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
What is a beta pleated sheet?
Hydrogen bonds form between residues of the primary sequence that are far away from each other.
B pleated sheets are stabilised by backbone hydrogen bonds between carbonyl on one strand and amine of the next.
Beta pleated sheets are not as ………. as alpha helix
regular
In beta pleated sheets the chains run ……………. or …………… . Which is the most common?
- parallel
- antiparallel
antiparallel is most common
Beta sheet maximises…
hydrogen bonding between the polypeptide chain
the secondary structure only involves …………. atoms
backbone
Secondary structure is held together by ………… ………………… interactions
non covalent
What is tertiary structure?
Non-covalent amino acid interactions of a single polypeptide chain that are not included in the secondary structure.
- Include all interactions between protein sidechains or between protein sidechains and the backbone.
- Tertiary structure often involves interactions between residues that are far apart in terms of primary sequence.
What is quaternary structure?
- The interactions holding multiple polypeptide chains together in one protein.
Each polypeptide chain in quaternary structure is referred to as….
a subunit
Subunits are held together by…?
the same non-covalent interactions as the tertiary structure.
protein with two subunits in their quaternary structure are called…?
dimers
protein with three subunits in their quaternary structure are called…?
trimers
protein with four subunits in their quaternary structure are called…? give an example
tetramers. Haemoglobin.
Give the non-covalent interactions we find in the tertiary and quaternary structure.
- hydrophobic interactions
- hydrogen bonds
- salt bridges (pairs of acid and basic amino acids close together in structure- interactions between permanent positive and negative charges AND also repulsive interactions)
- van der Waals interactions- interactions between either permanent or transient charges
- Disulphide bridges- a covalent S-S bond between the side chains of two cysteines close together in space.
How are protein structures broken?
heat, extreme pH, detergents, chemical modification.
