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1.7 Proteins

Syllabus
2025
Topic
1.7
Level
—

Learning objectives

1.7A—Describe the structure and function of proteinsDescribe the structure and function of proteins.• Proteins comprise linear chains of amino acids connected by the formation of covalent (peptide) bonds that form between a carboxyl group (−COOH) of one amino acid and an amine group (N−H)2 of the next amino acid, resulting in a growing peptide chain.• Amino acids are composed of a central carbon atom with a hydrogen atom, a carboxyl group, an amine group, and a variable R group covalently bound to it. The R group of an amino acid can be categorized by three possible chemical properties: hydrophobic/nonpolar, hydrophilic/polar, or ionic. The interactions of these R groups determine the structure and function of that region of the protein.• The specific sequence of amino acids in proteins determines the primary structure of a polypeptide as well as the overall shape of the protein.- Exclusion: The molecular structure of amino acids is beyond the scope of the AP Exam.• Secondary structures of proteins are made through the local folding that forms from interactions between atoms of the polypeptide backbone of the amino acid chain. Hydrogen bonding forms shapes such as alpha-helices and beta-pleated sheets.• The three-dimensional shape of the tertiary structure of a protein results from the formation of hydrogen bonds, hydrophobic interactions, ionic interactions, or disulfide bridges.• The quaternary structure arises from interactions between multiple polypeptides. All four levels of a protein structure determine the function of a protein.

Protein Function Emerges from Sequence and Folding

Proteins are linear chains of amino acids. Each amino acid has a central carbon bonded to hydrogen, a carboxyl group, an amine group, and a variable R group. A covalent peptide bond forms between the carboxyl group of one amino acid and the amine group of the next, extending the peptide chain.

R-group category Interaction tendency relevant to folding
Hydrophobic / nonpolar Associates away from water and with other nonpolar regions
Hydrophilic / polar Can interact with water and form polar interactions, including hydrogen bonds
Ionic Can attract or repel charged groups
Structural level What produces it
Primary The specific amino-acid sequence in one polypeptide
Secondary Local backbone folding stabilized by hydrogen bonds, including alpha-helices and beta-pleated sheets
Tertiary Overall three-dimensional shape from hydrogen bonds, hydrophobic interactions, ionic interactions, and disulfide bridges
Quaternary Interactions among multiple polypeptide chains

Primary sequence constrains which R groups can interact and where, so it influences higher-level folding. A sequence change can alter local chemistry, change protein shape, and therefore change binding, transport, movement, or another protein function. The effect depends on where the change occurs and which interaction is disrupted.

Secondary structure comes from backbone interactions; tertiary structure includes interactions involving R groups within one polypeptide; quaternary structure requires multiple polypeptides. The molecular structures of individual amino acids are explicitly outside AP Exam scope.