Chapter 3_Amino Acids, Peptides, and Proteins (print)

Amino Acids

The building blocks of proteins.

Peptides

Small condensation products of amino acids.

Proteins

Linear heteropolymers of α-amino acids.

Ionization

The process of gaining or losing protons.

Main agents of Protein Biological Function

Catalysis

Transport

Structure

Motion

Amino Acid Properties well suited to carry biological function (4)

capacity to polymerize (join together)

useful acid-base properties

varied physical properties

varied chemical functionality

A

Alanine

R

Arginine

N

Asparagine

D

Aspartic Acid

Asp

Aspartic Acid

Asn

Asparagine

C

Cysteine

E

Glutamic Acid

Glu

Glutamic acid

Glutamine

Gln

Q

Glutamine

Gly

Glycine

G

Glycine

H

Histidine

His

Histidine

Isoleucine

Ile

I

Isoleucine

Lys

Lysine

K

Lysine

Met

Methionine

Phe

Phenylalanine

F

Phenylalanine

P

Proline

S

Serine

T

Threonine

Thr

Threonine

Tryptophan

Trp

W

Tryptophan

Tyrosine

Y

Tyr

Tyrosine

V

Valine

pKa

The measure of acidity or basicity of a molecule.

Isoelectric Point (pI)

The pH at which an amino acid carries no net charge.

Buffers

Substances that resist changes in pH.

Polymerize

The process of joining amino acids together to form peptides.

N-terminal

The starting point of numbering and naming peptides.

Cofactors

Non-amino acid components of proteins.

Coenzymes

Organic cofactors of proteins.

Prosthetic groups

Covalently attached cofactors of proteins.

Posttranslational modifications

Changes made to proteins after they are synthesized.

Uncommon amino acids

Amino acids not typically incorporated by ribosomes.

Reversible modifications

Changes to amino acids that can be reversed.

Polypeptide

A chain of amino acids linked together by peptide bonds.

Residues

The individual amino acids in a protein or polypeptide chain.

Polypeptide chains

The individual chains that make up a protein.

Conjugated proteins

Proteins that are covalently bound to a nonprotein entity, such as a lipid or carbohydrate.

Prosthetic group

covalently attached cofactors

heme in myoglobin

The nonprotein entity that is covalently bound to a cofactor conjugated protein.

Sequence

The order of amino acids in a protein or polypeptide chain.

Three-dimensional structure

The spatial arrangement of atoms in a protein.

Native fold

The natural, functional conformation of a protein.

Biochemical role

The specific function or activity that a protein performs in a biological system.

Function regulation

The mechanisms by which a protein's activity is controlled or modulated.

Physico-chemical properties

The physical and chemical characteristics of a protein, such as solubility, charge, and hydrophobicity.

Purification

The process of isolating a protein from a mixture.

Chromatography

A technique used to separate and analyze mixtures based on differences in physical and chemical properties.

Column chromatography

A type of chromatography that uses a column packed with a solid phase to separate proteins.

Ion exchange

A type of chromatography that separates proteins based on their charge.

Size exclusion

A type of chromatography that separates proteins based on their size.

Affinity

A type of chromatography that separates proteins based on their specific binding interactions.

Electrophoresis

A technique used to separate and analyze proteins based on their charge and size.

SDS-PAGE

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis, a method for separating proteins based on their molecular weight.

SDS PAGE GEL: Ingredients and Function in Buffer

SDS: detergent denatures into linear shape and coats protein in negative charge

2-Mercaptoethanol: reduces disulfide bonds to denature protein

Glycerol: To weigh the sample down when you load the sample to fall into the well

Tris HCL: Ensures proper pH

to help pull the proteins along the gel. The negative charge of the Cl ions means they move faster through the gel than the proteins.

Bromophenol Dye: Able to see the protein’s movement

What makes SDS PAGE GEL separates only by

When proteins all have the same charge and shape the only thing that the structure can be separated by is by mass only

Molecular weight

The mass of a protein or polypeptide chain, calculated by summing the atomic weights of its constituent amino acids.

At low pH, the amino acid exists in a _____ charged form

positively (cation)

At high pH, the amino acid exists in a ____ charged form

negatively (anion)

Draw this molecule’s titration curves

Isoelectric focusing

A technique used to separate proteins based on their isoelectric point.

pI (isoelectric point)

The pH at which a protein has no net charge.

2D electrophoresis

A combination of isoelectric focusing and SDS-PAGE used to separate proteins in two dimensions.

UV-visible spectrophotometry

A method used to measure the concentration of proteins and peptides based on their absorbance of UV or visible light.

Specific activity

The ratio of a protein's activity to its total protein concentration, used to assess the purity of the protein.

Protein sequencing

Determining the order of amino acids in a protein or polypeptide chain.

native fold

the folded shape of a protein is most often referred to as its native "conformation" or "structure

Edman degradation procedure

Amino acid sequence is determined by breaking disulfide bonds, cleaving the protein into small fragments

Purifies protein by removing one residue at a time