CHE 476 Chapter 3

Amino Acids, Peptides and Proteins (1-14 for exam 1)

Proteins

Linear heteropolymers of alpha-amino acids, which are linked by peptide bonds formed through condensation reactions.

Amino Acids

Possesses properties such as the ability to polymerize, versatile acid-base characteristics, varied physical attributes, and diverse chemical functionalities, aching them suitable for a wide range of biological roles.

The alpha-carbon of each amino acid has…

A carboxyl group (—COOH), an amino group (—NH2), a hydrogen atom (—H), and a variable R group (side chain) that defines the identity and properties of the amino acid.

All amino acids are _____ except glycine

Chiral

Which isomers are found in proteins

L-isomers

Nonpolar, Aliphatic R Groups

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline.

Aromatic R Groups

Phenylalanine, Tyrosine, Tryptophan.

Polar, Uncharged R Groups

Serine, Threonine, Cysteine, Asparagine, Glutamine.

Positively Charged R Groups

Lysine, Arginine, Histidine.

Negatively Charged R Groups

Aspartate, Glutamate

Peptide Formation

Via the condensation of amino acids, resulting in peptide bonds. They are smaller than proteins (Mw < 10 kDa).

The sequence of amino acids in a peptide is denoted from the…

N-terminal (amino end) to the C-terminal (carboxyl end).

Peptides are named by…

Starting from the N terminal, using full names, 3 letter codes, or 1 letter codes for longer sequences.

Native protein structure can be deduced from…

molar mass differences in SDS-PAGE and size exclusion chromatography.

Amino Acids have ___ ionizable groups

At least 2: The alpha-carboxyl group and the alpha-amino group, each with distinct pKa values.

The alpha-carboxyl group…

is acidic (pKa ~2) and will donate a proton at low pH.

The alpha-amino group…

is basic (pKa ~9-10) and will accept a proton at high pH.

Amino Acids can exist in __ ionization states

3: cationic at low pH, zwitterionic at neutral pH, anionic at high pH.

Isoelectric Point (pI)

The pH at which the amino acid carries no net charge. It can be calculated as the average of the pKa values of the ionizable groups. Amino acids are least soluble in water and do not migrate in an electric field at this point.

Buffering Capacity

Amino acids and peptides can act as buffers, resisting changes in pH around their pKa values. This property is crucial for maintaining pH homeostasis in biological systems.

Cation Exchange

Proteins with pI < 7 will be negatively charged and will not bind strongly to the column.

Proteins with pI > 7 will be positively charged and will bind strongly to the column.

Chromatography

Techniques such as ion exchange chromatography (separates proteins based on charge), size exclusion chromatography (separates based on size), and affinity chromatography (separates based on specific binding interactions) are employed to purify proteins.

Electrophoresis

SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) separates proteins based on molecular weight. Proteins are denatured and given a uniform negative charge by SDS, allowing separation purely by size.

Isoelectric focusing separates proteins based on their isoelectric points, with proteins migrating in a pH gradient until they reach a region where their net charge is zero. 2D electrophoresis combines isoelectric focusing and SDS-PAGE for high-resolution protein separation.

Protein Sequencing- Classical Method:

Edman degradation involves successive rounds of N-terminal modification, cleavage, and identification, suitable for determining short peptide sequences.

Protein Sequencing- Modern Method

Mass spectrometry (MALDI-MS and ESI-MS) accurately determines the mass of peptides and sequences, identifies posttranslational modifications, and compares sequences to databases for protein identification.

Catalysis

Enzymes like enolase and DNA polymerase facilitate biochemical reactions.

Transport

Proteins like hemoglobin and lactose permease transport molecules across cell membranes.

Structure

Proteins like collagen and keratin provide support and shape.

Motion

Proteins like myosin and actin are involved in muscle contraction and cell motility.

The Side Chains/R Groups determine…

the properties and functions of amino acids, affecting protein structure, function, and interactions.

Peptide bonds are formed by…

condensation reactions between the carboxyl group of one amino acid and the amino group of another, creating the primary structure or proteins.

Primary Structure

Linear sequence of amino acids.

Secondary Structure

Local folding into alpha-helices and beta-sheets stabilized by hydrogen bonds.

Tertiary Structure

The overall 3D structure of a single polypeptide chain.

Quaternary Structure

The assembly of multiple polypeptide subunits.