F: Cell Fundamentals III: DNA Structure, DNA Synthesis And Enzymes Flashcards
What are the main structural features of the DNA helix?
- 2 anti-parallel polynucleotide chains form a RH (right-hand) helix
- Contains minor and major grooves
- Bases on inside of helix, phosphate + sugars on outside
- Nucleotides - repeating base-sugar-phosphate units linked by 3’->5’ phosphodiester bonds
- Bases adenine, guanine, cytosine, thymine
- Sugar = deoxyribose
Why are DNA strands described as anti-parallel?
- Strands run in opposite directions, hence one strand is 5’ -> 3’ and the other is 3’ to 5’
What are grooves in the DNA helix?
- Major groove = backbones far apart (big gap between the backbones)
- Minor groove = backbones close together (small gap between the backbones)
The grooves twist around molecule on opposite sides
What are the base pairs in the DNA helix and how many hydrogen bonds join each base pair?
- A + T = 2 H bonds
- G + C = 3 H bonds
What are purines and what bases are purines?
- Purines are an aromatic heterocyclic composed of carbon and nitrogen. Purines have 2 carbon-nitrogen ring bases
- Guanine + adenine are purine bases
What are pyrimidines and what bases are pyrimidines?
- Pyrimidines are a heterocyclic aromatic compound containing two nitrogen atoms at positions 1 and 3, and contain only one nitrogen-carbon ring
- Thymine, cytosine and uracil are pyrimidine bases
What are the three helical forms of DNA?
- A-DNA - RH helix
- B-DNA - RH helix
- Z- DNA - LH helix
Describe the A form of DNA and how it forms
- RH double helix
- 2 strands of DNA anti-parallel with each other, not symmetrical due to the glycosidic bonds between phosphate and sugar group
- Sugar phosphate chains on outsides, bases on inside
- Has 11 base pairs per helical turn
- Forms when relative humidity of environment is less than 75%, meaning it’s rarely present in normal physiological conditions
Describe the B form of DNA
- RH double helix
- Double strand of B-DNA run in opposite directions
- Structure is asymmetrical with major grooves and minor grooves present alternatively
- Sugar phosphate chains on outside, bases on inside
- In one turn, there are 10 base pairs
What is the difference between A-DNA and B-DNA?
- A-DNA has 11 base pairs per turn, B-DNA has 10 base pairs per turn
Describe the Z form of DNA and how it forms
- LH double helix
- Zigzag appearance of backbone allows it to be distinguished
- Has 12 base pairs per turn
- Occurs when processive enzymes such as polymerase and helicases generate underwound DNA in their wake, causing B-DNA to become Z-DNA
- Formed by 5’ GCGCGCGCGC… or 5’ GTGTGTGTGTG…
What form of DNA is tRNA?
- tRNA is an A-form helix
Describe the levels of DNA structure
- Primary - sequence of bases (DNA sequencing)
- Secondary - Helical structure (X-ray and chemistry)
- Tertiary - DNA supercoiling (Electron microscopy)
- Quaternary - Interlocked chromosomes
How do the sequences of bases in DNA carry the genetic blueprint of life?
- Sequences of bases in DNA ultimately determine the different proteins formed via protein synthesis, and henceforth, regulate protein synthesis
- Proteins are the basic unit of structure and function in organisms’ cells
What is the tetraplex structure of DNA?
What does it require?
- A four stranded DNA helix formed at telomeres
- Requires G-rich DNA sequences
What are telomeres and what do they do?
- A region of repetitive DNA sequences at the end of a chromosome
- Protect end of chromosome from degradation
- Naturally occurring
What is a Holliday junction?
- A 4-way nucleotide strand linking 2 double stranded DNA structures
- Arise naturally in living cells through DNA strand exchange between 2 homologous chromosomes
- Have important role in DNA repair
What is DNA supercoiling?
- Expression of strain on DNA strand, how twisted the double helix is. It’s a higher order DNA structure
- It’s the tertiary structure of DNA
What is Sanger sequencing?
- DNA strand copied with DNA polymerase in presence of inhibitor that arrest (halt) DNA synthesis at specifically A, C, G or T
- DNA strands separated by length on a polyacrylamide gel
- If DNA or incorporated inhibitor is radioactive or fluorescent, DNA bands can be visualised and sequence read
- 700-1000 bases per read
What is higher order structure of DNA?
- The formation of interlocked chromosomes by assemblage of nucleosomes
Describe the features of DNA in bacteria
- Most bacteria have haploid genome, and single chromosome composing of a circular, double stranded DNA molecule
- DNA supercoiled- ribbon is itself twisted in space
What enzymes causes DNA supercoiling?
DNA gyrase
What main protein is DNA complexed with in eukaryotic cells and what does this form?
- Histones (+ other proteins)
- Forms nucleoprotein complex called chromatin
What is a nucleosome?
- Basic building block of chromatin
How do nucleosomes form chromatin?
- They further coil and condense to form chromatin
How are nucleosomes identified in an electron microscope image?
- Look like beads on a string, like a pearl necklace
Outline the features of nucleosomes
- Linker DNA
- Core DNA
- Histone 1
- Histones 2A, 2B, 3, 4
Why is histone 1 important and what does it do?
- This is where linker DNA exits
- Histone 1 can regulate folding of chromatin fibres into more compacted higher-order structure
- Allows for compaction so DNA can fit into the nucleus
What is formed when chromatin undergoes higher order coiling and looping?
- Chromosomes
What are the different stages in the hierarchy of how genetic material is organised?
- 2 chromatids
- One coil
- One rosette
- One loop
- 30 nm fibre
- ‘Beads-on-a-string’ form of chromatin
- DNA
Which anticancer therapies rely on DNA damaging agents?
Radiation:
- UV light produces thymine dimers
- Ionising radiation (x-rays, gamma rays) break DNA chromosomes to cause leukaemia
In what ways can DNA be damaged to cause mutations in DNA?
- Spontaneous damage e.g. loss of bases, hydrolysis of C to U
- Chemicals and radicals generated by oxidative metabolism, causes change in base structure (but also cyclophosphamide) and can cause base insertion (interpolators such as doxorubicin widely used as anticancer drugs)
- Radiation:
- UV light produces thymine dimers (2 thymine molecules join together)
- Ionising radiation (X-rays, gamma rays) break DNA chromosomes to cause leukaemia
Why is the DNA repair system so important?
- Maintains genome stability
- Important as patients with xeroderma pigmentosum have defect in excision repair that deals with UV damage to DNA. Very prone to skin cancer
- Other cancer prone families have DNA repair defects e.g. predisposing to breast cancer and colon cancer
- DNA repair to crucial DNA structure and function