Intro to Nucleic acids Flashcards
Classes of Nucleic Acids
90% RNA
10% DNA
RNA
- -> rRNA (ribosomal)- 80%
- -> tRNA (transfer)- 15%
- -> mRNA (messenger)- 5%
Function of DNA
DNA - repository of genetic information.
Directs its own replication.
Directs transcription of complementary molecules of mRNA.
Function of mRNA
mRNA - carriers of genetic information.
Directs translation of genetic information into proteins.
Function of tRNA
tRNA - translator of genetic information.
Delivers amino acids during protein synthesis.
Function of rRNA
rRNA - components of ribosomes.
Have structural and functional roles.
Purines vs Pyrimidines
All genetic material is made from nucleotide bases.
Purine- PURE AG
Adenosine + Guanine
Pyrimidine-
Cytosine, Thymine, Uracil (RNA base)
Bases, nucleosides, nucleotides:
Nucleosides - bases + 5-carbon sugar.
Nucleotides - phosphorylated nucleoside (5’-position of the sugar).
When you phosphorylate a nucleoside like adenosine, you get adenosine monophosphate (AMP). Phosphorylate again and you get adenosine diphosphate (ADP). Phosphorylate one more time and you get adenosine triphosphate (ATP).
General structure of nucleic acids:
Sugar phosphate backbone
Watson-Crick base pairing:
A always pairs up to T and will form two hydrogen bonds.
G always pairs up to C and will form three hydrogen bonds.
G-C rich regions are more stable than A-T.
Structure of B-DNA
The most common structure of DNA found in cells.
B-DNA is a double-stranded double alpha helix.
Two grooves - major and minor.
Width of the molecule is 2nm.
The base pairs are planar and are oriented nearly at right angle to the axis of the helix.
The distance between each plane is 0.34nm.
One complete turn is 3.4nm and contains 10 base pairs.
The orientation of the strands in the DNA molecule is anti-parallel, they run in opposite directions.
DNA Replication
- The double helix is unwound by the enzyme helicase which splits the parental strand into a leading strand and a lagging strand.
1b. The point where the parental strand is split into the two strands is called the replication fork. - DNA primase adds RNA primers which are used by the DNA polymerase as starting points for the replication.
- The leading strand is replicated in a continuous fashion. As DNA synthesis proceeds in a 5’ to 3’ direction, the DNA polymerase cannot synthesis the lagging strand in a continuous piece. It does it in fragments called Okazaki fragments.
- RNA primers are removed by exonuclease activity of the DNA polymerase and are replaced with DNA.
- DNA ligase completes synthesis of the lagging strand.
Anti-retroviral therapeutic agents
The knowledge of how DNA replicates helps with the development of anti-viral chemotherapeutic agents e.g. Retrov’r, Zidovudine
3-dideoxycytidine
Hivid, Zalcitabine
Epivar, Lamivudine
These nucleosides analogues are phosphorylated at their 5’ position as normal nucleosides to form triphosphate analogues. Reverse transcriptase enzyme then incorporates the phosphorylated analogues into the viral genome. However, when the analogues have been incorporated into the DNA, DNA synthesis is blocked and no further chain elongation occurs. This is because these analogues do not have a hydroxyl group at 3’ position, but instead N3, H and S.
Structure of RNA
Single stranded molecules.
Consist of adenine, guanine, cytosine and uracil nucleotides which join together by phosphodiester bonds.
Start 5’ end, termination 3’ end.
Although they are single-stranded molecules, they have extensive secondary structure with intramolecular double stranded regions. Most common secondary structures are the hairpin loops.
RNA polymerases:
RNA polymerases synthesis RNA molecules.
Most eukaryotic cells have three different types of RNA polymerase.
They are distinguished from each other by the class of RNA molecule they synthesis.
RNA polymerase I: rRNA
RNA polymerase II: mRNA
RNA polymerase III: tRNA
RNA polymerase II is sensitive to inhibition by alpha-amanitin.
This poison is found in a mushroom - Amanita phalloides.
As alpha-amanitin inhibits RNA polymerase II, the intoxication process is slow.
This is because it takes time before all old mRNA molecules are degraded.
The onset of symptoms is about 8-16 hours after ingestion of the mushroom.
The symptoms are stomach pain, vomiting, diarrhoea and death after 7-10 days (in 10-15% of patients).
Transcription
Initiation - interaction of RNA polymerase with specific sites on the DNA.
Promotors - characteristic sequences of DNA usually in front or upstream of the gene that is to be transcribed.
Elongation - RNA polymerase selects appropriate ribonucleotides and forms phosphodiester bridges between them.
It is a rapid process: 40 nucleotides/sec
Double stranded DNA must be unwound: topoisomerases I + II - these enzymes are associated with a transcription complex and are targets for anti-cancer chemotherapy.
Termination: the three enzymes use different mechanisms to terminate transcription.
RNA polymerase I: uses specific proteins.
RNA polymerase II: uses specific termination sequence and protein factors.
RNA polymerase III: uses specific termination sequence.
Transcription pt.2
The double stranded DNA template is separated into a coding strand and a template strand. The coding strand has the same sequence as the RNA transcript except it replaces U. The template strand is complimentary to the RNA transcript. During the process of transcription, complimentary nucleotides are added by RNA polymerase to the growing RNA molecule. The template strand is read from 3’ to 5’, while the RNA is synthesised from 5’ to 3’.
