Nucleic Acids- 2 Flashcards
What are polynucleotides
Covalent bonds formed via phosphodiester linkages
- negatively charged backbone (diester means that there is an oxygen group at either end of phosphate group. When oxygen binds, it actually has two lone pairs of electron which are unused- so these oxygen atoms are electron rich= so negatively charged backbone.
DNA backbone is fairly stable
-Ancient DNA (mammoths, dinosaurs) the study of very old molecules of DNA
-Hydrolysis accelerated by enzymes (DNAses)
DNA can only be broken by enzymes called nucleases (e,g DNAses (DNAnuclease))
RNA backbone is unstable
-in water, RNA lasts for a few years
-in cells, mRNA is degraded in a few hours
RNA is made and because it is unstable, it is broken in a few hours by enzymes
So, DNA is a storage material and RNA is a metabolic material,
Although some viruses have RNA genome.
Linear polymers
-No branching or cross-links (unlike sugars)
Directionality
-5’ end (of the pentose sugar) is different from 3’ end (of the pentose sugar)
- we reas the sequence from 5’ to 3’.
What type of bond holds the sugar-phosphate backbone together
A type of covalent bond called phosphodiester bond links the sugar to phosphate groups on either end. So, the nucleotides share electrons to form a stable bond.
This is what links the nucleotides together forming a polynucleotide.
What links a phosphate group to the pentose sugar within a nucleotide is an ester bond.
Enzymes are needed to ensure that phosphodiester bonds form between nucleotides.
Diester meaning that there is an oxygen group at either end of the phosphate group.
Hydrolysis of RNA
RNA is unstable under alkaline conditions (at around pH of 9-10)
Hydrolysis is also catalysed by enzymes (RNase); enzymes such as RNA polymerases and RNAnucleases.
RNase enzymes are abundant around us:
-S-RNase in plants prevents inbreeding
-RNase P is a ribozyme (enzyme made or RNA) that processes tRNA precursors
Dicer is an enzyme that cleaves double-stranded RNA into oglionucleotides; dicer is important in RNA processing
- protection from viral genomes
- RNA interference technology
Hydrogen-bonding interactions
Two bases can hydrogen bond to form a base pair
For monomers, large number of base pairs is possible
In polynucleotide, only a few possibilities exist
Watson-Crick base pairs predominate in double-stranded DNA
A pairs with T
C pairs with G
This specific base pairing was discovered by Owen Chargaff
Purine pairs with pyrimidine
Discovery of DNA structure
One of the most important discoveries in biology Good illustration of science in action -missteps on the path to a discovery -value of knowledge -value of collaboration -cost of sharing your date too early
Complementarity of DNA strands
Two chains differ in sequence
(Sequence is read from 5’ to 3’)
Two chains are complementary
Two chains run antiparallel
Replication of genetic code
Strand separation occurs first
Each strand serves as a template for the synthesis of a new strand
Synthesis is catalysed by enzymes known as DNA polymerases
Newly made DNA molecule has one daughter strand and one parent strand.
How is DNA made
The two phosphate groups in the ATP/TTP/CTP/GTP breaks off as an inorganic phosphate molecule leaving the phosphate group binded to 3’ carbon of a pentose sugar in one nucleotide and 5’ carbon of a pentose sugar of another nucleotide.
An ester bond is an oxygen with substituent on either side of it
Both DNA and RNA have phosphodiester bonds
What makes DNA so stable
The length from the C-1’ glycosidic bond connecting the base Adenine (to its respective pentose sugar) to the C-1’ glycosidic bond connecting the base Thymine (to its respective pentose sugar) is 11.1A. A stands for Angstrom. This unit is 1/10 of 1 nm.
The length from C-1’ glycosidic bond connecting the base Guanine (to its respective pentose sugar) to C-1’ glycosidic bond connecting the base Cytosine (to its respective sugar) is 10.8A.
These lengths most stay constant (there is very little variability in these figures). Due to this, the DNA structure stays stable.
What did Rosalind Franklin and Raymond Gosling experiment with DNA
X-ray diffraction
What are major groove and minor groove
Due to the sugar puckering, we get major groove and minor groove in a strand.
Major groove is wide and shallow while minor groove is quite narrow and deep. These groove alternate along the strand.
When we add the sugars and phosphate groups to the length of base pairs, it adds up to 20A.
A complete 360 turn of the DNA adds up to a length of 36A.
The length between each base pair is 3.4A.
DNA is immensely long but hardly has width or depth to it. Nature’s 1D molecule: B-DNA.
