Lecture 4: BUILDING BLOCKS OF PROTEINS Flashcards
What do amino acids have?
An alpha carbon, amino group, carboxyl group and side chain (R)
What significance does amino acids having four different groups attached have?
It means that they are chiral
What forms can amino acids exist in?
L or D but are predominantly L
Chiral compounds can form…
Enantiomers
What are enantiomers?
Non-superimposable mirror images
What is the predominant form of amino acids in solution?
Zwitterion (COOH deprotonated and NH2 protonated)
What do the 20 amino acids have in common?
Backbone
What is different between the amino acids?
Their side chains
What does each amino acid have?
A full name, abbreviated 3 letter name and 1 letter name
What do the amino acids have due to their different side chains?
Different chemical properties
What do amino acid side chains do in proteins?
Carry out the biochemical reactions for which proteins are known
How are amino acids classified?
Based on their chemical properties
What are most non-polar amino acids?
Hydrophobic
Where are hydrophobic amino acids found?
Typically on the inside of a protein stabilising the structure
What is glycine’s 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 is cysteine commonly found in?
Proteases
What do phenylalanine and tryptophan have?
Aromatic side chains (resonance structures)
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
What side chain do negatively charged polar (acidic) amino acids have?
One containing an acidic carboxyl group
How are negatively charged polar (acidic) amino acids shown?
As the conjugate base where the protons are already donated
What side chain do positively charged polar (basic) amino acids have?
One containing a basic amine group
How are positively charged polar (basic) amino acids shown?
As conjugate acids where the protons are already accepted
What is characteristics of tyrosine?
Aromatic and can be phosphorylated
What amino acids contain amide groups?
Asparagine and glutamine
What can uncharged polar amino acids be involved in?
Polar, but uncharged hydrogen bonds
What are often learnt by biochemists and clinicians?
3 letter and 1 letter abbreviations
What are easy to remember?
3 letter abbreviations
What are one letter abbreviations useful for?
Sequence alignment and mutation
One letter abbreviations are …
A compact way to depict sequence and great for describing mutations
What does the first letter in the 3 symbol nomenclature represent?
The original amino acid
What does the second number in the 3 symbol nomenclature represent?
The location of the mutation in the protein
What does the second letter in the 3 symbol nomenclature represent?
The new or mutated residue
What do clinicians use the 3 symbol nomenclature for?
Noting resistance in proteins such as HIV
What is RT?
Reverse Transcriptase
What is reverse transcriptase?
An enzyme in the HIV virus that helps replicate the viral genome. It is essential for HIV survival
What are the amino and carboxyl groups of amino acids usually like in solution?
Charged
Some amino acid side chains are …
ionisable
What do ionisable side chains contribute to?
The net charge of the amino acid
How can ionisable side chains be classified?
By their pKa value
What is the pKa value for an ionisable group on an amino acid?
The pH of which the group is 50% ionised
What is the pI known as?
Isoelectric point
What is the isoelectric point?
The pH at which the net charge on an amino acid or protein is zero
What is the pKa value for alpha carboxylic acid groups?
About 2
What is the pKa value for alpha amine groups?
About 9/10
What os the pKa value for side chains?
Varies from about 4 to 12.5
What do almost all amino acids start as?
One of the standard 20
What are amino acids translated from?
RNA into proteins at the ribosome
What happens to some amino acids?
They are modified after they are added to a protein
What is amino acid modification called?
Post-translational modification
What does cysteine sometimes do?
Forms a covalent bond called a disulphide bond with another nearby cysteine.
When will disulphide bonds form?
In an oxidising environment
What does disulphide bonds forming do?
Gives rigidity to the structure
When will disulphide bonds break?
In a reducing environment
What are types of amino acid modification?
Phosphorylation, hydroxylation, carboxylation, metal ending, iodination, glycosylation and many others
What is phosphorylation?
Addition of a phosphate
What is hydroxylation?
Addition of an OH group
What is carboxylation?
Addition of a COOH group
What is iodination?
Addition of iodine which isn’t very common
What is glycosylation?
Addition of a carbohydrate
What is phosphorylation often used for?
To control enzyme activity like a chemical ON/OFF switch
What amino acids undergo phosphorylation?
Serine, threonine and tyrosine
What is hydroxylation needed for?
To prevent connective tissue diseases and scurvy
What amino acids are often involved in hydroxylation?
Proline and lysine
What is required for hydroxylation?
Vitamin C
What is carboxylation needed for?
Blood clotting
What is often involved in carboxylation?
Glutamate
What amino acids are often glycolysis?
Threonine and asparagine
What is glycosylated haemoglobin, HbA1c used for?
To diagnose and follow patients with diabetes
How can amino acids join together to form chains?
By covalent bonds called peptide bonds
What type of reaction is the formation of a peptide bond?
Dehydration where water is lost
What does the peptide bond partially have?
40% double bond character as there is resonance structures. This leads to planarity and planar conformation maximises pi bond overlapping
Can peptide bonds rotate freely?
No, there is a rotation barrier of approximately 80kJ/mol
What does the peptide bond have?
A dipole
What is the predominant form of a peptide bond?
Trans
What is a peptide?
A short chain of amino acids joined by peptide bonds
What is a protein?
A longer chain of amino acids joined by peptide bonds which have a defined function
What are amino acids known as in peptides or proteins?
Amino acid residues
What are amino acids known as amino acid residues in peptides or proteins?
Because they are no longer complete
What with regards to amino acids is often referred to?
Their location
What does M184 mean?
There is a methionine at position 184
