Unit 9 is about how scientists read, copy, cut, and rewrite DNA, and what they do with those abilities in medicine, farming, and research. By the end, you should be able to explain how PCR, gel electrophoresis, recombinant DNA, and CRISPR work, and read sequence data to compare organisms.
Read the overview first, then work through each topic's notes and checkpoint question before checking the common mistakes at the bottom.
This unit builds directly on DNA structure and protein synthesis. These techniques use properties of DNA, including predictable base pairing and a genetic code that is shared by nearly all organisms, with some exceptions.
Honors Biology Unit 9 covers biotechnology and genomics. You learn the main lab techniques (restriction enzymes, DNA ligase, plasmids, PCR, gel electrophoresis, and DNA sequencing), how they're applied (recombinant insulin, GMO crops like Bt corn, CRISPR gene editing, gene therapy, bioremediation), and how scientists study entire genomes using projects like the Human Genome Project and computer tools like BLAST. Expect questions that ask you to order the steps of a technique, read a gel, calculate PCR copies, or compare DNA sequences to decide which species are most closely related.
Restriction enzymes cut at specific sequences. Some leave sticky ends that pair with complementary ends, while others leave blunt ends. PCR primers find their target by base pairing too. Once you see that, the steps of each technique make sense instead of feeling like a list to memorize.
Bacteria can read a human insulin gene and build human insulin, because codons mean the same amino acids in nearly all life. This shared code helps scientists produce some GMOs and recombinant drugs by transferring genes between species.
Sequences that stay the same across species usually do something important. Species with more similar DNA usually share a more recent common ancestor, which is how scientists build phylogenetic trees from sequence data.
Sequencing reads the information, PCR copies it, and restriction enzymes or CRISPR edit it. Applications use different combinations of these tools. For example, scientists can insert an insulin gene into bacteria or edit blood stem cells to treat sickle cell disease. Ethical questions include who can access treatments and whether inherited edits could affect future generations.
Genetic engineering is a set of tools for cutting, copying, sorting, and moving DNA.
Biotechnology puts the tools from 9.1 to work in medicine, farming, and the environment.
Genomics studies whole genomes instead of single genes.
Genetic engineering is a set of tools for cutting, copying, sorting, and moving DNA. Each tool takes advantage of something DNA already does, like base pairing or being copied by a polymerase.
To build recombinant DNA, you cut a plasmid and the donor DNA with the same restriction enzyme. EcoRI, for example, cuts at GAATTC and leaves short single-stranded overhangs called sticky ends. Because both pieces were cut by the same enzyme, their sticky ends are complementary and base-pair with each other. DNA ligase then seals the sugar-phosphate backbone. Bacteria can take up the recombinant plasmid through transformation. The plasmid can replicate inside them, though some cells may lose it. To make human insulin, bacteria use an insulin coding sequence made from processed human mRNA and placed under bacterial controls.
PCR copies one target sequence. Each cycle has three steps. The sample is heated to about 95°C to separate the strands, cooled to about 55-65°C so primers can attach, then held at about 72°C while heat-stable Taq polymerase builds new strands. In the ideal model, each cycle doubles the target. Actual PCR efficiency can be lower, especially after many cycles.
Gel electrophoresis sorts DNA by size. DNA is negatively charged because of its phosphate groups, so it moves toward the positive electrode, and small fragments travel the farthest.
Worked example. You start with 50 copies of a target and run 20 cycles. Assume the target doubles in every cycle. Copies million. After 30 cycles, you'd have , or about 54 billion copies.
Check yourself: A gel shows two bands from the same sample, one near the wells and one near the bottom. Which fragment is smaller, and why? (Answer: The band near the bottom is smaller. Small fragments slip through the gel's pores faster, so they travel farther toward the positive electrode in the same amount of time.)
| Tool | What it does | Example use |
|---|---|---|
| Restriction enzyme | Cuts DNA at a specific sequence | Opening a plasmid to insert a gene |
| DNA ligase | Seals the sugar-phosphate backbone | Closing a recombinant plasmid |
| PCR | Makes billions of copies of one target sequence | Amplifying DNA from a hair follicle found at a crime scene |
| Gel electrophoresis | Separates DNA fragments by size | Comparing DNA fingerprints |
| DNA sequencing | Reads the exact order of bases | Finding a disease-causing mutation |
Biotechnology puts the tools from 9.1 to work in medicine, farming, and the environment. Most applications come down to one move. Scientists either get a new gene into a cell or change a gene that's already there.
A GMO carries DNA that was added or changed in a lab. Bt corn contains a gene from the bacterium Bacillus thuringiensis that makes a protein toxic to certain insect larvae, so farmers can spray less insecticide. Golden Rice was engineered to make beta-carotene, which your body converts to vitamin A.
CRISPR-Cas9 edits DNA at a chosen spot. A guide RNA pairs with the target sequence and leads Cas9 there. Cas9 also requires a suitable nearby DNA sequence called a PAM. After Cas9 cuts both strands, cell repair can disrupt the sequence or, with a suitable repair template, make a specific replacement. In 2023, a CRISPR-based treatment for sickle cell disease was approved in the US.
In medicine, recombinant human insulin produced by bacteria was approved in 1982 as an alternative to insulin from animal pancreases. Gene therapy can add, change, or silence genetic material in a patient's cells. Some gene therapies use modified viruses as vectors to deliver genetic material. Bioremediation uses microbes to break down pollutants such as spilled oil.
These tools raise real ethical questions. Edits to body cells are not inherited. Edits to eggs, sperm, or embryos can be passed to future generations, so germline editing is widely restricted.
Check yourself: A patient with cystic fibrosis receives gene therapy targeting lung cells. Will their future children inherit the corrected gene? (Answer: No. Only the lung cells were changed. Eggs and sperm still carry the original alleles, so the change is not inherited.)
| Approach | What changes | Example | Passed to offspring? |
|---|---|---|---|
| Transgenic GMO | A gene from another species is added | Bt corn with a bacterial toxin gene | Yes, through the plant's seeds |
| Gene editing (CRISPR) | An existing sequence is cut and changed | Editing a patient's blood stem cells to treat sickle cell disease | Only if eggs, sperm, or embryos are edited |
| Somatic gene therapy | A working gene is delivered into body cells | Treatment for spinal muscular atrophy | No |
Genomics studies whole genomes instead of single genes. To sequence a genome, scientists break the DNA into many overlapping fragments, read each one, and use computers to reassemble them by matching the overlaps.
The Human Genome Project produced a nearly complete reference sequence in 2003. In 2022, researchers published a gapless sequence of the non-Y chromosomes from a different human cell line. Humans have about 20,000 protein-coding genes, and less than 2% of human DNA codes for protein. Noncoding DNA includes regulatory sequences and many repeated sequences. Some noncoding regions have known functions, while the functions of others remain uncertain.
Bioinformatics is the computer side of biology. Databases like GenBank store sequences, and BLAST searches an unknown sequence against those databases to find matches. Sequence alignment lines up two or more sequences so you can count where they match. More similarity usually means a more recent common ancestor, which is how scientists build phylogenetic trees from DNA.
Comparative genomics looks for conserved sequences shared across species. If a stretch of DNA has barely changed between humans and mice over roughly 80 million years, natural selection has probably kept it because it does something important.
Worked example. A 20-base stretch of human DNA differs from the chimpanzee version at 1 position and from the mouse version at 6. Percent identity with chimp . Percent identity with mouse . The higher identity suggests humans and chimps share a more recent common ancestor.
Check yourself: The same aligned gene sequence from species A matches your sample at 88% of bases, species B at 97%, and species C at 75%. Which is the best candidate for the closest relative? (Answer: Species B, because it has the highest identity for this sequence. Comparing more genes can give a more reliable picture of the species' relationships.)
| Term | Definition |
|---|---|
| Recombinant DNA | DNA made by combining pieces from two or more different sources, such as a human gene inside a bacterial plasmid. |
| Sticky ends | Short single-stranded overhangs left by some restriction enzymes that base-pair with complementary overhangs. |
| DNA ligase | An enzyme that forms covalent bonds to seal breaks in the DNA sugar-phosphate backbone. |
| Polymerase chain reaction (PCR) | A technique that repeatedly heats and cools DNA with primers and Taq polymerase to make billions of copies of a target sequence. |
| Gel electrophoresis | A method that uses an electric current to separate DNA fragments by size through an agarose gel. |
| Primer | A short single strand of DNA that binds next to the target sequence and gives polymerase a starting point. |
| Transformation | The process of a bacterial cell taking up foreign DNA, such as a recombinant plasmid. |
| Guide RNA | The RNA in CRISPR that matches a target DNA sequence and leads Cas9 to the place it should cut. |
| Bioinformatics | The use of computers and databases to store, search, and analyze biological data such as DNA sequences. |
| Comparative genomics | Comparing the genomes of different species to find shared sequences, infer function, and trace evolution. |
It seems like bigger things should go farther, but the gel works like a sieve. Small fragments slip through the pores quickly, while large ones get slowed down. Bands near the wells are large, and bands near the bottom are small.
PCR targets the stretch of DNA between two primers. In a mixed sample, it can amplify that region from more than one contributor. The doubling formula () models the target copies under ideal conditions.
Mismatched ends may prevent the insert and plasmid from joining. One approach is to cut both pieces with the same enzyme so their sticky ends are complementary, then seal them with ligase. Scientists can also use different enzymes when they design compatible ends.
Changes to eggs, sperm, or embryos can be inherited, but changes limited to somatic cells are not passed to children. Most gene therapies and CRISPR treatments change somatic cells like blood or retina cells, so they affect only the patient.