Sequence Becomes Shape

AP Biology · Unit 1 · Topic 1.7

Sequence Becomes Shape

A protein's shape comes from the order of its amino acids and how their R groups interact. Change one and watch the fold move.

Learning objective 1.7.A Describe the structure and function of proteins.

The order of the R groups decides the shape

Press R groups to write a sequence. The chain folds itself as their interactions pull it together, and you can drag any residue to see the fold recover. Then disrupt it and watch the shape go.

Add an R group

Press R groups to write a sequence.
Amino acids0
Peptide bonds0
R group interactions0
Disulfide bridges0
How compact—

The four levels

Primary structure is the sequence itself

A protein is a linear chain of amino acids joined by covalent peptide bonds, each formed between the carboxyl group of one amino acid and the amine group of the next. That joining is a dehydration synthesis, the same reaction that builds every other polymer.

The specific sequence of amino acids is the primary structure, and it determines everything that follows. Nothing else about the protein is chosen — the shape falls out of the order.

R groups do the folding

An amino acid is a central carbon carrying a hydrogen, a carboxyl group, an amine group and a variable R group. Only the R group differs between one amino acid and the next, and R groups come in three chemical categories: hydrophobic/nonpolar, hydrophilic/polar, and ionic.

Those R groups interact with each other, and the interactions are what hold a folded shape together:

Four levels, one function

All four levels together determine what the protein does. Change the sequence and you change the shape; change the shape and you change the function.

Learning check

Answer these in your own words before you open the answers.

  1. Identify the process that forms the covalent peptide bonds joining amino acids into a polypeptide.
  2. Connect the primary structure of a protein to its overall shape.
  3. Two amino acids in a receptor are replaced, swapping hydrophobic R groups for charged ones. Explain why the receptor changes shape.
  4. Name the four interactions that hold tertiary structure together, and say which one is covalent.
Show answers

1. Dehydration synthesis, also called a condensation reaction. A water molecule is released as each peptide bond forms between the carboxyl group of one amino acid and the amine group of the next.

2. The amino acid sequence determines the overall shape of the protein, because the R groups in that sequence interact with each other and stabilize the folded structure.

3. The new R groups have different chemical properties, so different interactions form at that position. A hydrophobic R group clusters away from water in the core; a charged one is attracted to opposite charges and repelled by like ones. Because the interactions holding that region together change, the region folds differently and the overall shape changes.

4. Hydrogen bonds, hydrophobic interactions, ionic interactions and disulfide bridges. The disulfide bridge is the covalent one, which is why it is the hardest to break.