Protein Structure PDF

**Protein Structure** As we discussed earlier, a protein\'s shape is critical to its function. For example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind...

**Protein Structure** As we discussed earlier, a protein\'s shape is critical to its function. For example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary. **Primary Structure** Amino acids\' unique sequence in a polypeptide chain is its **primary structure**. For example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are linked together by disulfide bonds. The N terminal amino acid of the A chain is glycine; whereas, the C terminal amino acid is asparagine ([[Figure 3.25]](https://openstax.org/rex/releases/v4/6d3f24e/3-4-proteins#fig-ch03_04_04)). The amino acid sequences in the A and B chains are unique to insulin. **Figure 3.25** Bovine serum insulin is a protein hormone comprised of two peptide chains, A (21 amino acids long) and B (30 amino acids long). In each chain, three-letter abbreviations that represent the amino acids\' names in the order they are present indicate primary structure. The amino acid cysteine (cys) has a sulfhydryl (SH) group as a side chain. Two sulfhydryl groups can react in the presence of oxygen to form a disulfide (S-S) bond. Two disulfide bonds connect the A and B chains together, and a third helps the A chain fold into the correct shape. Note that all disulfide bonds are the same length, but we have drawn them different sizes for clarity. The gene encoding the protein ultimately determines the unique sequence for every protein. A change in nucleotide sequence of the gene's coding region may lead to adding a different amino acid to the growing polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin *β* chain (a small portion of which we show in [[Figure 3.26]](https://openstax.org/rex/releases/v4/6d3f24e/3-4-proteins#fig-ch03_04_05)) has a single amino acid substitution, causing a change in protein structure and function. Specifically, valine in the *β* chain substitutes the amino acid glutamic. What is most remarkable to consider is that a hemoglobin molecule is comprised of two alpha and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule---which dramatically decreases life expectancy---is a single amino acid of the 600. What is even more remarkable is that three nucleotides each encode those 600 amino acids, and a single base change (point mutation), 1 in 1800 bases causes the mutation.  **Figure 3.26** Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or "sickle" shape, which clogs blood vessels (Figure 3.27). The beta (β)- chain of hemoglobin is 147 amino acids in length, yet a single amino acid substitution in the primary sequence leads to changes in secondary, tertiary, and quaternary structures and sickle cell anemia. In normal hemoglobin, the amino acid at position six is glutamate. In sickle cell hemoglobin glutamate is replaced by valine. (credit: Rao, A., Tag, A. Ryan, K. and Fletcher, S. Department of Biology, Texas A&M University) Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or "sickle" shape, which clogs blood vessels ([[Figure 3.27]](https://openstax.org/rex/releases/v4/6d3f24e/3-4-proteins#fig-ch03_04_06)). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease. William Warrick Cardozo showed that sickle-cell anemia is an inherited disorder, meaning that the difference in the specific gene\'s encoding region is passed down from parents to children. As you will learn in the genetics unit, the inheritance of such traits is determined by a combination of genes from both parents, and these very small differences can have significant impacts on organisms. This electron micrograph shows red blood cells from a patient with sickle cell anemia. Most of the cells have a normal, disk shape, but about one in five has a sickle shape. A normal blood cell is eight microns across. **Figure 3.27** In this blood smear, visualized at 535x magnification using bright field microscopy, sickle cells are crescent shaped, while normal cells are disc-shaped. (credit: modification of work by Ed Uthman; scale-bar data from Matt Russell) **Secondary Structure** The local folding of the polypeptide in some regions gives rise to the **secondary structure** of the protein. The most common are the ***α*-helix** and ***β*-pleated sheet** structures ([[Figure 3.28]](https://openstax.org/rex/releases/v4/6d3f24e/3-4-proteins#fig-ch03_04_07)). Both structures are held in shape by hydrogen bonds. The hydrogen bonds form between the oxygen atom in the carbonyl group in one amino acid and another amino acid that is four amino acids farther along the chain.  **Figure 3.28** The *α*-helix and *β*-pleated sheet are secondary protein structures formed when hydrogen bonds form between the carbonyl oxygen and the amino hydrogen in the peptide backbone. Certain amino acids have a propensity to form an α-helix while others favor β-pleated sheet formation. Black = carbon, White = hydrogen, Blue = nitrogen, and Red = oxygen. Credit: Rao, A., Ryan, K. Fletcher, S. and Tag, A. Department of Biology, Texas A&M University. Every helical turn in an alpha helix has 3.6 amino acid residues. The polypeptide\'s R groups (the variant groups) protrude out from the *α*-helix chain. In the *β*-pleated sheet, hydrogen bonding between atoms on the polypeptide chain\'s backbone form the \"pleats\". The R groups are attached to the carbons and extend above and below the pleat\'s folds. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive hydrogen atom in the amino group and the partially negative oxygen atom in the peptide backbone\'s carbonyl group. The *α*-helix and *β*-pleated sheet structures are in most globular and fibrous proteins and they play an important structural role. **Tertiary Structure** The polypeptide\'s unique three-dimensional structure is its **tertiary structure** ([[Figure 3.29]](https://openstax.org/rex/releases/v4/6d3f24e/3-4-proteins#fig-ch03_04_08)). This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups create the protein\'s complex three-dimensional tertiary structure. The nature of the R groups in the amino acids involved can counteract forming the hydrogen bonds we described for standard secondary structures. For example, R groups with like charges repel each other and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the nonpolar amino acids\' hydrophobic R groups lie in the protein\'s interior; whereas, the hydrophilic R groups lie on the outside. Scientists also call the former interaction types hydrophobic interactions. Interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond that forms during protein folding. **Figure 3.29** A variety of chemical interactions determine the proteins\' tertiary structure. These include hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages. All of these interactions, weak and strong, determine the protein\'s final three-dimensional shape. When a protein loses its three-dimensional shape, it may no longer be functional. **Quaternary Structure** In nature, some proteins form from several polypeptides, or subunits, and the interaction of these subunits forms the **quaternary structure**. Weak interactions between the subunits help to stabilize the overall structure. For example, insulin (a globular protein) has a combination of hydrogen and disulfide bonds that cause it to mostly clump into a ball shape. Insulin starts out as a single polypeptide and loses some internal sequences in the presence of post-translational modification after forming the disulfide linkages that hold the remaining chains together. Silk (a fibrous protein), however, has a *β*-pleated sheet structure that is the result of hydrogen bonding between different chains. [[Figure 3.30]](https://openstax.org/rex/releases/v4/6d3f24e/3-4-proteins#fig-ch03_04_09) illustrates the four levels of protein structure (primary, secondary, tertiary, and quaternary).  **Figure 3.30** Observe the four levels of protein structure in these illustrations. Credit: Rao, A. Ryan, K. and Tag, A. Department of Biology, Texas A&M University. **Denaturation and Protein Folding** Each protein has its own unique sequence and shape that chemical interactions hold together. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence in what scientists call denaturation. Denaturation is often reversible because the polypeptide\'s primary structure is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is frying an egg. The albumin protein in the liquid egg white denatures when placed in a hot pan. Not all proteins denature at high temperatures. For instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the stomach\'s digestive enzymes retain their activity under these conditions. Protein folding is critical to its function. Scientists originally thought that the proteins themselves were responsible for the folding process. Only recently researchers discovered that often they receive assistance in the folding process from protein helpers, or **chaperones** (or chaperonins) that associate with the target protein during the folding process. They act by preventing polypeptide aggregation that comprise the complete protein structure, and they disassociate from the protein once the target protein is folded.