Amino acids/Proteins. Sugars --------> polysaccharides Nucleotides --------> nucleic acids Fatty...
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Transcript of Amino acids/Proteins. Sugars --------> polysaccharides Nucleotides --------> nucleic acids Fatty...
Amino acids/Proteins
Sugars --------> polysaccharides
Nucleotides --------> nucleic acids
Fatty Acids --------> Lipids
Amino acids -------> proteins
Four Critical Biological Molecules
Amino Acids
Carboxyl
Amino
Sterioisomers
The L amino acids have the amino grps to the leftAll three carbon atoms are in a row
Non polar
Aromatic
Polar uncharged
Polar positive
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 side-chains, such as glycine, have two pKa values:The pKa of the -carboxyl group is 2.34The pKa of the -amino group is 9.6
It can act as a buffer in two pH regimes.
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R groups
The pKa of the R group is designated here as pKR.
Peptide bond formationNucleophile= an atom or molecule that is electron-rich and seek positive charge
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Peptide bond resonance
Peptide
Peptides are 2-50 aa longMany peptides have function- hormones, neurotransmitters, sweetner Proteins are larger. Amino acids bind prosthetic groups such as metals, heme, phosphates etc.
Conjugated Proteins
ChromatographyTo understand a proteins, you need pure protein you need its sequence, you need its structure you need an assay to investigate activity.
Ion exchange
Gel Filtration (Size exclusion)
Affinity
SDS Gel Electrophoresis
Isoelectric focusing
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Purification table
Activity versus specific activity
Structure
Sequence
Protein Consensus sequence
Aligning sequences
Peptide sequencing