Molecular Biology Flashcards
What are the uses of molecular biology?
- Explains basis of diseases such as sickle cell anaemia and cystic fibrosis
- Useful for diagnostics and treatment of disease
- Building block of bioprocessing
How are prokaryotes distinguished from eukaryotes?
Prokaryotes do not have membrane bound organelles
Genomes are organised in different ways in each group
What is a genome?
The entire haploid set of genetic information that an organism needs to grow
What form does the majority of DNA take?
B form
Describe the B form of DNA:
Double helix- two polynucleotide chains in opposite orientations
Regular right handed double helix
Has a diameter of 2nm
What is the length between each turn in the B form of DNA
3.4nm
How many base pairs are there per turn of the helix in B form DNA?
~10.5
Why does the B form of DNA dominate?
B DNA is more flexible in its structure, the number of bases in each turn can be changed and the helix is coiled in 3D space so it can fit into smaller spaces
*bends can also occur at certain sequence features
Why does supercoiling occur in the genome of E. coli?
Extra turns are introduced into the DNA double helix or if turns are removed
What is the difference between positive and negative supercoiling?
-ve supercoiling= twist of the DNA is opposite to the right hand turn of the double helix
+ve supercoiling= twist of the DNA is in the same direction as the turn of the helix
How do we calculate torsional stress?
- Looking at the formation of super helices
- Looking at alterations of the number of base pairs per turn of the double helix
What does torsional stress measure?
Supercoiling in a molecule by giving us a linking number
What is the linking number (L)?
Total number of times the two strands of the double helix of a closed molecule cross each other when constrained to lie in a plane.
How do we calculate L?
Count the number of bases per turn (of the double helix)
What is a topoisomerase?
Enzymes that can change the linking number of DNA molecules. They alter the torsional stress on the molecule.
What is a type I topoisomerase?
An enzyme that breaks one strand of DNA and passes the other strand through the gas to then seal the break.
What is the change in L with type I topoisomerases?
±1
In E. coli, which gene encodes a type I topoisomerase?
topA
What is the role of topA in E. coli?
It relaxes negatively supercoiled DNA
What type of bond is formed when topo I nicks DNA?
A -ve DNA phosphotyrosine bond.
What is the role of type II topoisomerase?
Breaks both strands of DNA then passes another part of the helix through the gap.
What is the change in L with type II topoisomerase?
±2
How does type II topoisomerase affect torsional stress?
It removes it
How many supercoiled loops are in the single circular DNA molecule in E. coli?
40-50
How is the DNA arranged in E. coli?
Single circular loop arranged in 40-50 supercoils radiating from a central protein core
What maintains the supercoiled state of E. coli DNA?
DNA gyrase and topoisomerase I
What makes up the protein core of E. coli DNA?
DNA gyrase, topoisomerase and at least 4 proteins such as HU that are involved in packaging the DNA.
What is the role of the HU protein?
it forms tetramers around which DNA is wound
How many HU proteins are in an E. coli cell?
13,000
How many HU proteins are there in archaea?
They do not have HU proteins but instead they have proteins related to eukaryotic histones
What are some examples of bacteria that have linear genomes?
Borelia burgdorferi (Lyme disease), Streptomyces coelicolor (antibiotic producer) and Agrobacterium tumefaciens (plant tumours)
What is a multipartite genome?
Genomes divided into ≥2 molecules
Why are organisms with multipartite genomes difficult to study?
It is difficult to distinguish between the ‘essential genome’ components from plasmids.
What is a plasmid?
A (usually small) DNA molecule that usually codes for non essential genes.
What is special about obligate symbiont genomes?
They usually have very small genomes that can code for fewer genes than megaplasmids
How does horizontal gene transfer occur?
Plasmids are passed through conjugation between different bacterial cells.
Why is horizontal gene transfer important?
It leads to rapid changes in a organisms capabilities e.g antibiotic resistance.
