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Introduction to proteins and amino acids

Different types of proteins. The structure and properties of amino acids. Formation of peptide bonds.

Introduction

We tend to think of protein as a mass noun: a homogeneous substance, something that your diet should contain in a certain proportion. But if you ever work in a molecular biology lab (say, for a summer internship), protein may start to look very different to you.
How so? Well, you may see firsthand that protein isn’t just a single substance. Instead, there are lots and lots of different proteins in an organism, or even in a single cell. They come in every size, shape, and type you can imagine, and each one has a unique and specific job. Some are structural parts, giving cells shape or helping them move. Others act as signals, drifting between cells like messages in a bottle. Still others are metabolic enzymes, putting together or snapping apart biomolecules needed by the cell. And, odds are, one of these unique molecular players will become yours for the duration of your research!
Proteins are among the most abundant organic molecules in living systems and are way more diverse in structure and function than other classes of macromolecules. A single cell can contain thousands of proteins, each with a unique function. Although their structures, like their functions, vary greatly, all proteins are made up of one or more chains of amino acids. In this article, we will look in more detail at the building blocks, structures, and roles of proteins.

Types and functions of proteins

Proteins can play a wide array of roles in a cell or organism. Here, we’ll touch on a few examples of common protein types that may be familiar to you, and that are important in the biology of many organisms (including us).

Enzymes

Enzymes act as catalysts in biochemical reactions, meaning that they speed the reactions up. Each enzyme recognizes one or more substrates, the molecules that serve as starting material for the reaction it catalyzes. Different enzymes participate in different types of reactions and may break down, link up, or rearrange their substrates.
One example of an enzyme found in your body is salivary amylase, which breaks amylose (a kind of starch) down into smaller sugars. The amylose doesn’t taste very sweet, but the smaller sugars do. This is why starchy foods often taste sweeter if you chew them for longer: you’re giving salivary amylase time to get to work.

Hormones

Hormones are long-distance chemical signals released by endocrine cells (like the cells of your pituitary gland). They control specific physiological processes, such as growth, development, metabolism, and reproduction. While some hormones are steroid-based (see the article on lipids), others are proteins. These protein-based hormones are commonly called peptide hormones.
For example, insulin is an important peptide hormone that helps regulate blood glucose levels. When blood glucose rises (for instance, after you eat a meal), specialized cells in the pancreas release insulin. The insulin binds to cells in the liver and other parts of the body, causing them to take up the glucose. This process helps return blood sugar to its normal, resting level.
Some additional types of proteins and their functions are listed in the table below:
Protein types and functions
RoleExamplesFunctions
Digestive enzymeAmylase, lipase, pepsinBreak down nutrients in food into small pieces that can be readily absorbed
TransportHemoglobinCarry substances throughout the body in blood or lymph
StructureActin, tubulin, keratinBuild different structures, like the cytoskeleton
Hormone signalingInsulin, glucagonCoordinate the activity of different body systems
DefenseAntibodiesProtect the body from foreign pathogens
ContractionMyosinCarry out muscle contraction
StorageLegume storage proteins, egg white (albumin)Provide food for the early development of the embryo or the seedling
Table modified from OpenStax College, Biology.
Proteins come in many different shapes and sizes. Some are globular (roughly spherical) in shape, whereas others form long, thin fibers. For example, the hemoglobin protein that carries oxygen in the blood is a globular protein, while collagen, found in our skin, is a fibrous protein.
A protein’s shape is critical to its function, and, as we’ll see in the next article, many different types of chemical bonds may be important in maintaining this shape. Changes in temperature and pH, as well as the presence of certain chemicals, may disrupt a protein’s shape and cause it to lose functionality, a process known as denaturation.

Amino acids

Amino acids are the monomers that make up proteins. Specifically, a protein is made up of one or more linear chains of amino acids, each of which is called a polypeptide. (We'll see where this name comes from a little further down the page.) There are 20 types of amino acids commonly found in proteins.
Image of an amino acid, indicating the amino group, carboxyl group, alpha carbon, and R group.
Image credit: OpenStax Biology.
Amino acids share a basic structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (start text, N, H, end text, start subscript, 2, end subscript), a carboxyl group (start text, C, O, O, H, end text), and a hydrogen atom.
Although the generalized amino acid shown above is shown with its amino and carboxyl groups neutral for simplicity, this is not actually the state in which an amino acid would typically be found. At physiological pH (7, point, 2
7, point, 4), the amino group is typically protonated and bears a positive charge, while the carboxyl group is typically deprotonated and bears a negative charge.
Every amino acid also has another atom or group of atoms bonded to the central atom, known as the R group, which determines the identity of the amino acid. For instance, if the R group is a hydrogen atom, then the amino acid is glycine, while if it’s a methyl (start text, C, H, end text, start subscript, 3, end subscript) group, the amino acid is alanine. The twenty common amino acids are shown in the chart below, with their R groups highlighted in blue.
Chart depicting the 20 common amino acids in their predominant protonation forms at physiological pH (7.2-7.4).
Image by "Dancojocari." The image is licensed under a CC BY-SA 3.0 or GFDL, from Wikimedia Commons.
The properties of the side chain determine an amino acid’s chemical behavior (that is, whether it is considered acidic, basic, polar, or nonpolar). For example, amino acids such as valine and leucine are nonpolar and hydrophobic, while amino acids like serine and glutamine have hydrophilic side chains and are polar. Some amino acids, such as lysine and arginine, have side chains that are positively charged at physiological pH and are considered basic amino acids. (Histidine is sometimes put in this group too, although it is mostly deprotonated at physiological pH.) Aspartate and glutamate, on the other hand, are negatively charged at physiological pH and are considered acidic.
A few other amino acids have R groups with special properties, and these will prove to be important when we look at protein structure:
  • Proline has an R group that’s linked back to its own amino group, forming a ring structure. This makes it an exception to the typical structure of an amino acid, since it no longer has the standard NHstart subscript, 3, end subscriptstart superscript, plus, end superscript amino group. If you think that ring structure looks a little awkward, you’re right: proline often causes bends or kinks in amino acid chains.
  • Cysteine contains a thiol (-SH) group and can form covalent bonds with other cysteines. We'll see why this is important to protein structure and function in the article on orders of protein structure
Finally, there are a few other “non-canonical” amino acids that are found in proteins only under certain conditions.

Peptide bonds

Each protein in your cells consists of one or more polypeptide chains. Each of these polypeptide chains is made up of amino acids, linked together in a specific order. A polypeptide is kind of like a long word that is "spelled out" in amino acid lettersstart superscript, 4, end superscript. The chemical properties and order of the amino acids are key in determining the structure and function of the polypeptide, and the protein it's part of. But how are amino acids actually linked together in chains?
The amino acids of a polypeptide are attached to their neighbors by covalent bonds known as a peptide bonds. Each bond forms in a dehydration synthesis (condensation) reaction. During protein synthesis, the carboxyl group of the amino acid at the end of the growing polypeptide chain chain reacts with the amino group of an incoming amino acid, releasing a molecule of water. The resulting bond between amino acids is a peptide bond
Peptide bond formation between two amino acids. In a peptide bond, the carbonyl C of one amino acid is connected to the amino N of another.
Image modified from OpenStax Biology.
Because of the structure of the amino acids, a polypeptide chain has directionality, meaning that it has two ends that are chemically distinct from one another. At one end, the polypeptide has a free amino group, and this end is called the amino terminus (or N-terminus). The other end, which has a free carboxyl group, is known as the carboxyl terminus (or C-terminus). The N-terminus is on the left and the C-terminus is on the right for the very short polypeptide shown above.
How do we go from the amino acid sequence of a polypeptide to the three-dimensional structure of a mature, functional protein? To learn how interactions between amino acids cause a protein to fold into its mature shape, I highly recommend the video on orders of protein structure.

Want to join the conversation?

  • leafers ultimate style avatar for user chulman444
    N-terminus and C-terminus. What terminates extension of peptide linkage? Are they guaranteed not to react with other amino acids? If so how?...is it like how there aren't any random amino acids beside those 23 mentioned above, because i.e. for Lynsine, any more hydrocarbon backbone added to the hydrocarbon backbone of lynsine makes it unstable and is actually impossible or something?

    And would they be in zwitterion at physiological pH? Could this be why the terminus ARE terminus?
    (12 votes)
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    • leafers ultimate style avatar for user Travis Fisher
      To answer your first question, you need to look at the process of creating a peptide during Translation in the Ribosome. Messenger RNA is a sequence of nucleotides, three nucleotides is a codon, and codons code (go figure) for certain amino acids, codons also code a "start" and "stop". So in a example the ribosome will read a start codon and start building a peptide until it reaches a stop codon. There is your termination. I'm not sure how to explain the reasons for the differences in the 23 amino acids. Ribosomes are almost like computers robotically doing what the inputted code commands it to do.

      Also, I wanted to add that this isn't the end of the story. Things happen to the peptides after transcription within the cell. For example, insulin isn't transcribed fully functional but has to undergo several processes (cutting of pieces, adding) within the cell before it lives up to it's essential functions.
      (14 votes)
  • starky tree style avatar for user janez31
    how are proteins and phenotypes related to one another
    (5 votes)
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    • aqualine ultimate style avatar for user Prof. Matulik
      Provided that a protein has been transcribed and translated or "expressed" by the genes, that is the direct expression of phenotype. Large scale that may be seen in an organism as eye color, hair color, etc., as each protein has a different function.
      (7 votes)
  • aqualine ultimate style avatar for user Dexter Loh
    Should I make any distinction between the qualities: non-polar and hydrophobic or polar and hydrophilic? Can I use these terms interchangeably; which is to say, am I allowed to say non-polar instead of hydrophobic?
    (5 votes)
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    • aqualine ultimate style avatar for user Four21
      Yes, you should make a distinction. While it is definitely true that most of the time they are the same, it is a good idea to keep in mind the individual definitions of polar, non-polar, hydrophobic, and hydrophilic.
      (6 votes)
  • leaf grey style avatar for user Nelson9
    In the amino acid table, the proline is throwing me off. Isn't proline nonpolar?
    (6 votes)
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  • orange juice squid orange style avatar for user Jimena TA
    Hi, I remember that in the lipids lesson it said that a specific macromolecule (I don´t remember its name) was considered to be a lipid just because it was hydrophobic and in this article, I found this: "For example, amino acids such as valine and leucine are nonpolar and hydrophobic." So my question is what is the difference between the other macromolecule that was called a lipid because of its being hydrophobic and these proteins?
    (5 votes)
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  • orange juice squid orange style avatar for user Rmal1103401
    If enzymes are proteins, and they can function as a part of the digestive system, doesn't that mean that the enzymes will be breaking down other proteins in the eaten food? So proteins can break down other proteins?
    (4 votes)
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  • leaf green style avatar for user Ansar
    "Some amino acids, such as lysine and arginine, have side chains that are positively charged at physiological pH and are considered basic amino acids"
    "Aspartate and glutamate, on the other hand, are negatively charged at physiological pH and are considered acidic"

    What is going on? Positive charge means that it has excess of H+ protons, so why is it basic and vice versa?
    (2 votes)
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    • piceratops seed style avatar for user RogerP
      Lysine and arginine accept a proton and, in so doing, they act as bases and become positively charged. (Compare them with ammonia, which is a base and which becomes protonated in water to give NH4+ and OH- ions.)

      Aspartate and glutamate, on the other hand, lose protons and become negatively charged. They act as acids. (Compare them with acetic acid, which dissociates in water to give acetate ions and H3O+.)
      (2 votes)
  • blobby green style avatar for user Noor Ullah
    How the c and n terminus of a polypeptide are protected?
    (2 votes)
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  • blobby green style avatar for user Joe Wang
    Why is Carboxyl considered a acid but loses OH in the peptide formation and with same logic, Amino base?
    (1 vote)
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    • female robot grace style avatar for user tyersome
      Peptide bond formation is not an acid-base reaction.

      Peptide bonds are covalent bonds that form through dehydration (loss of a water molecule).

      Biological acid-base reactions typically involve transfers of hydrogen ions (aka protons or H⁺).

      Does that help?

      ————————————————————————————————————

      If you want to understand this material better, I strongly encourage you to work through the Chemistry material on Khan Academy starting here:
      https://www.khanacademy.org/science/chemistry

      That may look like a lot of work, but you've probably watched many of the videos already under "Chemistry of life". A deep understanding of chemistry is essential to anyone interested in modern biological sciences or medicine, so I really encourage you to take the time to work though all of the chemistry material (including the Organic Chemistry section: https://www.khanacademy.org/science/organic-chemistry).
      (3 votes)
  • female robot amelia style avatar for user Hajrah
    How is Carboxylic acid, an acid if it donates OH group during peptide bond formation?
    (1 vote)
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