Unit 6 Beta

Gene Expression and Regulation: the one-page sheet

6.1 DNA and RNA Structure

DNA is the hereditary material of all cells and many viruses; some viruses use RNA. Griffith's mice showed that something from dead S bacteria could transform live R bacteria; Avery, MacLeod and McCarty found that only destroying DNA stopped transformation; Hershey and Chase showed that a phage's DNA, not its protein, enters the cell and reaches the next generation. In the double helix, each base pair joins a two-ring purine to a one-ring pyrimidine, which keeps the width uniform and gives Chargaff's rules (A = T, G = C). Prokaryotes have one circular chromosome, often with plasmids, in the cytoplasm; eukaryotes have linear chromosomes in a nucleus, wound around histones into nucleosomes. Loose euchromatin can be read; tight heterochromatin is mostly silent.

Hereditary material is DNA in every cell and in many viruses; some viruses (RNA viruses, such as influenza) carry their genes in RNA.
Evidence: Griffith found transformation (1928); Avery, MacLeod and McCarty showed only DNase destroys the transforming principle (1944); Hershey and Chase showed phage DNA, not protein, enters the cell (1952).
Purines (A, G) have two rings; pyrimidines (T, C, and U in RNA) have one. Each pair is purine + pyrimidine, so the helix has a uniform width, and Chargaff's rules hold: A = T and G = C in double-stranded DNA.
Prokaryotes: one circular chromosome plus plasmids, no nucleus. Eukaryotes: several linear chromosomes in a nucleus, wound on histones as nucleosomes.
Euchromatin is loose and its genes can be read; heterochromatin is tight and mostly silent. A cell's full set of DNA is its genome.

Some R cells become S cells and pass the change to their offspring: a molecule from the dead cells changed their heredity. This is bacterial transformation. Only destroying DNA stops transformation, so DNA is the transforming molecule. The 32 P goes into the cells and into the next phages, but the 35 S stays outside: the phage's genes are DNA. Each strand sets the sequence of the other, which is what makes copying possible; and because every pair is a purine plus a pyrimidine, the helix has a uniform width. Its linear chromosomes are wrapped around histones as nucleosomes, then coiled and folded into chromatin; a bacterium keeps one circular chromosome, often with plasmids. Proteins that read genes can reach DNA in euchromatin but mostly not in heterochromatin, so packing helps decide which genes can be used.

transformation (bacteria): Bacterial transformation: a bacterium takes in DNA from its surroundings and gains new, inherited traits, as when harmless R cells became deadly S cells in Griffith's experiment.
virus: A small particle of nucleic acid (DNA or RNA) inside a protein coat, sometimes with an outer envelope. A virus is not a cell and can multiply only inside a host cell, using the host's machinery.
bacteriophage: A virus that infects bacteria (phage for short). Many phages attach to a cell's surface and inject their DNA, leaving the protein coat outside.
transforming principle: The experiments showing DNA is the hereditary material: Griffith's transformation of R bacteria by heat-killed S bacteria (1928); Avery, MacLeod and McCarty's finding that only DNase destroys the transforming principle (1944); and Hershey and Chase's phage labeling, in which DNA (³²P) entered the cells and protein (³⁵S) did not (1952).
hereditary material: The molecule that carries genetic instructions from one generation to the next: DNA in all cells and many viruses, RNA in some viruses.
RNA virus: A virus whose genes are carried in RNA instead of DNA, such as influenza, measles and the coronavirus that causes COVID-19.
plasmid: A small circle of DNA, separate from the main chromosome, that is copied on its own and can pass between bacteria. Plasmid genes are often useful but not essential, such as genes for surviving a drug.
linear chromosome: A chromosome with two ends, the kind found in the nucleus of eukaryotic cells (prokaryotes usually have one circular chromosome).
histone: A small, positively charged protein around which eukaryotic DNA winds. About two turns of DNA around a core of eight histones form a nucleosome, the first level of chromatin packing.
euchromatin: Loosely packed chromatin, whose genes can be reached and read. Its opposite, heterochromatin, is tightly packed chromatin whose genes are mostly silent.
purine: A nitrogenous base with two fused rings: adenine (A) and guanine (G). Pyrimidines have one ring: thymine (T), cytosine (C) and uracil (U). Each DNA base pair joins one purine to one pyrimidine.
uniform width of the double helix: The constant diameter of the DNA double helix (about 2 nm), which results from every base pair being one purine plus one pyrimidine.
Chargaff's rules: In double-stranded DNA, the amount of adenine equals the amount of thymine and the amount of guanine equals the amount of cytosine (A = T, G = C), because of base pairing. The share of A + T differs between species.
genome: One complete set of an organism's DNA: all of its genes plus the DNA between them. Human body cells carry two copies, one from each parent.

6.2 Replication

DNA replication is semiconservative: each parental strand is the template for a new partner, so each daughter helix has one old and one new strand, as Meselson and Stahl's density bands showed. Copying begins at origins of replication, which open into bubbles with two forks. Helicase unwinds the helix, single-strand binding proteins hold the strands apart, and topoisomerase relieves the twisting ahead. Primase makes a short RNA primer, and DNA polymerase III adds nucleotides to its 3′ end, building 5′ to 3′. Because the strands are antiparallel, the leading strand is made continuously and the lagging strand in Okazaki fragments; DNA polymerase I replaces the primers with DNA and ligase seals the nicks. Proofreading and mismatch repair keep errors rare. Linear chromosome ends shorten each round; telomeres buffer them, and telomerase can rebuild them.

Semiconservative replication: each new double helix keeps one parental strand. Meselson and Stahl's ¹⁵N/¹⁴N density bands ruled out the conservative and dispersive models.
Origins of replication open into bubbles with two replication forks. Bacteria have one origin; each eukaryotic chromosome has thousands.
Enzymes at the fork: helicase (unwinds), topoisomerase (relieves twisting), single-strand binding proteins, primase (RNA primer), DNA polymerase (adds to the 3′ end, 5′ → 3′), DNA ligase (seals nicks).
The leading strand is continuous; the lagging strand is made in Okazaki fragments because new DNA can only grow 5′ to 3′.
Proofreading by DNA polymerase and later mismatch repair keep errors rare. Telomeres buffer linear chromosome ends, which shorten each round unless telomerase rebuilds them.

Two replication forks form and move away from each other, opening a replication bubble. The strands separate; single-strand binding proteins keep them apart, and topoisomerase relieves the twisting that builds up ahead of the fork. Primase first lays down a short RNA primer, and DNA polymerase III extends it, always building 5′ to 3′ and pairing each new base with the template. One new strand (leading) grows continuously toward the fork; the other (lagging) grows away from it in Okazaki fragments, each with its own primer. DNA ligase seals the nicks, joining the fragments into one continuous strand. Each daughter molecule has one old strand and one new strand: replication is semiconservative, as Meselson and Stahl showed.

semiconservative replication: The way DNA is copied: each new double helix contains one strand from the parent molecule and one newly made strand. Meselson and Stahl's heavy-nitrogen experiment confirmed it and ruled out the conservative model (the parent helix stays whole) and the dispersive model (old and new DNA mixed along each strand).
origin of replication: A DNA sequence where copying begins. The helix opens there into a replication bubble with a replication fork at each side, and the forks move apart. Bacteria have one origin; each eukaryotic chromosome has many.
helicase: The enzyme that unwinds DNA at a replication fork by breaking the hydrogen bonds between base pairs, separating the two strands.
topoisomerase: An enzyme that cuts and rejoins DNA ahead of a replication fork to relieve the twisting strain caused by unwinding (in bacteria, gyrase).
single-strand binding protein: Single-strand binding proteins coat separated DNA strands at a replication fork and keep them from pairing up again before they are copied.
primer: A short nucleic acid strand paired to a template, whose 3′ end gives DNA polymerase a place to start adding nucleotides.
primase: The enzyme that builds the short RNA primers that start each new DNA strand and each Okazaki fragment.
DNA polymerase: The enzyme that builds new DNA by adding nucleotides, matched to the template, to the 3′ end of a growing strand, so new DNA grows 5′ to 3′. In bacteria, DNA polymerase III does most of the building and DNA polymerase I replaces RNA primers with DNA.
leading strand: The new DNA strand built continuously toward the replication fork, from a single primer.
lagging strand: The new DNA strand built away from the replication fork in short pieces, Okazaki fragments, each started by its own RNA primer and later joined together.
DNA ligase: DNA ligase: the enzyme that seals nicks in a DNA backbone, joining Okazaki fragments into one continuous strand (and joining DNA pieces in the lab).
proofreading: DNA polymerase's checking of each base it adds; a mispaired base is removed and replaced at once. Mismatch repair is a second system that fixes mispaired bases in the new strand after copying.
telomere: A long run of short repeated DNA at each end of a linear chromosome. Telomeres hold no genes, so they buffer the small loss at the ends in each round of copying. Telomerase is the enzyme that adds repeats back, in cells that divide throughout life, germ cells and many cancer cells.

6.3 Transcription and RNA Processing

Transcription copies a gene into RNA, the first step of the central dogma (DNA → RNA → protein). RNA polymerase binds at the promoter, needs no primer, reads the template strand 3′ to 5′ and builds RNA 5′ to 3′, so the RNA matches the coding strand with U for T. In bacteria a terminator ends transcription. In eukaryotes, RNA polymerase II makes pre-mRNA, which is processed in the nucleus: a 5′ cap and a poly-A tail are added, and spliceosomes remove introns and join exons. Alternative splicing joins different exons in different cells, so one gene can make several proteins. The mature mRNA leaves through nuclear pores to the ribosomes. Other genes make RNAs that work as RNA, such as tRNA and ribosomal RNA.

The central dogma: information flows DNA → RNA → protein. Transcription is the DNA → RNA step.
RNA polymerase starts at a promoter, needs no primer, reads the template strand 3′ to 5′ and builds RNA 5′ to 3′. The RNA matches the coding strand with U for T. A terminator ends it in bacteria.
Eukaryotic pre-mRNA is processed in the nucleus: 5′ cap, poly-A tail, and splicing by spliceosomes, which remove introns and join exons.
Alternative splicing joins different exons in different cells, so one gene can give several proteins.
Not every RNA is mRNA: tRNA carries amino acids and ribosomal RNA (rRNA) forms much of the ribosome; both work as RNA.

RNA polymerase opens a short stretch of the double helix and begins copying. The RNA grows 5′ to 3′ with the same sequence as the coding strand, except U for T. The RNA is released; in eukaryotes this primary transcript is pre-mRNA. The cap and tail protect the mRNA from breakdown, help it leave the nucleus, and help ribosomes bind it. Mature mRNA holds one continuous coded message; joining different sets of exons (alternative splicing) gives different mRNAs from one gene. Ribosomes there can use it to build a protein (topic 6.4).

central dogma: The usual flow of genetic information in cells: DNA is copied into RNA (transcription), and RNA's message is used to build a protein. Some viruses also copy RNA into DNA.
transcription: Making an RNA copy of a gene, using one DNA strand as the template. RNA polymerase builds the RNA 5′ to 3′, starting at the gene's promoter.
RNA polymerase: The enzyme that makes RNA from a DNA template. It binds at a promoter, unwinds a short stretch of DNA, needs no primer and adds nucleotides to the RNA's 3′ end. In eukaryotes, RNA polymerase II copies the genes for proteins.
promoter: A DNA sequence just before a gene where RNA polymerase (with helper proteins) binds; it sets where copying starts and which strand is read. Many eukaryotic promoters contain a TATA box a short distance before the transcription start site.
template strand: The DNA strand that RNA polymerase reads (3′ to 5′) to build a gene's RNA. The other strand, the coding strand, has the same sequence as the RNA, with T in place of U.
terminator: A DNA sequence at the end of a bacterial gene that, once copied, makes RNA polymerase release the RNA and leave the DNA.
pre-mRNA: The first RNA copy of a eukaryotic gene (primary transcript), which still contains introns and has not yet received its cap and tail.
RNA processing: The changes that turn eukaryotic pre-mRNA into mature mRNA in the nucleus: a modified G nucleotide (5′ cap) is added to the 5′ end, a poly-A tail of about 200 A nucleotides is added to the 3′ end, and introns are spliced out.
RNA splicing: RNA splicing: spliceosomes (complexes of proteins and short RNA molecules) cut the introns out of a pre-mRNA and join its exons. Exons are the parts kept in the mature mRNA; introns are the parts removed.
alternative splicing: Splicing the same pre-mRNA in different ways, including or leaving out particular exons, so that one gene gives several different mRNAs and proteins, often in different cell types.
tRNA: Transfer RNA: a short RNA, about 80 nucleotides long, that folds into a compact L shape and carries a specific amino acid to the ribosome. It is made by transcription but is never used as instructions for a protein.

6.4 Translation

Translation turns an mRNA's message into a polypeptide. The message is read in codons, three nucleotides each, in one reading frame set by the start codon AUG (methionine) and ended by a stop codon (UAA, UAG or UGA). Aminoacyl-tRNA synthetases load each tRNA with its amino acid; a tRNA's anticodon pairs with the codon in the ribosome. In initiation the ribosome assembles at the start codon; in elongation charged tRNAs enter the A site, peptide bonds form, and the ribosome moves one codon at a time, tRNAs passing from the A to the P to the E site; at termination a release factor frees the chain. The genetic code is nearly universal, evidence of common ancestry. Bacteria couple transcription and translation; polyribosomes make many copies at once. A signal peptide directs a chain into the rough ER. Retroviruses copy RNA into DNA with reverse transcriptase.

Translation builds a polypeptide from an mRNA's codons, three bases each, read 5′ to 3′ in one reading frame from the start codon AUG (methionine) to a stop codon.
tRNAs link the code to amino acids: each anticodon pairs with a codon, and aminoacyl-tRNA synthetases attach the right amino acid. Ribosomes have A, P and E sites.
The genetic code (a codon table) has 64 codons for 20 amino acids and stop; it is redundant but not ambiguous, and it is nearly universal, evidence of common ancestry.
Bacteria translate mRNA while it is still being made (coupled transcription and translation); many ribosomes can read one mRNA (polyribosome). A signal peptide sends a chain into the rough ER.
Retroviruses such as HIV use reverse transcriptase to copy their RNA into DNA.

Charged tRNAs carry amino acids, each tRNA with an anticodon that fits particular codons. The large subunit joins, with the methionine tRNA in the P site: initiation is complete and the reading frame is set. The ribosome forms a peptide bond, moving the growing chain onto that tRNA. The chain-carrying tRNA shifts to the P site, the empty tRNA leaves from the E site, and the A site is free: elongation repeats. A release factor binds, the finished polypeptide is released, and the ribosome comes apart: termination.

codon: A group of three mRNA nucleotides that stands for one amino acid or for stop. Codons are read one after another, 5′ to 3′, without gaps or overlaps.
translation: Building a polypeptide from the message in an mRNA. Ribosomes read the codons, and tRNAs bring the matching amino acids, which are joined by peptide bonds.
anticodon: The three bases on a tRNA that pair with an mRNA codon. It is complementary and antiparallel to the codon: codon 5′-UGG-3′ pairs with anticodon 3′-ACC-5′.
genetic code: The set of rules linking the 64 codons to the 20 amino acids and stop, usually shown as a codon table. It is redundant (most amino acids have several codons) but not ambiguous (each codon has one meaning).
start codon: AUG, the codon where translation begins. It codes for methionine, so new polypeptides start with methionine, and it sets the reading frame.
stop codon: One of the three codons, UAA, UAG and UGA, that code for no amino acid. When one reaches the ribosome's A site, a release factor binds and the polypeptide is released.
reading frame: The way an mRNA's bases are grouped into codons, set by the start codon. Shifting the start by one or two bases puts every later codon in a different frame.
aminoacyl-tRNA synthetase: Aminoacyl-tRNA synthetase: an enzyme that attaches a specific amino acid to the tRNAs for it, using energy from ATP, producing a charged tRNA.
A site (ribosome): The three tRNA-binding sites of a ribosome: the A site, where a new charged tRNA arrives; the P site, which holds the tRNA carrying the growing chain; and the E site, from which empty tRNAs exit. The ribosome has a small subunit, which binds the mRNA, and a large subunit, which forms peptide bonds.
initiation (translation): The three stages of translation. Initiation: the ribosome assembles at the start codon with the methionine tRNA. Elongation: tRNAs enter the A site, peptide bonds form, and the ribosome moves one codon at a time. Termination: a release factor binds a stop codon and the chain is freed.
coupled transcription and translation: In prokaryotes, which have no nucleus, ribosomes begin translating an mRNA while RNA polymerase is still making it.
polyribosome: Several ribosomes reading the same mRNA at the same time, one behind another, each making its own copy of the polypeptide (also called a polysome).
universal genetic code: The nearly universal genetic code: almost all organisms use the same codon assignments, with a few small exceptions such as in mitochondria. It is evidence that all life shares a common ancestor.
retrovirus: An RNA virus, such as HIV, whose enzyme reverse transcriptase copies its RNA genome into DNA (reverse transcription); the DNA is inserted into the host's DNA and its genes are then used like the host's own.
signal peptide: A short stretch at the start of a polypeptide that directs the ribosome making it to the rough ER, so the chain is threaded into the ER as it is made (protein targeting). It is usually cut off inside the ER.

6.5 Regulation of Gene Expression

Cells control which genes are transcribed and how much, using regulatory sequences in the DNA and the proteins that bind them. In bacteria, related genes are grouped in operons with one promoter and an operator. The lac operon is inducible: its repressor blocks the operator until allolactose, the inducer, binds the repressor and releases it; cAMP-CAP, an activator, boosts transcription when glucose is scarce. The trp operon is repressible: tryptophan, the corepressor, activates the repressor and switches the operon off. Repressors give negative regulation, activators positive regulation. Constitutive genes are always on; inducible genes are switched on when needed. In eukaryotes, transcription factors bind promoters and enhancers, and DNA looping brings them together. DNA methylation and histone acetylation change how open chromatin is; these epigenetic marks can be inherited without a sequence change. Gene products determine the phenotype.

Regulatory sequences (promoters, operators, enhancers) are DNA that proteins bind; regulatory proteins (repressors, activators, transcription factors) decide whether and how much a gene is transcribed.
An operon: promoter + operator + structural genes. Inducible (lac): usually off, an inducer inactivates the repressor. Repressible (trp): usually on, a corepressor activates it.
Negative regulation: a bound repressor lowers transcription. Positive regulation: a bound activator, such as cAMP-CAP, raises it.
Constitutive (housekeeping) genes are on all the time; inducible genes are switched on when needed.
Epigenetics: DNA methylation silences; histone acetylation opens chromatin. Marks can be inherited through divisions. Gene products (proteins and RNAs) set the phenotype.

They are copied into one mRNA and switched on or off together. RNA polymerase is blocked, so the lactose-digesting enzymes are not made. The repressor leaves the operator, and the genes are transcribed; if glucose is scarce, cAMP-CAP boosts transcription further. The active repressor binds the trp operator and switches off the genes for making tryptophan. RNA polymerase is recruited, and the combination of factors in a cell sets how much each gene is transcribed. Genes become easier or harder to transcribe, and these epigenetic marks can be passed to daughter cells without changing the DNA sequence.

regulatory sequence: A stretch of DNA that does not code for a product but is bound by proteins that control a gene's transcription, such as a promoter, an operator, an enhancer or a silencer.
transcription factor: A protein that binds DNA and controls transcription. General transcription factors gather at a promoter and recruit RNA polymerase II; specific ones (activators and repressors) bind enhancers or silencers and raise or lower a gene's transcription.
enhancer: A regulatory DNA sequence, often far from the gene it controls, where activator proteins bind; DNA looping brings them to the promoter, increasing transcription. A silencer is a similar site where repressor proteins bind and lower transcription.
operon: In bacteria, a group of structural genes with related jobs that share one promoter and one operator and are transcribed together into a single mRNA. The operator is the short DNA sequence a repressor binds.
repressor: A protein that binds an operator (or a silencer) and blocks transcription. Its shape, and so its grip on DNA, is changed by small molecules: an inducer inactivates it, and a corepressor activates it.
inducer: A small molecule that turns on an inducible operon by binding the repressor and making it release the operator; for the lac operon, allolactose, formed from lactose.
inducible operon: An operon that is usually off and is switched on when an inducer removes its repressor, such as the lac operon, whose enzymes take up and split lactose.
repressible operon: An operon that is usually on and is switched off when its end product, acting as a corepressor, activates the repressor, such as the trp operon, whose enzymes make tryptophan.
constitutive gene: A constitutive (housekeeping) gene is transcribed at a fairly steady level all the time, for products every cell needs. An inducible gene is transcribed only when a signal switches it on.
positive gene regulation: Positive gene regulation: a protein that binds DNA increases transcription, as the catabolite activator protein (CAP) with cAMP does at the lac operon when glucose is scarce. In negative gene regulation, a bound protein, such as a repressor, decreases transcription.
epigenetics: Changes in gene activity that do not change the DNA sequence and can be passed on when cells divide, such as DNA methylation and histone acetylation.
DNA methylation: Adding methyl groups to DNA, mainly to C nucleotides. Heavily methylated promoters are usually silent, because methylated DNA attracts proteins that pack chromatin tightly. The pattern is copied onto new DNA at each division.
histone acetylation: Adding acetyl groups to histone tails, which reduces their positive charge and loosens their hold on DNA, opening chromatin so genes are easier to transcribe. It is one kind of histone modification, part of chromatin remodeling.
gene product: What a gene makes: usually a protein, sometimes a working RNA. The amount and activity of gene products determine an organism's phenotype.

6.6 Gene Expression and Cell Specialization

All the cells of a body carry the same genome, as nuclear transfer experiments show; they become different by expressing different genes. Signals between tissues (induction) and morphogen gradients give cells in different positions different transcription factors. Each factor binds the enhancers of many genes, and genes switch on only with the right combination, so whole sets of genes are expressed together; master regulators such as Hox genes set the identity of whole body regions. This differential gene expression drives cell differentiation. Stem cells keep the ability to become other cell types: totipotent cells can form a whole organism, pluripotent cells any body cell. After transcription, microRNAs pair with target mRNAs and reduce their translation or speed their breakdown, and proteins are activated by post-translational modification or removed by the proteasome.

Differential gene expression: the same genome, different genes expressed. It is the basis of cell differentiation.
Specific transcription factors and combinations of enhancer elements decide which genes a cell uses; one master factor can switch on a whole set (coordinated gene expression).
Stem cells divide and can become other cell types: totipotent (any cell, including placenta), pluripotent (any body cell).
In embryonic development, induction (signals between tissues), morphogen gradients and homeotic (Hox) genes give cells positions and identities.
After transcription: microRNAs pair with mRNAs and reduce their use (post-transcriptional regulation); post-translational modification and protein breakdown in the proteasome control proteins.

Cells cannot differ in which genes they have, only in which genes they express. Cells in different places switch on different transcription factors. Whole sets of genes are switched on together (coordinated gene expression), and master regulators such as Hox genes set the identity of body regions. They make different proteins and become specialized cell types: cell differentiation. Each cell type's proteins are set at the level of mRNA and protein as well as at the gene.

differential gene expression: Differential gene expression: cells with the same genome expressing different sets of genes, because they contain different transcription factors and other regulators. It is the basis of cell specialization.
cell differentiation: The process by which a cell becomes specialized for one job, with the proteins and structures that job needs, by expressing a particular set of genes. A differentiated cell keeps its whole genome.
stem cell: A cell that can divide to renew itself and can give rise to specialized cells. Totipotent cells (the fertilized egg and its first descendants) can form any cell, including the placenta; pluripotent cells can form any cell of the body; adult stem cells form a few related types.
microRNA: A microRNA (miRNA) is a short RNA, about 22 nucleotides, that does not code for a protein; it pairs with target mRNAs and reduces their translation or speeds their breakdown. Small interfering RNAs (siRNAs) act similarly; using them to silence genes is RNA interference (RNAi). Both are noncoding RNAs.
post-transcriptional regulation: Control of gene expression after an RNA is made, for example by alternative splicing, by microRNAs, or by how fast an mRNA is broken down.
post-translational modification: Post-translational modification: changes made to a protein after translation, such as cutting it to an active form, or adding phosphate groups or sugars. Protein degradation by the proteasome, which breaks down proteins tagged for destruction, also controls protein levels.
embryonic development: Embryonic development: the process by which a fertilized egg becomes an organism, through cell division, cell differentiation and the shaping of tissues and organs (morphogenesis).
induction (development): Induction (development): one group of cells sends signals that change the gene expression and fate of neighboring cells, as when the optic cup induces skin to form a lens.
homeotic gene: A homeotic gene is a master regulatory gene that sets the identity of a body region by switching on the genes for its structures. In animals these are the Hox genes, which code for transcription factors expressed in order along the head-to-tail axis.
morphogen: A signal molecule that spreads from a source and forms a concentration gradient; cells switch on different genes at different levels, so the gradient tells them their position. Bicoid in fruit fly eggs is an example.
coordinated gene expression: Coordinated gene expression: switching on a whole set of genes together, because they share enhancer elements bound by the same transcription factor, as MyoD switches on many muscle genes.

6.7 Mutations

A mutation is a permanent change in DNA's base sequence. It arises from copying errors that escape repair or from damage by mutagens such as UV radiation and some chemicals, many of which are carcinogens, and it arises at random rather than in response to need. Point mutations replace one base and can be silent, missense or nonsense. Insertions and deletions that are not multiples of three shift the reading frame, changing every later codon. Changes to the amino acid sequence can change a protein's shape and function and so the phenotype, as in sickle cell disease. Whether a mutation is harmful, neutral or beneficial depends on the environment. Chromosomes can lose, repeat, flip or move segments, and whole sets can be added (polyploidy). Bacteria also gain genes by transformation, transduction and conjugation; transposons move within genomes; and viruses vary quickly through mutation and reassortment.

Point mutations: silent (same amino acid), missense (different amino acid), nonsense (stop codon). Insertions and deletions not in multiples of three cause frameshifts.
Causes: copying errors, and mutagens such as UV radiation and some chemicals (many are carcinogens). Mutations are random: not directed by need or by the environment.
Effects depend on context: neutral, harmful or beneficial. The same sickle-cell allele harms in two copies but protects carriers against malaria.
Chromosomal mutations: deletion, duplication, inversion, translocation; errors in number include nondisjunction and polyploidy.
Bacteria gain genes by horizontal gene transfer: transformation, transduction, conjugation. Transposons move within genomes; viruses vary through high mutation rates and reassortment.

The base sequence changes permanently: a mutation, passed to every cell that descends from this one. The codon may still mean the same amino acid (silent), a different one (missense) or stop (nonsense). The reading frame shifts, so every codon after the change is different and a stop codon often appears early (frameshift). Its folding and function may change, which can change the phenotype, as in sickle cell disease. A mutation can be harmful, neutral or helpful depending on the environment, and mutations in gametes add to the variety in a population.

point mutation: A mutation that changes a single base. The most common kind is a base substitution, in which one base pair is replaced by another.
silent mutation: The effects of a base substitution in a coding sequence. Silent mutation: the codon still codes for the same amino acid. Missense mutation: it codes for a different amino acid. Nonsense mutation: it becomes a stop codon, ending the chain early.
insertion mutation: An insertion mutation adds one or more bases to DNA; a deletion mutation removes them. Together they are called indels. If the number is not a multiple of three, they shift the reading frame.
frameshift mutation: A mutation that adds or removes a number of bases that is not a multiple of three, so every codon after it is regrouped; the amino acids change and a stop codon usually appears early.
mutagen: Something that raises the rate of mutation, such as UV radiation, X-rays or certain chemicals. Mutagens that can cause cancer are called carcinogens.
random mutation: The principle that mutations arise by chance, not in response to an organism's needs or to particular pressures in its environment; the environment affects which mutations persist, not which ones occur.
neutral mutation: A mutation can be neutral (no effect on survival or reproduction), harmful (deleterious) or beneficial, and which it is depends on the environment: one copy of the sickle-cell allele helps where malaria is common and has little effect elsewhere.
sickle cell disease: Sickle cell disease: an inherited disease caused by a missense mutation in the β-globin gene that puts valine in place of glutamic acid; the hemoglobin forms fibers at low oxygen, bending red blood cells into sickles that block small vessels. Carriers of one sickle-cell allele are protected against severe malaria.
chromosomal mutation: A change in the structure of a chromosome: a deletion (segment lost), a duplication (segment repeated), an inversion (segment flipped) or a translocation (segment moved to a nonhomologous chromosome).
polyploidy: Having more than two complete sets of chromosomes, such as triploid (3n) or tetraploid (4n). Common in plants; triploids are nearly sterile because their homologs cannot separate evenly in meiosis.
horizontal gene transfer: Horizontal (lateral) gene transfer: the movement of genes between organisms that are not parent and offspring, as when bacteria gain genes by transformation, transduction or conjugation.
transduction (bacteria): Transfer of bacterial DNA from one bacterium to another by a phage that packaged some of its previous host's DNA by mistake.
conjugation: Direct transfer of DNA, often a plasmid, from one bacterium to another through a connecting bridge formed with a pilus.
transposon: A transposable element: a DNA segment that can move or copy itself to new places in a genome. Inserting into a gene usually disrupts it.
viral recombination: The fast genetic change of viruses: RNA viruses copy their genomes without proofreading, giving a high viral mutation rate, and viruses with segmented genomes such as influenza can swap segments when two infect one cell (reassortment); others recombine parts of their genomes (viral recombination).

6.8 Biotechnology

Biotechnology uses the cell's own enzymes as tools. PCR copies a chosen stretch of DNA by repeating denaturation, primer annealing and extension with heat-stable Taq polymerase, doubling the target each cycle. Gel electrophoresis separates DNA fragments by size: DNA is negatively charged and moves toward the positive electrode, small fragments farthest, and a DNA ladder gives the sizes. Restriction enzymes cut specific sequences, often leaving sticky ends; joined with ligase, a gene and a plasmid make recombinant DNA, which bacteria take up by transformation and keep when a selectable marker lets only them grow. DNA sequencing reads the order of bases; DNA profiles compare short tandem repeats. CRISPR-Cas9 cuts DNA where its guide RNA pairs, allowing gene editing, and gene therapy adds working genes to a patient's cells. These tools are used in medicine, forensics, farming and research.

PCR copies a chosen stretch of DNA: denature, anneal primers, extend with Taq polymerase; copies double each cycle (2ⁿ).
Gel electrophoresis separates DNA by size: DNA is negative and runs toward +, small fragments farthest; a DNA ladder gives the sizes.
Restriction enzymes cut specific sequences, often leaving sticky ends; with ligase they make recombinant DNA. A plasmid carrying a gene and a selectable marker is put into bacteria by transformation (gene cloning).
DNA sequencing reads the order of bases. DNA fingerprinting compares short tandem repeats.
CRISPR-Cas9 cuts DNA where a guide RNA pairs, for gene editing. Gene therapy adds working genes to a patient's cells. These tools make genetically modified organisms.

The hydrogen bonds between bases break and the two strands separate (denaturation). The primers pair with their matching sequences on the single strands (annealing). Each strand gets a new partner, so every target molecule becomes two; 30 cycles make about a billion copies. Negatively charged DNA moves toward the positive electrode, small fragments fastest, so fragments separate by size and can be compared with a DNA ladder. Bacteria that grow on a selective plate carry the recombinant plasmid and make the gene's product, such as human insulin.

gel electrophoresis: A method that separates DNA fragments by size: samples are loaded into wells in an agarose gel and an electric current pulls the negatively charged DNA toward the positive electrode; small fragments move farthest. A DNA ladder of known sizes is run alongside to measure them.
restriction enzyme: A bacterial enzyme that cuts DNA at a specific short sequence, its restriction site, producing restriction fragments; many leave single-stranded overhangs (sticky ends) that pair with matching ends cut by the same enzyme.
PCR: The polymerase chain reaction: repeated cycles of heating to separate DNA strands, cooling so primers bind (annealing) and extension by heat-stable Taq polymerase, run in a thermal cycler. Each cycle doubles a chosen stretch of DNA.
recombinant DNA: DNA joined from different sources, for example a human gene in a bacterial plasmid, made with restriction enzymes and ligase. Organisms given such DNA are genetically engineered: genetically modified organisms (GMOs), or transgenic when the gene comes from another species.
gene cloning: Gene cloning (DNA cloning): making many copies of a gene by joining it into a cloning vector such as a plasmid, putting it into bacteria by transformation and growing a colony from one transformed cell.
selectable marker: A gene on a cloning vector that lets only cells carrying the vector grow under a chosen condition, for example a gene that lets cells survive an antibiotic, so that only transformed cells form colonies on plates containing it.
DNA sequencing: Determining the order of bases in DNA. Sanger sequencing copies a template with chain-stopping labeled nucleotides and reads the sequence from the lengths and end bases of the fragments; newer methods sequence whole genomes.
DNA fingerprinting: DNA profiling: comparing the lengths of DNA at sites that vary greatly between people, usually short tandem repeats (STRs), copied by PCR and measured by electrophoresis. Used in forensics and to test family relationships.
CRISPR: CRISPR-Cas9: a gene-editing system from bacteria in which a guide RNA pairs with a chosen DNA sequence and the Cas9 enzyme cuts both strands there; repair of the cut can disrupt the gene or insert a chosen change (genome editing).
gene therapy: Treating a disease by adding a working copy of a gene to a patient's cells, or editing a faulty one. When body cells are treated, the change is not passed to the patient's children.
biotechnology: The use of living things or their molecules to make products or solve problems; modern biotechnology uses tools such as PCR, gel electrophoresis, recombinant DNA, sequencing and gene editing.