AP Biology · Lesson 5 of 6 · Unit 1

Proteins: amino acids, peptide bonds and levels of structure

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Proteins execute nearly every cellular task—from enzymatic catalysis to membrane transport and signal transduction—because their specific three-dimensional shapes dictate their functions. On the AP Biology exam (CED Topic 1.7), you will frequently analyze models of polypeptides or amino acid charts to predict how an amino acid substitution alters protein folding, stability, and biological activity.

By the end you’ll be able to

Describe how peptide bonds form between the carboxyl group of one amino acid and the amine group of the next.
Describe the components of an amino acid and classify R groups as hydrophobic/nonpolar, hydrophilic/polar or ionic.
Explain how the amino acid sequence (primary structure) leads to secondary structures, alpha-helices and beta-pleated sheets, formed by hydrogen bonding in the backbone.

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Core ideas (continued)
Worked examples
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What the exam asks

Section I (Multiple Choice): Stimulus sets often show structural diagrams of amino acids or ribbon models of proteins (such as membrane channels or enzymes). You will be asked to classify R groups, identify where peptide bonds form, or predict how a mutation affects folding.
Section II (Free Response): Regularly appears in Q1/Q2 (Experimental Results), Q4 (Conceptual Analysis), and Q5 (Analyze a Model). Expect prompts asking you to describe the chemical interactions maintaining a specific level of structure or predict and justify how replacing one amino acid with another alters phenotype or enzyme rate.

Core ideas

Amino acid structure and R-group chemistry

Every amino acid monomer consists of a central carbon atom (alpha carbon, $\alpha$ -carbon) covalently bonded to four partners:

An amine group ( $\text{-NH}_2$ , or $\text{-NH}_3^+$ at cellular pH)
A carboxyl group ( $\text{-COOH}$ , or $\text{-COO}^-$ at cellular pH)
A hydrogen atom ( $\text{-H}$ )
A variable side chain (R group)

The physical and chemical properties of the R group determine how that region of the polypeptide interacts with its environment and other amino acids:

R-Group Class	How to Recognize on a Diagram	Folding Behavior in Aqueous Cytosol
Hydrophobic (Nonpolar)	Primarily hydrocarbons ( $\text{C}$ and $\text{H}$ chains or rings); lacks polar functional groups (such as $\text{-OH}$ or $\text{-NH}_2$ )