Chapter 3: Nonenzymatic Protein Function and Protein Analysis
🎯 Diagnostic: Test Your Starting Level 20 questions (2 per section). No prior reading required - see what you already know.
Aim to answer every question before checking. Missed questions point you to the sections you need most.
1. (3.1) Collagen's triple-helix structure is made possible by the unusually high content of which amino acids?
B. The repeating Gly-X-Y motif (X often Pro, Y often hydroxyproline) is essential. Glycine's tiny side chain fits where the three helices pack tightly; proline's rigid ring locks the left-handed individual helix that winds into the larger right-handed triple helix.
2. (3.1) Which cell-adhesion molecule requires calcium for function and mediates homotypic cell-cell binding?
C. Cadherins ("Ca-dependent adherins") bind to identical cadherins on neighboring cells via Ca2+-dependent interactions. Integrins anchor cells to extracellular matrix. Selectins are Ca-dependent carbohydrate-binders on leukocytes/endothelium.
3. (3.2) Myosin powers muscle contraction by:
A. The myosin head binds actin, hydrolyzes ATP, undergoes a power stroke (conformational change), releases, and re-binds further down - the "cross-bridge cycle." Repeated thousands of times per second across millions of myosin heads = muscle contraction.
4. (3.2) Kinesin typically walks toward the _____ end of microtubules, carrying cargo _____:
D. Kinesin = plus-end (anterograde) transport, away from the cell body and toward the periphery. Dynein = minus-end (retrograde) transport, back toward the nucleus. Both are ATP-powered motor proteins that walk on microtubules.
5. (3.3) An IgG immunoglobulin molecule is composed of:
C. Standard antibody structure: two heavy (H) chains + two light (L) chains, held together by inter-chain disulfide bonds. The two Fab "arms" contain the antigen-binding sites; the Fc stem triggers immune effector functions.
6. (3.3) Antibody specificity for antigens is determined by which region?
B. Each of the two Fab arms has a unique antigen-binding site formed by the variable (V) regions of one H chain and one L chain. Constant (C) regions are identical within an isotype and determine effector function, not specificity.
7. (3.4) G-protein-coupled receptors (GPCRs) are characterized by:
D. GPCRs are "7-transmembrane" receptors. Ligand binding on the outside causes a conformational change that activates an intracellular heterotrimeric G protein (Gα-GDP → Gα-GTP), initiating a signaling cascade.
8. (3.4) A receptor tyrosine kinase (RTK) differs from a GPCR in that it:
A. RTKs (e.g., insulin receptor, EGFR) carry their own kinase domain on the cytoplasmic tail. Ligand binding causes receptor dimerization and trans-autophosphorylation of tyrosines, creating docking sites for downstream signalers. No G protein needed.
9. (3.5) Hemoglobin's sigmoidal oxygen-binding curve results from:
B. Hemoglobin is a heterotetramer (α2β2) with four O2 binding sites. Binding at one site triggers a T→R state transition that raises the affinity at the other sites. Four binding events together produce the S-shaped curve.
10. (3.5) In a tissue with high CO2 and low pH (the Bohr effect), hemoglobin:
C. The Bohr effect: high CO2 and low pH (characteristic of active tissue) reduce hemoglobin's O2 affinity, so it dumps more oxygen where it's needed most. Curve shifts RIGHT.
11. (3.6) Myoglobin has a ______ oxygen-binding curve; compared to hemoglobin, its O2 affinity is:
A. Myoglobin is a single-chain, single-heme protein - no cooperativity, hyperbolic curve. Its tight O2 affinity lets it pull O2 out of hemoglobin for storage in muscle. Myoglobin > hemoglobin in O2 affinity at tissue PO2.
12. (3.6) Which statement correctly compares myoglobin and hemoglobin?
D. Myoglobin = single polypeptide, no quaternary structure. Hemoglobin = four chains (α2β2), quaternary structure enables cooperativity. Both have heme (eliminates B).
13. (3.7) Ion-exchange chromatography separates proteins based on:
B. A charged resin retains proteins with the opposite charge. Changing pH or salt concentration elutes bound proteins. Affinity chromatography (C) uses specific ligands; size-exclusion (A) uses pore-based sieving.
14. (3.7) In size-exclusion (gel-filtration) chromatography, which protein elutes first?
C. Large proteins cannot enter the beads' pores, so they take the shortest path through the column and elute first. Small proteins get trapped inside the pores and elute later. "Big is fast" - counterintuitive but memorable.
15. (3.8) SDS-PAGE separates proteins primarily by:
B. SDS (a detergent) coats proteins with a uniform negative charge proportional to length, masking their native charge. Under an electric field, they migrate through a gel matrix based on size only: small ones travel farther.
16. (3.8) Isoelectric focusing separates proteins based on:
A. A pH gradient is established in the gel. When a protein arrives at the pH equal to its pI, its net charge is zero and it stops moving. 2D-PAGE uses isoelectric focusing + SDS-PAGE to separate by both pI and size.
17. (3.9) Edman degradation sequences a peptide by:
D. Phenylisothiocyanate reacts with the free N-terminal amine, allowing cleavage of just the first residue as a PTH-derivative that can be identified. Repeat to sequence one residue at a time from N→C.
18. (3.9) The Bradford assay uses a dye that:
C. Coomassie Brilliant Blue G-250 binds to protein (particularly Arg residues), shifting its absorbance maximum from 465 to 595 nm. Read A595 to estimate protein concentration via Beer-Lambert. Fast, simple, and the standard protein quantification method.
19. (3.10) X-ray crystallography determines protein structure by:
B. A purified, crystallized protein diffracts X-rays. The diffraction pattern is mathematically transformed into an electron density map, which is interpreted to build the atomic model. Requires a well-ordered crystal, which is a key limitation.
20. (3.10) NMR spectroscopy is particularly useful for:
A. NMR exploits nuclear spin to extract structural information in solution. Works without crystals and reveals protein dynamics - but it struggles with large (>~30-50 kDa) proteins because of signal overlap.
Enzymes get all the attention, but most proteins in your body are not enzymes. Hemoglobin does not catalyze anything; it just carries oxygen. Collagen does not run a reaction; it holds your body together. Antibodies do not transform substrates; they grab specific shapes and flag them for destruction. This chapter is about everything proteins do that is not chemistry.
The second half of the chapter shifts gears. How do you find out what a mystery protein does? You separate it from the other 10,000 proteins in a cell, measure its size, sequence it, and sometimes solve its 3D structure. The techniques you learn here show up in almost every MCAT passage about a lab experiment.
Proteins are Specialized Machines
Keep in mind that everything a protein does comes from its 3D shape. A structural protein has a long, repetitive shape that resists stretching. A motor protein has a shape that changes when it binds ATP, which is how it walks along a track. An antibody has two matching arms that grab specific targets. Same 20 amino acids, same folding rules, thousands of different jobs.