6. Gene Expression and Regulation — AP BIOLOGY Revision Notes & Topical Questions

Section 1 of 24Packaging of genetic information

Heritable information

• DNA is the primary source, but some viruses use RNA.

Eukaryotes

• Eukaryotes multiple linear chromosomes of DNA, condensed by winding round histones and associated proteins.

Prokaryotes

• Prokaryotes most DNA is in a single circular chromosome, plus plasmids.
  • (small circular DNA molecules separate from the chromosome)

Section 2 of 24Nucleotides, base pairing and why DNA stores information

Nucleotides, base pairing and why DNA stores information

Nucleotides

• Nucleotides a pentose sugar, a phosphate group and a nitrogenous base.
  • (deoxyribose in DNA, ribose in RNA)

Purines have a double-ring structure: adenine (A) and guanine (G).

• Pyrimidines have a single ringcytosine (C), thymine (T, in DNA) and uracil (U, in RNA).

Polynucleotides

• Polynucleotides nucleotides join with a sugar-phosphate backbone; DNA forms a double helix,
  • while RNA is single-stranded but can fold into double-stranded regions.

Base pairing

• A pairs with T (or U in RNA) and C pairs with G, joined by hydrogen bonds.

A purine always pairs with a pyrimidine, giving base pairs of equal length.

• Specific base pairing has been conserved through evolution.

DNA as hereditary material

• DNA as hereditary material it suits information storage for three reasons.

Deoxyribose makes DNA more stable than RNA.

• Complementary pairing lets one strand be determined from the other, so DNA is easily replicated.
• Four bases give many combinations, so large amounts of information can be stored.

Section 3 of 24DNA replication

• When and what
  • replication happens in S phase, is accurate,
    • and is semiconservative: each new molecule has one original and one new strand, with one strand as template for a complementary strand.

1

Helicase unwinds the strands, exposing the template; topoisomerase relaxes the supercoiling that builds up ahead of the replication fork.

2

Short primers attach to the template strand, giving DNA polymerase a place to bind.

3

DNA polymerase builds new strands by joining nucleotides to form a new sugar-phosphate backbone; it adds nucleotides only to the 3′ end,

• so synthesis is always 5′ to 3′.

4

The leading strand is made continuously in the direction of the fork; the lagging strand is made discontinuously as short fragments in the opposite direction.

5

Ligase joins the fragments on the lagging strand to complete the new DNA molecules.

Section 4 of 24Types of RNA

RNA	Structure	Role
mRNA (messenger)	Single-stranded; sequence set by the DNA	Carries information from DNA to ribosomes as codons
tRNA (transfer)	Single strand folded in 3-D with hydrogen-bonded regions; one end carries an amino acid, another has an anticodon	Anticodon pairs with the mRNA codon during translation
rRNA (ribosomal)	Single strand folded in 3-D	Combines with proteins to form ribosomes

Section 5 of 24Transcription and mRNA processing

1

Part of the DNA unwinds, exposing the gene.

2

Free RNA nucleotides pair with the exposed bases on the template strand (the gene decides which strand is template).

3

RNA polymerase joins the nucleotides into a sugar-phosphate backbone, building mRNA 5′ to 3′ while reading the template 3′ to 5′.

4

The mRNA detaches and leaves the nucleus through a nuclear pore.

1Enzymes

• DNA polymerase joins DNA nucleotides in replication, whereas RNA polymerase joins RNA nucleotides in transcription.

2Poly-A tail

• Poly-A tail a chain of adenine nucleotides at the 3′ end that makes mRNA more stable and longer-lived in the cytosol.

35′ GTP cap

• 5′ GTP cap added at the 5′ end;
  • the small ribosomal subunit binds it, then scans to the start codon AUG, so without it translation is inefficient.

4Intron removal

• Intron removal introns (noncoding) are removed from pre-mRNA, leaving exons to form mature mRNA.

5Alternative splicing

• Alternative splicing exons can be joined in different combinations so one gene can give more than one mature mRNA.

Section 6 of 24Translation

• Site
  • ribosomes in the cytoplasm of prokaryotes and eukaryotes, and on rough ER in eukaryotes;
    • the process needs energy.

Translation

Initiation: the start codon AUG (methionine) of the mRNA interacts with the rRNA of the ribosome.

Elongation: tRNAs with complementary anticodons bind codons; two tRNAs sit on the ribosome at a time, a peptide bond forms between their amino acids,

• and the cycle repeats to lengthen the chain.

Termination: a stop codon signals the end, the amino acid chain is complete and the polypeptide is released.

• Prokaryotes
  • transcription and translation can occur at the same time on one mRNA because there is no nuclear membrane.

Section 7 of 24Reading the genetic code

Codon table

• Codon table each mRNA codon specifies an amino acid, which can be found with a genetic code chart.

The code is degenerate: many amino acids have several codons, e.g. GAU and GAC both code for aspartic acid.

• Nearly all organisms use the same code, which is evidence of common ancestry.

1

Worked example: sense strand TTC GAG CAT TAC GCC.

2

Template (antisense) strand by base pairing: AAG CTC GTA ATG CGG.

3

mRNA (U instead of T): UUC GAG CAU UAC GCC.

4

Read each codon on the chart: Phe, Glu, His, Tyr, Ala.

5

Sequence: Phe-Glu-His-Tyr-Ala.

Section 8 of 24Retroviruses

Retroviruses such as HIV

• Retroviruses such as HIV have RNA as genetic material and make viral proteins using the host cell.

Their RNA must be converted to DNA before transcription and translation; this is the reverse of the usual DNA to mRNA flow.

• The enzyme reverse transcriptase makes the DNA, which is inserted into the host genome.
• The host then carries out transcription and translation of viral genes.

Section 9 of 24Overview of regulating gene expression

1

Why regulate

• Why regulate the genes a cell expresses decide its structure and function.

2

Regulatory proteins

• Regulatory proteins bind specific DNA sequences to switch genes on or off, e.g. transcription factors.

3

Regulatory sequences

• DNA sequences that regulatory proteins bind, e.g. promoters.

4

Constitutive vs inducible genes

• Constitutive vs inducible genes constitutive genes are always expressed; inducible genes are expressed only when needed (e.g. lac operon enzymes).
  • (housekeeping genes)

5

Epigenetic changes

• Epigenetic changes reversible modifications to DNA or histones.

6

DNA methylation (methyl groups added) reduces transcription.

• Histone acetylation (acetyl groups added) loosens DNA wrapping and increases transcription.

7

siRNA

• siRNA single-stranded RNA that binds complementary mRNA and stops it being translated.

Section 10 of 24Operons in prokaryotes

Operons in prokaryotes

Operon

• Operon a cluster of genes under one promoter and operator, transcribed together as one mRNA so that proteins for one function are made together.
  • (the operator lies just upstream)

Inducible operon

• Inducible operon normally off, switched on by an inducer.

Repressible operon

• Repressible operon normally on, switched off when the end product is abundant.

Parts of the lac operon

• Parts of the lac operon structural genes (lacZ etc.) code for lactose-digesting enzymes;
  • regulatory genes code for the repressor;
  • the promoter binds RNA polymerase and the operator binds the repressor.

Operon	Condition	What happens
lac (inducible)	No lactose	Repressor binds the operator and blocks RNA polymerase; no enzymes are made
lac (inducible)	Lactose present	Lactose binds the repressor so it cannot bind the operator; RNA polymerase transcribes, enzymes are made and lactose is broken down
trp (repressible)	No tryptophan	Repressor cannot bind the operator; genes are transcribed and tryptophan is made
trp (repressible)	Tryptophan abundant	Tryptophan binds the repressor, which blocks the operator; synthesis stops and energy is conserved

• Exam point
  • you need to understand how such systems work and apply this to unfamiliar examples, not memorise them.

Section 11 of 24Regulation in eukaryotes: transcription factors, promoters and enhancers

1

Coordinate regulation

• Coordinate regulation eukaryotic genes are usually on different chromosomes,
• but share regulatory sequences that bind the same transcription factor;
  • e.g. heat-shock genes are activated together by one factor under stress.

2

Regulatory sequence location

• Regulatory sequence location upstream, downstream or within introns; cis-regulatory elements near a gene affect initiation,
  • and enhancers or silencers can lie far away.

3

Promoters

• DNA immediately upstream of a gene, the RNA polymerase binding site that marks where transcription starts.

4

Transcription factors

• Transcription factors proteins that bind promoter or nearby sequences and control how easily RNA polymerase binds.

5

Activators help recruit or stabilise RNA polymerase; repressors block its binding or movement.

• Eukaryotes use complexes of several factors; prokaryotes use fewer, with the same principle.

6

Enhancers

• Enhancers sequences that raise the transcription rate, bound by activators.

7

The DNA loops so activators contact the promoter, helping RNA polymerase bind and start, so enhancers act as boosters.

Feature	Prokaryotes (operons)	Eukaryotes (transcription factors)
Gene arrangement	Clustered in operons	Dispersed across the genome
Regulatory sequences	Promoter and operator next to the genes	Promoters, enhancers, silencers that may be far away
Coordination	All genes in an operon on one mRNA	Different genes share a regulatory element
Example	lac operon	Heat-shock genes

Section 12 of 24Gene expression and phenotype

1Phenotype basis

• Phenotype basis which genes are expressed and at what levels;
  • all cells hold the same DNA but different genes are active.

2Cell differentiation

• Cell differentiation stem cells hold the full genome but only some genes are activated,
  • so tissue-specific mRNA and proteins define cell structure and function.

3Development

• Development transcription factors turn gene sets on and off in sequence;
  • Hox genes encode factors that control body plan.

4Small RNAs

• Small RNAs microRNAs and siRNAs act after transcription by binding complementary mRNA.

5

They cause mRNA degradation or block ribosome binding, reducing protein synthesis.

6Overall effect

• Overall effect regulation controls which proteins are made,
  • when and in what amounts, underlying differentiation, development and response to the environment.

Section 13 of 24Types of mutation

Types of mutation

Mutation

• Mutation a change in DNA sequence that can alter the type or amount of protein and so the phenotype;
  • effects can be beneficial, detrimental or neutral.

Point mutations

• Point mutations a change to a single nucleotide.

Substitution swaps one nucleotide for another; because the code is degenerate it can be silent (no change to the amino acids).

• A substitution may be missense (changes one amino acid and the protein) or nonsense (creates a premature stop codon,
  • giving a shortened non-functional protein).

Insertion or deletion

• Insertion or deletion adding or removing a nucleotide shifts the reading frame, altering every codon downstream.
  • (frameshift mutation)

Section 14 of 24Mutation examples: cystic fibrosis and adaptive melanism

1Cystic fibrosis

• Cystic fibrosis a membrane disorder caused by mutations in the CFTR gene, some of them point mutations.

2

It disrupts ion transport, especially in the respiratory tract and reproductive organs, leaving thick sticky mucus that over time can damage the lungs.

• It is recessiveheterozygotes are carriers and homozygous recessive individuals have the disorder.

3Adaptive melanism in rock pocket mice (Chaetodipus intermedius)

• Adaptive melanism in rock pocket mice (Chaetodipus intermedius) dark (melanic) fur camouflages them on volcanic rock.

4

Mutations in the MC1R gene (melanocortin 1 receptor), which regulates melanin production, increase pigment and give darker fur.

• Natural selection favours dark mice in dark environments over generations.

Section 15 of 24Origin of mutations and their effect on phenotype

Origin of mutations and their effect on phenotype

Origin

• Origin random, spontaneous changes during DNA replication or repair, when DNA polymerase sometimes inserts a wrong nucleotide.

UV radiation and reactive chemicals raise mutation rates.

Context dependence

• Context dependence whether a mutation is detrimental, beneficial or neutral depends on the environment.

The sickle cell mutation gives resistance to malaria, so it is beneficial in malaria-prone regions.

Evolutionary role

• Evolutionary role mutations are a source of genetic variation;
  • new alleles give natural selection or genetic drift material to act on.

Section 16 of 24Chromosome-level mutations

Nondisjunction

• Nondisjunction errors in mitosis or meiosis that change chromosome number.

Aneuploidy: one or more individual chromosomes are extra or missing, e.g. trisomy 21 (Down syndrome) and Turner syndrome.

• Polyploidyextra complete sets, e.g. 3n (triploid) or 4n (tetraploid) instead of 2n.

Structural changes

• Structural changes inversions, translocations, duplications or deletions can alter gene expression.

Effect

• Effect changes in number or structure can cause disorders with developmental limitations.

Section 17 of 24Mutations and natural selection

Selection of new alleles

• Selection of new alleles advantageous alleles help individuals outcompete others, so they pass the allele to more offspring.

Sickle cell anaemia

• Sickle cell anaemia a mutation in the haemoglobin gene produces abnormal haemoglobin.

Homozygotes for the sickle allele (Hb^S) show symptoms.

• Heterozygotes (one normal, one sickle allele) have no symptoms but resist malaria, a survival advantage.
• So the allele is selected for where malaria is common (heterozygote advantage).

Section 18 of 24Other sources of genetic variation

1Why variation matters

• Why variation matters it drives natural selection, so sexual reproduction and recombination are conserved across many organisms.

2Horizontal gene transfer in prokaryotes

• DNA (often plasmids) passes between cells of the same generation.

3

Transformation: DNA from the environment is taken up and incorporated.

• TransductionDNA is carried by bacteriophages.
• Conjugationa pilus forms between two bacteria to exchange DNA.
• Transpositiona DNA segment moves within a chromosome or between DNA molecules, e.g. plasmids and chromosomal DNA.

4Viral recombination

• Viral recombination when two viruses infect one host cell, their genetic material interacts during replication using host machinery,
  • and progeny acquire genes from both strains.

Section 19 of 24Gel electrophoresis

Principle

• Principle separates DNA, RNA or proteins by size and electrical charge in a gel.

DNA is negatively charged, so it moves towards the positive electrode.

• Small molecules move faster through the gel pores, large ones more slowly.
• Fragments of unknown size can be sized by comparing the distance moved with fragments of known size.

Uses

• DNA profiles for relatedness, forensic analysis and helping DNA sequencing.
  • (e.g. DNA at a crime scene)

Exam focus

• Exam focus applications rather than full procedure.

Section 20 of 24Polymerase chain reaction (PCR)

• Purpose
  • makes many identical copies (amplifies) of a DNA fragment from a small sample, for profiling, phylogenetic analysis or transforming bacteria.
    • (criminals, paternity)

Polymerase chain reaction (PCR)

Denaturation: heat breaks the hydrogen bonds between the two strands.

Annealing: temperature falls so primers attach to the ends of the single strands.

Elongation: temperature rises to the optimum for DNA polymerase, which builds the complementary strands.

Equipment

• Equipment a thermal cycler automatically sets the temperature and time of each stage.

Speed

• DNA doubles every cycle, so amplification is rapid.

Section 21 of 24Bacterial transformation and DNA sequencing

Bacterial transformation

• Bacterial transformation introducing new DNA into bacteria so they make a useful non-bacterial protein.

Human insulin: the gene is inserted into plasmid vectors, bacteria take up the plasmid, and the gene is transcribed and translated.

• In vivo gene cloningvectors carry a DNA fragment into bacteria, which reproduce to give many identical copies.

Why bacteria are useful

• Why bacteria are useful the genetic code is universal, there are few ethical concerns, and plasmids act as convenient vectors.

DNA sequencing

• DNA sequencing identifies the base sequence of genetic material and is now rapid and automated;
  • computers compare sequences between organisms.

Many methods give a DNA fingerprint, a unique pattern of DNA fragments.

• Usesforensic identification, phylogenetic analysis, personalised medicine (identifying mutations for targeted treatment) and organism identification by comparing amplified fragments with databases.

Section 22 of 24Worked examples

1. A DNA template strand reads TAC GGA CTT. State the mRNA and explain how it is made. [3]3 marks

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2. Explain why the lagging strand is made in fragments. [3]3 marks

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3. Describe how lactose switches on the lac operon. [3]3 marks

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4. Explain the effect of a single base deletion in the middle of a gene. [3]3 marks

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5. Describe the three stages of one PCR cycle. [3]3 marks

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6. Explain why sickle cell trait persists in malaria regions. [3]3 marks

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Section 23 of 24Key terms

Term	Meaning
Semiconservative replication	Each new DNA molecule has one old and one new strand.
Codon	Three mRNA bases that specify an amino acid or stop signal.
Anticodon	tRNA triplet that pairs with an mRNA codon.
Intron	Noncoding region removed from pre-mRNA.
Operon	Cluster of genes under one promoter and operator.
Transcription factor	Protein that binds regulatory DNA to control transcription.
Frameshift mutation	Insertion or deletion that shifts the reading frame.
PCR	Technique that amplifies DNA by repeated heating and cooling cycles.
Gel electrophoresis	Separation of molecules by size and charge in a gel.
Reverse transcriptase	Enzyme making DNA from RNA in retroviruses.

Section 24 of 24Exam technique

1

Saying DNA polymerase makes mRNA — RNA polymerase does in transcription.

2

Writing thymine in mRNA — RNA has uracil.

3

Believing all mutations are harmful — effects depend on the environment and many are neutral.

4

Saying the lagging strand is made 3′ to 5′ — all synthesis is 5′ to 3′, just discontinuous on the lagging strand.

5

Confusing aneuploidy (individual chromosomes extra or missing) with polyploidy (whole extra sets).