Topic 2

Question 1

Structure of Adenine

Answer 1

• C6 amino group

Question 2

Structure of Guanine

Answer 2

• C6 oxy (C=O) group
• C2 amino group

Question 3

Structure of Cytosine

Answer 3

• C4 amino group
• C2 oxy group

Question 4

Structure of Thymine

Answer 4

• C2 oxy group
• C4 oxy group
• C5 methyl group

Question 5

Between the major and minor groove, which groove is deeper?

Answer 5

Major

Question 6

Size and diameter of minor groove

Answer 6

12 Å, 1.2 nm

Question 7

Size and diameter of major groove

Answer 7

22 Å, 2.2 nm

Question 8

From where are the angles measured for the major and minor grooves?

Answer 8

The glycosidic bonds

Question 9

The DNA sequence of operator sites that are recognized by the λ repressor and Cro are…

Answer 9

Palindromes
- not perfect palindromes, but very close
- The palindrome sequences are what allows the λ repressor and Cro to bind to the operators

Question 10

How many peptide bonds can an amino acid form?

Answer 10

2 (one at the amino end, one at the carboxyl end)

Question 11

In a polypeptide chain, where is the peptide backbone found?

Answer 11

On the inside (in contrast to DNA, where the sugar-phosphate backbone is on the outside)
- R groups protrude outward (in contrast to DNA: bases point inward)

Question 12

What does the 3D folding of a polypeptide determine about a protein?

Answer 12

The function/activity of a protein

Question 13

What are the two commonly found secondary structures?

Answer 13

• alpha helix (side chains protrude out)
• beta sheet (side chains project alternatively to either side of the backbone)

Question 14

Tertiary structure of proteins is found in…

Answer 14

Physiological conditions

Question 15

Quarternary structure of proteins is…

Answer 15

Composed of multiple polypeptide chains (each peptide chain is called a subunit)

Question 16

Proteins fold into discrete modules known as…

Answer 16

Domains

Question 17

In the cI repressor, how many helices are in the N terminus? How are they linked together?

Answer 17

5 helices in the N terminus linked together by a linker sequence.

Question 18

Which alpha helix in the lambda repressor recognizes and fits into the major groove of the operator DNA?

Answer 18

3

Question 19

Function of alpha helices 2 in the N domain of the cI repressor?

Answer 19

Important for positioning helix 3

Question 20

What do helices 2 and 3 form?

Answer 20

A helix-turn-helix (HLH) motif for OR binding

Question 21

Alpha helix 1 function in N domain of the cI repressor

Answer 21

Also helps position the DNA binding domain of the repressor onto the major groove

Question 22

The side chains of the λ repressor fit into the…

Answer 22

Major groove on the operator

Question 23

The lambda repressor is symmetrical. What does this indicate regarding its DNA binding?

Answer 23

Each monomer of the dimer binds to half of the palindromic operator sequence. This means the operator sequence is symmetrical, and the repressor dimer fits perfectly onto it.

Question 24

How does the lambda repressor enhance binding to the operator?

Answer 24

Repressor arms wrap around the operator to enhance binding

Question 25

Describe the tertiary structure of Cro

Answer 25

3 alpha helices and 3 beta sheets (rather than 5 alpha helices like lambda repressor)

Question 26

True or false: Cro binds to the same OR site as the repressor but in a different major groove

Answer 26

False. - Cro binds to the same OR site as the repressor in the same major groove (which leads to competition for binding)

Question 27

In general, what is it about the λ regulatory proteins that determine the relative affinity for OR sites?

Answer 27

Their amino acid residues.

Question 28

What are the conserved amino acid residues in helix 3 of Cro and λ repressor that are involved in base contact with the operators?

Answer 28

Gln and Ser

Question 29

In the λ repressor and Cro, there are Gln and Ser residues. How does this contribute to DNA binding?

Answer 29

Gln and Ser are both polar, which helps them interact with the DNA (which is also polar)

Question 30

In the λ repressor, there is an alanine residue. How does this residue contribute to DNA binding?

Answer 30

The alanine is nonpolar, so it's probably not directly interacting with the DNA, but can create a hydrophic environment which helps DNA and protein aggregate due to the hydrophobic effect.

Question 31

In the Cro protein, there is a Lys residue. How does this residue contribute to DNA binding?

Answer 31

The Lys residue is charged, which helps the protein interact with the negatively charged DNA.

Question 32

How does the glutamine in the repressor protein specifically interact with the adenine in the operator DNA?

Answer 32

2 hydrogen bonds form between the side chain of Gln and the base of A in the major groove.

Question 33

Alanine is found in helix 2 in the λ repressor and in Cro. What purpose does this alanine serve?

Answer 33

It interacts with Val (helix 3 in repressor) and Ile (helix 3 in Cro) through the hydrophobic effect to help maintain the structure of the protein and position helix 3.

Question 34

Glutamine is found in helix 2 in the λ repressor and in Cro. How does this Gln help in protein binding to the operator?

Answer 34

Gln is polar and interacts with the DNA phosphate backbone through ion-dipole interactions.

Question 35

What two regions in the RNA polymerase binding site are recognized?

Answer 35

The -10 and -35 regions

Question 36

What specific protein (transcription factor) recognizes the -10 and -35 regions in the RNA polymerase binding site, and what is its function?

Answer 36

The sigma factor recognizes these regions and recruits RNA pol

Question 37

The -10 region in the RNA pol binding site is known as _____ in eukaryotes, and _____ in prokaryotes

Answer 37

Eukaryotes: TATA box Prokaryotes: Pribow box

Question 38

When the λ repressor binds to OR2, it enhances RNA pol binding to PRM (λ repressor expression) but represses RNA pol binding to PR (Cro expression). How does this happen?

Answer 38

PR has 3 base pairs at its -35 region and PRM has 2 base pairs at its -35 region that overlap with OR2. When the repressor binds to OR2, these base pairs are covered. Since 3 base pairs are covered by the repressor in PR and only 2 in PRM, PRM is still able to bind RNA pol but PR cannot.

Question 39

How do the residues in the λ repressor contribute to enhanced cI gene expression?

Answer 39

2 amino acid residues along helix 2 and 1 in the loop between helix 2 and helix 3 are responsible for interacting with RNA polymerase to positively promote transcription initiation.

Question 40

What is the angle associated with the major groove?

Answer 40

210 degrees

Question 41

What is the angle associated with the minor groove?

Answer 41

150 degrees

Question 42

How can you determine the base pairing when looking at the major groove?

Answer 42

Look at the order of nitrogens and oxygens exposed to the major groove. If blue, red, blue, it’s GC. If blue, blue, red, it’s AT. If red, blue, blue, it’s TA.