Nucleic Acids Flashcards
Functions of nucleotide
Energy for metabolism (ATP) Enzyme cofactors (NAD+) Signal transduction (cAMP)
Function of nucleic acids
Storage of genetic info (DNA)
Transmission of genetic info (mRNA)
Processing of genetic information (ribozymes)
Protein synthesis (tRNA and rRNA)
Difference between nucleobase, nucleotide and nucleoside
Nucleobase:
Nitrogenous base
Nucleoside:
Nitrogenous base + pentose sugar
Nucleotide:
Nitrogenous base + Pentose sugar + phosphate
What are nucleobase
Derivative of pyrimidine (single ring) or purine (double ring)
Purines and pyrimidines both contain Nitrogen and carbon- so are called containing heteroaromatic molecules
Different to benzene rings which only have carbon
Planar or almost-planar structures (these ring structures are flat when you look at them from sideways)
Molecules that are flat are very good at absorbing photons of light
Thus, bases A,C T and G absorb UV light around 250-270nm range
The functional groups attached to the nitrogen or carbon gives its specific chemical structure that determine whether if its a T, C or a U.
At the position of N-9 of a purine, is where this purine connects to a sugar.
At the position of N-1 of a pyrimidine, is where the pyrimidine connects to a sugar.
Pentose sugar in nucleotides
beta-D-ribofuranose in RNA
beta-2’-deoxy-D-ribofuranose in DNA
Different puckered conformations of the sugar ring are possible
Finding a sugar in its chain form is very rare
Because the beta-D-ribofuranose has a very important aldehyde,it cycles itself into a ring pretty quickly
To refer to the position of the carbon in the pentose sugar, we say its number along with the word ‘prime’ e.g 1’ carbon. This prevents any confusion between the numbering of carbons (and nitrogens) of the bases.
When you hear the 5’ to 3’ formation of nucleotides in DNA and RNA, it is talking about the positions of the 5’ up to 3’ carbons of the pentose sugar.
The difference between a ribose sugar and deoxyribose sugar is that there is an oxygen (OH group) on the 2’ carbon in a ribose sugar whereas in a deoxyribose sugar it isn’t.
The pentose sugar is generally quite flat but in it puckers slightly (it bends). When the carbon at 2’ bends slightly above, it is called C-2’ endo and when it bends slightly down below of the main plane, it called C-2’ exo.
Similarly, when the C-3’ is slightly above the ring, it is called C-3’ endo and when its slightly below, its C-3’ exo.
The C-2’ endo is the more common form of sugar you will find in DNA.
The puckering of the sugar is what causes DNA to have a double helical structure.
What are nucleosides
In nucleosides the pentose ring is attached to the nucleobase via an N-glycosidic bond
The bond is formed to the anomeric 1’ carbon of the sugar in a beta configuration- the bond is formed from 1’ carbon of the pentose sugar up to the N1 of the pyrimidines or N9 of the purines.
This bond that attaches the pentose sugar to the base is a single glycosidic bond.
The bond is formed between position N1 in pyrimidines and position N9 in purines
It is a single (not double) bond
What is a phosphate group
Negatively charged (electron rich) at neutral pH (at the pH which of our cells are at)
Typically attached to 5’ position
- nucleic acids are built using 5’-triphosphates (triphosphates- three phosphates linked together)
ATP, GTP, TTP, CTP
- nucleic acids contain one phosphate per nucleotide
When nucleic acids are formed, what happens is, in these 5’-triphosphate groups, two phosphate groups are lost. So, we are left with one phosphate group that forms the backbone of the nucleic acids- sugar, phosphate, sugar, phosphate and so on.
The two phosphate groups are lost as an inorganic phosphate group. The loss of these groups is what drives the formation of DNA.
The phosphate group nearest to the pentose sugar is given the label alpha. The phosphate group is beta and the next will be gamma.
UV absorption of nucleotides
Absorption of UV light at 250-270nm is due to pie -> pie* electronic transitions
Excited states of common nucleobases decay rapidly via radiationless transitions
- effective photoprotection of genetic material
- no fluorescence from nucleic acids
In the C-N bonds, the pie and sigma bonds overlap forming an hybridised orbital called the SP2 orbital. This SP2 orbital produce an amazing electronic structure to the rings. When photons of light interact with these rings, it excites the pie bonds (the pie bonds absorb the energy of the photon). This makes them go from pie to pie. Pie is an activated form of the bond. The bases absorb the energy which is why we can detect them. The way they decay (give off that energy to go back to their ground state) is via radiationless transitions (so there is no fluorescence, radiation or release of harmful gases etc). This shows that bases are very stable structure. Due to this, there is effective photoprotection of genetic material.
Why these specific bases (A, T, C and G)
Their structure or their shape allows to either form hydrogen bonds or receive hydrogen bonds.
A- can make 2 hydrogen bonds
T, C and G- can make 3 hydrogen bonds
If you rotate the N-1 of the T purine structure, T will be able to form hydrogen bonds with A.
So, C and G make 3 hydrogen bonds
And A and T make 2 hydrogen bonds because
Difference between syn-Adenosine and anti-Adenosine
When the (purine) base, Adenine, is directly above the pentose sugar, it is called syn-Adenosine. When the purine base, Adenine, is twisted so it is not directly above the sugar, it forms anti-Adenosine. The base is further away from the sugar than the syn-Adenosine structure.
The same properties apply for other bases too.
How to name a nucleotide
First look at the type of base. Does it have two rings? If so, it is a purine- either adenine or guanine.
Guanine has amine group (NH2) attached to the C-2 whereas adenine only has H attached to the C-2. Always starting counting for N-1 for purines.
For example, if it has NH2 on C-2, then we know it is guanine.
After that, we have to check if its deoxyribose or ribose. If there is an oxygen present on the C-2’, then it is ribose otherwise it is deoxyribose.
The base will always be attached by a single glycosidic bond to C-1’ of the pentose sugar. This bond will either be attached to the N-9 of its a purine otherwise it will be N-1 of the pyrimidine.
In this case, since its a guanine, it will the N-9 to C-1’.
Lets assume in this case, the sugar is deoxyribose.
Lastly, check how many phosphate groups in the sugar attached to. Is it one (monophosphate), two (diphosphate) or three (triphosphate).
Lets assume its one phosphate, so it will be monophosphate.
So, overall it will be called dGMP.
d- deoxy
G-guanine
MP- monophosphate
