Lecture 11 - Protein structure Flashcards
What are the monomers of proteins?
amino acids
All amino acids have two common groups. What?
Amine - NH2
Carboxyl - COOH
Amino acids contain an amino acid side chain. R group. It is known as…
a variable side chain
Side chains may be…
- maybe a single hydrogen or contain 9 carbons with their associated hydrogen atoms
- side chains may be non-polar, polar but not ionized or polar ahdn ionized.
Draw the general formula of an amino acid.
What atom in an amino acid is an alpha carbon?
the carbon next to the carboxylic acid group is the alpha carbon
Most amino acids are chiral. What does this mean. Which is the only achiral amino acid?
- stereogenic centre, 4 different groups attached to the alpha carbon
- glycine is the only achiral amino acid.
What are proteogenic amino acids?
The name given to the 20 naturally occurring amino acids found in proteins. These amino acids are alpha amino acids and have the general formula that we know and understand.
How do amino acids form peptides?
The N terminus/ amine group of one amino acid react with the C terminus/carboxyl group of the next in a condensation reaction- covalent peptide bonds form between the amino acids
Draw the condensation reaction between two amino acids, showing the two isomers.
Define the primary structure of a protein
The sequence of amino acids in a polypeptide chain.
What is the primary structure of a protein determined by?
- the number of amino acids in the polypeptide chain
- the specific sequence of different amino acids.
Peptide bonds form the …………. of the polypeptide chain
backbone
What is the sequence of a backbone of a protein
N-C(alpha)-C-N-C(alpha)-C
How do peptide bonds break? Give an example.
broken by hydrolysis to yield individual amino acids- e.g. when we digest protein from the food we eat.
The peptide bonds is flat- aka…
planar
There is an equilibrium between the two isomers of the peptide bonds which results in…
- partial double bond characteristic/planar bond
- a reasonably stable bond
- the nitrogen and carbonyl are less reactive than you would think.
The double bond/peptide bond prevents….
rotation
There can be different isomers of the peptide. Which are more energetically favourable and why?
Trans - the groups are on opposite sides which reduces repulsion.
2 arrangements in secondary structure
- alpha helix
- beta pleated sheet
How does the secondary structure come about?
hydrogen bonds form between the polypeptide chain.
What are hydrogen bonds?
A hydrogen bond forms between an electronegative atom covalently bonded to a hydrogen atom and an electronegative atom with lone pair of electrons.
non-covalent
What is an alpha helix?
Non-covalent interactions between residues close together in primary sequence. Helixes are stabilised by hydrogen bonds between the backbone amine of one amino acid and the backbone carbonyl of the amino acid four residues earlier.
Alpha helix have a ……… arrangement
regular