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Lecture 2.2

Element 2- Biochemistry

What forces are there stabilising Proteins? Hydrogen Bonds Ionic Bonds (including disulphide bridges) Hydrophobic Interactions Hydrophilic Interactions
What is the Hydrophilic Effect? Polar side chains prefer to interact with the aqueous solvent where it can make hydrogen- bonds and ionic bonds. Hydrophilic amino acids stick together and fold around protein, burying the hydrophobic amino acids in the interior of the protein.
What is the hydrophobic effect? Water forms ordered 'cages' around non-polar molecules. Hydrophobic molecules stick together to minimise the ordering of water
Describe the shape of an alpha helix and the relative positions of the amino acid side chains A rod-like, right handed helical structure. All side chains sticking out of the helix (because all L optical isomers).
What is an amino acid residue? It's what's left of the amino acid after peptide bond formation and subsequent loss of the water molecule. So in alpha amino acid polypeptides its -NH-CHR-COO-
How is the alpha helix stabilised Alpha helix is stabilised by backbone hydrogen bonds. Formed of hydrogen bonding between the C=O of one amino acid residue and the N-H of the amino acid residue four units along (denoted= residue i and residue i+4)
Describe the beta pleated sheet. Antiparallel polypeptides
How is the beta pleated sheet stabilised? Through hydrogen bonding between N-H and C=O of different polypeptide strands, often running in opposite directions, or between the same polypeptide chain after an abrupt beta-turn
What is a beta turn? In a beta turn, a tight loop is formed when the carbonyl oxygen of one residue forms a hydrogen bond with the amide proton of an amino acid three residues down the chain.
Alpha- helix and beta-sheets are part of which type of amino acid structure Secondary structure
What group is responsible for disulphide bridges and which amino acid has this group? Thiol, Cysteine
What is tertiary Structure? Involves side chain- side chain interactions which are packed tightly to leave very little free space. Secondary structure elements pack together to form the territory structure.
How do proteins span the membrane? Using alpha helices
What is Quaternary Structure? Give an example The arrangement of sub units (single polypetide chains) in proteins containing more than one subunit. e.g. Disulphide bonds
Whats the difference between alpha helices inside the cell membrane and those outside the cell? Hydrophobic side chains are now on the outside of the helix
Created by: macdonkr
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