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26.2: Amino Acids and Proteins

Created by: CK-12

Lesson Objectives

  • Describe the general structure of an amino acid.
  • List the twenty common amino acids found in living organisms.
  • Describe how a peptide bond forms.
  • Define a protein and differentiate between the four levels of structure of a protein.
  • Describe the effect of an enzyme on a biochemical reaction and the general features of its reaction with a substrate.

Lesson Vocabulary

  • amino acid
  • enzyme
  • peptide
  • peptide bond
  • polypeptide
  • primary structure
  • protein
  • quaternary structure
  • secondary structure
  • tertiary structure

Check Your Understanding

Recalling Prior Knowledge

  • What is the structure of the carboxyl functional group?
  • What is the structure of the amino functional group?

Foods such as meat and fish are high in protein. Proteins are an essential class of biomolecules that actually make up more than half of the dry weight of your body. In this lesson, you will learn about small molecules called amino acids and how they link together to form larger protein molecules.

Amino Acids

An amino acid is a compound that contains both an amino group (−NH2) and a carboxyl group (−COOH) in the same molecule. While an infinite number of amino acids can be imagined, the term most commonly applies to a specific group of 20 amino acids that are used as fundamental building blocks by living organisms. Illustrated below (Figure below) is the general structure of these amino acids.

An amino acid is an organic molecule that contains an amino group, a carboxyl group, and a side chain (R). In the 20 most common amino acids found in living organisms, these groups are all bonded to the same carbon atom.

The amino and carboxyl groups of the basic 20 amino acids are both covalently bonded to a central carbon atom. That carbon atom is also bonded to a hydrogen atom and an R group. It is this R group, referred to as a side chain, that varies from one amino acid to another.

The nature of the side chains accounts for the variability in physical and chemical properties of the different amino acids. Some side chains consist of nonpolar aliphatic or aromatic hydrocarbons. Other side chains are polar, while some are acidic or basic (Figure below).

Five of the twenty biologically relevant amino acids, each with a distinctive side chain (R). Alanine’s side chain is nonpolar, while threonine’s is polar. Tryptophan is one of several amino acids whose side chain is aromatic. Aspartic acid has an acidic side chain, while lysine has a basic side chain.

Listed below (Table below) are the names of the 20 fundamental amino acids in biological organisms along with a three-letter abbreviation that is used when depicting sequences of linked amino acids.

Amino Acids and Abbreviations
Amino acid Abbreviation Amino acid Abbreviation
Alanine Ala Leucine Leu
Arginine Arg Lysine Lys
Asparagine Asn Methionine Met
Aspartic acid Asp Phenylalanine Phe
Cysteine Cys Proline Pro
Glutamine Gln Serine Ser
Glutamic acid Glu Threonine Thr
Glycine Gly Tryptophan Trp
Histidine His Tyrosine Tyr
Isoleucine Ile Valine Val

Peptides

A peptide is a combination of amino acids in which the amino group of one amino acid has undergone a condensation reaction with the carboxyl group of another amino acid. The result is an amide group (Figure below).

Two amino acids can join together to form a molecule called a dipeptide. The C−N bond between the carbonyl carbon of one amino acid and the nitrogen atom of another amino acid is called a peptide bond. By convention, chains of amino acids are drawn with the free amino group on the left and the free carboxyl group on the right.

A peptide bond is the amide bond that occurs between the amino nitrogen of one amino acid and the carboxyl carbon of another amino acid. The resulting molecule is called a dipeptide. Notice that the formation of a peptide bond is completely independent of the identities of the R groups, which do not participate in the condensation reaction, so any two amino acids can be joined together in this fashion.

The dipeptide has a free amino group on one end of the molecule and a free carboxyl group on the other end. Each is capable of extending the chain through the formation of another peptide bond. The particular sequence of amino acids in a longer chain is called an amino acid sequence. By convention, the amino acid sequence is listed in the order such that the free amino group is on the left end of the molecule and the free carboxyl group is on the right end of the molecule. For example, suppose that a sequence of the amino acids glycine, tryptophan, and alanine is formed with the free amino group as part of the glycine unit and the free carboxyl group as part of the alanine unit. The amino acid sequence can be abbreviated as Gly-Trp-Ala. This is a different molecule than Ala-Trp-Gly, in which the free amino and carboxyl groups would be on different amino acids.

Proteins

Longer chains of amino acids are referred to as polypeptides or proteins, depending on their approximate size. In general, a polypeptide is a sequence of ten or more amino acids, while a protein is a polypeptide with a molecular weight of more than about 10,000 g/mol. This corresponds to a polypeptide that is longer than about 80-100 amino acids in length, depending on the exact identities of the amino acids used. However, the boundary between these two categories is not definite, and many polypeptides in the 40-100 amino acid range will often be referred to as proteins if they perform functions that are similar to those of other larger proteins.

Proteins are very prevalent in living organisms. Hair, skin, nails, muscles, and the hemoglobin in red blood cells are some of the important parts of your body that are made of different proteins. The wide array of chemical, physiological, and structural properties exhibited by different proteins is a function of their amino acid sequences. Because proteins are so large, the number of possible amino acid sequences is virtually limitless. For example, even a "small" protein that is only 90 amino acids long could have 2090 = 1.24 × 10117 possible sequences. To put this number in perspective, the entire universe is estimated to contain about 1080-1082 atoms.

The three-dimensional structure of a protein is very critical to its function. This structure can be broken down into four levels. The primary structure is the amino acid sequence of the protein. The amino acid sequence of a given protein is unique and defines the function of that protein. The secondary structure is a highly regular sub-structure of the protein. The two most common types of protein secondary structure are the alpha helix and the beta sheet (Figure below).

The two most common secondary structures of a protein are the alpha helix and the beta sheet. An alpha helix consists of amino acids that adopt a spiral shape. A beta sheet consists of two or more rows of amino acids that line up in a side-by-side fashion. In both cases, the secondary structures are stabilized by extensive hydrogen bonding between the polyamide backbone.

The interactions between various nearby amino acids, particularly the hydrogen bonding between the amide groups that connect amino acids together, leads to the adoption of a particular secondary structure. The tertiary structure is the overall three-dimensional structure of the protein. A typical protein consists of several localized secondary structures (alpha helices or beta sheets) along with other areas in which the structure is less regular. These areas combine to produce the tertiary structure.

Some functional protein complexes consist of more than one protein molecule. For example, hemoglobin is a very large protein found in red blood cells. Its function is to bind and carry oxygen throughout the bloodstream. Hemoglobin consists of four subunits—two α subunits and two β subunits—that come together in a specific way through interactions between the side chains (Figure below). Each subunit is a single protein strand that is linked together by covalent bonds, while the overall complex is held together by large numbers of intermolecular interactions.

Hemoglobin is a very large protein consisting of four subunits. Two of the subunits are identical to one another and are called the alpha subunits (yellow). The other two subunits are also identical to one another and are called the beta subunits (gray). Hemoglobin also contains an atom of iron in the middle of each subunit. Each iron atom is positioned in the center of a smaller organic molecule known as a porphyrin, which is shown in red.

The quaternary structure of a protein refers to the interactions and orientations of the subunits in that protein. Some proteins consist of only one subunit and thus do not have a quaternary structure. The Figure below diagrams the four levels of protein structure.

The four levels of protein structure are primary, secondary, tertiary, and quaternary.

Enzymes

An enzyme is a protein that acts as a biological catalyst. Recall that a catalyst is a substance that increases the rate of a chemical reaction without itself being consumed in the reaction. Cellular processes consist of many chemical reactions that must occur quickly in order for the cell to function properly. Each of those biochemical reactions is catalyzed by an enzyme. The first enzyme to be isolated was discovered in 1926 by American chemist James Sumner. The enzyme was urease, which catalyzes the hydrolytic decomposition of urea, a component of urine, into ammonia and carbon dioxide.

\mathrm{H_2NCONH_2}(aq) \mathrm{+H_2O}(l) \mathrm{\overset {urease}{\rightarrow} 2NH_3}(g) \mathrm{+CO_2}(g)

Since that time, thousands of enzymes have been isolated and had their structures determined.

Enzymes catalyze most of the chemical reactions that occur in a cell. A substrate is the molecule or molecules on which the enzyme acts. In the urease catalyzed reaction above, urea is the substrate. Below (Figure below) is a diagram for a typical enzymatic reaction.

The sequence of steps for a substrate binding to an enzyme in its active site, reacting, then being released as products.

The first step in the reaction is that the substrate binds to a specific part of the enzyme molecule. The binding of the substrate is dictated by the shapes of each molecule. Side chains on the enzyme interact with the substrate in a specific way, weakening certain bonds and locking the molecule into a particular orientation. The active site is the region of an enzyme to which the substrate binds. Enzymes typically have just one active site, which is usually a pocket or crevice formed by the folding pattern of the protein. Because the active site of an enzyme has such a unique shape, only one particular substrate is capable of binding to that enzyme. In other words, each enzyme catalyzes only one chemical reaction with only one substrate. Once the enzyme/substrate complex is formed, the reaction occurs, and the substrate is transformed into products. Finally, the product molecule or molecules are released from the active site. Note that the enzyme is left unaffected by the reaction and is now capable of catalyzing the reaction of another substrate molecule.

Inhibitors

An inhibitor is a molecule that interferes with the function of an enzyme, either slowing or stopping the chemical reaction catalyzed by that enzyme. Inhibitors can work in a variety of ways, but one of the most common is illustrated below (Figure below).

A competitive inhibitor is a molecule that binds to the active site of an enzyme without reacting, thus preventing the substrate from binding.

The inhibitor binds competitively at the active site and blocks the substrate from binding. Since no reaction occurs with the inhibitor, the enzyme is prevented from catalyzing the reaction. Cyanide is a potent poison that acts as a competitive inhibitor. It binds to the active site of the enzyme cytochrome c oxidase and interrupts cellular respiration. The binding of the cyanide to the enzyme is almost completely irreversible, and the affected organism dies quickly.

Cofactors

Some enzymes require the presence of non-protein molecules or ions in order to function properly; these additional components are referred to as cofactors. Cofactors can be inorganic metal ions or small organic molecules. Many vitamins, such as the B vitamins, act as cofactors. Some metal ions that function as cofactors for various enzymes include zinc, magnesium, potassium, and iron.

Lesson Summary

  • Amino acids are the building blocks of proteins. An amino acid has a carboxyl group, an amino group, and a variable side chain all covalently bonded to a central carbon atom. There are twenty fundamental amino acids, each with a unique side chain, that are used as the building blocks of proteins in living organisms.
  • Amino acids can undergo a condensation reaction in which the carbon atom of the carboxyl group of one amino acid bonds to the amino nitrogen atom of another amino acid. The result is called a peptide bond. Polypeptides and proteins are long strings of amino acids.
  • Proteins have four levels of structure: primary, secondary, tertiary, and quaternary. The structure and function of a protein is ultimately governed by its amino acid sequence.
  • Enzymes are proteins that catalyze biochemical reactions. A substrate binds to an enzyme at its active site, where the chemical reaction occurs.

Lesson Review Questions

Reviewing Concepts

  1. What gives each of the twenty common amino acids its unique structure and properties?
  2. What type of organic reaction is required to form a dipeptide from individual amino acids?
  3. How many peptide bonds are present in the sequence Ala-Glu-Phe-Asn?
  4. Does the amino acid sequence Leu-Ser-His have the same structure as the His-Ser-Leu sequence? Explain why or why not.
  5. Distinguish between the primary structure and the secondary structure of a protein.
  6. Describe the two common secondary structures found in proteins. What interactions are primarily responsible for secondary structure?
  7. Distinguish between the tertiary structure and the quaternary structure of a protein.
  8. Why can a cell function normally even if the concentrations of essential enzymes in the cell are very low?
  9. Explain why multiple different molecules generally cannot act as substrates for a given enzyme.

Problems

  1. Draw the structure of the dipeptide given by the sequence Thr-Asp.

Further Reading / Supplemental Links

Points to Consider

The class of biomolecules called lipids is comprised of fats, oils, and other water-insoluble compounds.

  • What is the structure of a triglyceride?
  • What are phospholipids?

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