DNA structure and chromosomes Flashcards
How are nucleotides linked?
3’ position – linked via
phosphodiester bond to the
5’ position of the next base
in the polymer
What is the difference between DNA and RNA?
2’ position – OH in RNA, H in DNA
Where in DNA does H-bonding occur?
Hydrogen bonding between nitrogenous bases from each strand –
specific interactions – diameter of the double helix dictates a purine
base pairs with a pyrimidine
Where in DNA does hydrophobic interactions occur?
Hydrophobic interactions between the bases in the center of the
helix – π-stacking – nonspecific
Where in DNA does hydration occur?
Hydration – water solvates the sugar-phosphate backbone – not the
hydrophobic bases
Where in DNA does electrostatic repulsion occur? How is that dealt with?
Electrostatic repulsion between phosphates – potentially
destabilizing – neutralized by Mg2+
- polycationic molecules
Which set of base pairs is weakest?
A-T is weak- 2 hbonds
G-C is stronger - 3 hbonds
What is the convention for writing DNA sequences?
It is important to denote the 5’ and 3’ ends of a sequence.
If there is no 5’ or 3’ indicated, the convention is that the
sequence is written 5’ to 3’
What is Chargaff’s Rule?
Due to specific base pairing,
the amount of A = the amount of T
and the amount of G = the amount of C
Why are mutations rare?
Mutations are rare for two reasons
– high fidelity replication of DNA (few mistakes)
• Lectures 43 & 47
– DNA repair processes detect & correct damage
• Lecture 47
What are causes of DNA damage?
Causes of DNA damage
– UV radiation (sun light, tanning beds) skin cancer
– X radiation many types of cancer
– Benzo[a]pyrene in cigaretted smoke lung cancer
– Reactive oxygen species (ROS) formed in cells
– Radon gas
– Hundreds of chemicals
What are the different types of mutations?
Types of mutations
– point mutations – single nucleotide is changed
• Single nucleotide polymorphisms (SNPs)
• Transitions – pyrimidine to pyrimidine or purine to purine
• Transversions – purine to pyrimidine or vice versa
– insertions and deletions (indel)
• removal or addition of nucleotides to the sequence
– genomic rearrangements
• Translocation – a fragment of one chromosome is incorporated into a
different location
• Inversion – a fragment of DNA is flipped, i.e. opposite orientation
• Duplication – creates duplicates of DNA fragments
What are the different structural forms of DNA? Which is most common in cells?
DNA can exist in several forms, B,
A and Z. In cells; B is most common; A is
more like DNA-RNA during transcription; Z
may form in cells, but role is not clear.
How is DNA compacted to fit into cells?
DNA is supercoiled How? – DNA is nicked – break covalent bond in one sugarphosphate backbone – twist one strand around the other before sealing the nick – DNA is now supercoiled
What types of supercoils can exist in DNA?
Most DNA is negatively supercoiled (underwound)
Can be toroidal (spiral – left – wrapped around protein)
or can be plectonemic (right – coils wrapped around
coils)
