Week 15 · Chapter

Chapter 15 — Gene Regulation, Mutation & Biotechnology

Introduction to Biology Free sample edition

The module's primary reading · ~45–55 minutes · Objective 8 (describe how gene expression is regulated (the lac operon as the model), classify mutations and their effects, and explain what the core biotechnology tools do — PCR, gel electrophoresis, recombinant DNA, and CRISPR-Cas9 — including the ethical questions gene editing raises, weighed evenhandedly), with Objective 7 (explain the structure and semiconservative replication of DNA, apply Chargaff's rules and complementary base pairing, and trace gene expression through transcription and translation with the genetic code (the central dogma), decoding a sequence from template to protein) carried forward · Read it first this week; the lecture, the slides, the tutorial, the quiz, and the lab all build on it.

In plain language

Every cell in your body carries the same DNA, yet a muscle cell and a nerve cell look and act nothing alike. This week you learn why: cells use gene regulation (switching some genes on and others off) to read only the recipes they need. You also learn what happens when a recipe has a typo, a change called a mutation (a change in the DNA's sequence). Finally, you meet the tools people now use to copy, sort, cut, and edit DNA, and the hard questions those tools raise. Those questions stay open, and you will weigh both sides of them.

Why you already care about this

Look at your own arm. The muscle cells in your arm carry every one of your genes. So do the nerve cells that tell those muscles when to move. Same DNA, same cookbook, two very different cells. Last week you watched a cell copy one recipe at a time onto an mRNA card and turn it into a protein. This week you ask which recipes each cell decides to read.

Then the stakes rise. In 2020 the Nobel Prize in Chemistry went to Emmanuelle Charpentier and Jennifer Doudna for a way to edit DNA. In 2023 a therapy built on that tool was approved in the United States for sickle cell disease. A single typo in one gene, the codon GAG changed to GUG, causes that disease. One base, one amino acid, one life-changing condition, and now a tool that can reach into the cookbook and edit it.

By the end of this chapter you will be able to:

explain why cells with the same genome are different, and describe the lac operon as an on/off model;
sort a base change on a gene as silent, missense, nonsense, or frameshift, using a codon table;
explain why a mutation can be neutral, harmful, or beneficial;
say what PCR, gel electrophoresis, recombinant DNA, and CRISPR-Cas9 each do;
read a gel to match a DNA profile, and explain why an exclusion is firmer than a match;
lay out the case for and the case for caution on gene editing without picking a winner.

Carry this line with you: same cookbook; different recipes read.

Where we are

Already covered: Week 13 showed how DNA is built and copied; Week 14 showed how a gene is transcribed into mRNA and translated into protein, codon by codon. Weeks 10 and 11 showed how meiosis and inheritance shuffle versions of genes, and Week 1 named evolution by natural selection as biology's unifying framework.
This week: how cells switch genes on and off, the kinds of mutations and their effects, the biotechnology toolkit, DNA profiling on a virtual gel, and the ethics of gene editing.
How they connect: a mutation is a change in the template you transcribed last week, so you read its effect with the same codon table; the biotechnology tools work on the same double helix you built in Week 13.
Where we're going next: this is the last module of new material. Next comes finals week, with no new lessons; the cumulative final asks you to carry every process, in order and in its place, from the first week to this one.

Week 14 is the one this chapter leans on hardest. There you read Gene 1's template strand, 3′-TAC CGA ATA ACT-5′, and wrote its mRNA, 5′-AUG GCU UAU UGA-3′. You read that mRNA in codons of three from the AUG start, and it gave Met–Ala–Tyr and then stop. You also learned that the code has a cushion: GCU and GCC both code for alanine. Keep that mRNA and that cushion in view. This week you change one letter at a time and watch what happens to the protein.

1. Switch genes on and off: why cells differ

Think of a huge cookbook copied into every kitchen in a city. A bakery opens it to the bread pages. A soup kitchen opens it to the soup pages. Nobody cooks every recipe every day. Each kitchen reads the pages that fit its job.

Your cells work the same way. The genome is the complete set of DNA in an organism; nearly every cell in a body carries the whole genome, even though each cell uses only part of it. A muscle cell switches on the genes for the proteins that let it contract. A nerve cell, or neuron, switches on the genes for the proteins that carry signals. Both cells keep the other genes, closed, on the shelf.

Gene regulation is a cell's control over which genes are switched on and how much product each one makes, which saves energy and lets different cell types specialize.

Regulation pays off in two ways. First, it saves energy. Building a protein costs the cell ATP, so making proteins it does not need would waste fuel. Second, it makes specialization possible. A body can build muscle, nerve, and skin from one genome because each cell type reads a different set of recipes.

Worked example — two cells, one genome. You compare a muscle cell and a neuron from the same person.

Step 1. Ask what DNA each carries. Both carry the whole genome, because both came from one fertilized egg by rounds of mitosis, and the DNA is copied almost perfectly before each division.
Step 2. Ask which genes each uses. The muscle cell switches on its contraction genes; the neuron switches on its signaling genes.
Step 3. Name the cause of the difference. The difference is not in the DNA. It is in which genes are switched on: gene regulation.

In words: the two cells share a cookbook and differ in which recipes they read.

Misconception check. Students often think that every cell uses all of its genes all the time. It is tempting because every cell does carry every gene. The cure is to separate carrying from using. A cell carries the whole genome but switches on a subset, and that subset is what makes it a muscle cell or a neuron.

2. Flip the lac operon switch

Picture a bacterium living in a gut. Some days a meal brings milk, with its sugar, lactose. Other days there is no lactose at all. Making the proteins that digest lactose on a day with no lactose would waste the cell's energy. So the bacterium keeps those genes off until lactose shows up.

Biologists describe that switch with a model. An operon is a group of bacterial genes that share one on/off switch on the DNA, so they are turned on or off together. The lac operon is the classroom model of gene regulation: a bacterial operon holding the genes for digesting lactose, kept off by a repressor until lactose is present. Jacob and Monod (1961) described it in a paper on how cells regulate protein synthesis.

Two more terms carry the model.

A repressor is a protein that sits on the DNA at an operon and blocks its genes from being transcribed; in the lac operon, a molecule made from lactose pulls it off.
Allolactose is a molecule a bacterium makes from lactose; it binds the lac repressor and pulls it off the DNA, which turns the lactose-digesting genes on.

Worked example — two days in the gut. You run the switch under two conditions.

The lac operon switch under two conditions, in the classroom model
Condition	Where the repressor is	The lactose-digesting genes
No lactose present	sitting on the DNA, blocking the genes	off
Lactose present	pulled off the DNA by allolactose	on

Step 1. No lactose. The repressor sits on the DNA, so RNA polymerase cannot transcribe the genes. The genes stay off and the cell saves energy.
Step 2. Lactose arrives. The cell makes allolactose from it. Allolactose grabs the repressor and pulls it off the DNA.
Step 3. The genes turn on. RNA polymerase now transcribes them, and the cell makes the proteins that digest lactose.

In words: the repressor is the brake, and lactose, working through allolactose, takes the brake off. Full expression also needs glucose to be low; you name that second condition in words only.

Here is an honesty note about the model. The lac operon is a simple switch you can hold in one hand. It is not a picture of how every gene in every organism is controlled. Your own cells, which are eukaryotic, regulate genes at many levels: how tightly the DNA is packed, whether a gene is transcribed, what happens to the mRNA, whether it is translated, and what happens to the protein afterward. You name these levels this week; their machinery belongs to later courses.

Misconception check. Students often flip the switch and say the repressor turns the genes on. The name sounds like a part that does something, so it feels like the "on" part. The cure is the word itself: a repressor represses. When it sits on the DNA, the genes are off. Lactose, through allolactose, pulls it off, and only then do the genes turn on.

3. Sort the typos: silent, missense, nonsense

Copy a recipe by hand and you may slip a letter. Sometimes the slip changes nothing, like "colour" for "color." Sometimes it changes an ingredient. Sometimes it ends the recipe in the middle of a step. DNA typos fall into the same three groups.

A mutation is a change in the DNA sequence; it is the ultimate source of new genetic variation, and its effect can be neutral, harmful, or beneficial.
A point mutation is a mutation that changes a single base in the DNA.
A substitution is a point mutation that swaps one base for another; depending on the codon it creates, it is silent, missense, or nonsense.

Each kind of substitution has its own name.

A silent mutation is a substitution that changes a codon without changing the amino acid it codes for, so the protein stays the same, as when GCU becomes GCC and both code for alanine.
A missense mutation is a substitution that changes a codon so that it codes for a different amino acid, as when GAG becomes GUG and glutamic acid is replaced by valine in sickle cell disease.
A nonsense mutation is a substitution that turns a codon for an amino acid into a stop codon, so translation ends early and the protein is cut short.

Worked example — three typos on Gene 1. Gene 1's mRNA is 5′-AUG GCU UAU UGA-3′. It is 12 bases, and 12 ÷ 3 = 4 codons. With the codon table it reads Met–Ala–Tyr, then stop. You change one base at a time and read the table again.

Three single-base changes to Gene 1's mRNA and the protein each one gives
Change	Base changes	New codon means	Protein	Kind
none	0	—	Met–Ala–Tyr	the starting gene
GCU → GCC	1	Ala	Met–Ala–Tyr	silent
GCU → GAU	1	Asp	Met–Asp–Tyr	missense
UAU → UAA	1	stop	Met–Ala	nonsense

Silent. GCU → GCC changes 1 base, and GCC still codes for Ala, so the protein stays Met–Ala–Tyr. The code's cushion from last week absorbed the typo.
Missense. GCU → GAU changes 1 base, and GAU codes for Asp, so the protein becomes Met–Asp–Tyr. One amino acid is different.
Nonsense. UAU → UAA changes 1 base, and UAA is a stop codon, so the protein becomes Met–Ala; 3 − 1 = 2 amino acids instead of 3.

In words: one changed base can do nothing, swap one amino acid, or cut the protein short, and the codon table tells you which.

The disease from the opening fits here. In the gene for the beta chain of hemoglobin, the codon GAG codes for glutamic acid (Glu). In sickle cell disease it reads GUG, which codes for valine (Val). GAG → GUG changes 1 base and swaps Glu for Val, so it is a missense mutation.

Misconception check. Students often swap missense and nonsense. Both words start with a negative-sounding part, and both describe a changed codon. The cure is to ask what the new codon means. If it means a different amino acid, the message still makes sense but says something else: missense. If it means stop, the message ends early: nonsense. A second trap is thinking every mutation changes the protein. A silent mutation does not.

4. Slip the frame: frameshift mutations

Try reading a sentence in three-letter words: THE CAT SAW THE DOG. Now delete the first letter of CAT. You get THE ATS AWT HED OG. One missing letter scrambles every word after it.

A cell reads mRNA the same way, three bases at a time from AUG. That grouping is the reading frame you met last week.

A frameshift mutation is an insertion or deletion of bases, not in a multiple of three, that shifts the reading frame so every codon after it changes.

Worked example — delete one base from Gene 1. You delete the first base after AUG, the G at the start of GCU.

Step 1. Count the bases. The gene had 12 bases, so 12 − 1 = 11 remain.
Step 2. Regroup from AUG. The mRNA now reads AUG CUU AUU GA.
Step 3. Count the codons. 11 ÷ 3 = 3 whole codons with 2 bases left over.
Step 4. Compare the codons. After AUG, every codon has changed: CUU in place of GCU, AUU in place of UAU.
Step 5. Look for the stop. The UGA stop is gone from the frame.

In words: a single deleted base does not change one amino acid; it changes every codon after it. A frameshift usually leaves a protein that does not work.

Misconception check. Students often think that deleting one base changes only one amino acid, the way a substitution does. It is tempting because both are one-base changes. The cure is to regroup the letters in threes after the change. A substitution leaves the frame where it was, so only one codon changes. A deletion moves every boundary after it, so every codon after it changes.

5. Weigh the effects: neutral, harmful, beneficial

Most people hear "mutation" and picture something going wrong. Sometimes it does. But the word only means a change in the DNA sequence, and changes come in every flavor.

A mutation's effect ranges from neutral to harmful to beneficial.

Neutral. A silent change leaves the protein the same, so it has no effect on that protein.
Harmful. A nonsense change cuts the protein short, and a frameshift usually leaves a protein that does not work. The sickle-cell missense change alters hemoglobin's shape and job.
Beneficial. Once in a while a change suits an organism better to its environment. That rare change is the raw material adaptation is built from.

Things that damage DNA raise the rate of mutation.

A mutagen is anything that damages DNA and raises the rate of mutation.

Worked example — rank three changes on Gene 1. You rank the changes from Section 3 and Section 4 by how much of the protein each one alters.

Silent (GCU → GCC): 0 of the 3 amino acids change, because the protein stays Met–Ala–Tyr.
Missense (GCU → GAU): 1 of the 3 amino acids changes, Ala to Asp.
Nonsense (UAU → UAA): the chain stops after 2 amino acids, so the third one is never added.
Frameshift (one base deleted after AUG): every codon after AUG changes.

In words: the same small typo can leave a protein whole, nudge it, or break it, depending on where it lands and what it does to the codons.

This is where Week 1's big idea returns one last time. Evolution is change in the heritable traits of a population over generations. Mutation is the raw material of variation, and natural selection acts on that variation. Without mutations there would be no new versions of genes for selection to favor or remove. Meiosis and fertilization, from Week 10, shuffle the versions that exist; mutation makes new ones.

Misconception check. Students often think that all mutations are harmful. The word is linked with disease in everyday speech, so the belief is easy to pick up. The cure is the range: a silent change can be neutral, many changes break a protein, and a rare change helps. Without that rare helpful change, adaptation would have nothing to build from.

6. Copy, then sort: PCR and gel electrophoresis

Picture a tiny trace of blood left at a crime scene. It holds far too little DNA to study. You need two things: a way to make many copies of the DNA, and a way to sort the copies so you can read them. Biologists have one tool for each job.

Biotechnology is the use of living things and their molecules, such as DNA and enzymes, to make products or solve problems.
PCR (polymerase chain reaction) is a method that copies a chosen stretch of DNA over and over, each round running in the order denature, anneal, extend, using a heat-stable polymerase from the bacterium Thermus aquaticus.

Each PCR round runs in a fixed order. Denature: heat separates the two strands. Anneal: short starter pieces of DNA bind to the separated strands. Extend: the polymerase builds a new partner strand on each one. The order is a fact, and the polymerase has to survive the heat of the first step every round, which is why the heat-stable enzyme matters.

Gel electrophoresis is a method that sorts DNA fragments by size: the negatively charged DNA runs through a gel toward the positive end, and smaller fragments travel farther.
A size ladder is a lane of DNA fragments of known sizes run beside the samples on a gel, so the size of an unknown band can be read from how far it traveled.

Picture the gel as a slab with a row of small wells along one edge. You load DNA into the wells and switch on the current. DNA is negatively charged, so it moves away from the wells toward the positive end. The gel acts like a crowded room: small fragments slip through quickly, and big ones push through slowly. After a while, each fragment size has stopped at its own distance, as a band.

Worked example — read the ladder on the virtual gel. This week's virtual gel is illustrative, constructed for this course, and not real data.

Step 1. List the ladder. The size ladder has 4 bands at 500, 1,000, 2,000, and 4,000 bp.
Step 2. Spot the pattern. Each band is twice the one before, because 500 × 2 = 1,000, 1,000 × 2 = 2,000, and 2,000 × 2 = 4,000.
Step 3. Set the direction. DNA is negatively charged, so every band runs from the wells toward the positive end.
Step 4. Order by distance. Smaller fragments travel farther, so from farthest to nearest the wells the ladder reads 500, 1,000, 2,000, 4,000 bp. The 500 bp band is farthest and the 4,000 bp band is nearest.
Step 5. Size the gap. 4,000 ÷ 500 = 8, so the band nearest the wells is 8 times the size of the band farthest from them.
Step 6. Race two fragments. A 200 bp fragment outruns a 3,000 bp fragment, because it is smaller; 3,000 ÷ 200 = 15, so the slower fragment is 15 times larger.

In words: on a gel, distance reads size, and the smallest piece goes farthest. The 500 bp band versus the 4,000 bp band is an 8-fold size gap, and it shows up as the widest spread on the ladder.

Misconception check. Students often think bigger fragments travel farther, because a bigger thing seems stronger. The cure is the crowded room: big fragments get tangled in the gel and move slowly, so they stay near the wells. A second trap is calling PCR and gel electrophoresis the same thing. PCR copies; a gel sorts. A crime lab uses both, in that order.

7. Cut, paste, and edit: recombinant DNA and CRISPR-Cas9

Insulin is a human protein, made by human cells. One way to get a lot of it is to give the human insulin gene to bacteria and let them make it. That takes cutting and pasting DNA.

Recombinant DNA is DNA spliced together from two different sources, for example a human gene placed into a bacterial plasmid.
A restriction enzyme is an enzyme that cuts DNA at a specific base sequence, used to cut out a gene and open a plasmid so the two can be joined.
A plasmid is a small ring of DNA in a bacterium, separate from its main DNA, that biotechnologists use to carry a new gene into a cell.
A transgenic organism is an organism that carries a gene from another species, such as a bacterium that makes human insulin.

Worked example — put the insulin steps in order. You order the cut-and-paste steps for making human insulin in bacteria.

Step 1. Cut. A restriction enzyme cuts out the human insulin gene and cuts open a plasmid.
Step 2. Join. DNA ligase, the sealing enzyme you met in Week 13, joins the gene into the plasmid. The ring is now recombinant DNA.
Step 3. Carry. The plasmid carries the gene into a bacterium, which becomes a transgenic organism.
Step 4. Express. The bacterium transcribes and translates the gene, the way any cell expresses a gene, and makes human insulin.

In words: cut, join, carry, express, and the bacterium makes a human protein.

Cutting and pasting moves a whole gene. Editing changes a gene where it already sits. The newest editor came from bacteria too.

CRISPR-Cas9 is a gene-editing tool adapted from a bacterial immune defense, in which a guide RNA leads the Cas9 protein to a matching DNA sequence, where Cas9 cuts the DNA.
A guide RNA is the short RNA in CRISPR-Cas9 that is made to match the target DNA sequence and leads the Cas9 protein to the spot it should cut.

Think of the guide RNA as the address and Cas9 as the scissors. The guide RNA pairs with the matching DNA sequence by the same base-pairing rules you learned in Week 13, and Cas9 cuts there. Charpentier and Doudna shared the 2020 Nobel Prize in Chemistry for developing this method of genome editing.

Misconception check. Students often think Cas9 finds the right gene on its own. It is tempting because Cas9 is the part that cuts. The cure is to split the jobs: the guide RNA carries the address, matched to the target by base pairing, and Cas9 follows it there. Change the guide RNA and you change where Cas9 cuts.

8. Read a gel like a crime lab: DNA profiling

Back to the trace of blood at the crime scene. PCR has copied its DNA. Now a lab runs the copies on a gel beside samples from people it wants to compare. Each person's DNA gives a pattern of bands.

DNA profiling is comparing the band patterns of DNA samples on a gel to see whether they could come from the same person; a pattern that differs rules a person out more firmly than a matching pattern rules them in.

Worked example — whose DNA is it? The virtual gel, illustrative and constructed for this course, has three sample lanes beside the ladder.

Band sizes in each lane of the virtual gel, in base pairs (illustrative)
Lane	Bands (bp)	Bands that line up with the crime scene
Crime scene	500, 2,000, 4,000	—
Suspect 1	1,000, 2,000, 4,000	2 of 3
Suspect 2	500, 2,000, 4,000	3 of 3

Step 1. Order the tools. PCR copies the trace sample first, then the gel sorts the copies by size.
Step 2. Read the crime-scene lane. It has 3 bands, at 500, 2,000, and 4,000 bp.
Step 3. Compare Suspect 1. Its bands sit at 1,000, 2,000, and 4,000 bp. Two of 3 bands line up (2,000 and 4,000), and the smallest band differs: 1,000 bp instead of 500 bp. Suspect 1 is excluded.
Step 4. Compare Suspect 2. Its bands sit at 500, 2,000, and 4,000 bp. All 3 of 3 bands line up, so Suspect 2's pattern matches the crime scene.
Step 5. Weigh the two calls. One band that differs is enough to rule Suspect 1 out. Three matching bands only fail to rule Suspect 2 out.

In words: Suspect 2 matches, Suspect 1 is excluded, and the exclusion is the firmer of the two calls. An exclusion is firmer than a stand-alone match.

Here is a caveat about that last line. A match means the DNA could have come from Suspect 2. It does not by itself say that nobody else could share the pattern, and a lab weighs a match with other evidence. One mismatched band, by contrast, settles that the sample did not come from that person.

Misconception check. Students often treat a match as proof and an exclusion as a weaker result. A match feels like the exciting answer. The cure is to ask what each result rules out. A single band that differs rules a person out. A match leaves the person in, along with anyone else who might share the pattern. So a matching pattern needs more evidence before anyone draws a conclusion.

9. Weigh the questions: gene editing and its ethics

Suppose a tool could remove the typo behind a serious inherited disease. Should doctors use it in a sick person? In an embryo, so the change is passed down? Who decides, and who gets it? These are real questions now, and this course leaves them open.

The first step is a line between two kinds of editing.

Somatic editing is gene editing of body cells, which changes only the person treated and is not passed to that person's children.
Germline editing is gene editing of reproductive cells, such as eggs and sperm, or of an embryo, so the change can be passed to future generations.

Worked example — sort three edits by the line. You sort each described edit as somatic or germline by asking one question: could the change be passed to the person's children?

An edit to the skin cells of an adult changes body cells only. It cannot pass to that person's children, so it is somatic.
An edit to an early embryo can reach the cells that later make eggs or sperm, so it is germline.
An edit to a sperm cell before fertilization changes a reproductive cell, so it is germline.

Two real events sit on either side of the line. In 2023 a somatic CRISPR therapy for sickle cell disease was approved in the United States. In 2018 an announcement that human embryos had been edited drew international condemnation from scientists.

Now the two cases, each at full strength.

The case for editing. Some heritable diseases are devastating, and editing could prevent them, in one person through somatic therapy or across a family line through germline change.
The case for caution. Cas9 can cut in the wrong place, an off-target effect. Future generations cannot consent to a germline change made before they exist. A tool built for therapy could slide into enhancement, editing for traits rather than for disease. And a costly therapy raises the question of who gets access.

Here is a limitation of what biology alone can say. The science tells you what each edit does and whom it affects. It does not tell you which risks are worth taking. That is a question for people, weighing values, and thoughtful people land in different places.

Misconception check. Students often think the gene-editing debate has one right answer that experts already know. Clear science can make a policy question feel settled too. The cure is to separate the two kinds of question. Whether an edit is somatic or germline has a factual answer. Whether a germline edit should ever be made is a question of values, and both cases above are serious.

Pause and reflect. Choose one of these two prompts and think it through, or jot a few sentences in your notes.

(a) Pick one reason from the case for editing and one from the case for caution. Which one would weigh more for you, and what fact would change your mind?
(b) Think about access. If a somatic therapy works but costs a great deal, who should get it first, and how would you decide?

Back to the cookbook from the opening. Cells already decide which recipes to read, and a typo in one recipe can change a protein. Now people can copy, sort, and rewrite the recipes themselves. What should we do with that power?

Key terms

Genome — The complete set of DNA in an organism; nearly every cell in a body carries the whole genome, even though each cell uses only part of it. (first used: 1. Switch genes on and off: why cells differ)
Gene regulation — A cell's control over which genes are switched on and how much product each one makes, which saves energy and lets different cell types specialize. (first used: 1. Switch genes on and off: why cells differ)
Operon — A group of bacterial genes that share one on/off switch on the DNA, so they are turned on or off together. (first used: 2. Flip the lac operon switch)
Lac operon — The classroom model of gene regulation: a bacterial operon holding the genes for digesting lactose, kept off by a repressor until lactose is present. (first used: 2. Flip the lac operon switch)
Repressor — A protein that sits on the DNA at an operon and blocks its genes from being transcribed; in the lac operon, a molecule made from lactose pulls it off. (first used: 2. Flip the lac operon switch)
Allolactose — A molecule a bacterium makes from lactose; it binds the lac repressor and pulls it off the DNA, which turns the lactose-digesting genes on. (first used: 2. Flip the lac operon switch)
Mutation — A change in the DNA sequence; it is the ultimate source of new genetic variation, and its effect can be neutral, harmful, or beneficial. (first used: 3. Sort the typos: silent, missense, nonsense)
Point mutation — A mutation that changes a single base in the DNA. (first used: 3. Sort the typos: silent, missense, nonsense)
Substitution — A point mutation that swaps one base for another; depending on the codon it creates, it is silent, missense, or nonsense. (first used: 3. Sort the typos: silent, missense, nonsense)
Silent mutation — A substitution that changes a codon without changing the amino acid it codes for, so the protein stays the same, as when GCU becomes GCC and both code for alanine. (first used: 3. Sort the typos: silent, missense, nonsense)
Missense mutation — A substitution that changes a codon so that it codes for a different amino acid, as when GAG becomes GUG and glutamic acid is replaced by valine in sickle cell disease. (first used: 3. Sort the typos: silent, missense, nonsense)
Nonsense mutation — A substitution that turns a codon for an amino acid into a stop codon, so translation ends early and the protein is cut short. (first used: 3. Sort the typos: silent, missense, nonsense)
Frameshift mutation — An insertion or deletion of bases, not in a multiple of three, that shifts the reading frame so every codon after it changes. (first used: 4. Slip the frame: frameshift mutations)
Mutagen — Anything that damages DNA and raises the rate of mutation. (first used: 5. Weigh the effects: neutral, harmful, beneficial)
Biotechnology — The use of living things and their molecules, such as DNA and enzymes, to make products or solve problems. (first used: 6. Copy, then sort: PCR and gel electrophoresis)
PCR (polymerase chain reaction) — A method that copies a chosen stretch of DNA over and over, each round running in the order denature, anneal, extend, using a heat-stable polymerase from the bacterium Thermus aquaticus. (first used: 6. Copy, then sort: PCR and gel electrophoresis)
Gel electrophoresis — A method that sorts DNA fragments by size: the negatively charged DNA runs through a gel toward the positive end, and smaller fragments travel farther. (first used: 6. Copy, then sort: PCR and gel electrophoresis)
Size ladder — A lane of DNA fragments of known sizes run beside the samples on a gel, so the size of an unknown band can be read from how far it traveled. (first used: 6. Copy, then sort: PCR and gel electrophoresis)
Recombinant DNA — DNA spliced together from two different sources, for example a human gene placed into a bacterial plasmid. (first used: 7. Cut, paste, and edit: recombinant DNA and CRISPR-Cas9)
Restriction enzyme — An enzyme that cuts DNA at a specific base sequence, used to cut out a gene and open a plasmid so the two can be joined. (first used: 7. Cut, paste, and edit: recombinant DNA and CRISPR-Cas9)
Plasmid — A small ring of DNA in a bacterium, separate from its main DNA, that biotechnologists use to carry a new gene into a cell. (first used: 7. Cut, paste, and edit: recombinant DNA and CRISPR-Cas9)
Transgenic organism — An organism that carries a gene from another species, such as a bacterium that makes human insulin. (first used: 7. Cut, paste, and edit: recombinant DNA and CRISPR-Cas9)
CRISPR-Cas9 — A gene-editing tool adapted from a bacterial immune defense, in which a guide RNA leads the Cas9 protein to a matching DNA sequence, where Cas9 cuts the DNA. (first used: 7. Cut, paste, and edit: recombinant DNA and CRISPR-Cas9)
Guide RNA — The short RNA in CRISPR-Cas9 that is made to match the target DNA sequence and leads the Cas9 protein to the spot it should cut. (first used: 7. Cut, paste, and edit: recombinant DNA and CRISPR-Cas9)
DNA profiling — Comparing the band patterns of DNA samples on a gel to see whether they could come from the same person; a pattern that differs rules a person out more firmly than a matching pattern rules them in. (first used: 8. Read a gel like a crime lab: DNA profiling)
Somatic editing — Gene editing of body cells, which changes only the person treated and is not passed to that person's children. (first used: 9. Weigh the questions: gene editing and its ethics)
Germline editing — Gene editing of reproductive cells, such as eggs and sperm, or of an embryo, so the change can be passed to future generations. (first used: 9. Weigh the questions: gene editing and its ethics)

Summary

Every cell carries the whole genome but switches on only a subset of genes.
Regulation saves energy and makes specialization possible.
In the lac operon model, the repressor blocks the genes until allolactose pulls it off.
A mutation is a change in the DNA sequence and the source of new variation.
Silent keeps the amino acid; missense swaps it; nonsense makes a stop.
A frameshift moves the reading frame, so every codon after it changes.
Effects range from neutral to harmful to beneficial; mutagens raise the rate.
PCR copies; a gel sorts; smaller fragments travel farther.
Recombinant DNA is cut, joined, and carried in a plasmid; CRISPR-Cas9 edits where a guide RNA leads.
One band that differs excludes a person; an exclusion is firmer than a match.
Somatic edits stay with the person; germline edits can pass to children.

Check your understanding

Work these before looking at the answers — they are ungraded, and the answers (with reasoning) are at the bottom of the page.

An illustrative gene has the mRNA 5′-AUG CCC GAG UAG-3′, which reads Met–Pro–Glu, then stop. Classify two single-base changes: CCC → CCU, and GAG → UAG. Use these codon calls: CCU is Pro, and UAG is stop.
A backyard pond study runs an illustrative gel with a ladder at 300, 900, and 2,700 bp. Which ladder band travels farthest, which stays nearest the wells, and how many times larger is the biggest band than the smallest?
In the lac operon model, describe what the repressor is doing and whether the lactose-digesting genes are on or off: (a) in a bacterium with no lactose around; (b) right after a bacterium meets lactose.
A garden-center plant lab compares an illustrative mystery seedling's DNA with two known plant varieties. The seedling's lane has bands at 700 and 1,500 bp. Variety A shows 700 and 1,500 bp; Variety B shows 700 and 2,100 bp. Which variety is excluded, which matches, and which call is firmer?

Answers (worked reasoning — read after attempting)

CCC → CCU is silent: 1 base changes, and CCU still codes for Pro, so the protein stays Met–Pro–Glu. GAG → UAG is nonsense: 1 base changes (G to U at the first position), and UAG is a stop codon, so translation ends after Met–Pro and the protein has 2 amino acids instead of 3. The trap is calling the second change missense; it does not swap an amino acid, it ends the chain.
Smaller fragments travel farther, so the 300 bp band travels farthest and the 2,700 bp band stays nearest the wells. The size gap is 2,700 ÷ 300 = 9, so the biggest band is 9 times the size of the smallest. In words, the band that moved least is the biggest piece.
(a) With no lactose, the repressor sits on the DNA and blocks transcription. The lactose-digesting genes are off, and the cell saves energy. (b) When lactose arrives, the cell makes allolactose, which pulls the repressor off the DNA, so RNA polymerase can transcribe the genes and they turn on. The trap is calling the repressor the "on" part; it is the brake.
Variety B is excluded: its 2,100 bp band does not line up with the seedling's 1,500 bp band, and one band that differs rules it out. Variety A matches: both of its bands, 700 and 1,500 bp, line up with the seedling's. The exclusion of Variety B is the firmer call, because a match only fails to rule Variety A out, while a mismatch settles that the seedling is not Variety B.

Next up in this module: the Readings & Resources page, the lecture tutorial, the practice set, and the quiz. Next week is finals week, where the Final Practice Exam and the cumulative final ask you to use every ordered process and every model from the course, from the scientific method to the lac operon, at once.

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