Introduction

Proteins, along with carbohydrates and lipids, are a type of organic macromolecule that are fundamental building blocks of life. While you hear a lot about proteins in daily living – like in ads for protein shakes and protein powders– there are a few misconceptions about why proteins are important and how they work. After reading through this AP® Biology Crash Course Review, as well as the practice questions and quick recap at the end, you should feel that you have a good understanding of what proteins are and that you are ready to tackle that AP® Bio exam!

What Are Proteins?

Let’s start with a protein definition. Proteins are a type of complex macromolecule built up of monomers called amino acids that are linked into complex polymers by bonds known as peptide bonds.

Amino acids are formed by attaching an amine group, a carboxyl group, and a variable (R) to a central atom of carbon. While you are probably already familiar with carboxyl groups (COOH) and amine groups (NH2), the so-called R group may be new to you. There are 20 common amino acids, and they differ by their R Groups. For example, polar amino acids have polar bonds within their R group, while nonpolar amino acids have nonpolar bonding as in CH2 and CH3 in their R groups. Charged amino acids have bases or acids as their R groups. Some amino acids have very specialized functions, which their unique R groups allow them to carry out. R groups are also sometimes known as side chains or side groups.

Proteins are formed when amino acids join through peptide bonds, which is why they are also called polypeptides. The peptide bonds between the amino acids are formed by a process called dehydration synthesis. If you’ve read the other macromolecule AP® Biology Crash Course Reviews (carbohydrates and lipids), you might remember this process, as those polymers are bonded through dehydration synthesis as well. If not, you can read in depth about dehydration synthesis in this review specifically on the topic.

Although proteins, carbohydrates, and lipids are all essential macromolecules bonded through the same process, their structures are quite different. Proteins are unique in that their structure has four different levels of structure, due to the complex interactions that occur between amino acids in a long chain polypeptide. Let’s look at each of those levels more closely.

Levels of Protein Structure

Proteins have four main structural levels, each more complex than the next. Luckily, they’re in numerical order, so they are easy to remember. The four structure types are primary, secondary, tertiary, and quaternary. What type of structure a protein has determines its conformation, or its unique shape that allows it to perform whatever specific job is its function. We’ll look at the different possible functions proteins can have in more detail in the next section, but for now, just remember that a protein’s structure determines its function.

The primary structure of a protein is the unique sequence of a string of amino acids. This sequence is determined by the order of the nucleotides that code for that protein in DNA. One way to think of primary structure is to think of amino acids as the letters of the alphabet, and the primary structure as the words that are formed using those letters. Just like changing one letter in a word can change its meaning, changing a single amino acid in a protein sequence can have serious consequences. One example of this is the condition called sickle cell anemia, which occurs because of an amino acid substitution in molecules of hemoglobin, and has life-threatening effects.

Protein secondary structure refers to when the polypeptide molecule has hydrogen bonding within it. These hydrogen bonds cause the amino acid chain to fold or coil. This can result in two specific shapes. An alpha helix occurs when the hydrogen bonds form in a chain causing a spiraling pattern. Beta sheets form when chains that are parallel to each other link to create a pleated shape. Sometimes, alpha helixes and beta shapes can be combined in various forms to create a super-secondary structure or a motif, but you don’t need to worry about these for AP® Bio.

The tertiary structure of a protein refers to its 3D spatial conformation, or in other words, how its secondary structure (its alpha helix or beta sheet or both) folds itself up in its interior. This unique final folded shape determines the protein’s specificity. There are a couple of factors that contribute to the formation and maintenance of tertiary structures. You don’t need to know the nitty-gritty details of them, but it’s good to be able to able to list/recognize what a few of them are. One is Van der Waals interaction, which refers to the attraction (through van der Waals forces) of non-polar chains that are close to each other. Others are hydrogen bonds between R groups, ionic bonds between R groups, and hydrophobic interactions. Proteins with tertiary structures are often globular, like the sub-units in hemoglobin, an important protein in blood.

The final structure is quaternary structure. Not all proteins have this structure; only proteins that are made of two or more polypeptide chains do because this structure specifically refers to the connection of multiple polypeptides to form a functioning protein. A moment ago, we used hemoglobin sub-units as an example of tertiary structure. Hemoglobin exhibits quaternary structure as well since it consists of a combination of four polypeptide chains. In fact, hemoglobin shows all four levels of protein structure and is therefore a good example to give, should you need to explain the structures for the AP® Bio Exam.

Below, you can find an image that demonstrates each of the four levels of protein structure to help you visualize.

Protein Function

Proteins are one of the building blocks of life, because they perform such a variety of jobs throughout the body. For AP® Bio, you will need to know the seven main functions, which we will go through now (in no particular order).

The first main function is transport. Transport proteins carry small molecules and ions across cell membranes and throughout the body. Hemoglobin, which we’ve mentioned a few times now, is a transport protein in your blood that takes oxygen from your lungs to the other parts of your body. Proton pumps within cell membranes are also transport proteins, and regulate what can and cannot enter the cell.

A second important function of proteins is defense. Defensive proteins protect against disease by recognizing and attacking foreign microbes. Examples of these are antibodies and immunoglobins. They are a vital part of the immune system.

Proteins also serve a support function. Structural proteins, like keratin, collagen, and fibrin, make up things like hair, nails, scales, horns, and feathers. Similar to this, a fourth function of proteins is storage. Storage proteins store amino acids and can hold certain molecules like iron and calcium.

Regulation is also a function. Hormonal proteins coordinate body functions by sending and receiving information about body status to and from the brain. Insulin, which regulates blood sugar levels, is a good example.

Movement is a sixth major function. Contractile proteins, like actin and myosin, allow for motion by controlling muscle contractions.

The final main function you will need to know is enzyme catalysis. Enzymatic proteins facilitate chemical reactions by speeding them up. For example, digestive enzymes accelerate the hydrolysis of the polymers in your food. Enzymes are a topic worth looking at more in depth before the exam, so why not look at this AP® Biology Crash Course Review specifically on that subject?

Review Questions

Question 1. Which level of protein structure is determined mainly by hydrogen bonding?

A) Primary Structure

B) Secondary Structure

C) Tertiary Structure

D) Quaternary Structure

Question 2. Which of the following is not one of the main functions of proteins?

A) Transport across cell membranes

B) Protecting the body from disease

C) Encoding information

D) Catalyzing enzymes

Question 3. What sorts of bonds are used to link amino acids to each other?

A) Ionic bonds

B) Hydrogen bonds

C) Glycosidic bonds

D) Peptide bonds

Answers

Question 1. The correct choice is B: Secondary Structure.

Question 2. The correct choice is C: Encoding information.

Question 3. The correct choice is D: Peptide bonds.

Crash Course Review Recap

Congratulations, you’ve reached the end of this AP® Biology Crash Course Review on proteins! Hopefully, you now feel you have a better understanding of the protein definition and why proteins are so important for life as we know it. Here is a recap of the main points we covered:

• Proteins are organic macromolecules built up of amino acids joined by peptide bonds
• Amino acids are monomers made up of a carboxyl group, an amine group, and an R group attached to a central carbon
• There are four increasingly complex levels of protein structure
• Primary structure is the linear sequence of amino acids
• Secondary structures involve hydrogen bonding, which causes the chains to coil into alpha helixes or beta sheets
• Tertiary structure is the final folded 3D conformation
• Quaternary structure connects the subunits of proteins with multiple polypeptide chains
• Proteins have seven main functions: transport, defense, structure, storage, regulation, movement, and enzyme catalysis.

Do you feel confident about your knowledge of proteins? Let us know!

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