Nucleic acids & DNA replication

Question 1

What are the 3 components of a nucleotide

Answer 1

Nitrogenous base, pentose sugar and Phosphate

Question 2

What is the difference between a nucleotide and a nucleoside

Answer 2

Nucleoside doesn’t contain a phosphate

Question 3

Which bases are purines and pyrimidines, which bond to which, how many H bonds form and what is their general structure

Answer 3

Purines - A + G
Pyrimidines - C + T + U
A + T/U (2 H bonds) & C + G (3 H bonds)
Pyrimidines have 1 6 carbon ring
Purines have 1 6 carbon ring bound to 5 carbon ring

Question 4

What bond is between the backbone and the base

Answer 4

Beta-glycosidic linkage

Question 5

How do the 2 strands in DNA run

Answer 5

Antiparallel

Question 6

What is Chargaff’s rule

Answer 6

the ratio of G:C and A:T is always 1:1

Question 7

Which groove are the bases more accessible - give dimensions of both

Answer 7

Major groove (2.2nm in comparison to 1.2nm)

Question 8

What the 3 forces that form and stabilise the double helix

Answer 8

VDW interactions between stacked bases
Hydrophobic interactions between surrounding water and -vely charged backbone
Hydrogen bonds between bases

Question 9

How many nm does 1 bp correspond to

Answer 9

0.34 nm

Question 10

Name of the bond forming the backbone

Answer 10

Phosphodiester linkage

Question 11

How does a strand have ‘directionality’

Answer 11

The strands sugars are orientated in the same direction

Question 12

What is the melting temperature (Tm)

Answer 12

Temperature at which half of the helical structure is lost

Question 13

What are the 3 ways in which DNA can be denatured

Answer 13

Temperature
pH
Shear breakage

Question 14

What is the term used for renauration and when will it occur

Answer 14

Annealing - when temperature is lower than Tm

Question 15

Difference between denaturation and degredation

Answer 15

Denaturation leaves 2 separate but intact strands whereas degredation dessimates the DNA

Question 16

How can you degrade a DNA

Answer 16

Chemical or enzyme hydrolysis

Question 17

What is hyperchromicity

Answer 17

Increase in absorbance of a material

Question 18

What type of replication is it if the process proceeds from 2 replication forks

Answer 18

Bidirectional

Question 19

Difference in origins of replication between E and P

Answer 19

E have multiple whereas P only have 1

Question 20

Whose experiment showed semi-conservative replication and what were the 2 other possible outcomes

Answer 20

Meselson and Stahl
Dispersive - Segments of parental DNA and daughter DNA are interspersed between strands
Conservative - both parental strands remain together

Question 21

What happens at the origins of replication

Answer 21

Proteins bind to DNA causing local unwinding forming a replication bubble with 2 replication forks

Question 22

2 roles of helicase

Answer 22

Untwist the double helix at replication forks and breaks H bonds between bps

Question 23

What proteins bind to unpaired strands to stabilise them

Answer 23

Single strand binding proteins

Question 24

Which enzyme prevents supercoiling further along the strands

Answer 24

Topoisomerase

Question 25

DNA cannot initiate synthesis of a polynucleotide without an already existing chain that is base-paired with the template strand - What happens?

Answer 25

An initial RNA nucleotide chain called a primer is synthesised by primase

Question 26

What 2 enzymes play a major role in synthesising the strand

Answer 26

DNA polymerase III
DNA polymerase I

Question 27

Role of DNA polymerase III

Answer 27

Adds nucleotides to the RNA primer

Question 28

What nucleotides are added first during replication - how are these converted into nucleotides

Answer 28

dNTPs - nucleoside triphosphates
Polymerase III removes 2 extra phosphates - release of pyrophosphate

Question 29

To what end does DNA polymerase III add nucelotides to in the leading strand

Answer 29

Free 3’ end

Question 30

What direction does polymerase III add nucelotides in

Answer 30

5’ to 3’

Question 31

Role of DNA polymerase I

Answer 31

Removes RNA primer and replaces it with DNA nuceotides

Question 32

Name given to fragments in the lagging strand - which enzyme binds these together

Answer 32

Okazaki fragments - DNA ligase

Question 33

Why is the lagging strand discontinuous

Answer 33

Synthesis of the fragments occurs in the opposite direction from the movement of the replication fork

Question 34

What is a telomere and its function

Answer 34

Overhang on 3’ end preventing loss of genetic information