Reading Notes for Chapter 18

Chapter Summary:

Proteins are life. Every biological function is dependent upon proteins. That makes proteins a very important class of biomolecules. Proteins are biopolymers that are composed of amino acid units (often referred to as "residues"), and most biological proteins are composed of 20 (or fewer) different amino acid building blocks. The majority of the structure and function of a given protein is a result of the way these amino acid building blocks interact with (or don't interact with) water in biological systems.

Amino Acids:

Amino acids are interesting because they contain both a base (amine) and an acid (carboxylic acid) in the same molecule. While this is not unique to amino acids, it is critical to the diverse and ubiquitous function of proteins.

Focus on the different classifications of amino acids:

1. Non-polar R groups - These amino acid residues are least likely to interact with water.
2. Polar but neutral R groups - These amino acid residues will interact with water, but less strongly than charged R groups.
3. Negatively charged R groups - These are the carboxylate salts of carboxylic acid R groups. Being charged, they interact strongly with water as well as strongly interacting with positive charges, either positively charged ions in the solution or positively charged parts of the protein.
4. Positively charged R groups - These are all nitrogen-based. Being charged, they interact strongly with water as well as strongly interacting with negative charges, either negatively charged ions in the solution or negatively charged parts of the protein.

Amino acid are chiral (except for glycine). Only 1 enantiomer is typically biologically active.

Because the amino acids are both acids and bases, they undergo many typical acid-base reactions. In addition, many of the R groups in the sidechains are also acids or bases and can also undergo typical acid-base reactions.

Peptides & Proteins:

The amine of an amino acid can react with the carboxylic acid of another amino acid to form an amide linkage, also called a "peptide bond".

The formation of multiple peptide bonds leads to a biopolymer called a protein. The properties and function of proteins are determined by their structure and the specific amino acids that make up the polypeptide chain.

Protein Structure:

Protein structure is typically described as having 4 levels of structure:

1. Primary structure - This is the sequence of amino acids that make up the polypeptide backbone of the protein.
2. Secondary structure - This level of structure is determined by the interaction of "near-neighbor" amino acids in the polypeptide chain. The geometrical constraints of bond lengths and angles in the polypeptide backbone and the R groups of the sidechains lead to some very well-defined secondary structures including alpha-helix and beta-sheet.
3. Tertiary structure - This level of structure is determined (mostly) by the interaction of the various secondary structure components. Alpha-helices orient themselves in specific ways in relation to other alpha-helices and/or beta-sheets. Tertiary structure is largely responsible for the specific function and selectivity of proteins.
4. Quaternary structure - This level of structure exists when multiple separate proteins combine to form a larger structure.

When protein are "denatured", their structure is disrupted. The extent of this disruption depends on the strength of the interactions giving rise to the structure (ion-ion interactions, hydrogen-bonding, disulfide bonds, etc) and the denaturing conditions. Disrupting the structure of a protein alters or destroys its function.

Enzymes:

Enzymes are biological catalysts, most of which are proteins or contain proteins. Catalysts increase the rate of a chemical reaction without being consumed by the chemical reaction.

Enzymes are often extremely specific in the reaction(s) they will catalyze. This specificity is due to the very precise structure of the protein(s).

An enzyme and its substrate can be thought of as interacting like a lock and a key - if the key (substrate) doesn't fit the lock (enzyme) exactly, the reaction will not work.

In general, chemical reactions are faster at higher temperatures. This is also true of enzyme-catalyzed chemical reactions, but only until the heat starts to denature the protein.

Inhibitors are substances which decrease an enzyme's activity. In the case of many "poisons", the poison is something that sort of matches the substrate for an enzyme and binds at the active site of the enzyme, which blocks the correct substrate from binding.

Enzyme cofactors are additional "pieces" that are required for an enzyme to function. These cofactors often impact the structure at the active site or provide additional functional groups to complete the reaction that the enzyme catalyzes.