6.3: Proteins
- Page ID
- 131547
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- Describe some examples of how protein functions
- Discuss the relationship between amino acids and proteins
- Describe how amino acids are classified
- Explain the four levels of protein organization
- Describe the ways in which protein shape and function are linked
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
Types and Functions of Proteins
Enzymes, which living cells produce, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. The enzyme may help in breakdown, rearrangement, or synthesis reactions. We call enzymes that break down their substrates catabolic enzymes. Those that build more complex molecules from their substrates are anabolic enzymes, and enzymes that affect the rate of reaction are catalytic enzymes. Note that all enzymes increase the reaction rate and, therefore, are organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its substrate amylose, a component of starch.
Hormones are chemical-signaling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps regulate the blood glucose level. Table \(\PageIndex{1}\) lists the primary types and functions of proteins.
Type | Examples | Functions |
---|---|---|
Digestive Enzymes | Amylase, lipase, pepsin, trypsin | Help in food by catabolizing nutrients into monomeric units |
Transport | Hemoglobin, albumin | Carry substances in the blood or lymph throughout the body |
Structural | Actin, tubulin, keratin | Construct different structures, like the cytoskeleton |
Hormones | Insulin, thyroxine | Coordinate different body systems' activity |
Defense | Immunoglobulins | Protect the body from foreign pathogens |
Contractile | Actin, myosin | Effect muscle contraction |
Storage | Legume storage proteins, egg white (albumin) | Provide nourishment in early embryo development and the seedling |
Proteins have different shapes and molecular weights. Some proteins are globular in shape; whereas, others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, located in our skin, is a fibrous protein. Protein shape is critical to its function, and many different types of chemical bonds maintain this shape. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the protein's shape, leading to loss of function, or denaturation. Different arrangements of the same 20 types of amino acids comprise all proteins. Two rare new amino acids were discovered recently (selenocystein and pirrolysine), and additional new discoveries may be added to the list.
Amino Acids
Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom and an R group (Figure \(\PageIndex{1}\)). The R group varies between amino acids and is also referred to as the side chain.
Scientists use the name "amino acid" because these acids contain both amino group and carboxyl-acid-group in their basic structure. As mentioned, there are 20 common amino acids present in proteins. Nine of these are essential amino acids in humans because the human body cannot produce them and we obtain them from our diet. For each amino acid, the R group (or side chain) is different (Figure \(\PageIndex{1}\)).
With the exception of glycine (which has a single hydrogen as an R group), each amino acid can exist in two enantiomeric forms, because the central carbon is a chiral center. This difference may seem small to our eyes (Figure \(\PageIndex{2}\)), but in the cell, only L-amino acids are used to make proteins.
The chemical nature of the side chain determines the amino acid's nature (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the amino acid's standard structure since its amino group is not separate from the side chain (Figure \(\PageIndex{3}\)).
A three-letter abbreviation or a single letter represents amino acids. For example, the letter V or the three-letter symbol val represent valine.
Visual Connection
Give it a try! You don't need to memorize the amino acid's names or structures for this course, but you should be able to determine which group they belong to based on the chemical characteristics of their R groups.
Peptide Bonds
The sequence and the number of amino acids ultimately determine the protein's shape, size, and function. A peptide bond is formed between amino acids to create a polymer, through a dehydration reaction. One amino acid's carboxyl group and the incoming amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond (Figure \(\PageIndex{4}\)).
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 \(\PageIndex{5}\)). The amino acid sequences in the A and B chains are unique to insulin.
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 \(\PageIndex{8}\)). Both structures are held in shape by hydrogen bonds.
Tertiary Structure
The polypeptide's unique three-dimensional structure is its tertiary structure (Figure \(\PageIndex{9}\)). 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.
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.
Protein Structure Summary
Figure \(\PageIndex{10}\) summarizes the four levels of protein structure (primary, secondary, tertiary, and quaternary).
Sort the definitions below to the appropriate level of protein structure.
Video Summary
The video below reviews the structure of an amino acid and the levels of protein structure. Since proteins are so complex and diverse, it's also important to think about how we, as scientists, represent protein structures. Perhaps not surprisingly, there is more than one way to do this, each with its own strengths and weaknesses. Choosing which to use depends on the purpose of your diagram.
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.
Link to Learning
Complete the Protein Folding Interactive by slowing scrolling down the page. This interactive reviews the structure of an amino acid, classification of amino acids and the levels of protein structure discussed above.