). You use a 32P end-labelled, linear template DNA that contains two nucleosome positioning sites. You assemble two nucleosomes on the DNA template before incubation with and without the histone deacetylase. For some reactions, you use unmodified nucleosomes. For other reactions, you use nucleosomes that are methylated at lysine 36 of the histone protein H3.

A. The histone deacetylase binds nucleosome bound-DNA in lanes 1, 2, 3, and 4.

B. The histone deacetylase binds nucleosome bound-DNA in lanes 3& 4.

C. The histone deacetylase seems to recognize methylated nucleosomes at lysine 36 of histone H3 in lane 1, 2 & 3 better than unmethylated nucleosomes in lane 4 &5

D. The histone deacetylase seems to recognize methylated nucleosomes at lysine 36 of histone H3 in lane 1 & 2 better than unmethylated nucleosomes in lane 3 &4