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