AP® Biology review sheet from Aim for Five (aimforfive.com/bio/units/1/1-7)
Unit 1 · Topic 1.7
1.7 Proteins
Proteins are chains of amino acids that fold into precise three-dimensional shapes, and their shape decides their job: speeding reactions, carrying oxygen, building structures or sending signals. The order of amino acids sets the primary structure, and the chemical properties of each amino acid's R group drive how the chain folds through secondary, tertiary and sometimes quaternary structure.
Key terms
- amino acid
- peptide bond
- R group
- primary structure
- secondary structure
- tertiary and quaternary structure
Amino acids and peptide bonds
An amino acid has a central carbon atom bonded to four things: a hydrogen atom, an amino group (−NH₂), a carboxyl group (−COOH), and a variable side chain called the R group. There are 20 common amino acids, and they differ only in their R groups.
Amino acids are linked by dehydration synthesis (1.3). The carboxyl group of one amino acid bonds to the amino group of the next, forming a covalent bond called a peptide bond and releasing water. A chain of amino acids is a polypeptide. Each chain has two different ends: one with a free amino group (the N-terminus) and one with a free carboxyl group (the C-terminus). A protein is one or more polypeptides folded into a working shape.
R groups decide how a chain behaves
Because R groups interact with water and with each other, the sequence of amino acids determines where a chain will bend and fold.
| Type of R group | Behavior in water | Where it tends to end up |
|---|---|---|
| Nonpolar (hydrophobic) | Avoids water | Buried in the protein's core, or facing the fatty acid tails inside a membrane |
| Polar (hydrophilic) | Forms hydrogen bonds with water | On the protein's surface, exposed to the watery cytoplasm |
| Charged (ionic: acidic or basic) | Strongly attracted to water and to opposite charges | On the surface, or forming ionic bonds with oppositely charged R groups |
Four levels of structure
- Primary structure: the exact sequence of amino acids in the chain, held together by peptide bonds. It's determined by the gene that codes for the protein (Unit 6), and it determines all the higher levels of structure.
- Secondary structure: local, repeating folds held by hydrogen bonds between atoms of the polypeptide backbone (not the R groups). The two main shapes are the alpha (α) helix, a coil, and the beta (β) pleated sheet, where stretches of chain lie side by side.
- Tertiary structure: the overall three-dimensional shape of one polypeptide. It comes mostly from R-group interactions: hydrophobic interactions (nonpolar R groups cluster in the middle, away from water), hydrogen bonds, ionic bonds between charged R groups, and disulfide bridges, which are strong covalent bonds between the sulfur atoms of two cysteine amino acids.
- Quaternary structure: two or more polypeptides joined into one working protein. Hemoglobin, which carries oxygen in red blood cells, is made of four polypeptide subunits. Not every protein has quaternary structure.
Shape is function
All four levels together set the final shape, and the shape sets the function. An enzyme's active site, for example, only works if the right R groups sit in the right places (3.1).
Changing even one amino acid can matter. In sickle cell disease, one charged amino acid in a hemoglobin subunit is replaced by a nonpolar one. The new hydrophobic spot makes hemoglobin molecules stick together into long fibers when oxygen is low, which deforms red blood cells into a sickle shape.
Heat, pH changes and some chemicals can disrupt the weak bonds that hold the higher levels together. The protein unfolds (denatures) and loses its function, even though its peptide bonds stay intact (3.2). You don't need to memorize the structures of individual amino acids; focus on R-group properties and how they drive folding.
Worked examples
Try each one yourself first, then open the solution.
- Example 1
Predicting where amino acids sit
A protein crosses the plasma membrane once. Its sequence contains one stretch of about 20 amino acids that all have nonpolar R groups, with polar and charged amino acids on both sides of that stretch. Predict where each part of the protein sits relative to the membrane, and explain.
Show the solutionHide the solution
- Step 1: Recall the membrane's structure: the middle of the bilayer is made of hydrophobic fatty acid tails, and both surfaces face watery environments (2.3).
- Step 2: Match the nonpolar stretch: nonpolar R groups interact favorably with the hydrophobic tails, so that stretch should sit inside the membrane, spanning it.
- Step 3: Match the polar and charged regions: these interact with water, so they should stick out into the cytoplasm on one side and the fluid outside the cell on the other.
- Step 4: State the principle: where each region sits is decided by its R groups' interactions, which is the same logic that drives tertiary structure.
Answer: The nonpolar stretch spans the hydrophobic interior of the membrane; the polar and charged regions on either side sit in the watery cytoplasm and outside the cell.
- Example 2
Which level changed? (classic trap)
A mutation replaces one amino acid near a protein's core: a nonpolar amino acid is swapped for one with a negatively charged R group. A student says only the primary structure changes. Evaluate the claim and predict the effect on the protein.
Show the solutionHide the solution
- Step 1: The primary structure does change, because the sequence is different. That part is true.
- Step 2: The trap: higher levels depend on the primary structure. A change in sequence can change how the chain folds.
- Step 3: Reason about the new R group: a charged R group is hydrophilic. Buried in the core, it can't interact with water and can't join the hydrophobic interactions there, so that region is likely to fold differently.
- Step 4: Predict: the tertiary (and maybe quaternary) structure may change, which can change the protein's shape and reduce or destroy its function.
Answer: The claim is incomplete. The changed primary structure can alter folding, especially tertiary structure, because a charged R group doesn't fit in a hydrophobic core. The protein's shape and function may change.
Common mistakes
- Saying secondary structure comes from R-group interactions. Secondary structure is hydrogen bonding between backbone atoms; R-group interactions mainly drive tertiary structure.
- Thinking denaturation breaks peptide bonds. It disrupts the weaker interactions holding the shape; the amino acid sequence stays the same.
- Assuming every protein has quaternary structure. Only proteins made of two or more polypeptides do.
- Treating disulfide bridges as hydrogen bonds. They're covalent bonds between sulfur atoms in cysteine R groups.
On the exam
- Expect questions that give R-group properties (nonpolar, polar, charged) and ask where they'd end up in a folded protein or a membrane protein.
- For mutation questions, chain your answer: changed amino acid → changed R-group interactions → changed shape → changed function. Points come from each link.
Connected topics
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Check yourself
5 questions on 1.7 Proteins. Pick an answer to see if you got it, and why.
In a water-soluble protein, an amino acid with a nonpolar R group is normally buried in the protein's interior. A mutation replaces it with an amino acid that has a negatively charged R group. Which of the following is the most likely effect?
Hemoglobin is made of four polypeptide chains that fit together to form one functional protein. This arrangement is an example of which level of protein structure?
An α-helix is held in shape mainly by which of the following?
| Treatment | Enzyme activity (% of untreated enzyme) |
|---|---|
| 1. No treatment | 100 |
| 2. In chemical U | 0 |
| 3. In chemical U, then chemical U slowly removed | 92 |
| 4. Peptide bonds broken by a protease, then treated as in 3 | 0 |
Experimental data: chemical U disrupts hydrogen bonds, ionic interactions and disulfide bridges in proteins but does not break peptide bonds. A purified enzyme was given each treatment, and its activity was then measured under standard conditions.
Which of the following conclusions is best supported by the results for treatments 2 and 3?
In treatment 4, the enzyme's activity did not return after chemical U was removed. Which of the following best explains this result?
0 of 5 answered