Polymers Flashcards
What was the original idea of the Central Dogma proposed by Francis Crick in 1956?
What changed this in the 1970s?
What about in modern molecular biology?
Transfer of information from DNA -> RNA -> Protein in linear fashion
Retroviruses- reverse transcribing DNA back into RNA
Can now design genes that would produce a protein- PROTEIN -> DNA
What are the 3 key points of Watson-Crick base pairing?
How is this important for DNA repair enzymes?
Why are the hydrogen bonds between the base pairs particularly weak?
What are the number of H bonds between the pairs?
- Width between base pairs are same (and consequently distance between nucleotide sugars are same)
- A & G are purines (2 rings) and C & T are pyrimidines 1 ring
- Held by hydrogen bonds
Same width means any change can be corrected- purine:purine large bulge pyrimidine:pyrimidine dip
Propeller twist (between pairs) put strain on bonds
A-T 2 G-C 3
How is the phosphodiester bond formed?
In what direction does the DNA chain extend?
Between what elements of the nucleotide does the bond form?
What is the direction of chemical (non-biological) synthesis of DNA?
Condensation reaction
5’ to 3’
Phosphate (OH) on 5’ carbon and OH on 3’ of 2nd carbon
3’ to 5’
What is the cause of the twisted helix in DNA?
Why does this occur?
What is the stacking distance/rise per base pair between base pairs?
Base-stacking
Maximise hydrophobic interactions by stacking bases on inside- so base pairs associate with each-other above & below plane held by pi-pi interactions = twisting
3.4A
What is the stacking energy of DNA?
What kind of sequence has the lowest stacking energy?
Why is this significant?
What is the slight difference in energy between AT pairs and GC?
Amount of energy required to de-stack/melt a section of DNA
Alternating pyrimidine-purine (current DNA)
Requires least amount of energy to melt- easier to break hydrogen bonds for processes
AT has 2 H bonds- so lower stacking energy than GC with 3H
What is the propeller twist?
How is this different to the normal twist?
What is the significance of the propeller twist in the DNA structure?
What are the propeller twist properties in B-DNA?
The angle between 2 bases in a pair when they twist away slightly from eachother
Between bases horizontally rather than vertically stacked
A larger propeller twist = more rigid helix (less likely melt)
Smaller propeller twists (less rigid)
What type of helix is B-DNA?
What is the base per turn?
What is the rise per 360 turn?
What is the diameter?
Why is B-DNA most significant?
Is the structure of B-DNA always the same?
Right handed, anti-parallel double helix
10
33.2A/3.32nm
20A/2nm
Key form of Biology DNA
Same in crystal solution but local sequences can alter local structures/regions- it is the most common form DNA but also most variable in structure for those reasons
What is the significance of the major groove in B-DNA?
What does this mean about the minor groove?
How can B-DNA be altered with the major/minor groove relationship?
Which side is the minor groove always on?
What kind of nucleotide sequence does B-DNA favour? How can different sections alter the DNA?
Protein can bind to specific sequences of DNA & also sometimes accommodate a 3rd helix (triplet)
Proteins can non-specifically bind (chromatin proteins) as well as water & ions
Proteins bind & form A or Z-DNA
Closest to the sugar phosphates
Mixture - some areas melt more easily & others more rigid for protein binding
What nucleotide sequences are favoured in A-DNA?
Which orientation is the helix?
Where does A-DNA typically form?
Why is A-DNA wider than B-DNA? How does this account for its rigidity?
What is the base per turn?
Dehydrated
Right-handed
Stretches of purines (2 rings)
Bases are stacked off-centre - less flexible/stable
11
What are the two most common forms for A-DNA?
Why does RNA favour this config?
What areas of the nucleotide sequence is most likely to prefer the A-DNA config?
How else can A-DNA conformation form?
What other conformation of the helix prefers A-DNA?
DNA:RNA hybrid or double stranded RNA
The ribose on the sugar (OH) can’t fit as easily in the B-DNA structure
Stretches of purines
Proteins bind to B-DNA
Triplex
In what 2 conditions is Z-DNA favoured?
How is Z-DNA different to A & B? (5 ways)
When can Z-DNA naturally be found in genomes?
High salt & alternating pyrimidines:purines (CGCG)
- Left handed
- Minor groove is larger & deeper than major
- Narrower - 12bp per turn
- Irregular zigzag
- Nucleotides upside down relative to backbone
Acts as transcriptional factor for terminal differentiation
How is the phosphodiester backbone neutralised in solution?
How is this different in cells?
What are the two features of DNA methylation?
What is the difference between thymine and uracil?
Na+
Less Na+ in cell, so neutralised by polyamines, Mg2+ and DNA-binding proteins
- Regulate gene-expression (by DNA and histone)
- Mark the parent strand in prokaryotic DNA replication
Thymine has CH3 and uracil has CH here instead
Why is RNA no longer the primary store for genes?
Why is RNA single stranded?
How does RNA splicing affect linear information?
How does RNA editing affect the central dogma?
is RNA anionic or polyanionic?
Cytosine deaminates into uracil - cannot distinguish transcribed uracil & deaminated ones
Negative charge of ribose oxygen & phosphate backbone causes repel - energetically unfavourable
Can remove exons in the process
Modifies bases in RNA sequence - lead to variants of DNA or proteins
Polyanionic - multiple -ve charges from oxygen & phosphate
How does AUG have dual sense?
What is Sec and how is it incorporated into the polypeptide chain?
What is Pyl and how is it incorporated into the polypeptide chain?
Initiates protein synthesis & insert methionine
Selenocysteine - incorporated into polypeptides co-translationally as tRNA synthesises the Sec amino acid from selenium precursor
Pyrrolysine - co-translationally incorporated with its respective tRNA or lysine modification
The idea of the negative selection principle in the universal genetic code is based off what?
What is the idea with the central codon?
In what idea can P3 be important?
The codon with the fewest mutations is the most important (2nd is most & 3rd is least)
Gives the amino acid its property e.g U in P2 gives hydrophobic amino acids
Wobble position & the determination of purine/pyrimidine
