Proteins are polymers of amino acids. Each amino acid consists of an amino group, a carboxyl group, a H atom and a distinctive R group all of which are bonded to an alpha C. 

In proteins, the alpha carboxyl group of one amino acid is joined to the alpha amino group of another amino acid by a peptide bond which results from the loss of a water molecule. A polypeptide is many amino acids joined by such peptide bonds. By convention, the amino end is taken to be the start of a polypeptide. The bond between the carbonyl carbon and the N atom of the peptide bond is rigid (not free to rotate) because it has partial double bond character. In contrast, bonds between the alpha C and carbonyl C as well a between the alpha C and peptide N are single bonds with a large degree of rotational freedom.

The R group or side chain is what gives each amino acid its unique properties. There are 20 different side chains used to make up the 20 different amino acids which occur in nature which are grouped according to whether their side chains are acidic, basic, uncharged polar or nonpolar.

Acidic R Side Chains   (The residue has a negative charge due to a loss of H ion at physiological pH and the residue is attracted by aqueous solutions so as to seek the surface positions in the conformation of a peptide in which it is contained when the peptide is in aqueous solution. at a pH of greater than 4, the carboxyl side chains of D and E are negative.)

Basic R Side Chains (the residue has a positive charge due to association with H ion at physiological pH and is attracted by aqueous solution so as to seek the surface positions in the conformation of a peptide in which it is contained when the peptide is in aqueous medium at physiological pH)

Non Polar Side chains (1. neutral/non-olar: the residues are not charged at physiological pH and the residue is repelled by aqueous solution so as to seek the inner positions in the conformation of a peptide in which it is contained when the peptide is in aqueous medium. These residues are also designated “hydrophobic residues” 2. nuetral/polar: the residues are not charged at physiological pH, but the residues are attracted by aqueous solution so as to seek the outer positions in the conformation of a peptide in which it is contained when the peptide is in aqueous medium)

Uncharged Polar Side Chains

, pK and pI of proteins: The net charge of a protein depends on the .  For example, at a high pH, carboxylic acids tends to be charged and amines uncharged. At a low pH, carboxylic acids are uncharged and amines are charged. In the cell the pH is close to 7, and almost all carboxylic acids and amines are in their fully charged form. 

The at which exactly half the carboxylic acid or amine residues are charged is known as the pK of that amino acid side chain.For example, the pK of aspartic and glutamic acid is about 4.7. Below that value, these 2 acidic amino acids with take up an H and remain uncharged. Above that pK 1/2 of the residues will be in their charged negative form.

Peptides are short chains of amino acids connected sequentially by peptide bonds. Chains with 2-50 units are classified as pptides, while longer chains are usually classified as proteins. A skilled artisan can synthesize peptides by using an automated peptide synthesizer (for example, an Applied Biosynstems model 430A) using standard t-Boc chemistry as reported by Carpino, L.A., J. Am Chem Soc, 79:4427 (1957)

The primary structure of a protein refers to the linear arrangement of amino acids.

A protein’s secondary structure consists of regular, repeated pattern of orientation of parts of a polypeptide chain. One such regular structure is the alpha helix which is like a coil that turns in the direction a screw would turn. Short regions of alpha helix are especially abundant in proteins located in cell membranes, such as transport proteins and receptors. 3 types of are involved in secondary structure. These are the 1) all important hydrogen bond, 2) ionic bonds and 3) Van der Waals attractions.

A protein’s tertiary structure refers to the folding of regions between secondary features to give the overall shape of the protein or parts of it (domains) with specific functional properties.

A protien’s quaternary structures results from the association of 2 or more polypeptide chains.

All proteins bind or stick to other molecules. Any region of a protein’s surface that can interact with another molecule through sets of noncovalent bonds is called a binding site. The substance that binds to a protein is referred to as a ligand for that protein. 

If a binding site recognizes the surface of a second protein, the tight binding of 2 folded polypeptide chains at this site creates a larger protein molecule . Each polypeptide chain in such a protein is called a protein subunit. In a simple example, 2 identical folded polypeptide chains bind to each other in a head-to-head arrangement, forming a dimer. Hemoglobin contains 2 identical alpha globin subunits and 2 identical B globin subnits. Whena protein molecule is formed as a complex of more than 1 polypeptide chain, the complete structure is sometimes called the quaternary structure of that protein. 

In addition to the primary-quaternary structures, any part of a polypeptide chain can fold independently into a compact stable structure called a protein domain. Different domain of a protein are often associated with different functions. For example, the Src protein kinase fucntions in signaling pathways. This protein has 4 domains: the SH2 and SH3 domains which have regulatory roles with 2 other domains that are responsbile for kinase catalytic activity.

Linkages such as disulfide bonds can either tie 2 amino acids in the same protein together or connect different polypeptide chains in a multisubunit protein. Disulfide bonds do not change the conformation of a protein but rather act as atoic staples to reinforce its most favored conformation. Disulfide bond formation is catalyzed in the endoplasmic reticulum by an enzyme that links together 2 pairs of –SH groups of cysteine side chains that are adjacent in the folded protein. Such bonds usually fail to form in the cell cytosol where a high concentration of reducing agents converts S-S bonds back to cysteine –SH groups.

Proteins have impressive chemical ability because the neighboring  on their surface often interact in ways that enhance the chemical reactivity of amino acid side chains. For example, when amino acid side chains interact with one another through hydrogen bonds, normally unreactive side groups such as the CH2OH on the serine shown below can become reactive, enabling them to enter into reactions that make or break selected covalent bonds. This rearrangement of electrons is just one way that , a special class of proteins, can increase reaction rates.

Proteins often need small nonprotein molecule to be active. An example of a protein that contains a nonprotein pootion is hemoglobin (“hb”). A molecule of hb contains 4 subunits (polypeptide chains) called “heme groups” which are ring shaped molecules each with a single central iron atom.  By binding reversibly to O2 through its iron atom, heme enables hemoglobin to pick up oxygen in the lungs and release it in the tissues. Hemoglobin is an allosteric protein in that the binding of O2 is regulated by interactions between separate, nonadjacent sites. In one model of this allosteric nature of hb, binding of O2 to 1 subunit changes the conformation of this subunit from the tauter (T) to the relaxed (R) state but it does not change the conformation of the adjacent subunits. This change from T to R for all the subunits only occurs when at both the alpha and beta dimers of Hb contain at least 1 O2 which has bound. 

The binding of O2 to Hb is cooperative in nature in that binding of O2 enhances the binding of additional Hb to O2. It is this cooperative nature of Hb which gives Hb an usually high affinity for O2. If one compares. the binding to O2 of myoglobin (found in muscle tissue is composed of one subunit with only 1 heme to which O2 can bind) one will see that Mb has a higher affinity for O2. This can be seen by plotting Y, the fractional occupancy of all O2 binding sites in a solution on the Y axis versus PO2 on the x axis.  Mg exhibits a hyperbolic curve which will be to the left of the sigmoidal curve of Myglobin. The hyperbolic curve of Hb is sometimes rearranged to a straight line which is sometimes referred to as a “hill plot”.

There are various factors which decrease the affinity which hemoglobin has for O2. (1) lowering the pH (increased acidity), (2) increasing CO2 (forms salt bridges that stabilize the T form) and (3) a ligand called BPG all shift the O2 dissociation curve for Hb to the right.

Conservative Amino Acid Substitution

There is tremendous variability in the importance of individual amino acids in protein sequences. On the one hand, nonconcervative residue substitutions can be tolerated wtih no loss of activity at many residue positions, especially those exposed on the protein surface. On the other hand, destabilizing mutations can occur at a large number of different sites in a protein, and for many proteins such mutations account for more than half of the randomly isolated missene mutations that confer a defective phenotype. At sites that are key determinatans of stability or activity, even residue substituions that are generally considered to be conservative (.e.g, Glu-Asp, Asn-Asp, Ile-Leu, Lys-Arg and Ala-Gly) can have severe phenotypic effects. Unofrtunately, this means that there is no simple way to infer the likely effect of an amino acid substitution on the basis of sequence information alone. A nonconservative Gly-Arg substitution could be phenotypically silent at one position while a conservative Asn-Asp change could ldead to complete loss of activity at another position. (Pakula, “Genetic analysis of protein stability and funciton” Annu. Rev. Genet. 1989, 23: 289-310). 

Falkenstein (US 14/934866, published as US 2017/0066814) lists amino acids groups according to their common side chain properties.