Chemical behavior of the protein is studied such as activity, solubility, and electrical charge.

Protein molecules are polymers composed of amino acids (monomer).

There are 20 different amino acids. They are differentiated based on their R - Group.

Peptide Bonds - Hundreds of amino acids chained together.

A peptide bond is formed between the carboxyl group of one amino acid and the amino group of an adjacent one. This is called Dehydration Synthesis.

Amino acids bond together by forming long polypeptide molecules. This occurs in the ribosome of the cell.

A polypeptide chain is referred to as the primary structure.

The primary structure of a polypeptide chain is just the beginning of the complex folding process that creates a functional protein.

The secondary structure of a protein is formed by the folding of the polypeptide chain into patterns such as alpha helices and beta sheets. These patterns are stabilized by hydrogen bonds between the amino and carboxyl groups of the polypeptide backbone.

The tertiary structure is formed by the further folding of the secondary structure, creating a three-dimensional shape. This shape is crucial for the protein's function and is stabilized by various types of bonds such as disulfide bonds and hydrophobic interactions.

Finally, some proteins may have a quaternary structure, which involves the association of multiple polypeptide chains to form a functional protein complex.

The process of protein folding is complex and can be influenced by various factors such as pH, temperature, and the presence of other molecules. Any disruptions in this process can lead to misfolded proteins, which can have serious consequences for cellular function and human health.

1. Peptide bonds

2. Hydrogen bonds

3. Disulfide Bonds

4. Protein

Non - Polar = Share equally. Ex - Lipids

Polar - Do Not share equally. Ex - Water

Protein Functions

Structural - Provide structure and support for cells.

Enzyme - Act as catalyst to speed up biochemical reactions by building up or breaking down other molecules.

Transport - Bind and carry atoms and small molecules within cells and throughout the body.

Hormone - Act as messengers to transmit signals to coordinate biological processes between different cells.

Antibody - Bind to specific foreign particles to help protect the body.

Recognition - Receive chemical signals from the outside of a cell and translate chemical signals into intracellular action.

Enzymes are highly specific!! Most enzymes require cofactors.

Temperature of Reaction -

low temps - fewer substrates bump into enzymes and reaction rate is slow

high temps - too much stress of H-bonds holding the enzyme shape and enzyme begins to unravel so denaturing occurs.

Most enzymes kept cold to reduce chance of denaturing.

pH - Every enzyme has an optimum pH for maximum activity. In solutions with extreme pH, ions may interfere with enzyme activity or cause it to denature.

Studying Proteins

Polyacrylamide gel electrophoresis (SDS-PAGE) is a vertical polyacrylamide gel electrophoresis used to separate proteins based on size/mass. Sodium Dodecyl Sulfate (SDS Detergent) binds to the proteins to make them uniformly negative charged.

Western Blots - is a technique used to determined whether a protein band on a gel is actually the protein of interest with the help of a specific antibody. An enzyme linked antibody is added to colonize the protein bands.

ELISA - uses antibody to recognize specific proteins can be used to detect and measure the presence and concentration of a specific protein in a mixture. A spectrophotometer can be used to determine the concentration.

X-ray Crystallography - Determines the 3-D structure of a protein.

Spectrophotometer - Measures the protein concentration in a solution using the transmittance of light and the absorption of light in a protein sample. Reagents are added to visualize the protein.

Mass Spectrometry - an analytical tool useful for measuring the mass-to-charge ratio (m/z) of one or more molecules present in a sample. Used to calculate the exact molecular weight.

Bradford Assay - is based on the absorption of light as a function of wavelength. The coomassie G-250 dye exist in its catatonic state (Positive)

Protein Extraction and Purification

Intracellular - proteins are made and function inside the cell - to harvest the cells must burst open. Detergents can be used to open the cell, but it dentures many proteins and is difficult to isolate protein. Sonication uses high frequency sound waves to break open cells - disadvantage - thousands of proteins are released making it hard to isolate and purify.

Extracellular - Proteins are made in cells and function outside cell - much easier to isolate. Recovery begins by separating the protein from cell debris, either by filtering or centrifugation.

Purification separates other proteins from the desired proteins using column chromatography. The final product is run through a series of filters to concentrate the product and to remove small contaminate molecules - ULTRAFILTRATION.

Open Column - (gravity flow) chromatography uses a plastic or glass column packed with resin. Samples added to the top. Works well for small volumes.

Fast-Performance Liquid Chromatography - Uses pressure pumps to purify proteins - gives faster and better separation of similar compounds. Good for large volumes.

High Performance Liquid Chromatography - Uses tiny columns made of metal that can withstand very high pressures. Good for studying tiny amounts of protein, DNA, rNA

Immunoaffinity Chromatography - Uses the specific binding of an antibody to target the protein. The protein can be eluted by changing pH or salinity.

Gas Chromatography - One of the first types of chromatography. Uses boiling point, vapor pressure, and polarity to separate components of mixtures.

LAB

Enzyme - Cellobiase

Substrate - P-nitrophenyl Glucopyranoside

Product - P-nitrophenol and Glucose (Color Yellow)