AP Biology · Lesson 3

Protein structure and function

Know Know it

Every amino acid has the same backbone: a central carbon bonded to an amino group, a carboxyl group, a hydrogen and an R group. The 20 amino acids differ only in their R groups. An R group may be nonpolar, polar or charged, and that property decides how the amino acid behaves in a folded protein.

Amino acids are linked by peptide bonds, formed by dehydration synthesis, into a polypeptide with an amino (N) end and a carboxyl (C) end. Protein structure has four levels:

Primary: the order of amino acids. Secondary: alpha helices and beta pleated sheets, held by hydrogen bonds between backbone atoms. Tertiary: the full 3D fold of one chain, held by interactions among R groups, including hydrogen bonds, ionic bonds, hydrophobic clustering and disulfide bridges. Quaternary: two or more polypeptides fitted together, found in only some proteins.

Shape sets function. An enzyme's active site, for example, fits its substrate because of the R groups that line it. High heat or extreme pH can denature a protein: its weak interactions break, it unfolds and it stops working.

Trap Denaturing does not cut the chain

Denaturation disrupts the weak interactions that hold the fold, not the peptide bonds. The primary structure stays the same; the shape is what is lost.

Worked example Easy

What makes one amino acid different from another?

  1. Its amino group
  2. Its R groupAnswer
  3. Its carboxyl group
  4. Its central carbon

How to solve it

  1. List the parts all amino acids share: central carbon, amino group, carboxyl group, hydrogen.
  2. The remaining part, the R group, is the one that varies.

Why each choice is right or wrong

  • A. Incorrect. Every amino acid has the same amino group, so it cannot tell them apart.
  • B. Correct. The side chain is the only part that differs among the 20 amino acids.
  • C. Incorrect. Every amino acid has the same carboxyl group, so it does not make them differ.
  • D. Incorrect. Every amino acid has a central carbon, so it is shared rather than distinct.

Explain Explain it

Task verbs: explain, predict

To predict the effect of a change in a protein, follow the chain: the changed amino acid has an R group with a new property, that property changes how the chain folds or binds, and the changed shape changes the function.

Worked example Hard

In a protein that works in the watery cytoplasm, one amino acid buried in the core has a nonpolar R group. A mutation replaces it with an amino acid whose R group carries a negative charge. What is the most likely result?

  1. The protein gains a second polypeptide chain
  2. The peptide bonds next to the change break
  3. The protein keeps the same shape, since one amino acid is too few to matter
  4. The core no longer packs normally, so the protein may fold incorrectlyAnswer

How to solve it

  1. Note where the amino acid sits: the nonpolar core, away from water.
  2. The new R group is charged, so it is hydrophilic.
  3. A hydrophilic group in the core disturbs the R group interactions that hold the tertiary structure.

Why each choice is right or wrong

  • A. Incorrect. Changing one amino acid does not add a second polypeptide, so quaternary structure is not created.
  • B. Incorrect. A new R group does not break peptide bonds; the backbone stays linked.
  • C. Incorrect. One changed amino acid can alter folding, as a charged group in a nonpolar core shows.
  • D. Correct. A charged R group is drawn toward water, so it disrupts the nonpolar core and can change the fold.

Predict Your turn

An enzyme from a pond bacterium is heated to 75 degrees C for 20 minutes and then cooled back to 25 degrees C. Predict the enzyme's activity after cooling compared with before heating, and explain your prediction in terms of protein structure.

Write it, then compare. Nothing you type here is saved or graded.

Compare with a model answer

A full answer does this

  • Predicts that activity is lower after heating than before
  • Explains that heat breaks the weak interactions holding the 3D shape, so the protein unfolds (denatures)
  • Links the lost shape to an active site that no longer fits the substrate

Model answer

The enzyme will be less active after cooling than before heating. High heat breaks the hydrogen bonds and other weak interactions among R groups that hold the enzyme's 3D shape, so the enzyme denatures. Its active site loses the shape that fits the substrate, so fewer substrate molecules bind and the reaction slows.

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