DNA

Question 1

Composition of nucleotides

Answer 1

• Cyclic nitrogenous bases
• Pentose sugars
• Phosphate groups

Question 2

Structural difference between Uracil and Thymine

Answer 2

CH3 on C3 of Thymine

Question 3

Structural differences between Thymine and Cytosine

Answer 3

1. Cytosine has NH2 instead of O on C4
2. 2 double bonds 1 between C4 and C5 in Cytosine
3. C5 has N instead of HN on cytosine

Question 4

Structural differences between Adenine and Guanine

Answer 4

1. Adenine has double bond between C7 and C8
2. Adenine has NH2 instead of O on C7
3. Guanine has NH2 instead of H on C = CN across from O/ NH2 group

Question 5

Structural differences between ribose and deoxy ribose sugar

Answer 5

Ribose - OH OH

Deoxyribose - OH H

Question 6

Bases are connected to sugars by

Answer 6

Beta - N glycosidic bonds

Question 7

How are successive deoxyribose resides joined?

Answer 7

By phosphate group between 3’ of one sugar and 5’ of next -> one end (left) free 5’ end and the other is 3’ end

Question 8

B-form DNA characteristics

Answer 8

• Wide + deep major groove, narrow + less deep minor groove
• bp/ turn : 10.4
• av. rise/ bp : 0.34 nm
• helical diameter: 2.4nm
• pitch: 3.5 nm

Question 9

Nucleases cleave ______ which contribute to _____ with products X and Y

Answer 9

Phosphodiester bond , 5’ and 3’C polarity
X = 5’phosphate + 3’hydroxyl group
Y = 3’ Phosphate + 5’ hydroxyl group

Question 10

Types of nucleases:

Answer 10

1. DNAses + RNAses
2. Endo + exonucleases
3. Specific for ds DNA/ ssDNA
4. Restriction endonucleases cleave both strands of dsDNA at specific sequences
   type 2 : palindromic

Question 11

Ligase

Answer 11

catalyse formation of ppd between 5’ and 3’ end

Question 12

Chargraff principle

Answer 12

purine : pyrimidine 1:1

Question 13

Packing ratio

Answer 13

Length B-form DNA / actual length

Question 14

Nucleosome characteristics

Answer 14

30nm fiber : DNA xomplexed with histones

-> 8 histones each wrapped by DNA 1.65 times

Question 15

Histone

Answer 15

Basic repeating unit of 11nm chromatic fibre

Question 16

Chromatosome

Answer 16

Nucleosome + H1

Question 17

Chromatid is produced by

Answer 17

Tight coiling of 250 nm fiber

Question 18

Core Histones are :

Answer 18

H2A, H2B, H3 and H4

Question 19

Which is the linker histone and how does it differ to the core histones?

Answer 19

H1 , Much higher Mr and higher Lys/arg percentage

Question 20

A histone octamer consists of

Answer 20

2 H2A-H2B dimers and a H3-H4 tetramer

Question 21

In a histone octamer DNA wraps around how many times?

Answer 21

Twice

Question 22

Functions of H1

Answer 22

Fastens DNA to nucleosome core

Question 23

Length and configuration of DNA in metaphase chromosome

Answer 23

1400 nm with condensed scaffold - associated chromatin at 700 nm

Question 24

Length and configuration of DNA in interphase chromosome

Answer 24

Extended scaffold associated chromosome - 300 nm whole beads on a string form chromatin -> DNA double helix -> condensed

Question 25

How does the packing ratio differ between interphase and mitotic chromosome?

Answer 25

1K to 10K

Question 26

Histone tails are generally…

Answer 26

Methylated and acetylated

Question 27

Stacking is when

Answer 27

Induced dipole interactions between bases

-> electrostatic repulsion of anionic phosphate bonds are counteracted by cations

Question 28

What does hydrophobic effect cause in conformation of DNA?

Answer 28

Purine and pyrimidine rings are burried in interior which increases stability

Question 29

Microarray overview

Answer 29

cDNA of known identified sequenced genes printed on glass -> spot with DNA fragments of interest -> appearance of single genes of interest

Question 30

FISH overview

Answer 30

1. Cells in metaphase treated to swell
2. Fixed onto slide
3. Treated so Chr DNA SS + proes hybridise with comp. sequence
4. Excess probes washed
5. Fluorescent microscope