DNA structure and function Flashcards
What are nucleotides?
Monomers of nucleic acids
8 common varieties
Made from: nitrogenous base, sugar and at least one phosphate group
Either purine or pyrimidine
What are the purines and pyrimidines?
Purines - two rings (larger)
Adenine and Guanine
Pyrimidines - one ring (smaller)
Cytosine, Thymine and Uracil
All use a pentose sugar
What are some properties of the nucleotide bases?
Planar
Aromatic rings
Sp2 hybridised C
Polar functional groups around the edges of the rings
What are some properties of the nucleotide sugars?
Based on the pentose – ribose (RNA) or 2’-deoxyribose (DNA)
Not flat
Not an aromatic ring
Sp3 hybridised C
Polar functional groups around and in the ring
What are the bases, nucelosides (without PO4-) and the nucelotides of A, G, C, U and T?
Adenine - Adenosine - Adenylic acid Guanine - Guanosine - Guanylic acid Cytosine - Cytidine - Cytidylic acid Uracil - Uridine - Uridylic acid Thymine - Deoxythymidine - Deoxythymidylic acid
What is the most well known nucleotide?
ATP - adenosine triphosphate
Contains: adenine, ribose and 3 phosphate groups
Used as an energy carrier/tranfer agent
What are nucleic acids?
Polymers of nucleotides
The phosphates bridge the 3’ and 5’ positions of niehgbouring ribose units
The phosphates of these polynucleotides are acidic, so at physiological pH, nucleic acids are polyanions
Describe the bond between nucleotides?
The linkage between nucleotides are phosphodiester bonds
The phosphate is esterified to two ribose units
What is the 5’ end and the 3’ end?
5’ end - the terminal residue whose C5′ is not linked to another nucleotide
3’ end - the terminal residue whose C3′ is not linked to another nucleotide
Nucleic acids are written left to right - 5’ end to 3’ end
What is Chargaff’s rule?
Chargaff’s rule 1:1 ratio of A=T and G=C, with each having the same amount (meaning same amount of A as T)
What is the structure of DNA?
A double helix of antiparallel strands of polynucleotides - forms right handed helices
Complementary base pairs (the basis of inheritance) joined by hydrogen bonds
The bases occupy the core and the sugar-phosphate chains run along the perihpery to minmise repulsion between charged PO4- groups
The surface contains two grooves of unequal widths:
Major and minor
What can purines and pyrimidines assume?
They can assume different tautomeric forms
Tautomerisation - the ability of the nucleotide bases to form differing chemical forms with the same chemical formula = isomers
What does tautomerisation affect?
Which form is dominant affects H bond donor/acceptors
This would allow variant base pairing = mutation destroying the genetic material
However, equilibria is strongly leaning towards the keto form = not a problem
What different formations can DNA adopt?
B-DNA - Right handed helix, wide major groove, narrow minor groove and pitch 34 A
A-DNA - Right handed helix, narrow major groove, wide minor groove and pitch 34 A
Forms when dehydrating B-DNA
Z-DNA - Left handed helix, flat major groove, narrow minor groove and pitch 44 A
Hypothetical structure but should exist in vivo
B-DNA is the most common form
Describe B-DNA structural features?
Two antiparallel polynucleotide strands in a right handed manner
Planes of nucleotide bases perpendicular to the helix axis - only edges of the base pairs are exposed to solvent
Each base pair has approximately the same width = near perfect symmetry
Ideal B-DNA has 10 base pairs per turn and pitch (rise per turn) of 34 A
Why does DNA have limited flexibility?
There are 7 degrees of freedom per nucleotide:
6 torsion angles of the sugar-phosphate backbone and 1 torsion angle describing the orientation of the base around the glycosidic bond
These torsion angles have internal constrainst to restrict freedom - mainly the rotation around the glycosidic bond
=Stiff sugar-phosphate backbone
What are the sterically allowed orientations?
Purines - syn and anti conformations
Pyrimidines - anti conformation
Most double-helical nucleic acids have anti conformation bases except Z-DNA
Aside from torsion angles what limits flexibility of DNA?
The ribose ring
The ring is puckered in half chair conformation in order to avoid steric hinderences
The out-of-plane atom is almost always C2’-endo or C3’-endo
What are Nucleic acids stabilised by?
Hydrogen bonds between base pairing
Stacking interactions - above and below each ring there is a set of pi orbitals = stable due to van der Waals interaction (enthalpically driven and entropically opposed)
Ionic interactions - cations sheild negative charges of phoshate groups
Na+, K+, Mg2+, Co2+ etc… (divalent 2+ are more effective)
Describe DNA denaturation?
We can separate the two complementary strands
The DNA will have decreased viscosity and increased flexibility
UV absorbance increases due to disruption of electronic interactions between bases (hyperchromic effect)
Stability depends on the nature of the solvent
What is the renaturing of DNA?
The DNA can reanneal upon cooling in hybridisation
This can form new strands
What can DNA do?
Supercoiling:
More compact than ‘relaxed’ molecules
L - linking number: the number of times that one DNA strand winds around the other
T - Twist: the number of complete revolutions that one polynucleotide strand makes around the duplex axis
W - Writhing number: the number of turns that the duplex axis makes around the superhelix axis
L = T + W
What alters supercoiling?
Topoisomerases
Breaks the DNA if there isn’t the correct superhelical tension
Type I - single-strand breaks in DNA
Type IA - relax negatively supercoiled DNA
Typer IB - can relax both positive + negative DNA via controlled rotation
Type II - make double-strand breaks
What is RNA?
A single stranded nucleic acid
Ribose and Uracil (noT)
Base pairing can occur intramolecularly, giving rise to stem-loop structures
Some double stranded RNA is the genetic material of some viruses (similar to B-DNA structure)
How is RNA stablised and how is it conformationally flexible?
stabilized by the same forces that stabilize DNA, and its conformational flexibility is limited by many of the same features that limit DNA conformation
However, RNA is more rigid than DNA due to more H2O molecules forming H bonds
What are some different RNA’s in the cell?
Structural components of cellular machinery; ribosomal RNAs, tRNAs, spliceosomal RNAs (transcribed and post-transcriptionally modified) mRNA molecules (transcribed, post-transcriptionally modified & substrates for splicing and translation) Regulatory RNAs (transcribed & ligand binding)
Give an example of a ribozyme?
Hammerhead ribozyme
participates in the replication of certain virus-like RNAs that infect plants and also occurs in schistosomes (species of parasitic flatworms)
It catalyzes the site-specific cleavage of one of its own phosphodiester bonds
It’s not a true catalyst as it is its own substrate (can’t return to original state) - but undergoes many turnovers before being affected
Give an overview of DNA replication?
Semiconservative replication
The DNA strand acts as a template for the formation of its complementary strand
Each contains a parental strand and a daughter strand
What is the central dogma of molecular biology?
DNA is transcribed to produce RNA (complementary)
RNA is translated into amino acids to form a protein
What is genomics?
Study of the genomes size, organisation and gene content
What is transcriptomics?
The study of gene expression
What is proteomics?
The study of proteins (proteome) produced as a result of transcription and translation
