Comprehensive Guide to Amino Acids, Peptides, and Protein Structure

Amino Acids

Building blocks of protein.

Proteins

Main agents of biological function.

Catalysis

The process by which enzymes accelerate chemical reactions.

Transport

The function of proteins that involves moving substances across cell membranes.

Structure

The role of proteins in providing support and shape to cells and tissues.

Motion

The function of proteins that enables movement in muscle tissue.

α-amino acids

The building blocks of proteins, characterized by having an amino group, a carboxyl group, and a unique R group.

Chirality in Amino Acids

All amino acids are chiral except glycine.

L amino acids

The form of amino acids that proteins only contain.

Classification of Amino Acids

Common amino acids can be classified into five groups based on their R substituents.

Nonpolar, aliphatic amino acids

A group of amino acids that includes 7 members.

Aromatic amino acids

A group of amino acids that includes 3 members.

Polar, uncharged amino acids

A group of amino acids that includes 5 members.

Positively charged amino acids

A group of amino acids that includes 3 members.

Negatively charged amino acids

A group of amino acids that includes 2 members.

UV light absorption by amino acids

Amino acid side chains absorb UV light at 270-280 nm.

Hydrogen bonds in amino acids

Amino acid side chains can form hydrogen bonds.

Disulfide bonds

Cysteine can form these types of bonds.

One Letter Code for Amino Acids

A system where each amino acid is represented by its first letter or a unique letter.

Cysteine

Amino acid represented by the letter C.

Histidine

Amino acid represented by the letter H.

Isoleucine

Amino acid represented by the letter I.

Methionine

Amino acid represented by the letter M.

Serine

Amino acid represented by the letter S.

Valine

Amino acid represented by the letter V.

Alanine

Amino acid represented by the letter A.

Glycine

Amino acid represented by the letter G.

Leucine

Amino acid represented by the letter L.

Proline

Amino acid represented by the letter P.

Threonine

Amino acid represented by the letter T.

Arginine

Amino acid represented by the letter R.

Phenylalanine

Amino acid represented by the letter F.

Tyrosine

Amino acid represented by the letter Y.

Tryptophan

Amino acid represented by the letter W.

Aspartate

Amino acid represented by the letter D.

Glutamate

Amino acid represented by the letter E.

Asparagine

Amino acid represented by the letter N.

Glutamine

Amino acid represented by the letter Q.

Lysine

Amino acid represented by the letter K.

Free energy (ΔG)

The values reflect the free energy (ΔG) of transfer of the amino acid side chain from a hydrophobic solvent to water.

Favorable transfer

This transfer is favorable (ΔG < 0; negative value in the index) for charged or polar amino acid side chains.

Unfavorable transfer

This transfer is unfavorable (ΔG > 0; positive value in the index) for amino acids with nonpolar or more hydrophobic side chains.

Hydropathy index

A scale combining hydrophobicity and hydrophilicity of R groups.

Cysteine classification

Cysteine is generally classified as polar despite having a positive hydropathy index.

Sulfhydryl group

The ability of the sulfhydryl group to act as a weak acid and to form a weak hydrogen bond with oxygen or nitrogen.

Proline surface occurrence

As originally composed, the hydropathy index takes into account the frequency with which an amino acid residue appears on the surface of a protein.

pKa values

The values at which protons can be ionized from an amino acid, with each group having its own pKa.

Zwitterion

A form of an amino acid that has both a positive and negative charge, existing between the pKa values of the amino and carboxyl groups.

Isoelectric Point (pI)

The specific pH at which an amino acid carries a net charge of zero, calculated as pI = (pK1 + pK2)/2.

Cation

The positively charged form of an amino acid that exists at low pH.

Anion

The negatively charged form of an amino acid that exists at high pH.

Buffer

A substance that prevents changes in pH, with amino acids acting as buffers in two pH ranges based on their pKa values.

Ionizable side chains

Side chains of amino acids that can influence the pI and can also be titrated.

Titration curves

Graphs that show how the pH of a solution changes as acid or base is added, becoming more complex with ionizable side chains.

pK1

The pKa value associated with the carboxylic acid group of an amino acid.

pK2

The pKa value associated with the amino group of an amino acid.

Chemical Environment

Factors that affect the pKa values of amino acids, making the α-carboxy group more acidic and the α-amino group slightly less basic.

Protonation

The process of adding a proton (H+) to a molecule, occurring at low pH for the carboxylic acid and at high pH for the amino group.

Hydrophilic

Referring to molecules that are attracted to water, often associated with charged or polar amino acid side chains.

Hydrophobic

Referring to molecules that repel water, often associated with nonpolar amino acid side chains.

Average occurrence

The frequency of an amino acid's presence in more than 1,150 proteins, providing insight into its biological significance.

pKa of α-carboxyl group

The pKa value of the α-carboxyl group, which is 2.34 for glycine.

pKa of α-amino group

The pKa value of the α-amino group, which is 9.6 for glycine.

pI

Isoelectric point, calculated as (pKR + pK2)/2.

pI Calculation

To calculate the pI when the side chain is ionizable, identify the species with net zero charge, the pKa value defining acid strength (pKR), the pKa value defining base strength (pK2), and take the average of these two pKa values.

Peptides

Small condensation products of amino acids, typically with a molecular weight less than 10 kDa.

N-terminal

The amino terminus of a peptide where numbering and naming starts.

Insulin

A hormone involved in sugar metabolism.

Oxytocin

A hormone associated with childbirth.

Substance P

A neuropeptide that acts as a pain mediator.

Polymyxin B

An antibiotic effective against Gram-negative bacteria.

Bacitracin

An antibiotic effective against Gram-positive bacteria.

Amanitin

A toxin found in mushrooms.

Conotoxin

A toxin from cone snails.

Chlorotoxin

A toxin from scorpions.

Cofactors

Functional non-amino acid components that can be metal ions or organic molecules.

Coenzymes

Organic cofactors, such as NAD+ in lactate dehydrogenase.

Prosthetic groups

Covalently attached cofactors, such as heme in myoglobin.

Posttranslational modifications

Other modifications that proteins may undergo after translation.

Cytochrome c

A protein with a molecular weight of 12,400 and 104 polypeptide residues.

Ribonuclease A

A protein with a molecular weight of 13,700 and 124 polypeptide residues.

Lysozyme

A protein with a molecular weight of 14,300 and 129 polypeptide residues.

Myoglobin

A protein with a molecular weight of 16,700 and 153 polypeptide residues.

Chymotrypsin

A protein with a molecular weight of 25,700 and 245 polypeptide residues.

Hemoglobin

A protein with a molecular weight of 64,500 and 574 polypeptide residues.

Serum albumin

A protein with a molecular weight of 66,000 and 609 polypeptide residues.

Hexokinase

A protein with a molecular weight of 107,900 and 972 polypeptide residues.

Polypeptides

Chains of amino acids that can have differing sequences and arrangements, giving them unique chemical characteristics.

Chromatography

A technique used for the separation of proteins based on their physical and chemical properties.

Column Chromatography

A method that allows separation of a mixture of proteins over a solid phase using a liquid phase.

Ion Exchange Chromatography

A separation technique based on the charge of proteins.

Size Exclusion Chromatography

A separation method that separates proteins based on their size.

Affinity Chromatography

A technique that separates proteins based on their binding affinity for a specific ligand.

Specific Activity

The ratio of activity to total protein concentration, indicating the purity of the protein of interest.

Electrophoresis

A method for separating proteins based on their charge and size using an electric field.

SDS-PAGE

A type of electrophoresis that separates proteins by molecular weight using sodium dodecyl sulfate.

Isoelectric Focusing

A technique used to determine the isoelectric point (pI) of a protein.

2D Electrophoresis

A method that combines isoelectric focusing and SDS-PAGE for protein separation.

Lambert-Beer Law

A principle used in UV-visible spectrophotometry to relate absorbance to concentration.

Edman Degradation

A classical method for determining the amino acid sequence of a protein by successive rounds of modification and cleavage.