Chapter 6: DNA and Biotechnology
🎯 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. (6.1) A DNA nucleotide is composed of:
C. DNA nucleotide = base + deoxyribose + phosphate(s). Ribose-based = RNA nucleotide. A nucleoside is base + sugar only (no phosphate); a nucleotide is base + sugar + phosphate.
2. (6.1) Which nitrogenous bases are purines?
B. Purines = Adenine, Guanine (two fused rings). Pyrimidines = Cytosine, Thymine, Uracil (single ring). Mnemonic: "Pure As Gold" for purines (A, G); "CUT the py" for pyrimidines.
3. (6.2) Chargaff's rules state that in any DNA sample:
D. A pairs with T, G pairs with C. So amounts of A and T are equal; same for G and C. This was key evidence that A-T and G-C are specific pairing partners in the double helix.
4. (6.2) The two strands of a DNA double helix are:
A. Antiparallel orientation; hydrogen bonds between bases (A=T is 2 H-bonds, G≡C is 3 H-bonds - so G-C rich DNA is more stable and has a higher melting temperature).
5. (6.3) DNA polymerase adds new nucleotides:
B. DNA (and RNA) polymerases extend from the 3' end. Incoming nucleotide's 5' phosphate attacks the chain's 3' -OH. This directionality is why the lagging strand is synthesized discontinuously (Okazaki fragments).
6. (6.3) Okazaki fragments are synthesized on the:
C. Because polymerase only goes 5'→3', the lagging strand must be built in short chunks moving away from the fork, each primed by its own RNA primer. These fragments are later joined by DNA ligase.
7. (6.4) Mismatch repair corrects errors by:
A. After replication, mismatch repair scans for distorted helix geometry (mispaired bases) and excises a patch from the daughter strand (distinguished in bacteria by transient methylation asymmetry; in eukaryotes by other marks). Defective mismatch repair → Lynch syndrome (hereditary colorectal cancer).
8. (6.4) Nucleotide excision repair (NER) is responsible for fixing:
D. NER removes bulky adducts, including UV-induced pyrimidine (thymine) dimers. Defective NER → xeroderma pigmentosum (extreme UV sensitivity, high skin cancer risk).
9. (6.5) Restriction enzymes are:
B. Restriction enzymes (e.g., EcoRI, BamHI) cut DNA at specific 4-8 bp palindromic sequences. Evolved by bacteria to destroy invading viral DNA. The cell's own DNA is methylation-protected. Foundation of all recombinant DNA technology.
10. (6.5) "Sticky ends" produced by some restriction enzymes:
C. Staggered cuts leave 4-6 nt single-stranded overhangs. Two DNA fragments cut with the same enzyme have complementary overhangs that base-pair spontaneously, then DNA ligase seals the backbone. This is how a gene of interest can be inserted into a plasmid.
11. (6.6) The three temperature steps in each PCR cycle are:
A. Melt the template (95°C), let primers bind (50-65°C, depends on primer Tm), extend with Taq polymerase (72°C - Taq's optimum). Each cycle doubles the target, giving exponential amplification (n cycles → copies).
12. (6.6) PCR uses Taq polymerase because:
D. Mesophilic polymerases (E. coli's) would denature in the 95°C step. Taq, from a hot-spring bacterium, maintains function after each cycle. The discovery of Taq enabled automated thermocycling PCR.
13. (6.7) On a DNA gel, fragments separate based on size; the direction of migration is:
C. DNA's phosphate backbone gives it uniform negative charge per length. All fragments migrate to the positive electrode. Small fragments move faster through the gel matrix; large fragments are impeded. Bands are visualized with ethidium bromide (or safer alternatives like SYBR) under UV.
14. (6.7) A ladder (standard) of known DNA sizes is run alongside samples so that:
B. The ladder is a size-reference; comparing your band's position to the nearest ladder bands gives a size estimate. Migration distance scales as log(1/size) roughly.
15. (6.8) Which blotting technique detects specific DNA sequences?
D. "SNoW DRoP" mnemonic: Southern=DNA, Northern=RNA, Western=Protein. Separate by gel, transfer to membrane, probe. Southern uses DNA probes; Northern uses RNA probes; Western uses antibodies.
16. (6.8) A Western blot uses _____ to detect the target:
A. Western blot: proteins separated on SDS-PAGE, transferred to nitrocellulose/PVDF membrane, then probed with a specific primary antibody. A labeled secondary antibody produces the visible signal.
17. (6.9) Sanger dideoxy sequencing works by:
C. ddNTPs lack a 3'-OH, so when incorporated they terminate DNA extension. Each of the 4 ddNTPs carries a distinct fluorescent color. Capillary electrophoresis separates all terminated fragments by size, revealing the sequence one base at a time.
18. (6.9) Next-generation (massively parallel) sequencing differs from Sanger because it:
B. NGS platforms (Illumina, etc.) sequence millions to billions of fragments in parallel, each typically 100-300 bp. Short reads, but massive numbers. This enabled whole-genome sequencing in days rather than years, and drove the cost per genome from \$100M to under \$1000.
19. (6.10) The CRISPR-Cas9 gene-editing system uses a guide RNA to:
A. The guide RNA base-pairs with a target genomic sequence (adjacent to a PAM motif). Cas9 makes a double-strand break there. The cell's repair machinery then introduces indels (if non-homologous end joining) or a specified change (if a donor template is provided for homology-directed repair).
20. (6.10) CRISPR originally evolved as a:
D. Bacteria insert short viral DNA "memories" into their CRISPR loci, then use those as guides to recognize and destroy the same virus in a future infection. Scientists hijacked this system for programmable gene editing in any cell type.
Every cell in your body has the same ~3 billion DNA base pairs. That text encodes everything you are. How that sequence is read, copied, repaired, cut, and rewritten in the lab is the subject of this chapter.
The MCAT treats DNA in two parts. First, the molecular biology: what DNA looks like, how it replicates, how errors are corrected. Second, the lab toolkit: how to copy, cut, separate, sequence, and edit DNA. Most MCAT passages about experiments draw on these techniques.
DNA is a Twisted Ladder
Keep in mind that the double helix is really just two sugar-phosphate rails holding up rungs of paired bases. The rails give the structure. The rungs encode the information. Everything else - replication, transcription, repair, PCR - is a variation on “let the rungs apart, copy them, and put them back together.”