BMP: protein structure Flashcards
Discuss rotation of bonds in terms of polypeptides
- The peptide bond has a partial double bond character – it is shorter than a single bond and therefore is rigid and planar.
- This prevents free rotation around the bond between the carbonyl carbon and the nitrogen of the peptide bond.
- However, the bonds between the a-carbons and the a-amino or a-carboxyl groups can be freely rotated and thereby allow the polypeptide to assume a variety of possible configurations.
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Is the peptide bond trans or cis? why?
Trans due to steric interfence of R groups in cis form
What contributes to the charge of a polypeptide/ protein? Explain
The -C=O and -NH groups of peptide bonds neither accept or donate protons over pH range of 2-12 therefore are uncharged. The charged parts result from:
- N terminal amino group
- C terminal carbocyl group
- ionisable groups on side chains
Describe the secondary stucture of alpha helixes
Spiral structure consiting of tightly packed coiled polypeptide back bone with R group side chains extending outwards from the centeral axis to avoid steric interferecne
What bonding is involved in alpha helixes?
Hydrogen bonding between the carbonyl oxygen and amide Hydroigen of the peptide bonds
indivdually weak, but collectively strong
Describe the AA per turn and what this means
What are the exceptions?
- 3.6 AA per turn so AA residues 3/4 from each other are close in the helix
- Exceptions:
- Proline - imino group isn’t geometrically compatiable with the right handed spiral of the a-helix so inserts a kink
- Large numbers of charged AA cause ionic bond formation or electrostatically repel each other
- AA with bulky side chains e.g. tryptophan or branched chain AA interefere with alpha helix
Describe the forces in B-sheets
B-sheets are formed from 2 or more polypeptide chains that can be arranged in antiparallel or a parallel direction.
All components of peptide bond are involved in Hydrogen bonding . The H-bonds are perpindicular to polypeptode back bone
If the bonds are formed between the polypeptide back bone of seperate polypeptide chains its called interchain bonding. If they are formed between the polypeptide back bone of a single stand folding back on itself its called intrachain bonding
What are the differences between a helix and b-sheet
In B-sheets there is 2 polypeptides used (b-strands) as opposed to the one in the alpha-helix
What are beta bends?
- reverse the direction of the polypeptide chain helping to form a globular shape
- usually found on the surface of protein molecules and often have charged moieties
- often connect with AP B-sheets
Describe tertiary structures
- Refers to the overall 3D shape of the protein
- Non-covalent interactions between the side chains of amino acid residues help to stabilise the tertiary structure.
- Proteins tend to fold so that the atoms are close together and enhancing potential for Van der Waal interactions as well.
- In some proteins a few side chains are covalently cross-linked by disulphide bonds.
Give an example of a globular protein and describe it
- Myoglobin is a single chain polypeptide with 153 amino acid residues. Almost all the hydrophobic residues are on the inside of the structure so they are not in contact with water.
- Proteins like myoglobin which consist of one polypeptide (one subunit) are called monomeric. Such proteins have no quaternary structure.
Describe quaternary structure
- Proteins composed of more than one polypeptide chain (subunit) are said to be polymeric.
- Quaternary structure involves the clustering of several polypeptide chains into a final specific shape.
- Quaternary structure describes the way in which these subunits interact by the various non-covalent interactions.
- 2 major protein categories are fibrous and globular.
describe insulin
- Human insulin consists of 2 polypeptide chains, A and B
- The two chains are connected by disulphide bonds
- The protein assumes a global configuration
Describe haemoglobin
- Haemoglobin is a polymeric protein consisting of 4 subunits consisting of 2a and 2b-subunits.
- Each chain contains a haem prosthetic group and therefore haemoglobin can bind 4 oxygens.
Describe Lactate dehydrogenase
- LDH is tetrameric composed of 2 monomeric subunits M and H
- Five types (isoenzymes) of LDH tetramer can therefore be formed
- Quaternary structure of:
–LDH 1 = H4
–LDH 3 = H2M2
–LDH 5 = M4
