Chaperonin is the enzyme responsible for folding nascent polypeptide chains into the correct and functional 3-dimensional structure. Lipase is an enzyme that breaks down lipids, or fats. Amylase breaks down starches and complex carbohydrates or sugars. Helicase helps unwind the DNA helix during replication, and topoisomerase II helps keep the DNA untangled and acts as adhesive during DNA repair or replication.

Primary structure revolves around the sequence of amino acids, while secondary structure is achieved through hydrogen bonds interacting along the backbone of the polypeptide. Tertiary structure is achieved through interactions between the various side chains of amino acids and is required for the protein to be functional. Quaternary structure involves the interaction of two or more polypeptide subunits, and adds efficiency to their ability to catalyze a reaction.

Proteins have four levels of structure: primary, secondary, tertiary, and quaternary. These refer to the types of binding and folding that occur in the molecule that cause it to take on a stable shape. Hydrogen bonds occur between parts of the molecule containing slightly positive hydrogen, and other parts that may be slightly negative (generally containing oxygen). These bonds stabilize the protein's secondary structure, allowing more complicated folding into tertiary and quaternary structures. Alpha-helices and beta-pleated sheets form the common secondary protein structures.

Primary structure is driven by peptide bonding, while tertiary structure is derived from disulfide bonds and hydrophobic interactions. Quaternary structure describes the congregation of multiple subunits driven by hydrophobic interaction and protein-mediated assembly.

The formation of -helices and -pleated sheets constitute the secondary structure of a protein. These conformations are reinforced by hydrogen bonds between the atoms in the polypeptide chain.

Primary structure is determined by peptide bonds, which link adjoining amino acids in sequence. Tertiary structure is determined by disulfide bonds between cysteine residues and hydrophobic interactions. Quaternary structure is determined by interactions between multiple subunits of a protein.

Hydrogen bonding is responsible for giving shape to the secondary structures of proteins. The amino acids in the protein all carry carboxyl and amino termini, which are capable of forming hydrogen bonds. Secondary protein structure refers to the formation of alpha-helices and beta-pleated sheets through hydrogen bonding in the amino acid backbone. The R-groups are not involved in secondary structure.

Covalent bonds are used to permanently join atoms together, and are not seen in protein folding. Peptide bonds are a special class of covalent bonds that are responsible for holding the individual amino acids together, forming the protein's primary structure. Ionic bonds are generally formed between metals and non-metals, and are not generally seen in proteins.

Quaternary protein structure is distinguished by the fact that several polypeptide chains come together to make a functional protein. This is different than the first three levels of protein structure, which only involve one polypeptide chain. Quaternary structure is held together primarily by hydrophobic interactions between the polypeptide chains (ionic and/or hydrogen bonding is often seen as well). Each polypeptide chain forms a subunit of the protein.

Disulfide bridges are formed between the sulfhydryl (-SH) groups of two cysteine residues. These bonds are covalent, and are important in stabilizing the tertiary structure of many proteins.

Proteins have different levels of structure. Primary structure is the sequence of amino acids, joined by peptide bonds. Secondary structure is determined by hydrogen bonding in the amino acid chain backbone. Tertiary structure is the entire protein's shape, determined by R-group interaction and hydrophobic forces. Quaternary structure is only found in certain proteins, and results from the joining of multiple polypeptide subunits into a functional protein.

Chaperones are proteins that are vital for the proper folding of some polypeptide chains. Without chaperones, proteins may be folded incorrectly and become nonfunctional. Chaperones are particularly essential to tertiary and quaternary structure.

The other answers describe functions of other types of proteins.

The generation of new protein begins in the nucleus with the transcription of a gene’s DNA sequence into mRNA. The mRNA is then translated into protein by ribosomes in proximity to the rough endoplasmic reticulum. The rough endoplasmic reticulum functions to accept the growing protein sequence and ensure that it is appropriately folded and modified (i.e. addition of carbohydrate) appropriately. The protein is then transported to the Golgi apparatus for additional maturation of the protein, such as carbohydrate modifications. Lastly, the protein is transported to the cell surface based on signals or motifs in protein sequence that determine where it is transported.

Note that only proteins that are transported in vesicles (i.e. membrane proteins and secreted proteins) require intervention by the rough endoplasmic reticulum and Golgi apparatus. Cytoplasmic proteins can be translated by free-floating ribosomes and folded by chaperone proteins.