Exploring the Molecules of Life:  Proteins

What is the major function of proteins in the human body?

Why does having a perm (or permanent) make your hair curly?  

Proteins are the most important biological compounds needed for life and are used for many purposes in the human body.  They act as the structural materials in humans and animals as cellulose does in plants.  Enzymes are proteins that catalyze the body's chemical reactions.  Proteins make up muscles that aid in movement.  The curl from a perm involves the resetting of attractive forces in the protein of hair.

Proteins are made up of chains of amino acids.  For example, here is the simplest amino acid glycine.  Can you find what element is present in proteins that is not present in carbohydrates?  What is the oxygen-containing functional group?

Amino acids are organic compounds that contain an amine group (-NH2) bonded to a carbon atom that is bonded to a carboxylic acid group (-COOH) as seen below.  Remember you saw the carboxylic acid group in fatty acids.  Can you find the two functional groups above?

For glycine the R group is a hydrogen, H.  Other side chains or R groups make up other amino acids.  There are about 20 amino acids that naturally form in nature. We can classify amino acids into four major groups, each characterized by its type of side chain: non-polar, polar but neutral, acidic, and basic.  Click here to go to a good site displaying the amino acids.

Amino acids can bond together forming what is called a peptide bond (which is also called a amide linkage) .  The amine group (-NH2) of one amino acid bonds to the carboxylic acid group (-COOH) of another amino acid as seen below for the general case, where the R groups are different.  

Here is an example of phenylalanine and lysine combining together.  The product, phe-lys, does not have any hydrogen showing to make viewing easier.  Orient the individual amino acids to help see how they combine.  For the two linked amino acids or phe-lys, you may want to right click and select 2D structure to compare to the reaction above.


phenylalanine                          lysine                              the two linked

Can you see where these two amino acids will come together to form a bond?  Describe it.

Looking at the structure of combination of the two, what is lost when the two amino acids bond together?

Peptide bonds are formed by loosing an (-OH) and a  (-H).  

What do you call two amino acids bonded together?

Could you bond a third amino acid to the two-bonded amino acids above?  Why or why not?

Two amino acids bonded together produce a dipeptide.  Di means two, therefore if three are bonded together the product is a tripeptide.  If many amino acids are bonded together the product would be a polypeptide.  Notice that there is still an amine group and a carboxylic acid group in the final product. 

What do long chains of amino acids produce?

When many amino acids bond together they form a protein, which is used in many functions in living organism.

Can phenylalanine and lysine  be bonded a different way to get the same product?

As you can see (phe-lys) and (lys-phe) are not the same products.  These are two different dipeptides.  They have the same formula but they both have different properties.  They are known as isomers.  Isomers are compounds that are different in properties but they have the same molecular formula.

To link a pair of amino acids together requires one peptide linkage.  How many peptide linkages occur in a tripeptide?  How many in a tetrapeptide?  Click here to go to a website that will allow you to build a polypeptide.

Here is a longer chain of amino acids.   Does the main part of the amino acid chain look like a hydrocarbon chain?  

Can you count how many amino acid linkages make up this chain?  How many amino acids actually make up this chain?

There are six amino acids present in this chain.   Can you see them?  Can you also name each individual amino acid in this chain?

Click here to go to the site to see the individual structures, names and official abbreviations of the 20 amino acids found in nature. 

Here is the sequence of amino acids that make up hexapeptide above:  


The order of the linkage of amino acids or the sequence is the basis of the primary structure of proteins.   Here is a brief table of proteins with their function, number of amino acids, and the resultant molar mass.

Protein Function Number of amino acids Molar Mass (g/mole)
Insulin enzyme for sugar metabolism 51 6000
Cytochrome c enzyme for cell respiration 104 16000
Growth Hormone used in anti-aging treatment 191 49000
Hemoglobin oxygen transport in blood 574 65000
Hexokinase enzyme for glycolysis 730 96000
Gamma Globulin part of immune system in blood 1320 176000
Myosin muscle action 6100 800000

Modified from: Seager & Slabaugh , Organic and Biochemistry for Today, 4th ed, Brooks/Cole (2000)

Here is a simplified protein structure that is made up of nine amino acids.  How does this structure in terms of the backbone (not the number of amino acids) differ from the hexapeptide above?  How would you describe the shape of each structure?   Be sure to click on the molecule to move it around so you can see this.  Selected hydrogen atoms have been removed to make viewing of the structure easier.

The structure above is an alpha helix that has been simplified by removing the side chains, or R groups.  What attractive force holds the helix in its shape? (Right click on the image, go to options, then select display hydrogen bonds.)

The structure below is more realistic as it displays different amino acids in the helix.  Be sure to click on the molecule to move it around so you can see the nature of the helix.

Now look at the simplified structure composed of only glycine below. 

What is the structural difference between this one and the two helix proteins above?

Do you think that you can find where hydrogen bonding will take place?

The three chains in this structure above are aligned parallel to each other and they are held together by hydrogen bonding.

Here is a real sheet protein, composed of many amino acid.  See if you can see the sheet structure.  If you right click, go to display and then select cartoon, you may be able to visualize the structure easier.

These proteins are known as sheet proteins.  The helix and sheet structures are the two most common secondary structures in proteins.

The structure of myoglobin, which aids in oxygen transport to muscles, is given below.  How does myoglobin compare to the other proteins shown above?

Let's change the display of the protein- Right click on the image, go to display, then select cartoons.  Is the chain of amino acids one continuous chain? 

Myoglobin is one continuous chain of amino acids that is folded and twisted.  This folding and twisting forms the basis of the tertiary structure of a protein.  What attractive forces do you think keeps the folds in place?

The structure of insulin is given below.  Do you see any similarities in the structure with those of the helix and sheet structures you have seen already?

Let's change the display of the protein- Right click on the image, go to display, then select cartoons.

Now what do you notice about the structure of insulin?  

Is the chain of amino acids one continuous chain? 

Is there any sulfur in the protein?

Insulin is the hormone in the body that regulates the blood's glucose level.  It is a small protein that only consists of 51 amino acids and contains two polypetide chains linked together.  The structure of insulin is an example of a protein with a quaternary structure.  The adjacent sulfurs in the cysteine forms disulfide linkages to help hold the structure along with hydrogen bonding.  Here is an excellent tutorial on insulin- click here.  (must use Netscape to view)

Compare the structure of hemoglobin, which transports oxygen in blood, given below with that of insulin.  

Be sure to right click on the image, go to display, then select cartoons.  

What do you notice about the difference in structure?

Now right click again on the image of hemoglobin, go to color, then select chain.  How many subunits in hemoglobin?

Insulin and hemoglobin are examples of proteins with quaternary structure.  Quaternary structure is the highest level of protein organization and it only applies to proteins with more than one polypeptide chain.  The four subunits of amino acids are held tightly together in a compact shape as you can see with hemoglobin.  However not all proteins have a quaternary structure.

The tertiary and quaternary structures of proteins are aided by a number of attractive forces which include hydrogen bonding and the three below:

 1.    disulfide linkages between -SH groups to form -S-S- from the occurrence of cysteine

2.    salt bridges between ionized -COO- and -NH3+

3.    hydrophobic interactions between non-polar groups such as phenyl groups from phenylalanine

The molar mass of a protein can be experimentally determined by osmotic pressure measurements.  How might you estimate the number of amino acids in a protein from its molar mass?

In a protein with a very specific biological function, does changing one of the amino acids in the sequence make any different how the protein functions?  Do a web search on sickle cell anemia to find out. 

Here is the structure of concanavalin A monomer.  How would you describe this protein in terms of its primary, secondary, tertiary, and quaternary structure?  This monomer has a molar mass of 18,000 g/mole.  How many amino acids in the monomer?  Is this a continuous chain of amino acids?

For more information on the concanavalin A monomer- click here.

An excellent website on proteins and amino acids can be found at UCSB by Duane Sears - click here.  Then click on the TABS near the top of the page.

Many of the structures on this page are from the molecules collection available at the NSF-funded C4 Project at Cabrillo Community College.

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