Nucleic acids Flashcards
What is the basic composition of a nucleic acid?
- 4 different nucleotides
- Sugar-phosphate (ribose or deoxyribose)
How are the nucleotides linked together?
Phosphodiester bond forming between the 5’ and 3’ hydroxyl group on adjacent nucleotides
Which nucleic acid are purines and which are pyrimidines?
purines - Adenine, Guanine
pyrimidines- Cytosine, Uracil, Thymine
How does the bond between the sugar and base differ for purines and pyrimidines?
glycosidic linkage between C1’ of sugar and:
N9 of purine
N1 of pyrimidine
What is a nucleoside?
Base + Sugar
What are the nucleoside names for A, C, G and T?
A - deoxyadenosine
C - deoxycytidine
G - deoxyguanosine
T - deoxythymidine
What are the main structural elements of DNA?
- Right-handed double helix
- 2 anti-parallel strands
- sugar-phosphate backbone
- Alternating major and minor grooves
What are the main interactions between components of DNA?
- H-bonds occurring between base pairs
- Base stacking accumulates van der Waals forces
- Core is hydrophobic
- Exterior phosphate groups interact with water
How many H-bonds are formed between:
a) A + T
b) G + C
a) 2
b) 3
What is the most common conformation of the sugar?
- One atom ‘puckered’ (out of plane)
- Called ‘endo’ as on the same side as C5’
- Most commonly C2’ and C3’
Describe the B form of DNA
- most common
- bases are perpendicular to the helical axis
- ~10 bases per turn
- C2’ endo pucker
- Uneven grooves
Describe the A form of DNA
- Less common and usually occurs when DNA is dehydrated, on double stranded RNA or DNA/RNA hybrids
- Bases tilted with respect to the helix axis
- C3’ endo pucker
Describe the Z form of DNA
- extremely uncommon, adopted by DNA with alternating G & C residues
- Left handed helix
- Phosphoryl groups of the backbone are ‘zigzagged’
- C2’ and C3’ endo puckers
- 12 bases per turn
How does DNA replication differ on the leading and lagging strand?
Leading strand - DNA polymerase, continuous replication
Lagging strand - Primase synthesises RNA to act as a ‘primer’ for DNA elongation to form Okazaki’s fragments which are later joined by the enzyme ligase
What catalyses the pairing of t-RNA with an amino acid?
aminoacyl-tRNA synthase
What are the start codons and stop codons?
start - UAA, UAG, UGA
stop - AUG
What is exogenous and endogenous DNA damage?
exogenous - external factors
endogenous - celullar processes
What can a chemical change to the DNA structure cause?
Abnormal base-pairing can propagate during cell division and cause altered function/carcinogenesis
What can physical changes to the DNA cause?
Can prevent replication/transcription leading to cell death
Define spontaneous deamination
Where cytosine undergoes spontaneous deamination to uracil which can go on to pair with adenine instead of guanine
How is spontaneous deamination repaired?
Enzyme DNA-glycosylase removes any uracil found in DNA
How does DNA alkylation occur?
- Electrophilic chemicals can alkylate DNA at various positions blocking translation/transcription
- Commonly O6 methylguanine can pair with T instead of C, inducing a mutation
What are thymine dimers and how are they caused?
- UV radiation can cause photochemical cross-linking of pyrimidine bases forming cyclobutane ring which distorts the DNA strand
How are thymine dimers repaired?
bacteria - DNA photolygase
higher organisms - excision repair
