Nucleic Acids Flashcards
What are the parts of the primary structure of DNA?
bases, nucleosides, nucleotides then single strands
What are bases?
nitrogenous bases = have high nitrogen content
- purine
- pyrimidine
What is tautomerism?
DNA nucleotides recognise each other by their hydrogen bonds
- in the correct tautomeric form these bases have hydrogen bond acceptors and donors = which allow formation of hydrogen bonds and recognition of each other
What are tautomers?
isomers of a compound the only differ in the position f their electrons and protons
What are the purine bases?
single benzene ring - 6C
cytosine - found in DNA and RNA
thymine - found in DNA
uracil - found in RNA
What are the pyrimidine bases?
two benzene rings - 6C and 5C
adenine - found in DNA and RNA
guanine - found in DNA and RNA
Where are the hydrogen bond donors and acceptors for thymine and cytosine?
pyrimidine acceptors - nitrogen and oxygen atoms donors - hydrogen atoms on the nitrogen atoms
Where are the hydrogen bond donors and acceptors for adenine and guanine?
purine acceptors - nitrogen and oxygen atoms donors - hydrogen atoms on the nitrogen atoms
What is a nucleoside?
nitrogenous base attached to a sugar
sugar - ribose or deoxyribose
What is the difference between ribose and deoxyribose sugar?
RNA = ribose - has 2 OH groups on the ribose sugar ring DNA = deoxyribose - has only 1 OH group on the ribose sugar ring (1 is missing from C2)
What is a nucleotide?
phosphate esters of nucleosides
- base, sugar and phosphate
- phosphates are attached to the sugar by the free hydroxyl group on C5
phosphate groups give the nucleotides an overall negative charge
What are the roles of nucleotides?
movement of energy within an organism - ATP
ATP = 3 phosphates, ribose sugar, adenine
metabolic regulator - cAMP
components of major coenzymes - NAD, FAD, coenzyme A
activated intermediates in biosynthesis
How are the nucleotides in a single strand of DNA linked?
nucleotides are linked phosphate groups bridging two sugar units
sugar-phosphate groups form the backbone of the strand with the bases hanging off it
What is the different between RNA and DNA?
RNA - usually single stranded
DNA
- usually double stranded
- the two strands are held together by hydrogen bonds
- the bonds runs in opposite directions forming a duplex
How does Watson - Crick base pairing work?
dominant pattern of base pairing is formed
A-T has 2 hydrogen bonds
C-G has 3 hydrogen bonds
= A-T < C-G
What features of the base pairing in Watson-Crick base pairing allows for isomorphous geometry?
For each pair the distance between the C-1’ atoms and the angle between the glycosidic bonds is the same.
What is the primary structure of DNA?
order of attachment of nucleotides
What determines the secondary structure of DNA?
shape of the base pairs interaction between base pairs duplex of DNA packing of DNA structure of RNA
What is the shape of the nucleotide pairs?
bases are in an aromatic ring - are planar
hydrogen bonds between the bases ensure that both bases are in the same plane
the sugars are more or less perpendicular to the plane of the bases - are puckered
sugar phosphate backbone is quite flexible - not responsible for the helical shape of DNA
What is meant by pi stacking?
pi stacking occurs as heterocyclic bases in DNA tend to try to line up above one another = overlap
it occurs as aromatic rings have electrons above and below the plane of the ring and it is energetically favourable for them to overlap with other p-orbital in adjacent rings
- it is energetically favoured as it allows for the delocalisation of electrons
the bases tend to line up on top of each other at angle of approximately 30-40 degrees
How does pi stacking affect the secondary structure of the DNA?
the overlap of the heterocyclic bases (aromatic) is a constraint on the sugar-phosphate backbone
- results in the formation of the helical shape = forced to twisting
What is the difference between right handed and left handed DNA?
DNA is normally right handed but can be found as left handed under certain conditions
right handed - viewed as clockwise
left handed - viewed as anticlockwise
What determines the shape of DNA?
the sequence of bases and the chemical environment
- the negative charges on the backbone phosphate will repel and stretch the strand
- if the bases are not all in the same plane but tilted to one another then the strand will bend
What are the grooves in DNA and their causes?
minor and major grooves
- each is a different shape, size and contains a different chemical environment
minor
- occurs when strands are closer together
major
- occurs when strands are further apart
Why are grooves important for drug discovery?
drugs binds to different grooves
proteins binds to different grooves
What are histones and what is their function?
proteins that associate with DNA
enable it to fit inside the nucleus
- neutralises the negative charges on the phosphates groups = stops repulsion and separation
- histones can wrap around them and can enter the nucleus
What are the areas in DNA that anti-cancer drugs can bind to?
two areas
- intercalation = between the base pairs
- groove binding = in the groove
What is gene therapy?
involves the introduction of small pieces of DNA into a cell, which then allows for the synthesis of a required protein
- could be a required protein (cystic fibrosis) or a foreign toxic protein (targeting cancer cells)
