DNA structure Flashcards
What is the name of the backbone?
Phosphodiester
Name the bond that forms between 2 bases
Glyosidic bond
Describe the structure of the sugar
Primary Alcohol on 5’
Secondary on 3’
What is a nucleoside?
sugar + base
Name the 4 nucleosides
Adenosine
Thymidine
Guanosine
Cytidine
Who created the double helix model?
James Watson and Crick
What did Rosalind Franklin discover?
Obtained X-ray Diffraction patterns on DNA fibres
Name Chargaff’s rules?
Number of A=T and C=G The purines (A+G) = pyrimidines (C+T)
What did Watson and Crick discover about DNA bases?
Bases are on the inside and hydrophobic CG pairings have 3 H bonds AT pairings have 2 H bonds But pairs are same size and shape Separation distance of stacked bases are optimal for Van Der Wal forces Bases and connected by H bonds
What is nucleotide?
Nucleoside and phosphate
Where are the phosphates on DNA helix?
on the outside
The DNA molecule has what charge?
Highly negative
Describe what is meant by antiparallel?
2 strands. One runs 5’ to 3’ the other 3’ to 5’
Named Sense/coding strand and template strand
Is the DNA helix left or right handed?
Right Handed
Where is the base pairs in comparison to the helix axis?
Base pairs perpendicular to helix axis, the centre of the helix runs through the axis
What is the most stable conformation of DNA ?
B-DNA
What grooves does B-DNA have ?
2 grooves of unequal size
What are the 3 forms of DNA?
B-DNA Z-DNA A-DNA
A-DNA Left or right handed? How is it formed? What is its difference between this and B-DNA? How many bases per turn
Right Handed
Formed when DNA is dehydrated
Wider, bases tilted of set from axis
11 bases per turn
Z-DNA
Left or right handed?
How is it formed?
How many bases per turn
Left handed
Formed by some GC containing sequences at high salt concentrations
12 bases pairs per turn
Describe DNA melting
The process by which double-stranded deoxyribonucleic acid unwinds and separates into single-stranded strands through the breaking of hydrogen bonding between the bases.
In the lab how do we seperate DNA strands in solution?
heating or addition of acid/alkali agents to alter the pH
Why is strand separation beneficial for DNA?
What causes it?
Allows for DNA replication or transcription
Helicases carry this out
What is the hyperchromic effect?
The hyperchromic effect is the striking increase in absorbance of DNA upon denaturation
What is the difference in the maximal absorbance of single and double stranded DNA?
Single stranded have higher absorbency than double stranded
When is the midpoint of the translation in DNA melting?
Tm(‘C) 50% double 50% single stranded
What is the relationship between absorbance and denaturing in DNA melting?
Absorbance increases as it denatures
Which melt at a higher temperature GC or AT and why?
GC melt at higher temperature due to 3 H bonds
Which melts at a higher temperature longer or shorter DNA fragments?
Longer
Which salt concentration melts at a higher temperature and why?
Higher salt concentration due to positive ions neutralising repulsive negative phosphate groups
Which melts at a higher temperature low or high ionic strength?
Low ionic strength= greater melting
