Nucleic acids & DNA replication Flashcards
What are the 3 components of a nucleotide
Nitrogenous base, pentose sugar and Phosphate
What is the difference between a nucleotide and a nucleoside
Nucleoside doesn’t contain a phosphate
Which bases are purines and pyrimidines, which bond to which, how many H bonds form and what is their general structure
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
What bond is between the backbone and the base
Beta-glycosidic linkage
How do the 2 strands in DNA run
Antiparallel
What is Chargaff’s rule
the ratio of G:C and A:T is always 1:1
Which groove are the bases more accessible - give dimensions of both
Major groove (2.2nm in comparison to 1.2nm)
What the 3 forces that form and stabilise the double helix
VDW interactions between stacked bases
Hydrophobic interactions between surrounding water and -vely charged backbone
Hydrogen bonds between bases
How many nm does 1 bp correspond to
0.34 nm
Name of the bond forming the backbone
Phosphodiester linkage
How does a strand have ‘directionality’
The strands sugars are orientated in the same direction
What is the melting temperature (Tm)
Temperature at which half of the helical structure is lost
What are the 3 ways in which DNA can be denatured
Temperature
pH
Shear breakage
What is the term used for renauration and when will it occur
Annealing - when temperature is lower than Tm
Difference between denaturation and degredation
Denaturation leaves 2 separate but intact strands whereas degredation dessimates the DNA
How can you degrade a DNA
Chemical or enzyme hydrolysis
What is hyperchromicity
Increase in absorbance of a material
What type of replication is it if the process proceeds from 2 replication forks
Bidirectional
Difference in origins of replication between E and P
E have multiple whereas P only have 1
Whose experiment showed semi-conservative replication and what were the 2 other possible outcomes
Meselson and Stahl
Dispersive - Segments of parental DNA and daughter DNA are interspersed between strands
Conservative - both parental strands remain together
What happens at the origins of replication
Proteins bind to DNA causing local unwinding forming a replication bubble with 2 replication forks
2 roles of helicase
Untwist the double helix at replication forks and breaks H bonds between bps
What proteins bind to unpaired strands to stabilise them
Single strand binding proteins
Which enzyme prevents supercoiling further along the strands
Topoisomerase
DNA cannot initiate synthesis of a polynucleotide without an already existing chain that is base-paired with the template strand - What happens?
An initial RNA nucleotide chain called a primer is synthesised by primase
What 2 enzymes play a major role in synthesising the strand
DNA polymerase III
DNA polymerase I
Role of DNA polymerase III
Adds nucleotides to the RNA primer
What nucleotides are added first during replication - how are these converted into nucleotides
dNTPs - nucleoside triphosphates
Polymerase III removes 2 extra phosphates - release of pyrophosphate
To what end does DNA polymerase III add nucelotides to in the leading strand
Free 3’ end
What direction does polymerase III add nucelotides in
5’ to 3’
Role of DNA polymerase I
Removes RNA primer and replaces it with DNA nuceotides
Name given to fragments in the lagging strand - which enzyme binds these together
Okazaki fragments - DNA ligase
Why is the lagging strand discontinuous
Synthesis of the fragments occurs in the opposite direction from the movement of the replication fork
What is a telomere and its function
Overhang on 3’ end preventing loss of genetic information
