Lecture 4 - building blocks of proteins Flashcards
are amino acids usually found in the L or D form in biological systems
L form
are amino acids chiral
yes
what is a zwitterion
when they have both a positive and negative charge
are non polar side chains hydrophobic or hydrophilic
hydrophobic
how to tell if the amino acid is non polar
if it has only C or H at the end of their side chain
how to tell if the amino acid is polar
if it also has -OH, -NH2 or -O in their side chain
if it is able to form bonds with other atoms
are polar amino acids hydrophilic or hydrophobic
hydrophilic
how to know if a amino acid is positively charged polar
same as polar but has + charge at pH 7
how to know if a amino acid is negatively charged polar
same as polar but has - charge at pH 7
how to know if something is ionisable or not
- its polar
- has an H atom that can participate in acid base reactions
- donates and accepts electrons
what does the pKa of an ionisable group on amino acid or protein equal
the pH at which the group is 50% ionised
what does the pI or isoelectric point equal
the pH at which the net charge on an amino acid or protein is zero
what is post translational modification
a chemical group can be added to an amino acid residue AFTER translation has occurred
what happens due to post translational modification
the protein is modified which can switch it on or off
what amino acid is different to the others in terms of post translational modification
cystine = forms a disulfide bond instead of adding something
what type of bond is a peptide bond
a covalent bond
what are other features of a peptide bond that are important for preventing steric hinderance
planar = flat
trans = a-carbons go on opposite sides
dipole = ends have opposite charges
what is special about the peptide bond in terms of the double bond
it has partial double bond character (when the double bond can switch from the O to the N ?)
what do amino acids have
An alpha carbon, amino group, carboxyl group and side chain (R)
what are enantiomers
non superimposable mirror images
what is cystine commonly found in
proteases
what is glycines R group
A hydrogen making it non-chiral, flexible because its R group is small meaning it is found in regions which need to get tight and close together
What does the R group in proline do?
Bends back to the main chain N forming a 5 membered covalently closed ring. This makes it rigid and an imino acid rather than an amino acid as it contains an amine
How are negatively charged polar (acidic) amino acids shown?
As the conjugate base where the protons are already donated
how is the peptide bond formed
via dehydration between C-terminal of one amino acid and N-terminal of another
what is a peptide
short stretch of amino acids joined by peptide bonds
what is a polypeptide
a longer stretch of amino acids joined by peptide bonds
what is a protein
longer chain of amino acids, usually with a biological function
what is an amino acid residue
amino acids that are covalently joined together in peptide of a protein
When will disulphide bonds form?
In an oxidising environment
When will disulphide bonds break?
In a reducing environment
what are types of post translational modification
Phosphorylation, hydroxylation, carboxylation, metal ending, iodination, glycosylation and many others
