Amino acid nomenclature and stereochemistry Flashcards
What is the basic structure of all amino acids?
A central carbon bonded to a hydrogen atom, a carboxyl group, an amino group and an R group/side chain.
What is the R group on glycine?
A hydrogen atom.
What is the side chain of proline?
The nitrogen of the amino group attached to the alpha carbon.
What is the relationship between the the two versions of each amino acid?
They are enantiomers.
What are the names of the two versions of each amino acid?
D- form and L- form.
What form of amino acid is used in the formation of proteins?
L- form
How many ionisable groups does each amino acid have?
At least 2
What is ionisation?
The conversion of an atom to an ion.
What is a zwitterion?
A molecule with two ionised groups but no net charge.
What makes amino acids amphoteric?
Their ionisable carboxyl and amino groups.
What determines whether amino and carboxyl groups are ionised?
pH
Is glycine ionised at pH 4-8?
Yes but it is a zwitterion.
What happens to glycine at pH 0-4?
Some molecules are ionised.
What is the carboxyl Pka?
The point where there are an equal number of ionised and non- ionised carboxyl groups.
When do non-ionised carboxyl groups predominate?
At a lower pH.
What happens to amino groups at pH 8?
Some lose protons.
What is the Pka of amino groups?
The point when the number of molecules with and without ionised amino groups are the same.
When do the non-ionised amino groups predominate?
At pH values above the Pka.
At what pH can the zwitterions of each amino acid operate?
pH 7.4
Why do aspartic acid and glutamic acid act as proton acceptors in biochemical reactions?
As they are fully ionised at pH 7.4.
Why do arganine and lysine act as bases at pH 7.4?
As they have a positively charged side chain.
Are the side chains of cysteine and tyrosine ionised at pH 7.4?
No
Why can histidine act as a proton donor or acceptor?
As it has ionisable side chains and at pH 7.4 some molecules are ionised and some are non - ionised.
By what is the polarity of some side chains caused?
Uneven distribution of electrons on the R group.
What are the two rare amino acids not usually found in living systems?
Selenocysteine and pyrrolysine.
What is the simplest post-translational modification?
The addition of hydroxyl, methyl and phosphate groups to the side chain.
What regulates protein activity?
Amino acid modification.
Where does the peptide bond form in a polypeptide?
Between the carboxyl group of one amino acid and the amino group of another.
How does the polypeptide terminate?
With either a free amino group (N terminus) or a free hydroxyl group (C terminus).
What is chemical direction of polypeptides?
Either N->C or C->N.
In what direction does protein synthesis occur?
N->C, every amino acid is added to a free carboxyl.
What is the structure of a peptide group?
2 alpha carbons with a carbon, nitrogen, oxygen and hydrogen between them.
What are the characteristics of peptide groups?
The have a flat structure and are rigid; there is no rotation.
What is the angle rotation around the alpha carbon - carbon bond called?
Psi
What is the rotation angle around the nitrogen - alpha carbon bond called?
Phi
What is the angle of psi and phi when two adjacent peptide groups are orientated on the same plane?
180 degrees.
What happens to phi and psi when the bond is rotated clockwise?
They increase
What happens to phi and psi when the bond is rotated counterclockwise?
They decrease
Why do 77% of possible psi and phi combinations never occur?
Because of steric effects.
What does the Ramachandran plot demonstrate?
the phi and psi combos that occur.
What is primary structure?
The sequence of amino acids in the polypeptide.
What is secondary structure?
The series of conformations i.e. helices, sheets and turns.
What is tertiary structure?
The 3D configuration of a protein.
What is quaternary structure?
Association between different subunits to form a subunit protein.
