protein structure- week 2 Flashcards
What is the secondary structure of a protein?
spatial arrangement of amino acids near to each other in the linear sequence
Why are there proteins and hydrogen bonding?
due to polar backbone
How can peptides in the backbone rotate and why?
- rotation possible around non-peptide bonds in chain
- because of steric hinderance only 2 angles possible
Who and what was proposed 1952?
- pauling and Corey
- idea that proteins could fold into regular repeating units: alpha helix and beta pleated sheet
How is the alpha helix formed?
- by H-bonds in same polypeptide chain (backbone not side chains)
- H-bonds formed between peptide bond carbonyl-O and H of N-H every 4th peptide
- regular right-handed helix
- stabilised by H-bonds
- R group on the outside
- rigid cylinder shape, acts as architectural support for protein
What is the structure of the alpha helix?
- structure is a regular tight coil
- stabilised by H-bonds between NH and CO groups 4 residues apart in backbone
- 100 degree rotation fo one residue to next
- 3.6 residues per turn
- 1.5 A rise between residues
- coil diameter of ca. 5A
What forms can an alpha helix have?
- right and left handed helices possible, RH more energetically favourable
Why are RH alpha helices more favourable?
there re fewer steric clashes between the side chains and the main chain
In an aloha helix residue which amino acids are very close ?
4 aa apart are spatially very close
How much percent of haemoglobin is an alpha helix?
60%
What is missing when a peptide linkage includes proline? What’s the consequence?
no H atom bound to nitrogen
- H is not available for hydrogen bond
- structure restricts rotation
- ends alpha helix
What stabilises an alpha helix?
hydrogen bonds between NH and CO groups
Describe the beta pleated sheet
-consists of 2 or more strands of polypeptide Calle beta strands
- consists of 2 or more strands or polypeptide (beta strands)
- H bonds between adjacent strands stabilise structure
What is the difference between alpha helix residues and beta sheets?
in beta sheets the residues are almost fully extended
What two forms of beta pleated sheets are there?
antiparallel and parallel
What does the antiparallel beta sheet look like?
beta hairpin bend
- widespread in globular proteins
What does the parallel beta sheet look like?
arrows point to C terminus
What version of the beta pleated sheet is more stable?
anti-parallel, as h bonding is not distorted
What is the distance between the adjacent residues in a beta pleated sheet?
around 3.5 A
What is the position of the side chains in a beta pleated sheet?
alternate above and below plane of strand
Give an example of proteins with beta pleated sheet
transmembrane proteins eg. porin
Describe the structure of a beta pleated sheet
- made up of 5 strands, but can also be up to 10
- can be anti-parallel, parallel or a mixture of both
Name proteins with a high percentage of beta sheets
-fibrillar proteins - silk fibres
- has high tensile strength but no elasticity
What is the tertiary structure of a protein?
spatial arrangement of amino acids, usually far apart form each other in the primary sequence
What is myoglobin?
- oxygen and iron binding protein found in muscles
- single polypeptide chain
- exist in unique 3D conformation
What happens to the position of residues in 3D structures?
residues that are far apart in amino acid sequence are located close together
what is the quaternary structure of a protein?
spatial arrangement in a protein made up form more than one polypeptide chain
What is a subunit in the quaternary structure?
a poly peptide chain in a protein
- can be homo or hetero
name a protein with a quaternary structure
Haemoglobin
- tetrameric protein with 2 identical alpha subunits and 2 identical beta subunits
alpha2beta2 configuration
What is haemoglobin configuration?
alpha2beta2 configuration
What does the quaternary structure allow for?
- smaller quantities of generic material to create large proteins and structures
- cooperative regulation of enzymes
Describe the structure of the human rhinovirus (causes common cold)
uses 60 repeats of 4 unit structure ti produce its coat
what is the allosteric effect?
- causes cooperative regulation of enzymes
- change in one subunit induces a change in another
