2: Nucleic acid fundamentals

Question 1

What is the central dogma of molecular biology?

Answer 1

DNA makes RNA makes protein

Question 2

Building blocks of DNA

Answer 2

sugar, phosphate, bases

Question 3

Characteristics of nucleobases

Answer 3

• nitrogenous heterocycle
• planar
• endocyclic nitrogens are basic and can function as hydrogen acceptors

Question 4

nuceloside vs nucleotide

Answer 4

nucleoside - two groups (sugar and base)
nucleotide - sugar, base, and phosphate

Question 5

Difference between DNA and RNA sugars

Answer 5

2’ carbon of DNA has a hydrogen attached and RNA has a hydroxyl group attached

Question 6

Phosphodiester bonds hold together…

Answer 6

nucleotides in single stranded DNA (ssDNA)

Question 7

true or false: Directionality of genetic information in DNA is carried from 5’ to 3’

Answer 7

True!

Question 8

How do base pairs bind?

Answer 8

They bind through H-bonding which forms dimers between A:T and G:C

Question 9

Cell cycle of typical mammalian cell

Answer 9

1. DNA synthesis (46 pairs of chromosomes)
2. G2 - post dna synthesis (46 pairs of chromosomes)
3. mitosis - splits into two cells (23 pairs of chromosomes)
4. pre-dna synthesis (23 pairs of chromosomes)

Question 10

What are the steps to adding nucleotides to the 3rd-H terminus of a growing strand?

Answer 10

1. based on the base pairs of the template strand, the next nucleotide is added
2. the 3’ hydroxyl group at the 3’ end of the growing strand attacks the inner most phosphate group from the incoming trinucleotide
3. A bond is formed between the O and P of the new nucleotide
4. The other two phosphates are released (pyrophosphate)

Question 11

Role of gyrase (topoisomerase II)

Answer 11

Holds the twisted section of DNA so that the stress of the twisting is relieved and it doesn’t unravel.

Question 12

Role of helicase

Answer 12

unbinds the base pairs and opens the double stranded DNA (like a zipper)

Question 13

Role of single-strand binding proteins

Answer 13

prevent the unwound DNA strand from pre-maturely twisting itself.

Question 14

Role of DNA polymerase complex (contains Pol III)

Answer 14

responsible for adding new base pairs

Question 15

Role of RNA primase complex (primosome)

Answer 15

Synthesizes primers (start template DNA) in order for polymerase to add onto the 3’ end of the primer.

Question 16

Role of ligase

Answer 16

“glue of the DNA strand”
seals any gaps in the lagging strand

Question 17

How are primers removed in lagging strand synthesis?

Answer 17

DNA polymerase I
1. primer nucleotide is cleaved and rejected
2. next DNA nucleotide is added
3. done until all RNA nucleotides are ejected
(similar concept to ripping up train tracks to lay down new ones)

Question 18

How is DNA packed in the body as chromosomes?

Answer 18

1. the dna double helix wraps around histones (that make nucleosomes) “beads on a string”
2. the “beads on a string” chromatin coils and forms a chromatin fibre of tightly packed nucleosomes
3. a chromosome is a densely packed thing of chromatin

Question 19

Why are grooves in DNA important for ligand interactions?

Answer 19

major grooves and minor grooves allow for interactions with proteins (e.g. transcription factors)

Question 20

What is a DNA motif?

Answer 20

an amino acid sequence pattern with a high affinity for binding DNA

Question 21

helix-turn-helix motif

Answer 21

two alpha-helixes held together by a strand of amino acids (AKA the turn)
- first helix stabilizes interaction with DNA
- second helix interacts with base pairs in the major groove

Question 22

Zinc finger motif

Answer 22

contain finger-like projections and bind to zinc
- Arg 46 and His 49 form sequence-specific contacts
- nonspecific contacts between PO4 groups and side chains

Question 23

3 steps of transcription

Answer 23

1. initiation - RNA polymerase recognizes the promoter then de-basepairs the DNA (unzips helix)
2. elongation - creates a copy of DNA strand (RNA)
3. termination - there is a signal that releases the RNA

Question 24

Role of mRNA

Answer 24

• single stranded with some self-interactions
• serves as a template and for protein biosynthesis

Question 25

Role of tRNA

Answer 25

• 73-93 ribonucleosides with a cloverleaf structure
• transfers the amino acids during protein synthesis

Question 26

Role of rRNA

Answer 26

• makes up ribosomes (along with protein)
• where protein synthesis actually occurs