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Biology LibreTexts

3.11: Proteins

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  • Protein_shake.jpg

    Figure 1

    Protein Shake

    Drinks like this shake contain a lot of protein. Such drinks are popular with people who want to build muscle because muscle tissue consists mainly of protein. Making up muscles is just one of a plethora of functions of this amazingly diverse class of biochemicals.

    What Are Proteins?

    Proteins are organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and, in some cases, sulfur. These compounds may many essential functions within the cell (see below). Proteins are made of smaller units called amino acids. There are 20 different common amino acids needed to make proteins. All amino acids have the same basic structure, which is shown in Figure below. Only the side chain (labeled R in the figure) differs from one amino acid to another. These side chains can vary in size from just one hydrogen atom in glycine to a large heterocyclic group in tryptophan. The variable side chain gives each amino acid unique properties. The side chains can also characterize the amino acid as (1) nonpolar or hydrophobic, (2) neutral (uncharged) but polar, (3) acidic, with a net negative charge, and (4) basic, with a net positive charge at neutral pH.

    Proteins can differ from one another in the number and sequence (order) of amino acids. It is because of the side chains of the amino acids that proteins with different amino acid sequences have different shapes and different chemical properties. Small proteins can contain just a few hundred amino acids. Yeast proteins average 466 amino acids. The largest known proteins are the titins, found in muscle, which are composed from over 27,000 amino acids.


    Figure 2

    General Structure of Amino Acids. This model shows the general structure of all amino acids. Only the side chain, R, varies from one amino acid to another. For example, in the amino acid glycine, the side chain is simply hydrogen (H). In glutamic acid, in contrast, the side chain is CH2CH2COOH. Variable side chains give amino acids acids different chemical properties. The order of amino acids, together with the properties of the amino acids, determines the shape of the protein, and the shape of the protein determines the function of the protein. KEY: H = hydrogen, N = nitrogen, C = carbon, O = oxygen, R = variable side chain.

    Protein Structure

    Amino acids join together to form a molecule called a dipeptide. The –OH from the carboxyl group of one amino acid combines with a hydrogen atom from the amino group of the other amino acid to produce water. This is called a condensation reaction. It  is a reaction in which two molecules combine to form a single molecule with a release of water (see figure below).  When two amino acids combine in a condensation reaction, a covalent bond forms between the amine nitrogen of one amino acid and the carboxyl carbon of the second amino acid. A molecule of water is then removed as a second product. This reaction forms a molecule called a dipeptide and the carbon-nitrogen covalent bond is called a peptide bond. When repeated numerous times, a lengthy molecule called a polypeptide is eventually produced. Very lengthy polypeptides with functions configuration are called proteins. 


    Figure 3

    Amino acids join together to form a molecule called a dipeptide. The C−N bond is called a peptide bond. The order of amino acids is by convention shown with the free amino group on the left and the free carboxyl group on the right.

    Proteins may have up to four levels of structure, from primary to quaternary, as described and shown in the diagram below, giving them the potential for tremendous diversity:

    • A protein’s primary structure is the sequence of amino acids in its polypeptide chain(s). This sequence of amino acids determines the higher levels of protein structure and is encoded in genes.
    • A protein's secondary structure consists of regularly repeating local structures stabilized by chemical bonds. The most common secondary structures include the alpha helix and beta sheet. Because secondary structures are local, many regions of different secondary structure can be present in the same protein molecule.
    • A protein's tertiary structure refers to the overall three-dimensional shape of a single protein molecule. It is determined by the spatial relationship of weak and covalent bonds between the "R" groups of distant amino acids in a polypeptide. The tertiary structure is what controls the basic function of the protein.
    • Not all proteins have a final, quaternary structure. This is a structure formed by several protein molecules that function together as a single protein complex.


    Figure 4

    This diagram shows the levels of structure of a protein called hemoglobin.


    Functions of Proteins

    The diversity of protein structures explains how this class of biochemical compounds can play so many important roles in living things. What are the roles of proteins?

    • Some proteins have structural functions. They may help cells keep their shape or make up muscle tissues.
    • Many proteins are enzymes that speed up chemical reactions in cells. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Thousands of different biochemical reactions are known to be catalyzed by enzymes, including most of the reactions involved in metabolism.  A reaction without an enzyme might take millions of years to complete, whereas with the proper enzyme, it may take just a few milliseconds!
    • Other proteins are antibodies. These are proteins that bind to specific foreign substances, such as proteins on the surface of bacterial cells. This targets the cells for destruction.
    • Still other proteins carry messages or materials. For example, a protein called myoglobin is an oxygen-binding protein found in the muscle tissues of most mammals including humans. You can see a model of the tertiary structure of myoglobin in the figure below.


    Figure 5

    Myoglobin is a protein found in the muscle tissues of most mammals. It binds with oxygen to supply the cells with this element.

    The chief characteristic of proteins that allows their diverse set of functions is their ability to bind other molecules specifically and tightly. For example, myoglobin can bind specifically and tightly with oxygen. The region of a protein responsible for binding with another molecule is known as the binding site. This site is often a depression on the molecular surface, determined largely by the tertiary structure of the protein.

    Protein Consumption, Digestion, and Synthesis

    Proteins are necessary in the diets of humans and other animals. We cannot make all the different amino acids we need, so we must obtain some of them from foods we consume. Through the process of digestion, we break down the proteins in food into free amino acids that can then be used to synthesize our own proteins. Protein synthesis from amino acid monomers takes place in all cells and is controlled by genes. Once new proteins are synthesized, they generally do not last very long before they are degraded and their amino acids are recycled. A protein's lifespan is generally just a day or two in mammalian cells.


    • Proteins are a major class of biochemical compounds made up of small monomer molecules called amino acids, of which more than 20 are commonly found in the proteins of living things. Proteins have tremendous diversity of structure and function.
    • Long chains of amino acids form polypeptides via condensation reaction. The sequence of amino acids in polypeptides makes up the primary structure of proteins. Proteins also have higher levels of structure. Secondary structure refers to configurations such as helices and sheets within polypeptide chains. Tertiary structure is a protein's overall three-dimensional shape, which controls the molecule's basic function. A quaternary structure forms if multiple protein molecules join together and function as a complex.
    • Functions of proteins include helping cells keep their shape, making up muscle tissues, acting as enzymes or antibodies, and carrying messages or materials. The chief characteristic that allows proteins' diverse functions is their ability to bind specifically and tightly with other molecules.
    • We cannot make all the amino acids we need to synthesize our own proteins, so we must obtain some of them from proteins in the foods we consume.


    1. What are proteins?
    2. How two amino acids combine together to make a dipeptide? 
    3. Outline the four levels of protein structure.
    4. Identify four functions of proteins.
    5. Explain why proteins can take on so many different functions in living things.
    6. What is the role of proteins in the human diet?
    7. Can you have a protein with both an alpha helix and a beta sheet? Why or why not?
    8. If there is a mutation in a gene that causes a different amino acid to be encoded than the one that is usually encoded in that position within the protein, would that affect:

      a. The primary structure of the protein? Explain your answer.

      b. The higher structures (secondary, tertiary, quaternary) of the protein? Explain your answer.

      c. The function of the protein? Explain your answer.

    9. a. What is the region of a protein responsible for binding to another molecule called?

      b. Which level or levels of protein structure creates this region?

    10. Arrange the following in order from the smallest to the largest level of organization:

      peptide; protein; amino acid; polypeptide

    11. True or False. You can tell the function of all proteins from their quaternary structure.

    12. Explain what the reading means when it says that amino acids are “recycled.”

    Explore More

    Watch the video below to learn about how proteomics, the study of proteins, can be used in cancer research.


    Learn about muscle protein synthesis and breakdown in the video below.


    The video below discusses the different levels of protein structure.

    Image Attributions

    [Figure 1] 
    Credit: By Sandstein (Own work) [CC BY 3.0 (], via Wikimedia Commons; 
    License: CC BY-NC 3.0

    [Figure 2] 
    Credit: YassineMrabet/Wikimedia Commons; 
    License: CC BY-NC 3.0

    [Figure 3] 
    Credit: User:YassineMrabet/Wikimedia Commons; 
    License: CC BY-NC 3.0

    [Figure 4] 
    Credit: By OpenStax College [CC BY 3.0 (], via Wikimedia Commons; 
    License: CC BY-NC 3.0

    [Figure 5] 
    Credit: By →AzaToth (self made based on PDB entry) [Public domain], via Wikimedia Commons; 
    License: CC BY-NC 3.0