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Protein Classification

Introduces the four levels of structure for polypeptides.

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Illustration of sickle cell anemia

Credit: The National Heart, Lung, and Blood Institute (NHLBI)
Source: http://commons.wikimedia.org/wiki/File:Sickle_cell_01.jpg
License: CC BY-NC 3.0

A Serious Shift

Hemoglobin is a complex protein which has a quaternary structure and contains iron. There are four subunits in the hemoglobin molecule – two alpha subunits and two beta subunits. Each subunit contains one iron ion, whose oxidation state changes from +2 to +3 and back again, depending upon the environment around the iron. When the oxygen binds to the iron, the three-dimensional shape of the molecule changes. Upon release of the oxygen to the cells, the shape changes again.

With hemoglobin of normal structure, this shift in conformation does not present any problems. However, individuals with hemoglobin S do experience serious complications. This hemoglobin has one amino acid in the two beta chains that is different from the amino acid at that point in the primary structure of normal hemoglobin. The result of this one structural change is aggregation of the individual protein molecules when oxygen is released. Adjacent hemoglobin molecules come in contact with one another and clump up, causing the red cells to deform and break.

This abnormality, known as sickle cell, is genetic in nature. A person may inherit the gene from one parent and have sickle cell trait (only some of the hemoglobin is hemoglobin S), which is usually not life-threatening. Inheriting the gene from both parents will result in sickle cell disease, a very serious condition.


A polypeptide is a sequence of amino acids between ten and one hundred in length. A protein is a peptide that is greater than one hundred amino acids in length. 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 and physiological properties of proteins is a function of their amino acid sequences. Since proteins generally consist of one hundred or more amino acids, the number of amino acid sequences that are possible is virtually limitless. 

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. An alpha helix consists of amino acids that adopt a spiral shape. A beta sheet is alternating 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 side chains. The interaction of the various side chains in the amino acid, specifically the hydrogen bonding, leads to the adoption of a particular secondary structure.

Structure of alpha helices and beta sheets

Credit: Alpha: User:Ayacop/Wikimedia Commons; Beta: User:Dcrjsr/Wikimedia Commons
Source: Alpha: https://commons.wikimedia.org/wiki/File:CALC1_2GLH.png; Beta: http://commons.wikimedia.org/wiki/File:1gwe_antipar_betaSheet_both.png
License: CC BY-NC 3.0

Secondary structure: alpha helix and beta sheet. [Figure2]

The tertiary structure is the overall three-dimensional structure of the protein. A typical protein consists of several sections of a specific secondary structure (alpha helix or beta sheet) along with other areas in which a more random structure occurs. These areas combine to produce the tertiary structure.

Some protein molecules consist of multiple protein subunits. The quaternary structure of a protein refers to the specific interaction and orientation of the subunits of that protein Hemoglobin is a very large protein found in red blood cells and whose function is to bind and carry oxygen throughout the bloodstream. Hemoglobin consists of four subunits – two α subunits (yellow) and two β subunits (gray) – which then come together in a specific and defined way through interactions of the side chains (see Figure below). Hemoglobin also contains four iron atoms, located in the middle of each of the four subunits. The iron atoms are part of a structure called a porphyrin, shown in red in the figure.

Ribbon diagram of hemoglobin

Credit: Courtesy of Todd L. Mollan, CBER, US Food and Drug Administration
Source: http://blogs.fda.gov/fdavoice/index.php/tag/blood-substitutes/
License: CC BY-NC 3.0

Hemoglobin [Figure3]

Some proteins consist of only one subunit and thus do not have a quaternary structure. The Figure below diagrams the interaction of the four levels of protein structure.

Diagram of the four levels of protein structure

Credit: Mariana Ruiz Villarreal (Wikimedia: LadyofHats)
Source: http://commons.wikimedia.org/wiki/File:Main_protein_structure_levels_en.svg
License: CC BY-NC 3.0

The four levels of protein structure. [Figure4]


  • Peptide and proteins are defined.
  • The four levels of protein structure are listed and defined.



Watch the video at the link below and answer the following questions:


  1. What is part of what determines how a protein folds?
  2. What holds secondary structure together?
  3. What holds the tertiary structure together?



  1. A protein has the following sequence: ser-his-thr-tyr. What component of protein structure is this?
  2. What do we call the overall three-dimensional shape of a protein?
  3. A protein has one subunit. Would it have a quaternary structure?

Image Attributions

  1. [1]^ Credit: The National Heart, Lung, and Blood Institute (NHLBI); Source: http://commons.wikimedia.org/wiki/File:Sickle_cell_01.jpg; License: CC BY-NC 3.0
  2. [2]^ Credit: Alpha: User:Ayacop/Wikimedia Commons; Beta: User:Dcrjsr/Wikimedia Commons; Source: Alpha: https://commons.wikimedia.org/wiki/File:CALC1_2GLH.png; Beta: http://commons.wikimedia.org/wiki/File:1gwe_antipar_betaSheet_both.png; License: CC BY-NC 3.0
  3. [3]^ Credit: Courtesy of Todd L. Mollan, CBER, US Food and Drug Administration; Source: http://blogs.fda.gov/fdavoice/index.php/tag/blood-substitutes/; License: CC BY-NC 3.0
  4. [4]^ Credit: Mariana Ruiz Villarreal (Wikimedia: LadyofHats); Source: http://commons.wikimedia.org/wiki/File:Main_protein_structure_levels_en.svg; License: CC BY-NC 3.0

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