Problem set-2.1 & 2.2

Question 1

Which is less stable, DNA or RNA? Briefly describe how the difference in chemistry affects stability

Answer 1

RNA is less stable than DNA because the hydroxyl group on the C2’ position of the ribose acts as a nucleophile in a displacement reaction with an adjacent phosphate group and hydrolyzes the RNA
backbone to yield a cyclic nucleotide and a shortened RNA chain. Because deoxyribose in DNA is missing this nucleophilic hydroxyl group, it is a more stable structure.

Question 2

What secondary structural motif can occur in a nucleic acid chain with a palindromic repeat?

Answer 2

hairpins and cruciforms.

Question 3

What is a hairpin structure

Answer 3

A hairpin
occurs when a self-complementary palindromic repeat base pairs with itself to form a stem with a loop at
the end

Question 4

What is a cruciform structure

Answer 4

A cruciform occurs when there are two complementary strands of a nucleic acid chain that form
hairpins opposite one another to make a cross-shaped secondary structure

Question 5

What are 3 common non-enzymatic reactions that can occur to nucleotides in a nucleic acid chain?

Answer 5

1. Deamination
   2.Depurination
2. Thymine dimers

Question 6

Deamination

Answer 6

-converts cytosine to uracil
-can occur on adenine/guanine. -Results in altered base pairing that can cause a permanent mutation if not repaired.

Question 7

Depurination

Answer 7

-loss of purine bases through hydrolysis (can also occur with pyrimidines, but much more
slowly)
– results in an abasic site in which the coding information is lost and can further destabilize the
backbone because the furanose can open up to the linear aldehyde form of the pentose sugar

Question 8

Thymine dimers

Answer 8

occur when UV light catalyzes formation of a cyclobutyl ring between adjacent
pyrimidines.

Question 9

What enzyme edits mRNA to convert adenosine bases to inosine?

Answer 9

-ADAR (Adenosine deaminase acting on RNA)
-deaminates adenosine to inosine

Question 10

List five common RNA functions that are facilitated by secondary structure

Answer 10

1. makes tRNAs for translation
2. Controls whether non-standard amino acids are incorporated into a protein (e.g. 3’ SECIS and
   selenocysteine incorporation)
   3.gene silencing via recognition and maturation of precursor miRNAs by DICER1
3. Regulation of whether an mRNA transcript is translated (i.e. riboswitches)
4. Catalytic activity (i.e. ribozymes) that can degrade or splice other RNA, or can form peptide
   bonds

Question 11

What is a riboswitch?

Answer 11

A riboswitch is a secondary structural element in mRNA (usually in the 5’ untranslated region) that binds
ligands to regulate mRNA transcription or translation.

Question 12

Aptamer domain

Answer 12

binds the ligand

Question 13

Switching Sequence

Answer 13

changes secondary structure upon ligand binding and spans
regions of both the aptamer domain and the expression platform domain,

Question 14

Expression platform

Answer 14

protein encoding domian

Question 15

What is a ribozyme? What are some common activities of ribozymes?

Answer 15

-ribonucleic acid chain that can catalyze reactions
-does cleavage and ligation
of RNA and DNA
-links amino acids during protein synthesis
-splicing and tRNA biosynthesis.

Question 16

What is the structure of the DNA binding domain of the TATA box-binding protein (TBP)?
How does
it interact with DNA?
What molecular events does TBP binding promote?

Answer 16

-10 stranded beta sheet that forms a SADDLE SHAPE
-causes a deformation of DNA across the saddle shaped surface a
-acts as a scaffold for the recruitment of transcriptional machinery to initiate
transcription of the downstream gene.

Question 17

Why do transcription factors so commonly use an alpha helix to physically interact with DNA?

Answer 17

-The width (12 angstroms) of alpha helix fits perfectly intp the groove of the major groove of DNA
-The bases on the DNA major groove can make hydrogen bonds with specific nucleotide bases

Question 18

What structural family do homeobox transcription factors belong to?
What part of the DNA is bound by homeobox transcription factors? What DNA residue motif is bound with very high affinity by homeobox transcription factors?

Answer 18

-helix-turn-helix
-The alpha 3 (recognition) helix binds to the major groove of DNA, and arginines in the amino terminus tail bind to the minor groove.
-Stabilization
occurs through several salt bridges and hydrogen bonds between the DNA backbone and HOX protein
side chains.
-The alpha 3 helix binds to the sequence 5’-ATTA-3’ with very high affinity

Question 19

Mutations in certain arginine residues of p53 promote tumor formation. What are the functions of these arginine residues in p53? Why does mutating them promote cancers?

Answer 19

-occur in arginine residues of the p53 DNA binding domain
-Depending on their location,
mutations of Arg residues can cause an overall loss of stability of loop structure in the DNA binding region
and compromised binding to the sugar-phosphate backbone or nucleotide bases, thereby disrupting p53’s
function in suppressing tumors.

Question 20

Describe the structure of zinc-finger transcription factors. Explain how tandemly-arrayed zinc finger
transcription factors interact with DNA.

Answer 20

-adjacent alpha helix and beta strand stabilized by a zinc
ions
-coordinated by two cysteine residues from the beta strand and two histidine residues
from the alpha helix.
-alpha helix binds the major groove of DNA
-interacting with three residues. Tandemly-arrayed zinc fingers wrap entirely around the DNA, with the recognition helix of each finger sitting contiguously in the major groove.

Question 21

Describe the structure of Leucine zipper (bZIP) transcription factors, how they function, and how
they contact DNA

Answer 21

-composed of two long alpha helices.
-helices interact through
a zipper region, which assumes a coiled-coil conformation primarily stabilized by hydrophobic interactions
-The ends of each helix form the DNA binding or basic region, which binds DNA.
-thetwo halves of the dimer grip the DNA like chopsticks, binding to successive major grooves
on opposite sides of the DNA helix using Lys and Arg residues to interact with the DNA backbone and conserved Asn and Arg residues to make contact with specific nucleotides.

Question 22

What are the primary domains in a helix-loop-helix transcription factor? Which helix binds DNA and how does it contact the DNA strand?

Answer 22

-helix-loop-helix (HLH) transcription factors are composed of two alpha helices
separated by a loop.
-The HLH monomers form dimers with one another, with the loops extended from each side like wings.
- When HLH transcription factors bind DNA, the H1 helices partially dissociate from one another and instead form a rigid structure that binds E-box response elements in the major groove
on opposite sides of the DNA helix.