All of these affect protein function and give rise to the many functions of proteins. The order in which the individual residues (amino acids) are bonded contributes to the overall shape of a protein due to interactions between each amino acid side chain. This order matters so that the proper side chains can interact. The secondary structure of a protein consists of alpha helices and beta pleated sheets. Both of which play widely different roles structurally in cells. The quaternary structure categorizes interactions between different subunits of protein. Several subunits come together to perform a function they otherwise could not.

The different properties of the amino acid side chains are perhaps the most important aspect of protein function. Some are hydrophobic which are found in the centers of proteins (when the protein is globular). Others are hydrophilic and are found on the exterior of proteins. Yet are others are protonated or unprotonated in certain pH ranges. All of these give rise to incredibly diverse protein functions. As an example, there are pores in cell membranes called aquaporins that resemble hollow barrels or cylinders. These barrels are beta pleated sheets and the interior (the hole the membrane) is coated with hydrophilic amino acids while the exterior (which is hidden in the lipid bilayer of the cell membrane) consists of hydrophobic amino acids.

Polymers of amino acids are called polypeptides. A protein is made up of one or more polypeptide chains that has folded and coiled in specific 3D configurations. Nucleic acids are polymers of nucleotides. Examples of nucleic acids are RNA and DNA. Ribosomes are the site of protein synthesis and are made of rRNA and protein.

All proteins are made up of amino acids. Even though proteins are highly diverse they all can be built from the same set of 20 amino acids. Thus, the order in which these amino acids are linked together (primary structure, which is directly determined by the DNA sequence) determines its structure and function.

Amino acids are made up of carboxyl and amino groups. Hence their name, amino acids describes the functional groups found in all proteins, regardless of their R-groups. Carboxyl groups are also known as carboxylic acid groups. Glycerol is found in lipids, specifically fats where it is linked to fatty acid chains. Hydroxyl groups are also known as alcohol groups and are not present in all amino acids, although, some R-groups contain hydroxyl functional groups. 

The covalent bond between two amino acids is called a peptide bond. This is formed by positioning two amino acids so the carboxyl group of one is adjacent to the amino group of another. An enzyme then joins the two via a dehydration synthesis reaction. Ester bonds link fatty acids to glycerol heads, and phosphodiester bonds are formed between the sugar and phosphate backbone of a nucleic acid.

The primary structure of a protein is its amino acid sequence. The coils and folds of a protein are its secondary structure. Irregular contortions in the protein structure due to interactions between amino acid side chains is the tertiary structure. The overall structure when two or more polypeptides aggregated is the quaternary structure.  

Conformation is the the term for the three dimensional structure of proteins. Though the types of proteins are incredibly diverse they are all polymers made up of the same set of 20 amino acids. A protein's molecular weight involves the sum of all the atoms and their abundances, molecular weight is often used to approximate the size of a protein when determining if it will pass through a pore or channel in a membrane. The amino acid sequence is the primary structure, and is held together by peptide bonds.

Disulfide bonds may be formed in both tertiary and/or quaternary structures of a protein. These bonds result from the oxidation of the R-group (side chain) of the amino acid cysteine.

The linear sequence of amino acids in a polypeptide chain gives rise to the protein's primary structure.

The formation of disulfide bridge occurs in the tertiary and/or quaternary level of protein structure. This involves two sulfur atoms sharing a lone pair of electrons to form a covalent bond, which enhances the integrity of the protein's structure. The amino acid that is involved in forming disulfide bridges is cysteine.