Peptide bonds form between the amine group of one amino acid and the carboxylic acid of another via a covalent linkage. The formation of a polypeptide chain from amino acid residues constitutes the protein primary structure.

Secondary structure is formed by hydrogen bonding between the amino and carboxyl backbone units of the polypeptide. Tertiary structure is formed by disulfide covalent bonds, hydrophobic interactions, and R-group hydrogen bonding. Quaternary structure is the joining of multiple polypeptide subunits.

Peptide nuerohormones are synthesized in the rough endoplasmic reticulum of the cell body of the neuron. They are then packaged in the Golgi complex and transported along the axon to the nerve endings. Since peptide hormones must be transported out of the cell in vesicles, they are not likely to be synthesized by cytoplasmic ribosomes. These ribosomes are primarily involved in synthesizing cytoplasmic proteins that do not leave the cell.

The nucleus houses DNA and is the site of transcription. The nucleolus is the site of ribosomal submit synthesis. The smooth endoplasmic reticulum is responsible for certain waste disposal and other functions.

Euchromatin is the most active part of the genome and is almost always in active transcriptional mode. mRNA is formed via transcription from DNA in the nucleus, in the form of euchromatin, as opposed to heterochromatin. Heterochromatin is characterized by tight winding of DNA around histones, such that it cannot easily be accessed by RNA polymerase and transcription proteins. Most DNA resembles euchromatin during interphase, when transcription is most active, and condenses to heterochromatin during mitosis.

Note that assembly of eukaryotic ribosomal subunits takes place in the nucleolus, but mRNA is always transcribed directly from DNA within the greater nuclear structure.

Denaturation of a protein involves the breakdown of noncovalent bonds between amino acid residues. The formation of noncovalent bonds, such as hydrogen bonding and van der Waals forces, lead to higher order structures such as secondary, tertiary, and quaternary structure. Upon denaturation these noncovalent bonds in the protein chain are broken and the protein reverts back to its primary structure. The primary structure of a protein consists of the amino acid sequence joined together by peptide bonds (covalent bond). Covalent bonds are much stronger and more permanent that hydrogen bonds and other intermolecular forces, and can endure denaturation. Environmental conditions such as temperature and pH contribute to denaturation of a protein.

Recall that all amino acids have a carboxylic acid, amino group, hydrogen, and a functional group attached to their central carbon. In nonpolar amino acids the functional group will not contain any groups capable of protonation or deprotonation. The changes due to the pH in a nonpolar amino acid will only involve the amino and carboxylic acid groups.

A solution with pH of 13 is very basic. The carboxylic acid will be deprotonated and the amine will be intact (neither protonated nor deprotonated). The deprotonated carboxylic acid will give an overall charge of  to the molecule.

Hydrolysis reactions involve breakdown of molecules (lysis) in the presence of water. Water is a reactant in hydrolysis reactions. Dehydration synthesis reactions involve formation of bonds between molecules (synthesis) and removal of water at the end of the reaction (dehydration). Water is a product in dehydration synthesis reactions.

During the formation of peptide bonds a hydroxyl group from carboxylic acid and a hydrogen atom from the amino group are released and form water. Formation of peptide bonds is a dehydration synthesis reaction because bonds are synthesized and water is released.

Formation and destruction of bonds within macromolecules always involve a hydrolysis or a dehydration synthesis reaction. Esterification and hydrogenation reaction refer to other organic chemistry processes.

Proteins are made up of amino acids that undergo a series of dehydration reactions, which link them together to form the primary structure of a protein. Amino acids are linked together by peptide bonds, while nucleic acids are linked via phosphodiester bonds. The secondary structure of the protein is formed by hydrogen bonding between the amino acid backbones. Every protein will have primary and secondary structure, and thus will have hydrogen bonding.

Disulfide bridges help to construct tertiary structure, but only occur between cysteine residues. Cysteine will not necessarily be present in every protein, and there are some proteins that cannot form disulfide bridges. Similarly, not all proteins will contain glycine.

Aldehyde groups are frequently found in carbohydrates, but do not often appear in proteins.

Whenever you think about disulfide bonds you should think about cysteine. Cysteine contains a sulfur atom in a sulfhydryl group that is capable of forming a disulfide bridge with another sulfur atom in another cysteine residue. These disulfide bridges contribute to the overall three-dimensional structure of the protein, namely the tertiary structure).

Quaternary structure results from the joining of multiple polypeptide subunits and is driven by hydrophobic interactions. Tertiary structure is also driven by hydrophobic interactions, but also relies on intermolecular forces between amino acid function groups, such as the cysteine sulfhydryl.

To block a receptor protein, a molecule must structurally resemble the natural ligand. The active sites of proteins are highly specific, and will only bind certain molecules. The chemical formula, electrons, and bonding in the molecule can all influence small regions of the molecule's structure, but the overall shape must ultimately match the active site of the target protein.

Though proteins may be found on the cellular membrane, they are not a primary component. The cell membrane is known as the "phospholipid bilayer," as it is primarily composed of a double layer of lipids. Proteins may be attached to the surface or fully integrated into the bilayer, and serve as a means of signaling, transport, and adhesion.

Proteins are a primary component of the endocrine system, and several signaling hormones are made of peptides. The proteins action and myosin are directly involved in muscle contraction and for the structural basis of the sarcomere. Enzymes are a special class of catalytic proteins. Chaperone proteins and ion channels help transport molecules through the body; many nonpolar molecules must bind to a protein to travel through the blood.