Intro to protein structure Flashcards
Amino acid side-chains
Amino acids can have:
- Non-polar side chains (hydrophobic) e.g. glycine, proline, alanine, valine
- Polar side chains (hydrophilic) e.g. serine, threonine, tyrosine, aspartate, glutamate, cysteine
- Charged side chains e.g. arginine, lysine, aspartate, glutamate
Chirality of amino acids
- Amino acids have a chiral centre (central carbon atom), it has 4 different substituents attached to it
- Results in enantiomers of each amino acids, they are mirror images of each other
- All amino acids in the body are in the L-form
- Glycine only exception - no side chain so no enantiomer
What holds a protein together?
- Covalent bonds - strongest bonds in protein, exist in primary structure. Also exist as disulphide bridges when cysteine side chains within a protein are oxidised. Disulphide bond is between 2 S.
- Hydrogen bonds - occur when two atoms bearing partial negative charges share partially
positive charged hydrogen - they are in a hydrogen bond. They occur between atoms on
different side chains and the backbone of the protein or between water molecules - Ionic interactions - occur when there is electrostatic attraction between charged side chains - relatively strong bonds, particularly when the ion pairs are in the protein interior and excluded from water
- Van der Waal forces - re transient, weak electrostatic attractions Although relatively weak and transient in nature, important due to their presence in large numbers.
- Hydrophobic interactions - are a major force driving the folding of proteins into their correct conformation. They juxtapose hydrophobic side chains by packing them into the interior of the protein. This creates a hydrophobic core and a hydrophilic surface to the majority of proteins
Alpha-helix and Beta-pleated sheet
- Helices are stabilised by hydrogen bonds
- The side chains in an α-helix project outwards. The helix is right handed due to the use of L-amino acids
- In a β-pleated sheet, the N-H and C=O groups point out at right angles to the line of the backbone, making a pleat
- Alternate strands of the sheet can run in the same direction to give a parallel sheet or in opposite directions to give an antiparallel sheet
- The pleating in each case allows for the best alignment of the hydrogen bonded groups
Primary, secondary, tertiary and quaternary structure of proteins
Primary- linear sequence of amino acids that make up the protein. Written from amino terminus to the carboxyl terminus
Secondary- defined as local structural motifs within a protein e.g. a-helices and b-pleated sheets.
Tertiary- arrangement of the secondary motifs into compact globular structures called domains, 3D structure of the protein
Quaternary- 3D structure of a multimeric protein (one that has multiple polypeptide chains)
How do amino acids exist at neutral pH
As dipolar ions, Zwitterions.
NH3+ and COO-
How do proteins usually fold?
What do chaperones do in protein folding?
-fold into a structure with the lowest free energy
These bind to the partly folded polypeptide chain and ensure that the folding continues along the most energetically favourable pathway.
What denaturants break hydrogen bonds and disulphide bonds?
- urea to break hydrogen bonds
- 2-mercaptoethanol breaks disulphide bonds
Which amino acid can form disulphide bonds?
Cysteine
What form can amino acids exist in?
What is the exception
L and D forms but cells can only use L forms
Exception is glycine because it cant form isomers, due to not being chiral.
What word confirms we are talking about Quaternary structure?
The term subunits confirms we are talking about quaternary structure, which describes the arrangement of several protein chains or subunits within a multimeric protein.
Which 2 amino acids can mammals not make?
Isoleucine and Leucine are distinct essential amino acids which cannot be synthesized by mammals and have to be ingested in their diet.
In several proteins of the blood clotting pathway, the amino acid glutamate undergoes post-translational modification to generate gamma-carboxyglutamate.
The addition of the carboxyl group introduces an increased affinity for calcium ions which is necessary for clotting to occur. The anti-coagulant warfarin works by inhibiting this post-translational modification.
when are ionic bonds particularly strong?
When the ion pairs are within the protein interior and excluded from water.
Glycosylation of side chains within a protein is an example of what?
post-translational modification
