Nucleic Acids- 3 Flashcards
DNA and RNA secondary structures
DNA sequences can contain palindromes or repeats
Palindromes: words or phrases that are the same when read backward or forward
Secondary structure: primary, secondary sequence
DNA and RNA denaturation
Covalent bonds remain intact
-genetic code remains intact (DNA is particular in very stable)
Hydrogen bonds between strands are broken (heating up the strands can break the hydrogen bonds thus separating the strands; this is called denaturation)
-two strands separate
Since the strands separate, the stacking of the bases is unravelled- Base stacking is lost
-UV absorbance increases
Denaturation can be induced by high temperature, or change in pH
Denaturation may be reversible: annealing
Annealing is the process in which as you cool down the separated strands, the strands automatically come together in a specific manner and wind up.
As you heat up a DNA molecule, the strands separate or a bulge forms.
For annealing, as you start to cool it back down to its original temperature, the bases start pairing up with its complementary bases and start to wind up, forming the double helix.
The denaturation and annealing of DNA and RNA strands in useful in many experiments- e.g PCR.
Damage to nucleic acids
UV light induces dimerization of pyrimidines (especially thymine); this may be the main mechanism for skin cancers.
There are enzymes that recognise these pyrimidine dimers in the DNA and come and cut it and then replace it with correct pyrimidines.
Ionizing radiation (X-rays and gamma-rays) causes ring opening and strand breaking.
X-rays and gamma rays which are extremely high energy particles can cause damage to proteins, DNA, RNA, lipids, carbohydrates
In particular, they can break the sugars in RNA and DNA causing the ring to open and the DNA/RNA to fall apart.
These are difficult to fix.
Cells can repair some of these modifications, but others cause mutations. Accumulation of mutations is linked to ageing and carcinogenesis.
What is a polynucleotide
Many nucleotides linked together forming a 3D structure
How many forms of DNA are present and which ones are common
The one that we are the most familiar with is B-form DNA but A and Z forms exist too. Z-DNA only forms in special conditions of salt concentration; hardly ever seen in biological context. B-DNA is the most common among A and Z DNA.
A form just like the B form is also right handed helix and has major and minor grooves.
A form is seen more in biological context.
Z form DNA is left handed helix.
A form DNA is formed under particular condition of stress in the DNA.
In A form, the base pairs are stacked at an acute angle and are away from the axis of the helix; unlike in B-DNA, where the base pairs are flat. In the A-form, the DNA is compressed (only 28A).
The B form DNA uses the C-2’ endo sugar pucker.
Triple Helical DNA
When a third strand wraps itself around the double strand along its major groove.
Four stranded DNA (quadruplexes or tetraplexes)
E.g Guanosine tetraplex.
Four guanine bonded to each other through hydrogen bonds. When these are stacked together, it forms the G-quadruplex secondary DNA structure.
These type of structures form in the promoter Sequences of genes of eukaryotes.
Because promoters have long runs of guanine.
DNA can contain palindromes and/or mirror repeats
Palindromes: read the same forwards as backwards (e.g Bob)
Mirror repeats: even though the strands run antiparallel, they can made a single strand (from the point it mirrors with each other) and fold up on its self.
Hairpin DNA structure
A small sequence of bases is complementary to the a small sequence of bases further down the strand.
If the bases between these sequences fold inwards, a double helix can be formed since these complementary bases can form hydrogen bonds
The flexible bases that fold inwards form a curve similar to the one in a hairpin-hence this structure is called hairpin structure.
This structure is only possible in single stranded DNA or RNA molecule
Complicated forms of hairpins are called cruciforms
What are hairpin structures, palindrome + mirror, quadrulexes structures all called
Secondary structures
Where do you normally find complex secondary structures
In RNA, you can find single strand regions, bulges, internal loops and hairpins etc.
Single strands- the complementary bases are not bonded by hydrogen bonds
Bulge- where a base does not have its complementary base on the other strand; however, as it is surrounded by stable bonded complementary bases, it can remain as a bulge.
Internal loops- a set of bases which bulge out and are unpaired (are not bonded) but again due to being surrounded by stable bonded complementary bases.
And lastly, hairpins etc.
To note, DNA cannot do this.
The enzyme RNAse P
This is a protein and RNA together and this comes from E.coli
The protein recognises the RNA structure to make a machine called RNAse P.
RNA folding up to form complex 3D structures + amino tRNA (specifically phenylalanine tRNA)
tRNA has a dual role- one end contains an amino acid cargo and the other end recognises the nucleic acid in the mRNA (codon) and it decodes the mRNA to link a specific amino acid to the next amino acid. (Codon is complementary to the anticodon and the amino acid that the anticodon translates to is on the other end-so while the codons are being decoded, a peptide bond is forming between the amino acids).
There are 20 normal amino tRNAs and all of them would have a codon and anticodon look at one end. And for the phenylalanine tRNA, phenylalanine would be attached on the other end. In this type of tRNA, the structure is double helical and has bulges and hairpins.
Hammerhead ribozyme
Discovered much earlier
But is a RNA that can act as an enzyme
Self-cleaving intron (also a ribozyme)
Part of mRNA molecule
This can link back to its mRNA molecule and self-splice.
This goes to show how RNA was around at the early stages of Earth and is very crucial in how life came to be.
