Chapter 3: Proteins

Proteins

Cell’s building blocks and execute the majority of cell’s functions.

Most abundant protein on earth

RubisCo

Most abundant protein in mammals

Collagen

Polypeptides

A polypeptide is a chain of amino acids linked together by peptide bonds.

Peptide bond

A peptide bond is a covalent bond that forms between the carboxyl group (-COOH) of one amino acid and the amino group (-NH2) of another amino acid during a condensation reaction.

Disulphide bridges

Disulfide bridges, also known as disulfide bonds, are covalent bonds that form between two sulfur atoms in different cysteine residues within a protein or peptide.

Hydrogen bond

A hydrogen bond is a relatively weak, non-covalent interaction that occurs between a hydrogen atom covalently bonded to an electronegative atom (such as nitrogen, oxygen, or fluorine) and another electronegative atom in a different molecule or within the same molecule.

Ionic bond

An ionic bond is a type of chemical bond that forms between two atoms or ions with significantly different electronegativities.

Hydrophobic interactions

Hydrophobic interactions are interactions between nonpolar molecules or regions of molecules that occur in the presence of water.

Amino acids

Amino acids are organic compounds that serve as the building blocks of proteins.

Zwitter ions

Dipolar ions

Acidic amino acid

* It contains an extra COOH group.
* Aspartic acid, Glutamic acid.

Basic amino acid

* It contain extra NH2 group.
* Histidine, Lysine, Arginine.

Neutral amino acid

* It contains one NH2 group and one COOH group.
* Asparagine, serine, tyrosine, etc.

Amino acid with aliphatic group

Glycine, Alanine, Valine, Isoleucine, Leucine

Amino acids containing hydroxyl (-OH) groups

Serine, Threonine

Sulphur containing amino acids

Cysteine, Methionine

Acidic amino group

Aspartic acid, Asparagine, Glutamic acid, Glutamine

Basic

Leucine, Arginine, Histidine

Aromatic

Phenylalanine, Tryptophan, Tyrosine

Imino

Proline

Non-polar amino acids

no charge on the R-groups

Polar amino acids

charge on the R-group

Essential amino acid

* Not synthesized in our bodies.
* Need to be taken in our diets.

Non-essential amino acids

Synthesized in their body cannot be taken in diet.

Semi-essential amino acids

Produced at a very slow rate can be synthesized by the adult body but not in growing children.

Simple protein

Made up of amino acids.

Conjugate protein

Made up of protein + nonprotein part.

Derived protein

* Primary: Due to denaturation of protein.
* Secondary: formed due to digestion.

Complete protein

All 20 essential amino acids are present.

Incomplete protein

One/two essential amino acids lacking.

Monomeric protein

made up of one polypeptide chain.

Oligomeric protein

made up of two/more polypeptide.

primary structure

It is a linear chain of amino acids linked by peptide bonds.

secondary structure

It comprises of alpha helix and beta plated sheet.

Alpha helix

a most common type of secondary structure and rigid rearrangement of polypeptide chain.

Beta-plated sheet

made up of 2 or more polypeptide chains are held together by intermolecular-H bonding.

Tertiary structure

protein of tertiary structure are highly folded and globular in nature.

Quaternary structure

it is made up of two or more than two polypeptide chain

largest enzyme

peroxidase

smallest enzyme

catalase

Oxidoreductase

* enzymes involved in oxidation-reduction reaction.
* alcohol dehydrogenase, cytochrome oxidase.

Transferase

* Enzyme that catalyze reactions the transfer of functional group.
* e.g.: hexokinase, trans-aminase.

Hydrolase

* Enzyme catalyzing hydrolysis of ester, ether, peptides etc.
* These enzyme breaks large molecules into smaller molecules by the introduction/presence of H2O molecules.

Lyases

* They break specific covalent bonds and remove a group without hydrolysis, oxidation etc.
* e.g. Aldolase, fumarase.

Isomerase

Rearrangement of molecular structure to form isomers.

Ligases

Enzyme catalysing the synthetic reaction where two molecules are joined together.

Simple enzyme

consist of only proteins and catalyze their substrate specific reactions.

Conjugate enzyme

Made up of protein and non-protein parts.

Prosthetic group

A prosthetic group is tightly bound organic co-factor.

Coenzyme

A coenzyme is a loosely bound/organic co-factor. It can be easily removed.

Lock and key hypothesis

* According to this theory:
* Enzymes are rigid and pre-shaped.
* Substrate fit to the active site just as a key fit into a proper lock.

Induced fit theory

* Proposed by Kosh land.The monomer
* Most accepted hypothesis on the basis of enzyme action.
* Enzymes are not rigid and pre-shaped.

Inhibitors

chemical molecules that inhibit enzyme activity

Competitive inhibitors

* Inhibitors are structure similar to substrate.
* They favor lock and key hypothesis.
* Reversible in nature.
* Km increase but Vmax remain constant.

Non-competitive inhibitors

* Some inhibitors do not compete for active site of enzyme but destroy the structure of enzyme, the physical structure of enzyme is altered as a result and do not form enzyme-substrate complex.
* They favor induced-fit theory.
* Irreversible in nature.
* Km remain constant but Vmax change.