How many polypeptides are needed to make a protein

This end is called the N terminal, or the amino terminal, and the other end has a free carboxyl group, also known as the C or carboxyl terminal. When reading or reporting the amino acid sequence of a protein or polypeptide, the convention is to use the N-to-C direction. That is, the first amino acid in the sequence is assumed to the be one at the N terminal and the last amino acid is assumed to be the one at the C terminal.

Although the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically any polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have folded properly, combined with any additional components needed for proper functioning, and is now functional. Each successive level of protein folding ultimately contributes to its shape and therefore its function.

The shape of a protein is critical to its function because it determines whether the protein can interact with other molecules. Protein structures are very complex, and researchers have only very recently been able to easily and quickly determine the structure of complete proteins down to the atomic level.

The techniques used date back to the s, but until recently they were very slow and laborious to use, so complete protein structures were very slow to be solved. To determine how the protein gets its final shape or conformation, we need to understand these four levels of protein structure: primary, secondary, tertiary, and quaternary. Really, this is just a list of which amino acids appear in which order in a polypeptide chain, not really a structure. But, because the final protein structure ultimately depends on this sequence, this was called the primary structure of the polypeptide chain.

For example, the pancreatic hormone insulin has two polypeptide chains, A and B. Primary structure : The A chain of insulin is 21 amino acids long and the B chain is 30 amino acids long, and each sequence is unique to the insulin protein. The gene, or sequence of DNA, ultimately determines the unique sequence of amino acids in each peptide chain. So, just one amino acid substitution can cause dramatic changes. People affected by the disease often experience breathlessness, dizziness, headaches, and abdominal pain.

Sickle cell disease : Sickle cells are crescent shaped, while normal cells are disc-shaped. Secondary structures arise as H bonds form between local groups of amino acids in a region of the polypeptide chain.

Rarely does a single secondary structure extend throughout the polypeptide chain. It is usually just in a section of the chain. This holds the stretch of amino acids in a right-handed coil. Every helical turn in an alpha helix has 3. The tertiary structure of a polypeptide chain is its overall three-dimensional shape, once all the secondary structure elements have folded together among each other.

Interactions between polar, nonpolar, acidic, and basic R group within the polypeptide chain create the complex three-dimensional tertiary structure of a protein. When protein folding takes place in the aqueous environment of the body, the hydrophobic R groups of nonpolar amino acids mostly lie in the interior of the protein, while the hydrophilic R groups lie mostly on the outside.

Cysteine side chains form disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding. All of these interactions, weak and strong, determine the final three-dimensional shape of the protein. When a protein loses its three-dimensional shape, it will no longer be functional. Tertiary structure : The tertiary structure of proteins is determined by hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages.

The quaternary structure of a protein is how its subunits are oriented and arranged with respect to one another. As a result, quaternary structure only applies to multi-subunit proteins; that is, proteins made from more than one polypeptide chain.

Proteins made from a single polypeptide will not have a quaternary structure. In proteins with more than one subunit, weak interactions between the subunits help to stabilize the overall structure.

Enzymes often play key roles in bonding subunits to form the final, functioning protein. For example, insulin is a ball-shaped, globular protein that contains both hydrogen bonds and disulfide bonds that hold its two polypeptide chains together. Four levels of protein structure : The four levels of protein structure can be observed in these illustrations.

Since certain amino acids can interact with other amino acids in the same protein, this primary structure ultimately determines the final shape and therefore the chemical and physical properties of the protein. The secondary structure of the protein is due to hydrogen bonds that form between the oxygen atom of one amino acid and the nitrogen atom of another. In globular proteins such as enzymes, the long chain of amino acids becomes folded into a three-dimensional functional shape or tertiary structure.

This is because certain amino acids with sulfhydryl or SH groups form disulfide S-S bonds with other amino acids in the same chain. As will be seen later in this unit, during protein synthesis, the order of nucleotide bases along a gene gets transcribed into a complementary strand of mRNA which is then translated by tRNA into the correct order of amino acids for that polypeptide or protein.

Therefore, the order of deoxyribonucleotide bases along the DNA determines the order of amino acids in the proteins. But in combination with other data, e. The genetic code. By compiling observations from experiments such as those outlined in the previous section, the coding capacity of each group of 3 nucleotides was determined.

This is referred to as the genetic code. It is summarized in Table 3. This tells us how the cell translates from the "language" of nucleic acids polymers of nucleotides to that of proteins polymers of amino acids. Knowledege of the genetic code allows one to predict the amino acid sequence of any sequenced gene.

The complete genome sequences of several organisms have revealed genes coding for many previously unknown proteins. A major current task is trying to assign activities and functions to these newly discovered proteins. The Genetic Code. Position in Codon. Of the total of 64 codons, 61 encode amino acids and 3 specify termination of translation.

The degeneracy of the genetic code refers to the fact that most amino acids are specified by more than one codon. The degeneracy is found primarily the third position. Consequently, single nucleotide substitutions at the third position may not lead to a change in the amino acid encoded.

These are called silent or synonymous nucleotide substitutions. They do not alter the encoded protein. This is discussed in more detail below. The pattern of degeneracy allows one to organize the codons into " families " and " pairs ". In 9 groups of codons, the nucleotides at the first two positions are sufficient to specify a unique amino acid, and any nucleotide abbreviated N at the third position encodes that same amino acid.

These comprise 9 codon "families". An example is ACN encoding threonine. There are 13 codon "pairs", in which the nucleotides at the first two positions are sufficient to specify two amino acids. A purine R nucleotide at the third position specifies one amino acid, whereas a pyrimidine Y nucleotide at the third position specifies the other amino acid.

The UAR codons specifying termination of translation were counted as a codon pair. The codons for leucine and arginine, with both a codon family and a codon pair, provide the few examples of degeneracy in the first position of the codon.

Degeneracy at the second position of the codon is not observed for codons encoding amino acids. Chemically similar amino acids often have similar codons. Hydrophobic amino acids are often encoded by codons with U in the 2nd position, and all codons with U at the 2nd position encode hydrophobic amino acids.

The major codon specifying initiation of translation is AUG. Using data from the genes identified by the complete genome sequence of E. AUG is used for genes. GUG is used for genes. UUG is used for genes.

AUU is used for 1 gene. CUG may be used for 1 gene. Regardless of which codon is used for initiation, the first amino acid incorporated during translation is f-Met in bacteria. Of these three codons, UAA is used most frequently in E.

UAG is used much less frequently. UAA is used for genes. UGA is used for genes. UAG is used for genes. The genetic code is almost universal.

In the rare exceptions to this rule, the differences from the genetic code are fairly small. In addition, chemical forces between a protein and its immediate environment contribute to protein shape and stability.

For example, the proteins that are dissolved in the cell cytoplasm have hydrophilic water-loving chemical groups on their surfaces, whereas their hydrophobic water-averse elements tend to be tucked inside. In contrast, the proteins that are inserted into the cell membranes display some hydrophobic chemical groups on their surface, specifically in those regions where the protein surface is exposed to membrane lipids.

It is important to note, however, that fully folded proteins are not frozen into shape. Rather, the atoms within these proteins remain capable of making small movements. Even though proteins are considered macromolecules, they are too small to visualize, even with a microscope.

So, scientists must use indirect methods to figure out what they look like and how they are folded. The most common method used to study protein structures is X-ray crystallography. With this method, solid crystals of purified protein are placed in an X-ray beam, and the pattern of deflected X rays is used to predict the positions of the thousands of atoms within the protein crystal. In theory, once their constituent amino acids are strung together, proteins attain their final shapes without any energy input.

In reality, however, the cytoplasm is a crowded place, filled with many other macromolecules capable of interacting with a partially folded protein. Inappropriate associations with nearby proteins can interfere with proper folding and cause large aggregates of proteins to form in cells.

Cells therefore rely on so-called chaperone proteins to prevent these inappropriate associations with unintended folding partners. Chaperone proteins surround a protein during the folding process, sequestering the protein until folding is complete.

For example, in bacteria, multiple molecules of the chaperone GroEL form a hollow chamber around proteins that are in the process of folding. Molecules of a second chaperone, GroES, then form a lid over the chamber. Eukaryotes use different families of chaperone proteins, although they function in similar ways. Chaperone proteins are abundant in cells. These chaperones use energy from ATP to bind and release polypeptides as they go through the folding process.

Chaperones also assist in the refolding of proteins in cells. Folded proteins are actually fragile structures, which can easily denature, or unfold. Although many thousands of bonds hold proteins together, most of the bonds are noncovalent and fairly weak. Even under normal circumstances, a portion of all cellular proteins are unfolded. Increasing body temperature by only a few degrees can significantly increase the rate of unfolding. When this happens, repairing existing proteins using chaperones is much more efficient than synthesizing new ones.

Interestingly, cells synthesize additional chaperone proteins in response to "heat shock. All proteins bind to other molecules in order to complete their tasks, and the precise function of a protein depends on the way its exposed surfaces interact with those molecules.