MCB Lecture 4 & 5 Amino Acids Flashcards
L and D amino acids are…
Optical isomers
Describe what is meant by L and D amino acids
This is the different conformations around the alpha carbon
What do the L and the D refer to?
The direction they rotate light
L : left
R : right
Describe the stereochemistry of an amino acid (looking down the H – alpha-carbon bond)
CORN when read clockwise
What is the name of the dihedral/torsion angles in the side chain?
Chi
X1, X2 etc
What is the preffered conformation of the side chain atoms?
Staggered
What are amino acids synthesised from?
L glyceraldehyde
What are the acidic side chains?
Aspartic acid (Asp, D)
Glutamic acid (Glu, E)
What are the basic side chains?
Arginine (Arg, R)
Histadine (His, H)
Lysine (Lys, K)
What are the polar amino acids?
Asn Gln Tyrosine Serine Threonine
Which are the aromatic amino acids?
Trp
Phe
Tyr (also polar)
What is the ionic status of the acidic side chain?
Completely ionised at physiological conditions
What is physiological pH?
7.4
What do the acidic side chains often do?
At as chelators on metal ions
What is the ionic status of lysine?
Completely ionised at physiological pH
Which is the predominate form of histadine at physiological pH?
Both ionised and not are found
What are the aliphatic amino acids?
Cysteine Gly Ala Val Leu Ile Pro Met
Which amino acids are highly used in enzyme active sites?
Histadine
Cysteine
How is Histadine chemically ambidextrous?
It’s a nucleophile
It’s an electrophile
Describe the reactivity of Asparagine and Glutamine
Not very reactive
Describe the reactivity of the hydroxyls (Thr & Ser)
Not very chemically reaction
Describe the reactivity of Phenylalanine
Very unreactive
Describe the reactivity of Tyr
OH can hydrogen bond
What is special about Trp
It absorbs UV and fluorescent
Describe the reactivity of the aliphatic side chains
Unreactive
What are the two possible conformations of Pro? Which is favoured?
Trans and cis
Trans is favoured
Compare the reactivity of cysteine and methionine
Though they both have sulfur, cysteine is very reactive and methionine is very unreactive
Inside the cell (cytosol) is a … environment
Reducing
Describe the formation of disulfide bridges
Oxidise, two protons released, and a bond between the two sulfurs
In what environments will disulfide bridges be present in protein?
In the blood (oxidising)
Inthe cell is reducing, so there will be no disulfide bridges
What does the presence of di-sulfide bonds mean for a protein?
Eg ?
Increased stability
Eg. The disulfide bridges in insulin
Describe the inner structure of a protein
No water
Hydrophobic region
Describe the localisation of polar and non polar side chains in amino acids
Polar: outside
Non polar: inside
Where are Glycine and Proline predominantly found?
In alpha and beta turns
Which forces drive protein folding?
Van Der Waals
Hydrogen bonding
Electrostatic
Hydrophobic force
What is the native state of amino acids?
What is the other state?
Folded is native
Denatured is not the native state
What is renaturing?
Protein denaturing is reversible.
After it has been denatured, if the solvent is removed, it will denature and be folded
What is meant by protein folding is cooperative?
It is all or none. There is no such thing as a half folded protein
If any part of the protein has it’s interactions disturbed, …
The whole protein will denature
Describe what happens in the cases where proteins can not fold by themselves?
Chaperones will help them fold
Chaperones prevent the proteins from folding badly whilst they are still being synthesised
What are amyloid diseases?
These are diseases in which there are complexes of protein where all the protein is mis folded.
Eg. Huntington, Parkinson’s, Creurzfeld-Jacob
Identify the direction of a dipole in a peptide bond
Up
Describe van Der Waals interactions
Once the atoms get to a certain proximity, there is an attractive force
Closer than this, and the electrons repulse the two atoms
Further away and there is no attraction
Describe hydrogen bonds
Two electronegative atoms share a hydrogen atom
Describe hydrophobic interactions and entropy in proteins
Hydrophobic molecules stick together
It is more favourable for the protein to fold up for that all the hydrophobic residues are together in the middle. This way, all the water molecules are released. This represents a higher level of disorder
Which amino acid is ambidextrous in terms of bonding reactivity?
Histadine
It is both a electrophile and a nucleophile
Which amino acid acts as a chelator?
Aspartic acid and glutamic acid
