I . DNA & RNA | 1. Chemical structure of nucleotides....

Question 1

3 types of nucleotides

Answer 1

nucleosidemonophosphate
nucleosidediphosphate
nucleosidetriphosphate

Question 2

What are the 2 purine bases?

Answer 2

Question 3

What are the 3 pyrimidine bases?

Answer 3

Question 4

What does Nucleoside contain?

Answer 4

nucleobase + pentose

Question 5

What does nucleotide contain?

Answer 5

nucleoside + 1 phosphate
group (at least)

Question 6

What are Nucleobases?

Answer 6

N-containing heteroaromatic compounds, substituted purine or pyrimidine rings.

Question 7

Structural features of Purines and pyrimidines

Answer 7

They are nitrogen- containing heterocycles. They contain, in addition to carbon, other (hetero) atoms, such as nitrogen. Their six-atom rings are numbered in opposite direction.
- Pyrimidines: with the clock
- Purines: against the clock

Question 8

Oxo-enol tautomerism of nucleobases
-> What are Tautomers?

Answer 8

isomers of a compound which differ only in the position of protons (H) and electrons.

Question 9

• The oxo and amino groups of purines and pyrimidines exhibit ___ (which phenomenon)

Answer 9

oxo-enol and amine-imine tautomerism

Question 10

oxo-enol and amine-imine tautomerism
-> Physiological conditions favor which forms?

Answer 10

They favor oxo + amino forms

Question 11

In RNA, the sugar moiety to which the phosphates and purine + pyrimidine bases are attached to ___

Answer 11

is ribose, rather than the 2’ deoxyribose of DNA.

Question 12

What are Bonds between the phosphate

Answer 12

ester bond, and 2 acid anhydride bonds

Question 13

Acid anhydride bonds are considered as ___

Answer 13

macroergic bonds (store high energy)

Question 14

Nucleosides are derivatives of ____

Answer 14

purines and pyrimidines

Question 15

What is Steric hindrance by the heterocycle?

Answer 15

there is no freedom of rotation about the beta-N-glycosidic bond of nucleosides/nucleotides

Question 16

2 forms of Heterocyclic N-glycosides

Answer 16

• Heterocyclic N-glycosides exist as syn- and anti-conformers

Question 17

What are Nucleic acids?

Answer 17

polynucleotides specialized for information storage and transmission. They
are composed of multiple nucleotide units connected by phosphodiester bonds.

Question 18

Similarity and Difference in primary structures of DNA and RNA

Answer 18

DNA and RNA are linear polymers composed of nucleotides which are linked by phosphodiester bonds

Question 19

Explain why we read 5’ -> 3’ direction of polynucleotide chains

Answer 19

• In a single chain of DNA, there is a hydroxyl group at 3’ end and a phosphate group at 5’ end on their terminal sugars
• The phosphodiester bonds link adjacent nucleotides
• By this convention (+ synthesis proceeds 5’ to 3’), the polynucleotide sequences are written and read in the 5’ to 3’ directionality

Question 20

What is The secondary (3D) structure of polypeptide chains?

Answer 20

Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers.

Question 21

What is The secondary (3D) structure of DNA?

Answer 21

1/ DNA is a right-handed double helix with 2 polynucleotides chained running antiparallel to each other.
2/ The two sugar phosphate backbones are on the outside of the double helix, whereas the bases project into the interior
3/ Base-bair complementary:
- A-T base pair: 2 hydrogen bonds
- G-C base pair: 3 hydrogen bonds (stronger
interaction)
=> A consequence of the size, shape, and chemical composition of the bases
4/ Hydrogen bonds -> main contributor stability of the double helix
Hydrophobic and van der Waal interactions further stabilize

Question 22

How is the phosphodiester bond formed?

Answer 22

A bond consisting of 2 phosphoester bonds, one on the 5’ side of the phosphate and another on the 3’ side

In DNA and RNA, the phosphodiester bond is the linkage between the 3’ carbon atom of one sugar molecule and the 5’ carbon atom of another, deoxyribose in DNA and ribose in RNA.

Question 23

describe the secondary structure of RNA?

Answer 23

Stem-loops, hairpins and other secondary structures can form by base pairing between distant complementary segments of an RNA molecule
- In stem-loops, the single-stranded loop between the base-paired helical stem maybe hundreds or event thousands of nucleotides long
- in hairpins, the short turn may contain as few as 4 nucleotides

Base pairing:
A - U: 2 H-bonds
G - C : 3 H-bonds