DNA Structure Flashcards
What is DNA present as in the nucleus?
Chromatin
What are the 4 major forms of DNA?
B form, A form, Z form and C form
What is the structure of the B form of DNA?
- 10 base pairs per turn in B-form
- B-form has major and minor grooves
- DNA in most of our cells is present as B form
- Angle between the glycosidic bonds of major groove is 240 while for the minor groove it is 120
What is the structure of the A form of DNA?
- Less common than B-form
- 11 base pairs per turn for A-form
- A-form of DNA found under dehydrating conditions (when relative humidity less than 75%)
- A-form 20-25% shorter than B-form (A-form also wider than B-form)
- Major and minor grooves of A-form a lot closer in size compared with B-form
- Bases aren’t perpendicular to the helical axis like they are in the B-form
What is the structure of the Z form of DNA?
- left hand conformational
- 12 base pairs per turn
- Transient (only active for short amount of time and then disappears) in high salt conditions
- Phosphodiester backbone forms a zigzag pattern thus causing the DNA to be named the Z-form
- Contains negative supercoiling
What is the structure of the C form of DNA?
- Found at relatively low humidity (66%)
2. Found in the presence of certain ions, e.g. Li+ and mg2+
Why are major and minor grooves present on DNA?
Because the glycosidic bonds that form within a base pair aren’t directly opposite each other
What is the function of the major and minor grooves of DNA?
DNA binding Proteins can bind to bases within the major and minor grooves to alter the structure of the DNA or to regulate transcription
Do proteins bind more favourably to the major or minor groove? Why?
Proteins bind more favourably to bases within major groove as there is more space for them to bind compared to minor groove
How do proteins gain the energy to bind to DNA?
Proteins gain energy needed to bind to bases within major and minor grooves by displacing H20 molecules associated with the major and minor grooves
Basic structure of DNA
- DNA made up of repeating sugar phosphate units linked by 3’-5 phosphodiester bonds
- Sugar called deoxyribose
- Both the 3’ and the 5’ positions connected to a deoxyribose sugar
- DNA base bonded to carbon 1 of the deoxyribose sugar
Why does single stranded DNA have polarity?
DNA strands have polarity due to the presence of the negatively charged phosphate group. This means DNA is acidic in nature.
Is DNA or RNA more stable? Why is this the case?
DNA more stable than RNA due to the extra oxygen present in the deoxyribose sugar compared with the ribose sugar found in RNA
What types of bases are the 4 different DNA bases?
Cytosine = Pyrimidine base Guanine = Purine base Thymine = Pyrimidine base Adenine = Purine base
What are the complementary base pairs in DNA?
Cytosine and Guanine
Adenine and Thymine
Why do the bases pair up in the combinations that they do?
C and G pair up because they are able to form 3 hydrogen bonds
A and T pair up because they form 2 hydrogen bonds when they pair up
What form of DNA does tRNA fold into?
A form of DNA
Examples of unusual forms of DNA
Holliday junction
Tetraplex DNA
C and Z forms of DNA
When is the Holliday junction used and what is it for?
Formed during homologous recombination. Homologous recombination used to fix double strand break repair (When breakages occur on both strand son DNA).
Levels of DNA structure
Primary: Sequence of bases
Secondary: Helical structure
Tertiary structure: DNA supercoiling
Quaternary structure: Interlocked chromosomes
What process allow for DNA to be packaged into the nucleus?
DNA supercoiling
What is a nucleosome?
Basic building block of chromatin that represents the first level of chromatin structure
How is a nucleosome formed?
Formed when the DNA double helix is wound around 8 histone proteins (an octamer of histones)
The octamer of histones includes 2 molecules each of 4 different types of histone protein: Histone 2A, 2B, 3 and 4.
How are chromosomes formed?
Once DNA is coiled into the nucleosome Histone 1 binds to the outside of the nucleosome and to the linker DNA.
This allows for multiple nucleosomes to stick together thus forming a 30 nm fibre called the solenoid fibre
Solenoid fibre is then subject to higher order coiling and looping to become chromatin
Chromatin then condenses and coils even more to form chromosomes
How do the histone proteins interact with DNA?
positively charged N-terminal tail interacts electrostatically with the negatively charged phosphate present with the DNA strands
What is the structure of an E.coli chromosome?
Circular and organised into 50 independently supercoiled domains
What does DNA damage cause the DNA to become?
DNA becomes mutated
Examples of DNA damage and how each type damages the DNA
Deamination - Hydrolytic reaction which causes entire amine group of a DNA base to be removed. This causes cytosine to be hydrolysed to form uracil
Oxidative stress - Occurs when there’s an imbalance between processes that produce oxygen free radicals and the production of the antioxidants that detoxify them or repair the resulting damage
Radiation – UV light can cause area of DNA with 2 adjacent thymine bases to form thymine dimers by causing formation of cyclobutyl ring between the bases
Ionising radiation, E.g. x-rays and gamma rays, can break DNA chromosomes to cause leukaemia.
Why is DNA repair is important?
- Maintains genome stability as DNA is chemically unstable
2. 50-100 different enzymes/proteins involved which means that there is a large investment for the cell
What are the different types of DNA repair?
Direct repair - E.g. DNA photoreactivation (occurs when photons cleave the c-c bond of cyclobutyl ring formed during thymine dimerisation to reproduce the thymine monomers)
Base excision repair - Endonucleases cleave the DNA backbone on 5’ side of abnormal base, remove the damaged base. Other DNA strand used as a template for replacement of damaged base. Then DNA ligase catalyses formation of phosphodiester bonds once new base inserted.
Which endonucleases are involved in base excision repair?
UvrA and UvrB recognise damage
UvrC makes incision in the DNA strand
UrvD removes abnormal base
