What are Proteins?

Proteins are the building blocks from which cells are assembled.

They adopt the philosophy “structure dictates function”

Proteins are assembled from a set of 20 different a-amino acids.

They are called alpha amino acids because the amine is attached to the carbon alpha to the carbonyl group.

A protein molecule is made from a long chain of these amino acids, each linked to its neighbor through a covalent peptide bond.

Proteins, therefore, are also called polypeptides.

Each amino acid in a polypeptide chain is referred to as a residue.

There are twenty standard amino acids, each of which include a carboxyl group, a amino group, a hydrogen, and a side group all bonded to a chiral carbon center.

They typically differed only in their side chain/group, often designated as R group

Amino acids are the structural units (monomers) that make up proteins. Created with BioRender.

All amino acids residues are L-stereoisomers.

All amino acids, other than glycine, have a chiral carbon.

The position and nature of charges will depend on the pH of the solution.

Free amino acids are zwitterion at neutral pH.

The amino group is protonated and the carboxylic group is deprotonated.

Digested proteins reach the cells of the human body as single amino acids.

There are also 10 essential amino acids in humans, which means that these amino acids can’t be formed, so we must ingest them.

The amino acids are joined by peptide bonds from dehydration from the alpha- carboxyl group of one amino acid and the alpha-amino group of another.

Formed via a condensation (dehydration) reaction.

The peptide bond can exist in two conformations, cis and trans.

Peptide bonds are generally in the trans formation.

This key fact influences the types of secondary structure that form.

The sequences of peptides are always written from the N-terminal end to the C- terminal end.

Folding Patterns of Proteins

The final folded structure, or conformation, adopted by any polypeptide is determined by energetic considerations: a protein generally folds into the shape in which the free energy is minimized.

Hydrophobic, nonpolar, molecules including the nonpolar side chains of some amino acids tend to be forced together inside the folded protein thus avoiding contact with the aqueous cytosol and not disrupting hydrogen bonds that the hydrophilic, polar, amino acids are creating on the outside with H2O.

Amino acid sequence, primary structure, dictates the folding conformation of the protein and is unique to every protein.

Folding generally occurs in a step by step or hierarchical manner; local secondary structures come together to form tertiary structure etc

Types of Proteins

There are two (2) types of proteins:

1) Globular Proteins:

In which the polypeptide chain folds up into a compact shape like a ball with an irregular surface.

Enzymes are usually globular proteins.

2) Structure/Fibrous Protein:

Relatively simple, long polymers

Maintain and add strength to the cellular and matrix structure

Example: Collagen, made from a unique type of helix (triple helices of polypeptides rich in glycine and proline) and is the most abundant protein in the body.

It is very tough because it crosslinks with itself.

Most common extracellular matrix protein in the body.

Glycoproteins are proteins with a carbohydrate group attached and they are a component of cellular plasma membranes.

Also serve as markers for cellular recognition.

Proteoglycans are also a mixture of proteins and carbohydrates, buy they generally consist of more than 50% carbohydrates.

Major component of extracellular matrix.

Cytochromes are proteins which require a prosthetic (nonproteinaceous) heme group in order to function.

Cytochromes get their name from the color they add to the cell.

They are present in the METC and are responsible for electron shifting there.

Protein Structure

Primary Structure of Protein

The number and sequence of amino acids in a polypeptide is called the primary structure.

Secondary Structure of Protein

Secondary structure of proteins can be one of two (2) conformations, and result from hydrogen bonding between N-H and C=O:

a. alpha-helix:

A hydrogen bond is made between every forth peptide bond, linking the C=O of one peptide bond to the N-H of another.

Sometimes 2 a-helices will wrap around each other to form coiled-coil structure.

Occurs when the 2 a-helices have most of their nonpolar side chains on one side, so they can twist around each other.

b. beta-pleated sheets:

Made when hydrogen bonds form between segments of polypeptide lying side by side.

B-pleated sheets can be arranged into parallel B sheets and antiparallel B sheets

Parallel B sheets both neighboring polypeptides run in the same direction N-C terminus’s or C-N terminus’s

Antiparallel B sheets both neighboring polypeptides run in different directions N-C terminus’s and the other in C-N terminus’s

Secondary folding patterns aren’t uniform, they are usually broken up in the protein folding pattern with multiple alpha helices and B sheets in the protein.

The amino acid proline will disrupt both a-helix and B-pleated sheets, which assists in the creation of the tertiary structure.

Tertiary Structure of Protein

3. Tertiary structure:

The curls and folds of secondary structure to form an overall three-dimensional structure.

Most hydrophobic side chains are buried away from water

Typically compact

Most charged chains are on the outer face hydrated to water molecules

The biggest contributing factor to tertiary structure come from the hydrophobic forces

Tertiary structures are stabilized by Hydrogen bonding, Electrostatic interactions, van der Waals forces, hydrophobic forces, covalent disulfide bonds, between two cysteine amino acids on different parts of the chain.

Quaternary Structure of Protein

4. Quaternary structure:

When two or more polypeptide chains bind together.

The same 5 forces at work in tertiary structure can also act to form the quaternary structure.

Protein Stablization

When a cell is exposed to extracellular conditions they will create covalent cross- linkages , both intra and inter.

Most often they are disulfide bonds, and they do not change the conformation of the protein, but instead reinforce it.

Disulfide bonds occur between 2 cysteine amino acids.

Disulfide bonds usually don’t form in the cell cytosol, because of a high concentration of reducing agents

A protein can be unfolded, or denatured, by treatment with certain solvents that disrupt the noncovalent interactions holding the folded chain together.

When a protein is denatured all that remain is the primary structure.

When the denaturing solvent is removed the protein often refolds spontaneously, or renatures, into its original conformation, this indicates that the primary structure is what determines the folding pattern of the protein.

Many proteins require helper proteins called molecular chaperones to help fold into the proper energetically favorable tertiary native structure.

Protein Destabilizing Agents

Denaturing Agents	Forces Disrupted
Urea	Hydrogen bonds
Salt or pH change	Electrostatic forces
Mercaptoethanol	Disulfide bonds
Organic solvents	Hydrophobic forces
Heat	All forces