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2.3: Protein

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    Protein is another major macronutrient that, like carbohydrates, are made up of small repeating units. But instead of sugars, protein is made up of amino acids. In the following sections, you will learn more about how protein is synthesized and why it is important in the body.

    Amino Acids

    Similar to carbohydrates, proteins contain carbon (\(\ce{C}\)), hydrogen (\(\ce{H}\)), and oxygen (\(\ce{O}\)). However, unlike carbohydrates (and lipids) proteins also contain nitrogen (\(\ce{N}\)). Proteins are made up of smaller units called amino acids. This name, amino acid, signifies that each contains an amino (\(\ce{NH2}\)) and carboxylic acid (\(\ce{COOH}\)) groups. The only structural difference in the 20 amino acids is the side group represented by the \(\ce{R}\) below.

    clipboard_e647133ad0d1e4a05502d2529741d3e0b.png
    Figure \(\PageIndex{1}\): Structure of an amino acid

    To illustrate the differences in the side group we will consider glycine and alanine, the two simplest amino acids. For glycine the \(\ce{R}\) group is hydrogen (\(\ce{H}\)), while in alanine the \(\ce{R}\) group is a methyl (\(\ce{CH3}\)). The structures of these two amino acids are shown below.

    clipboard_e0781edef6acb91a45f1812337272e3c8.png
    Figure \(\PageIndex{2}\): Structure of glycine
    clipboard_e469b139339d97c2f8cb03bfaafc32388.png
    Figure \(\PageIndex{3}\): Structure of alanine
    ADAPT \(\PageIndex{1}\)

    Individual amino acids are joined together using a peptide bond (green) and is shown in the figure below.

    clipboard_e26d60c13db2fc07f2e19159621dabbb5.png
    Figure \(\PageIndex{4}\): Peptide bond formation1

    Amino acids can also come together to form tripeptides (three amino acids), oligopeptides (medium size peptide, there isn’t a formal cutoff), and polypeptides (large size). A polypeptide is a chain of amino acids as shown below.

    clipboard_e59ff7ddb82ab331a361e9f641de6721c.png
    Figure \(\PageIndex{5}\): A polypeptide chain2
    ADAPT \(\PageIndex{2}\)

    Protein Synthesis

    The process of protein synthesis is not as simple as stringing together amino acids to form a polypeptide. As shown below, this is a fairly involved process. DNA contains the genetic code that is used as a template to create mRNA in a process known as transcription. The mRNA then moves out of the nucleus into the cytoplasm where it serves as the template for translation, where tRNAs bring in individual amino acids that are bonded together to form a polypeptide.

    clipboard_eb1191854446db6735f8e16c23d05c6f0.png
    Figure \(\PageIndex{6}\): The process of creating a polypeptide3

    Proteins, known as ribosomes, assist with translation. After translation, the polypeptide can be folded or gain structure as shown below and will be discussed in the next subsection (Protein Structure).

    clipboard_ea7ddb6f177c54765c070287babdf7ef8.png
    Figure \(\PageIndex{7}\): Protein synthesis and processing4

    These videos do an excellent job of showing and explaining transcription and translation, respectively.

    Video \(\PageIndex{1}\): Transcription is the process by which the information in DNA is copied into messenger RNA (mRNA) for protein production. https://www.youtube.com/watch?v=5MfSYnItYvg
    Video \(\PageIndex{2}\): mRNA Translation. https://www.youtube.com/watch?v=8dsTvBaUMvw
    ADAPT \(\PageIndex{3}\)

    Protein Structure

    Protein structure is the orientation of the amino acids within a protein. There are four levels of protein structure. Primary structure is the linear polypeptide chain. Secondary structure occurs when hydrogen bonding between amino acids in the same polypeptide chain causes the formation of structures such as beta-pleated sheets and alpha-helices. Tertiary structure occurs as a result of an attraction between different amino acids of the polypeptide chain and interactions between the different secondary structures. Finally, certain proteins contain quaternary structure where multiple polypeptide chains are bonded together to form a larger molecule. Hemoglobin is an example of a protein with quaternary structure. The figure below illustrates the different levels of protein structure.

    clipboard_ee20e29e952b57de8f34cfe8e192c9816.png
    Figure \(\PageIndex{8}\): Different Protein Structures5

    This video does a nice job of illustrating and explaining the different protein structures.

    Video \(\PageIndex{3}\): A short video about protein primary, secondary, tertiary and quaternary structure. https://www.youtube.com/watch?v=lijQ3a8yUYQ
    ADAPT \(\PageIndex{4}\)

    Protein Functions

    There are various functions of proteins in the body that are described below.

    Structural

    Proteins, such as collagen, serve as the scaffolding of the body, and thus are important for the structure of tissues.

    clipboard_eda611090e8320250eba6f6eb7a1b3e1e.png
    Figure \(\PageIndex{9}\): Triple-helix structure of collagen6

    Enzymes

    We will discuss a number of enzymes throughout this class, and the vast majority are proteins. An enzyme catalyzes (enhances the rate of) a chemical reaction. The key part of an enzyme is its "active site". The active site is where a compound to be acted on, known as a substrate, enters. Enzymes are specific for their substrates; they do not catalyze reactions on any random compounds floating by. You might have heard the "lock and key" analogy used for enzymes and substrates, respectively. After the substrate enters the active site and binds, the enzyme slightly changes shape (conformation). The enzyme then catalyzes a reaction that, in the example below, splits the substrate into two parts. The products of this reaction are released and the enzyme returns to its native or original shape. It is then ready to catalyze another reaction. The figure and video below nicely illustrate the function of an enzyme.

    clipboard_e632845371c857a0cab26fe24714eabc7.png
    Figure \(\PageIndex{10}\): The function of enzymes7
    Video \(\PageIndex{4}\): Enzymes allow many chemical reactions to occur within the homeostasis constraints of a living system. Enzymes function as organic catalysts. A catalyst is a chemical involved in, but not changed by, a chemical reaction. https://www.youtube.com/watch?v=cbZsXjgPDLQ

    Enzymes’ names commonly end in -ase, and many are named for their substrate. For example the enzyme amylase cleaves bonds found in amylose and amylopectin.

    Hormones

    Many hormones are proteins. A hormone is a compound that is produced in one tissue, released into circulation, then has an effect on a different organ. Most hormones are produced from several organs, collectively known as endocrine organs. Insulin is an example of a hormone that is a protein. The video below describes and illustrates the functions of hormones.

    Video \(\PageIndex{5}\): Many of the body's most basic functions are regulated by the endocrine system—eight different glands located throughout the body. The endocrine system constantly and quietly does its work—secreting liquid chemical messengers called hormones. https://www.youtube.com/watch?v=kIPYVV4aThM

    Fluid Balance

    Proteins help to maintain the balance between fluids in the plasma and the interstitial fluid. Interstitial fluid is the fluid that surrounds cells. Interstitial fluid and plasma (fluid part of blood) are the two components of extracellular fluid, or the fluid outside of cells. The following figure illustrates the exchange of fluid between interstitial fluid and plasma.

    clipboard_e01485e84125700aa242bf143c9347935.png
    Figure \(\PageIndex{11}\): Interstitial Fluid and plasma8

    Acid-Base Balance

    Proteins serve as buffers, meaning that they help to prevent the pH of the body from getting too high or too low.

    Transport

    Transport proteins move molecules through circulation or across cell membranes. One example is hemoglobin that transports oxygen through the body. We will see a number of other examples as we move through class.

    Immune Function

    Antibodies are proteins that recognize antigens (foreign substances that generate antibody or inflammatory response) and bind to and inactivate them. Antibodies are important in our ability to ward off disease.

    Other Functions

    Proteins can also serve as neurotransmitters and can be used for energy by forming glucose through gluconeogenesis.

    ADAPT \(\PageIndex{5}\)

    Types of Amino Acids

    There are 20 amino acids our body uses to synthesize proteins. These amino acids can be classified as essential, non-essential, or conditionally essential. The table below shows how the 20 amino acids are classified.

    Table \(\PageIndex{1}\): Essential, conditionally essential, and nonessential amino acids9
    Essential Conditionally Essential Nonessential
    Histidine Arginine Alanine
    Isoleucine Cysteine Asparagine
    Leucine Glutamine Aspartic Acid or Aspartate
    Lysine Glycine Glutamic Acid or Glutamate
    Methionine Proline Serine
    Phenylalanine Tyrosine  
    Threonine    
    Tryptophan    
    Valine    

    The body cannot synthesize nine amino acids. Thus, it is essential that these are consumed in the diet. As a result, these amino acids are known as essential, or indispensable, amino acids. As an example of how amino acids were determined to be essential, Dr. William C. Rose at the University of Illinois discovered that threonine was essential by feeding different diets to graduate students at the university as described in the following link.

    Web Link

    Discovery of Threonine by William C. Rose

    Nonessential, or dispensable, amino acids can be made in our body, so we do not need to consume them. Conditionally essential amino acids become essential for individuals in certain situations. An example of a condition when an amino acid becomes essential is the disease phenylketonuria (PKU). Individuals with PKU have a mutation in the enzyme phenylalanine hydroxylase, which normally adds an alcohol group (OH) to the amino acid phenylalanine to form tyrosine as shown below.

    clipboard_eb3d8264c8a3c654f873b0d5f55e8040f.png
    Figure \(\PageIndex{12}\): Phenylketonuria (PKU) results from a mutation in the enzyme phenylalanine hydroxylase10,11

    Since tyrosine cannot be synthesized by people with PKU, it becomes essential for them. Thus, tyrosine is a conditionally essential amino acid. Individuals with PKU have to eat a very low protein diet and avoid the alternative sweetener aspartame, because it can be broken down to phenylalanine. If individuals with PKU consume too much phenylalanine, phenylalanine and its metabolites, can build up and cause brain damage and intellectual disabilities. The drug Kuvan was approved for use with PKU patients in 2007 who have low phenylalanine hydroxylase activity levels. You can learn more about this drug using the link below.

    Web Link

    Kuvan

    ADAPT \(\PageIndex{6}\)
    ADAPT \(\PageIndex{7}\)

    Amino Acid Structures

    It is a good idea to have a general idea of the structure of the different amino acids and to be able to recognize them as amino acids. You are not expected to memorize these structures. Often I say the name of amino acids and not all students understand that I am talking about an amino acid. Each amino acid differs only by its side group, which is circled in red in each figure below. Also, the more familiar you become with chemical structures, the more prepared you will be for later classes.

    clipboard_e0613a3162217f1c3d98dd8e5c75ed61a.png
    Histidine12
    clipboard_ec17746f0388110c33e4b14225d44b9d3.png
    Isoleucine13
    clipboard_ec8b9e17cc19431cd1a0bada6cd1e9f5d.png
    Leucine14
    clipboard_e8eabd6d0dede0c1a45d3f930bc65e2e4.png
    Lysine15
    clipboard_e43aefc8afc5d42ada1936bf34e39daff.png
    Methionine16
    clipboard_ece221ea7750ff26a46a33a0e3770e409.png
    Phenylalanine17
    clipboard_ea85b5534a76f8641e456153716255909.png
    Threonine18
    clipboard_eafb7eec54d2bd366a5a439bc63d565fe.png
    Tryptophan19
    clipboard_e33e1a7d67fa3be290db030eaf5c28f6d.png
    Valine 20

    Figure \(\PageIndex{13}\): Essential amino acids12-20

    You may hear someone talk about the branch chain amino acids, which are all essential amino acids, but they are singled out in the figure below. These amino acids have branched carbons in their side chains.

    clipboard_e6337bf643d85c0ae33a9de4e23ee429c.png
    Valine20
    clipboard_e2b842575115f0b59b6e24cf77e8344ce.png
    Leucine14
    clipboard_e445b87b43dfc755768c689770e16b968.png
    Isoleucine13

    Figure \(\PageIndex{14}\): Branched chain amino acids20,14,13

    clipboard_ee14043d826eecbb8cf1b9ba36160bb17.png
    Arginine21
    clipboard_e695b8585473a39bca31731b495bcbc74.png
    Cysteine22
    clipboard_e9222c53f23d279fbca7a36eb9c8b1f7c.png
    Glutamine23
    clipboard_e40b1db574e39fd65e3e973025c45d780.png
    Glycine24
    clipboard_e49089b8fe906c604f98ba66a7c2236a8.png
    Proline25
    clipboard_eca524cf5a4ce44899611cb5ecc29c567.png
    Tyrosine26

    Figure \(\PageIndex{15}\): Conditionally essential amino acids21-26

    clipboard_e0003c46e8759150cf26091b066e1d990.png
    Alanine27
    clipboard_ecef2adcf928f12f1be265240b1ee72af.png
    Asparagine28
    clipboard_efdc7fc55ebfea8b825a056399b588040.png
    Aspartate (aspartic acid)29
    clipboard_e40031552c788cc094ae8aea2e75bb192.png
    Glutamate (glutamic acid)30
    clipboard_e6c1828b8a93b3c18c1a27b9e1e8ac5fc.png
    Serine31

    Figure \(\PageIndex{16}\): Nonessential amino acids27-31

    ADAPT \(\PageIndex{8}\)

    References

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    3. www.genome.gov/Pages/Hyperion...essenger%20RNA
    4. en.Wikipedia.org/wiki/File:Pr...nsynthesis.png
    5. "225 Peptide Bond-01" by OpenStax College - Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013.. Licensed under CC BY 3.0 via Commons - commons.wikimedia.org/wiki/F...de_Bond-01.jpg
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