Amino acids/Proteins
Four Critical Biological Molecules
Sugars --------> polysaccharides
Nucleotides --------> nucleic acids
Fatty Acids --------> Lipids
Amino acids -------> proteins
Amino Acids
Amino
Carboxyl
a
Sterioisomers
The L amino acids have the amino grps to the left
All three carbon atoms are in a row
Non polar
Aromatic
Polar uncharged
Polar positive
a
b
g
d
e
Polar negative
Disulfide bonds
Uncommon amino acids
Zwitterions
pI
Each amino acid has a characteristic isoelectric point which is the pH at
which the positive equals the negative charge. This varies based on the side
chain.
For amino acid without ionizable side chains (non-polar), the Isoelectric Point
(equivalence point, pI) is pI= pK1+pK2/2
At this point, the net charge is zero. The AA is least soluble in water and the
AA does not migrate in electric field (important in electrophoretic
separation of peptides)
Ionization and pH
At acidic pH, the carboxyl group is protonated and the amino acid is in the cationic form
At neutral pH, the carboxyl group is deprotonated but the amino group is protonated.
The net charge is zero; such ions are called Zwitterions
At alkaline pH, the amino group is neutral –NH2 and the amino acid is in the anionic form.
The R groups also gets protonated. This varies from amino acid to amino acid. Thus
different amino acids have different pKa.
Amino acid titration
Amino acids with uncharged sidechains, such as glycine, have two pKa
values:
The pKa of the a-carboxyl group is
2.34
The pKa of the a-amino group is 9.6
It can act as a buffer in two pH
regimes.
R groups
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The pKa of the R group is designated here as pKR.
Peptide bond formation
Nucleophile= an atom or molecule that is electron-rich and seek positive charge
Peptide bond resonance
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Peptide
Peptides are 2-50 aa long
Many peptides have functionhormones,
neurotransmitters,
sweetner
Proteins are larger.
Amino acids bind prosthetic groups such as metals, heme, phosphates etc.
Conjugated Proteins
To understand a proteins,
you need pure protein
you need its sequence,
you need its structure
you need an assay to investigate activity.
Chromatography
Ion exchange
Gel Filtration (Size exclusion)
Affinity
SDS Gel Electrophoresis
Isoelectric focusing
Purification table
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Activity versus specific activity
Structure
Sequence
Protein Consensus sequence
Aligning sequences
Peptide sequencing