Protein structure Flashcards
Which amino acid is different?
Proline has also a secondary amino group.proline’s side chain and the alpha amino group form a rigid five-member ring structure. Its unique geometry contributes to the formation of the fibrous structure of the collagen and often interrupts the alpha helices found in globular proteins.
Non-polar side chain amino acids
Hydrophobic interactions
aqueous solution or in a polar environment as the cytoplasm, the side chains of the non-polar amino acids tend to cluster together in the interior of the protein.
proteins that are located in a hydrophobic environment such as a membrane the non-polar groups are found on the outside surface of the protein interacting with the lipid environment.
Polar, uncharged side chain amino acids
uneven distribution of charges due to the different electronegativity of specific atoms
serine, threonine and tyrosine contain a polar hydroxyl group that can participate to the formation of hydrogen bonds
Acidic side chain amino acids
amino acid aspartic acid and glutamic acid are proton donors as their side chain is fully ionised, negatively charged carboxylate group
Basic side chain amino acids
lysine and arginine accept protons becoming fully and positively charged. In contrast, histidine is weakly basic and the free amino acid is largely uncharged at physiological pH. However, when histidine is incorporated into a protein it can be neutral or positive depending on the ionic environment surrounding the protein.
Why are peptide bonds generally in a trans configuration instead of a cis?
steric hindrance between side chains of adjacent amino acids when in a cis position.
What is an alpha helix?
spiral structure consisting of a tightly packed coiled polypeptide backbone core with the side chains of the component amino acids extending outwards from the central axis to avoid interfering sterically with each other
How can alpha helixes be disrupted?
- not compatible with the right handed spiral of a α-helix. -Proline secondary amide group 5 member ring.
- Charged amino acids such as glutamate, aspartate, histidine forming ionic bonds or by electrostatic repelling each other
- bulky side chains such as tryptophan that branch at the β carbon can interfere with the α-helix if present in large amounts.
What are heme proteins?
group of specialized proteins that contain heme as a tightly bound prosthetic group
Heme is a complex of protoporphyrin IX and ferrous iron
The iron is held in the centre of the heme molecule by binding to four nitrogen atoms of the protoporphyrin ring. The heme Fe2+ can form two additional bonds one on each side of the protoporphyrin ring. In myoglobin and haemoglobin one of this binding is with the side chain of an histidine residue of the globin molecule whereas the other position is available to bind oxygen.
What is myoglobin?
consists of a single polypeptide chain. Myoglobin is a compact molecule containing approximately 80% of its molecule folded into 8 stretches of α-helices. These α-helices are terminated at least in part by the presence of proline
What is a collegene molecule?
long rigid structure in which three polypeptides are wound around one another in a rope-like triple helix
