Lecture 4 - Building Blocks of Proteins Flashcards
Zwitterion
Both positive and negative charges
Non polar
hydrophobic
Amino acids have
incl hows its classed
ionisable groups
Classed using pKa
pKa
pH where an ionisable group is half ionized
pI
isoelectric point
pH where the whole molecule has a charge of 0
Amino acid properties
Amino Group (NH2) Carboxyl Group (COOH) Sidechain (R)
Amino acid are
Chiral
What do 20 amino acids have?
Same backbone Different sidechains (R)
Each amino acid has a different
name
Sidechains of amino acids in proteins are arranged to
carry out chemical reactions
Amino acid sidechain perform
biochem of proteins
attach to protein backbone
Non polar amino acids
Glycine Alanine Valine Leucine Isoleucine Methionine F (Phenylalanine) W (Tryptophan) Cysteine Proline
“Grandma Always Visits London In May For Winston’s Christmas Party”
Negatively charged (acidic) polar amino acids
Aspartic acid (D) Glutamic acid (E)
Positively charged (basic) polar amino acids
K (Lysine)
R (Arginine)
Histidine
“Knights Riding Horses”
Uncharged polar amino acids
Threonine (Thr) Q (Glutamine, Gln) Serine Y (Tyrosine, Tyr) N (Asparagine, Asn)
“The Queen Stole Your Nose”
Why are 1 letter abbreviations for amino acids useful?
Sequence alignment
Describe mutations
Why are 1 letter abbreviations for amino acids useful example
Old way
“From a glutamate to a valine at position 6”
whats the new way
E6V
1st letter - wild type or native amino acid
Number - Location of mutation
2nd letter - Mutated residue
Some amino acids have
ionisable groups
what parts of amino acids in solution are usually charged?
amino and carboxyl ends
Some amino acid side chains are
Incl which contribute to?
ionisable
net charge of the amino acid
How can ionisable side chains of amino acids be classified?
pKa value
Amino acids ionisable side chains examples
Aspartic acid Glutamic acid Histidine Lysine Arginine Cysteine Tyrosine
pKa value for an ionizable group on an amino acid or
protein is
pH at which the group is 50% ionized
pI, or isoelectric point is
pH at which the net
charge on an amino acid (or protein) is zero
all amino acids start out as
standard 20
standard 20 of amino acids are
“translated” from RNA into proteins at the ribosome
“post-translational modification”
amino acids modified after they are added to a
protein
“post-translational modification” example
disulfide bond between 2 cysteines
Other Amino Acid Modifications
- Phosphorylation (add phosphate)
- Hydroxylation (add hydroxyl)
- Carboxylation (add carboxyl)
- Metal Binding (add metal)
- Iodination (add iodine)
- Glycosylation (add glucose)
Phosphorylation
control enzyme activity –
ON/OFF
Hydroxylation
prevent connective tissues diseases and scurvy
Carboxylation
need for blood clotting
metal binding
Examples of Some Amino Acids that can be modified after translation
Phosphoserine
Phosphothreonine
Phosphotyrosine
Glycosylation of Threonine
How are proteins made?
joining amino acids together with a covalent peptide bond
Peptide
short stretch of amino acids joined together by peptide bonds
Protein
long chain of amino acids joined together with a biological function
amino acid residues
amino acids bond together
no longer complete, individual, amino acids.
How did Linus Pauling and Robert Corey determine structure of peptide bond?
X ray Crystallography
The Peptide Bond
Planar
Trans
Dipole
What do we mean by “amino acids are chiral”?
exist in two forms have D- and L-isomers of amino acids.
have at least one chiral centre.
central carbon has four different groups attached
What are the 4 main groups of amino acids, as discussed in the lecture?
Non Polar
-‘ve Polar (acid)
+‘ve Polar (basic)
Uncharge Polar
Where in a protein would you expect to find non-polar amino acid residues?
Interior
hydrophobic
away from water
What chemical groups would we expect to find in the R-group of an ionizable amino acid?
Aspartic Acid (pKa = 4) Glutamic Acid (4)
Histidine (6)
Lysine (10)
Arginine (12.5)
Cysteine (8)
Tyrosine (10)
What is the name of the bond that links amino acids in the polypeptide chain?
Peptide bond (Covalent bond)
What are the key properties of peptide bond?
Planar, trans, dipole
List some common examples of post-translational modifications.
- Phosphorylation (add phosphate)
- Hydroxylation (add hydroxyl)
- Carboxylation (add carboxyl)
- Metal Binding (add metal)
- Iodination (add iodine)
- Glycosylation (add glucose)
What are some important functions of posttranslational modifications?
control enzyme activity –
ON/OFF
prevent connective tissues diseases and scurvy
need for blood clotting
metal binding
