Exam 1 ( Ppt 5)

Question 1

Differences between DNA and RNA

Answer 1

1) backbone of RNA contains ribose instead of 2’-deoxyribose

2) RNA contains Uracil in place of Thymine in the DNA

Question 2

Pairing Comparison of T:A and U:A

Answer 2

Both bind A at its 1,6 position via their 3,4 position

Question 3

RNA is usually found as a…?

Answer 3

single polynucleotide chain

RNA Chains Fold Back to Form “Looped Out” Forms (i.e bulge, internal loop, hairpin, pseudoknot)

Question 4

Some Viruses Can Control Protein Synthesis through…?

Answer 4

Pseudoknot

Question 5

RNA Can Form ___-____-____ Base Pairing

Answer 5

“Non-Watson-Crick base pairs can be found in all combinations in RNA, in which GA and GU are the most abundant in ribosomal RNA.” Prof Ye

RNA can fold up into complex tertiary structures frequently involving these unconventional base pairing

Question 6

How to identify the highly varied and complex RNA structures

Answer 6

1) Mutate and Map Method

Question 7

Mutate and Map Method

Answer 7

Each nucleotide is replaced with its complement;
Each mutant is chemically modified by SHAPE
Treated with a chemical reagent (N-methylisatoic anhydride) selectively acylates 2’-OH of nucleotoides that are unpaired;
The position of unpaired nucleotides is then determined by reverse transcriptase using a DNA primer. It will be ceased when encountering 2’-acylated nucleotide.

Question 8

Directed Evolution Selects RNAs that…?

Answer 8

Bind Small Molecules (ligands)

then gets selected for and recovered and amplified by PCR or mutagenesis

Question 9

Ribozymes

Answer 9

Ribosomal enzymes

Question 10

RNase P

Answer 10

1st ribozyme discovered

cleaves a segment of RNA from the end of a precursor tRNA and transforms it into a mature tRNA molecule.

Question 11

Why is DNA not similarly susceptible to alkaline hydrolysis?

Answer 11

??? it is often in its condensed form unless a specific region is being acted on.
Stability via nucleosome structure and histone tail associations

Question 12

Where does the protein synthesis take place?

Answer 12

Ribosome, CYTOPLASM (RER)

Question 13

Building Block of protein

Answer 13

Amino acids =>

contains Amino group, Carboxyl group, Side chain

Question 14

Importance of Amino acids

Answer 14

1) divalent cation

2) Salt bridge (Ionic lock)

Question 15

Peptide bond:

Answer 15

the covalent link between amino acid in a protein, which is formed by a condensation reaction with a water molecule elimination.

Question 16

Torsion angles

Answer 16

The Ψ (phi) torsion angle corresponds to the rotation about the Cα—C bond;

The φ (psi) torsion angle corresponds to the rotation about the N—Cα bond.

Question 17

3 Important Amino Acids

Answer 17

Glycine: R group = proton, not chiral, most
conformational freedom than any other amino
acid.
Proline: side chain has a covalent bond already, making
it the least conformational freedom
Cysteine: disulfide bond and it can dimerize

Question 18

Protein structures can be described at __ levels. What are they?

Answer 18

Primary: Peptide bond, vanderwaal forces
Secondary: H bonding, dimers, Pi stacking forces, covalent bonds?
Tertiary: 1 polypeptide chain, 3D config,
Quaternary: more than 1 polypeptide chain, 3D config

Question 19

Which one can form the bigger pleated beta-pleated sheet?

Answer 19

“The parallel arrangement is less stable because the geometry of the individual amino acid molecules forces the hydrogen bonds to occur at an angle, making them longer and thus weaker. Contrarily, in the anti-parallel arrangement the hydrogen bonds are aligned directly opposite each other, making for stronger and more stable bonds.” -https://chem.libretexts.org/

Question 20

Most common Post-Translation Modification (PTM)

Answer 20

phosphorylation

Question 21

Anfinsen Refolding Experiment

Answer 21

showed that Gene not only encode amino acid sequence but also 3D structure