Week 2 Lectures Flashcards
What is the function of nucleic acids
Encode all of the genetic information for an organism
Two types: DNA and RNA
What bases are known as purines
Adenine
Guanine
What bases are known as pyrimidines
Cytosine
Thymine (in DNA only)
Uracil (in RNA only)
Difference in RNA structure compared to DNA
DNA - deoxyribose sugar H poking out on 2nd C,
RNA - ribose sugar OH poking out on 2nd C
What makes up a nucleotide
Base + sugar
Polynucleotide chain has a direction?
One end has an unreacted 5’ phosphate and the other (3’) unreacted hydroxyl group
DNA Sequences are written 5’ to 3’ direction
What is joined by a phosphodiester link in DNA/RNA
The hydroxyl group on carbon-3’ of one sugar, that’s joined to a hydroxyl-5’ of another
1953 - Landmark in Science
Watson and Crick
Analysed X-ray diffraction patterns from DNA fibres and deducted that cross pattern was typical of a helical structure,
As the layer line spacing is 1/10 the pattern repeat must be 10 residues per turn with a distance of 3.4nm
Bases in DNA must form specific pairs (A-T 2bond) (G-C 3bond)
Key features of DNA double helix
Constant diameter (2nm)
There are 10 nucleotides per turn of the helix
Phosphate groups / sugar groups lie on the outside of the helix next to water environment
Bases lie flat on inside of helix and form hydrogen bonds between two strands
Van Der Waals bonds form between successive bases in same strand
Strand run in opposite direction
Two strands are complementary, acting as a template.
Structure of amino acid
Amino group (NH2), Carboxyl group (COOH), Hydrogen atom and variable side chain (R) all attached to a central Carbon alpha
How do side chains of amino acids differ?
Size, shape, charge, hydrophilicity/phobicity and how chemically reactive they are / what they react to
How do side chains of amino acids differ?
Size, shape, charge, hydrophilicity/phobicity and how chemically reactive they are / what they react to
Which amino acid doesn’t have an optical isomer ?
Optical isomers are mirror images of one another, but amino acid glycine doesn’t do this. As it’s side chain is a hydrogen atom
Acidity definition
Concentration of H ions in a solition
Amino acids in a low pH (1) compared to high pH (14)
Low pH - pick up H ions easy, carboxyl group can’t easily remove H (gains positive charge)
High pH - Struggle to pick up H, but carboxyl group can easily remove a H (gains negative charge)
Why is Histidine a special amino acid
Has a pKa around physiological pH (6.8)
The ability for it to change its charge status at physiological pHd is important in the folding of many proteins and in the activity of many enzymes
pKa is the pH at which an ionisable group is one-half charged and one-half neutral
Structure of an amino acid
Amino group (NH2), carboxyl group (COOH), Hydrogen atom (H) and a variable side chain (R) all attached to a central carbon atom (Carbon alpha)
What direction is an amino acid always written in?
N —> C direction
The peptide bond has partial double bond character … what does this mean?
Rotation is restricted (Peptide unit is rigid and planar)
Therefore polypeptide chain can only rotate around the bonds on either side of the peptide unit
Where is a PSI angle vs PHI angle in a polypeptide
PSI = C (alpha) - C bond
PHI = N - C (alpha)
Most are not allowed due to steric collisions between side chains and main polypeptide chain, the shape of the protein is determined by the values of the psi and phi angles for each amino acid
What forms a hydrophobic core in water soluble proteins?
Pack hydrophobic side chains into the interior of the protein to ‘hide’ them from surrounding water molecules
As the main polypeptide chain is hydrophilic due to the polar C=O and N-H groups, protein must adopt structures which ‘neutralise’ these groups by hydrogen bonding
What are the two main types of hydrogen bonding in amino acids (secondary structure folding)
Alpha helix
Beta pelted sheet
They’re formed when a number of continuous amino acid residues have the same psi and phi angles
