structure of an amino acid?
Which form are all amino acids in ?
L optical isomer
- the alpha carbon is the chiral centre and four different things bond to the central carbon
- this gives rise to optical isomers
glycine is the only nonchiral amino acid as it has no side chain
what are the characteristics of a peptide bond?
- there is no free rotation
- C – O and N-H are in the same plane
- Other two bonds in the backbone of the peptide are able to rotate
- Only conformation in which the side chains do not clash with the main chain (steric hindrance) are allowed
how are peptide formed?
what is the anatomy of a peptide?
- formed by condensation reactions
- functionality requires a definite 3D structure or conformation of the polypeptide chain
Hydrophobic
Glycine Alanine Proline Valine Leucine Isoleucine Tryptophan Phenylalanine, Methionine
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leucine and isoleucine may take pharmacology
Hydrophilic
Serine Thereonine Tyrosine Asparagine Glutamine Cysteine
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amino acids with positively charged side chain
Arginine Lysine always protonated at physiological pH
Histidine is protonated (+) under pH 6
Negatively charged
Glutamate Aspartate are always negatively charged at physiological pH
Why can proteins not tolerate a great change in pH?
Ionisation state of amino acids is essential for function. Changes in pH = change in ionisation state = change in property.
Amino acids can take up and release protons which gives them some buffering capacity = gives them capacity to resist some changes in pH
what hold a protein together?
what bonds?
covalent bonds
hydrogen bonds
ionic interactions
van der waals forces
hydrophobic interactions
When do disulphide bridges form?
Cytosine chains are oxidised
Covalent bond between 2 amino acids
explain covalent bonds
- The strongest bonds within a protein and exist in the primary structure
- Covalent bonds can also exist as DISULPHIDE BRIDGES
explain hydrogen bonds?
- Occur when two atoms bearing partial negative charges share a partially positively charged hydrogen
- These can occur between atoms on different side chains and the backbone of the protein OR between water molecules
explain ionic interactions?
- Arise from the electrostatic attraction between CHARGED SIDE CHAINS
- Relative STRONG bonds
- Within any particular protein molecule, the majority of charged groups are at the surface of the folded protein - there they can be neutralised by counter ions such as salts
explain van der waals forces?
- Transient, weak electrostatic attractions between two atoms - due to the fluctuating electron cloud surrounding each atom which has a temporary electric dipole
- the transient dipole in one atom can induce a dipole in the other atom
- The appropriate distance required for Van der Waals attractions differs based on the size of each electron cloud - referred to as the Van der Waals radius
- because there are lots of van der waals forces they can be strong all together
explain hydrophobic interactions?
- They put hydrophobic side chains close together by packing them into the interior of the protein
- This creates a hydrophobic core and a hydrophilic surface to the majority of proteins
Why does proline cause a kink in the peptide chain?
- When proline is added to a polypeptide chain there is a loss of NH group of the amino acid
- Side chain can’t form hydrogen bonds with C=O of another part of chain
- this distorts the helical conformation
- it puts a kink into it
how are proteins usually folded?
- proteins are generally folded into the single conformation of the lowest energy
- Chaperones may be involved to make sure that folding occurs in the most energetically favourable way
what does functionality require?
requires a clear 3D structure or conformation of the polypeptide chain
What is a parallel beta strand?
- Beta sheets run parallel to each other
Beta sheets run in opposite directions = antiparallel beta sheet
the pleating in each case allows the best alignment of the hydrogen-bonded groups
how are beta pleated sheets held together?
how are alpha helices held together?
- Hydrogen bonds between the C=O and the N-H of two or more beta strands hold the entire structure together
- they are held together by hydrogen bonds
what is a domain?
compact globular structure that the secondary structure motifs are arranged into
what is denaturing
what are common denaturants?
- urea breaks hydrogen bonds
- 2-mercaptoethanol (breaks disulphide bonds)
what is the post-modification of proteins?
- the starting set of 20 amino acids can be modified to create novel amino
acids enhancing the capabilities fo the protein
- The formation of g-carboxyglutamate residues within several proteins of the blood clotting cascade is critical for their normal function by increasing their calcium binding capacities
