Proteins

Essential Question

How does the shape of a protein determine what it can do?

Proteins do more jobs in a cell than any other class of molecule. They speed up reactions, build structures, carry oxygen, and fight infection. All of them are built from the same 20 amino acids, and yet each one has its own shape and its own job. In this lesson, you’ll learn how amino acids join into chains, how a chain folds into a 3-D shape, and why a change in shape can stop a protein from working.

What Proteins Do

• Proteins are the most varied class of large molecules
• Each protein has its own shape and its own job
• Enzymes are proteins that speed up reactions
• Proteins always contain nitrogen

Job	Example	What it does
Enzyme	Amylase	Speeds up the breakdown of starch
Structure	Collagen	Strengthens skin and tendons
Transport	Hemoglobin	Carries oxygen in red blood cells
Defense	Antibody	Recognizes and binds to invaders
Signaling	Insulin	Tells cells to take up glucose

Proteins carry out most of the work of a cell. A human cell makes thousands of different proteins, and each one has a specific job. The table shows a few examples. The wide range of jobs comes from a wide range of shapes, and all of those shapes are built from the same set of small monomers.

Amino Acids

• Amino acid: the monomer of a protein
• Every amino acid has an amino group and a carboxyl group
• The R group (side chain) is different in each of the 20 kinds
• R groups are different sizes and have different chemical properties

The monomers of proteins are amino acids. Every amino acid has the same backbone: a central carbon bonded to an amino group, a carboxyl group, and a hydrogen atom. What makes one amino acid different from another is its R group, also called the side chain. Cells use 20 different amino acids. Some R groups are attracted to water, some are not, and some carry an electric charge. These differences are what cause a chain of amino acids to fold up into a specific shape.

Peptide Bonds and Polypeptides

• Amino acids join by dehydration synthesis
• The bond between them is a peptide bond
• A chain of amino acids is a polypeptide
• A chain of n amino acids has n − 1 peptide bonds

When two amino acids join, the carboxyl group of one bonds to the amino group of the next, and a molecule of water is released. This is dehydration synthesis, and the new bond is a peptide bond. A chain of amino acids is called a polypeptide, and a protein is made of one or more polypeptides. Because the 20 kinds of amino acids can be placed in any order, the number of possible chains is enormous. A chain of only 3 amino acids already has 20 × 20 × 20 = 8,000 possible sequences.

Four Levels of Protein Structure

• Primary: the order of amino acids
• Secondary: coils and pleats held by hydrogen bonds
• Tertiary: the whole chain folds into a 3-D shape
• Quaternary: two or more chains join together

Biologists describe the shape of a protein at four levels. The primary structure is the sequence of amino acids. Hydrogen bonds between parts of the chain pull it into coils called helices and zigzags called pleated sheets, which are the secondary structure. The coils and sheets then fold into a particular 3-D shape, the tertiary structure, held in place by bonds between R groups. Some proteins, such as hemoglobin, are made of more than one chain. How the chains fit together is the quaternary structure. The sequence of amino acids decides all the other levels, because it decides which R groups can attract or avoid each other.

Shape Decides Function

• A protein works only in its folded shape
• Heat, acid, or other changes can unfold a protein
• Unfolding is denaturation
• A denatured protein usually cannot do its job

The graph shows sample data for an enzyme heated for 10 minutes at different temperatures. Up to about 40°C almost every molecule keeps its shape, and between 50°C and 70°C most of them lose it. Losing the folded shape is called denaturation. Heat breaks the weak bonds that hold the folds in place, but it does not break the peptide bonds, so the amino acid sequence stays the same. Because the shape is gone, the protein can no longer do its job. Cooking an egg is an everyday example: the proteins in the egg white denature and the clear liquid turns white and firm.

One Change in the Sequence

• A change in one amino acid can change the shape
• Sickle cell disease is caused by one changed amino acid in hemoglobin
• Hemoglobin has 4 chains and 574 amino acids
• A tiny change in sequence can have a large effect

Position in the beta chain	1	2	3	4	5	6	7	8
Normal hemoglobin	Val	His	Leu	Thr	Pro	Glu	Glu	Lys
Sickle cell hemoglobin	Val	His	Leu	Thr	Pro	Val	Glu	Lys

Hemoglobin is made of four chains, two of one kind and two of another, with 574 amino acids in all. The table shows the first 8 amino acids of one of these chains. In people with sickle cell disease, the amino acid in position 6 is valine (Val) instead of glutamic acid (Glu). This one change has a different R group, which changes how hemoglobin molecules interact. They stick together into long fibers that bend red blood cells into a sickle shape. A change in the primary structure led to a change in shape, and a change in shape led to a change in function.

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Worked Examples

Try each problem on your own first, then open the solution to check your work.

Example 1: Counting Peptide Bonds

(a) A tripeptide is a chain of 3 amino acids. How many peptide bonds does it have, and how many molecules of water are released when it forms? (b) How many different tripeptides can be made from the 20 amino acids? (c) Hemoglobin has 574 amino acids in 4 separate chains. How many peptide bonds does it have?

Show the solution

1. (a) Bonds: a chain of 3 has 3 − 1 = 2 peptide bonds. Each bond releases 1 water molecule, so 2 molecules of water are released.
2. (b) Possible sequences: there are 20 choices for each of the 3 positions. 20 × 20 × 20 = 8,000 tripeptides.
3. (c) Hemoglobin: each chain of n amino acids has n − 1 bonds, so 4 chains have 574 − 4 = 570 peptide bonds. The chains are held together by other, weaker bonds and not by peptide bonds.
4. Answer: (a) 2 bonds, 2 water. (b) 8,000. (c) 570 peptide bonds.

Example 2: Heating an Enzyme

Use the graph of an enzyme heated for 10 minutes. (a) What percent of the molecules were still in working shape at 50°C? (b) By how many percentage points did this drop from 40°C to 70°C? (c) Explain why the enzyme stopped working at high temperatures even though its peptide bonds were not broken.

Show the solution

1. (a) At 50°C: 85% of the molecules were still in working shape.
2. (b) Drop: 98% at 40°C and 8% at 70°C. 98 − 8 = 90 percentage points.
3. (c) Explanation: heat breaks the weak bonds that hold the secondary, tertiary, and quaternary structure in place, so the protein unfolds. The peptide bonds and the primary structure are not changed, but the enzyme no longer has the shape it needs to work.
4. Answer: (a) 85%. (b) 90 percentage points. (c) Heat unfolds the protein (denaturation), so its shape and function are lost.

Example 3: Sickle Cell Hemoglobin

Use the table of the first 8 amino acids of the hemoglobin chain. (a) In which position do normal and sickle cell hemoglobin differ? (b) Two of the four chains in a hemoglobin molecule have this change. What percent of the 574 amino acids is that? (c) Explain how a change in one amino acid can change the function of the whole protein.

Show the solution

1. (a) Position: position 6. Normal hemoglobin has Glu and sickle cell hemoglobin has Val.
2. (b) Percent changed: 2 changed amino acids ÷ 574 × 100 = 0.35%, so well under 1% of the amino acids are different.
3. (c) Explanation: the new R group changes how the chain interacts with other molecules. This changes the shape of hemoglobin, and the hemoglobin molecules stick together, so red blood cells bend out of shape.
4. Answer: (a) Position 6 (Glu in normal, Val in sickle). (b) About 0.35%. (c) The new R group changes the shape, and shape decides function.

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Practice

Name the four levels of protein structure, count peptide bonds and water molecules, read a graph of an enzyme being heated, and explain how one changed amino acid can change a protein. Try it on your own first, then check your work with the answer key.

• Proteins Practice Worksheet (PDF)
• Proteins Practice Answer Key (PDF)

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Lesson Slides

• 5.4 Proteins Slides (PDF)

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Big Ideas

• Amino acids are the monomers of proteins
• Peptide bonds join amino acids by dehydration synthesis
• Four levels of structure: primary, secondary, tertiary, quaternary
• The sequence of amino acids decides the shape, and the shape decides the function
• Denaturation unfolds a protein and stops it from working

Back to the essential question: a protein’s shape determines what it can do. The sequence of amino acids decides how the chain folds, and the folded shape fits the protein to its job. When the shape changes, because of heat or because of a change in the sequence, the function can be lost. Next, you’ll look at the molecules that carry the instructions for building proteins: nucleic acids.

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