4. Genetics, Variation and Interdependence — AQA A Level Biology 7402 Revision Notes & Topical Questions

Section 1 of 29DNA in prokaryotes, eukaryotes and organelles

DNA in prokaryotes, eukaryotes and organelles

Prokaryotic DNA

• Prokaryotic DNA a single circular chromosome (nucleoid) not bound to proteins, plus plasmids.
  • (small circular DNA with a few genes, often for antibiotic resistance, easily accessible for quick expression)

Eukaryotic chromosomes

• Eukaryotic chromosomes long linear DNA wound round positively charged histone proteins, forming chromatin.
• Other proteins are enzymes for copying and repairing DNA.
• Chromatids are made of chromatin; telomeres seal the ends.

Mitochondrial and chloroplast DNA

• Mitochondrial and chloroplast DNA short, circular and not associated with protein, in the matrix and stroma respectively.

Section 2 of 29Genes, loci and the triplet code

Gene

• Gene a base sequence of DNA that codes for the amino acid sequence of a polypeptide or for a functional RNA.
  • (mRNA, tRNA, rRNA)

Locus

• Locus the position of a gene on a chromosome; alleles are different forms of the gene at the same locus.

Triplet code

• Triplet code each triplet of bases codes for one amino acid.
• 64 possible triplets (4³) but only 20 amino acids, so the code is degenerate.
• Start (TAC, giving methionine) and stop signals mark the gene boundaries.
• The code is non-overlapping and almost universal.

Exam care

• Exam care check whether a question gives DNA triplets or mRNA codons (complementary).

Section 3 of 29Non-coding DNA, introns and exons

1Non-coding DNA

• Non-coding DNA found between genes as multiple repeats and within genes as introns, between coding exons.

2Transcription and splicing

• Transcription and splicing the whole gene is transcribed into pre-mRNA;
  • introns are removed and exons joined (splicing) before the mature mRNA leaves the nucleus.

Section 4 of 29Genome, proteome and RNA structure

Genome, proteome and RNA structure

Genome

• Genome the complete set of genes in a cell; proteome — the full range of proteins a cell can make.
• The proteome is larger than the genome because of alternative splicing and post-translational modification (for example in the Golgi).

RNA

• RNA single-stranded polynucleotide with ribose and uracil instead of thymine.

mRNA

• mRNA a transcript copy of a gene carrying the code to ribosomes.

tRNA

• tRNA a folded single strand held by hydrogen bonds, with an anticodon complementary to an mRNA codon and a site for one specific amino acid.

Section 5 of 29Transcription

1

In the nucleus, helicase breaks hydrogen bonds and unwinds the gene.

2

The strand copied is the template strand; the other is the non-template (coding) strand.

3

Free activated RNA nucleotides pair with complementary bases on the template strand.

4

RNA polymerase joins the nucleotides to form the sugar-phosphate backbone, moving 3' to 5' along the template so mRNA grows 5' to 3'.

5

The mRNA detaches, the DNA rewinds, and mRNA leaves via a nuclear pore.

1Sequence relationships

• Sequence relationships mRNA matches the non-template strand (with U for T);
  • tRNA anticodons match the template strand.

2Enzymes

• DNA polymerase is for replication; RNA polymerase is for transcription.

Section 6 of 29Eukaryotic versus prokaryotic transcription, and alternative splicing

Eukaryotes

• Eukaryotes pre-mRNA contains introns and exons; splicing gives mature mRNA of exons only.

Alternative splicing

• Alternative splicing exons are joined in different combinations, so one gene can code for several polypeptides.
  • (one reason the proteome is bigger than the genome)

Prokaryotes

• Prokaryotes no introns and no pre-mRNA;
  • mRNA is made directly, and translation can begin during transcription because both occur in the cytoplasm.

Section 7 of 29Translation

1

mRNA attaches to a ribosome in the cytoplasm.

2

tRNA molecules bring their specific amino acids.

3

The anticodon of each tRNA pairs with a complementary mRNA codon.

4

Two tRNAs fit the ribosome at a time, holding amino acids side by side.

5

A peptide bond forms between them, using ATP from mitochondria.

6

The ribosome moves along until a stop codon is reached, and the polypeptide is released.

• Locations
  • transcription in the nucleus, translation in the cytoplasm.

Section 8 of 29Working with codons and amino acid sequences

1Degeneracy

• Degeneracy several codons code for one amino acid, so some mutations do not change the protein.
  • (UGU and UGC both code for cysteine)

2Start and stop

• AUG is always methionine; stop codons such as UAA code for no amino acid.

3Counting

• Counting amino acids = – 1 for the stop codon.
  • (coding nucleotides ÷ 3)
• 303 nucleotides gives 101 codons, so 100 amino acids.
• Given amino acids, multiply by 3 and add 3 for the stop codon.

4Worked example

• DNA TAC CCG AAA ACT.
• mRNA: AUG GGC UUU UGA.
• Amino acidsMet–Gly–Phe, then stop.

Section 9 of 29Gene mutations

Gene mutation

• Gene mutation a change in the base sequence, occurring continuously and at random;
  • most do not alter the polypeptide because the code is degenerate.

Deletion

• Deletion loss of a nucleotide changes every later triplet (frameshift) and can change the protein dramatically.

Substitution

• Substitution swapping one base affects only one triplet.
• Silentsame amino acid.
• Missenseone amino acid changes (sickle cell anaemia).
• Nonsensepremature stop codon, giving a shortened protein (as in some cystic fibrosis cases).

Effects

• Effects altered active site shape or weaker structural proteins such as collagen.

Mutagenic agents

• Mutagenic agents ultraviolet and ionising radiation (X-rays) and toxic chemicals such as peroxides raise the mutation rate beyond cell proofreading and repair.

Section 10 of 29Chromosome mutations and meiosis

Non-disjunction

• Non-disjunction chromosomes fail to separate in meiosis, producing gametes with an extra or missing chromosome.
• Down's syndromethree copies of chromosome 21, giving 47 chromosomes.

Meiosis

Meiosis produces four genetically different haploid cells in two divisions.

Independent segregation

• Independent segregation homologous pairs line up randomly in metaphase I, so each pair separates independently of the others.

Crossing over

• Crossing over in prophase I, homologous chromosomes form bivalents and non-sister chromatids exchange segments, giving recombination of alleles.

Section 11 of 29Stages of meiosis

Stage	Events
Prophase I	Chromosomes condense and pair as homologous pairs; crossing over; spindle forms; nuclear envelope breaks down
Metaphase I	Homologous pairs line up randomly on the equator (independent segregation)
Anaphase I	Whole chromosomes pulled to opposite poles; centromeres do not divide
Telophase I	Two groups of chromosomes; nuclear envelopes reform; cytokinesis gives two haploid cells
Prophase II to Metaphase II	No interphase or DNA replication; new spindle at right angles; chromosomes line up singly
Anaphase II	Centromeres divide and chromatids move to poles
Telophase II	Four haploid nuclei; cytokinesis gives four cells

1Counting

• Counting chromosomes are counted by centromeres, so a replicated cell still has 46 chromosomes but 92 chromatids.

2Identifying stages

• Identifying stages pairs of chromosomes side by side means meiosis I;
  • two cells formed means meiosis I and four means meiosis II.

Section 12 of 29Sources of variation and calculating combinations

1Sources

• Sources crossing over, independent segregation and random fertilisation, plus mutation.

2After meiosis

• After meiosis number of chromosome combinations = 2ⁿ, where n is the haploid number.
• Humans2²³ = 8 388 608.
• A plant with diploid number 16: n = 8, so 2⁸ = 256.

3After random fertilisation

• (2ⁿ)².
• Humans(2²³)² = about 7.04 × 10¹³.
• The plant(2⁸)².

4Note

• Note ignore crossing over in these calculations.

Feature	Mitosis	Meiosis
Use	Growth and repair	Gamete production
Divisions	One	Two
Daughter cells	Two, diploid, identical	Four, haploid, genetically different
Location	Throughout the body	Sex organs

Section 13 of 29Genetic diversity and fitness

Genetic diversity

• Genetic diversity the number of different alleles in a population, increased by mutation.
• New alleles may be advantageous, disadvantageous or neutral and can stay hidden for generations.

Selection pressures

• Selection pressures environmental factors that change survival; individuals with favoured phenotypes have higher fitness.
  • (ability to survive and pass on alleles)

Small gene pools

• Small gene pools cheetahs went through a population bottleneck about 10 000 years ago,
  • so inbreeding and low diversity make them vulnerable to environmental change.

Section 14 of 29Logarithms in bacterial investigations

Logarithms in bacterial investigations

Why use logarithmic scales

• Why use logarithmic scales bacteria grow rapidly, giving very large and small values;
  • log scales fit a wide range on one axis.

Order of magnitude

• Order of magnitude a tenfold change; each unit on a log₁₀ axis is one order of magnitude.

Recognising log scales

• Recognising log scales uneven intervals between values; examples are yeast growth curves and the pH scale.

Section 15 of 29Natural selection and types of selection

Natural selection and types of selection

Natural selection

• Natural selection random mutation produces new alleles;
  • under some conditions an allele helps survival and reproduction, is passed on and rises in frequency.
• Rabbit examplebrown fur (dominant) camouflages better than white (recessive), so foxes eat more white rabbits and the white allele frequency falls.

Stabilising selection

• Stabilising selection keeps the mean constant by selecting against extremes.
• Human birth weightvery low and very high weights have higher mortality.

Directional selection

• Directional selection shifts the mean towards one extreme when the environment changes or a new allele arises.
• Antibiotic resistanceantibiotics select for resistant bacteria, so the resistance allele frequency rises.

Section 16 of 29Adaptation, evolution and speciation

1Adaptation

Adaptation types

Type	Description
Anatomical	white polar bear fur, long limbs in desert animals.
Physiological	anticoagulants in mosquito saliva, hibernation.
Behavioural	reptiles basking, bird migration.

2Evolution

• Evolution change in adaptive features of a population over time through natural selection;
  • no change in environment means no change in selection.

3Speciation

• Speciation isolated populations accumulate differences until they cannot interbreed to produce fertile offspring.

4Sequence for any example

• Sequence for any example variation by mutation, advantage, more survival and reproduction, allele becomes common,
  • and eventually possibly a new species.

Section 17 of 29Practical: aseptic technique and disc diffusion

• Aseptic technique
  • sterilise Petri dishes and agar, disinfect surfaces, work near a Bunsen flame, flame loops before and after use, keep lids on and lift at an angle only briefly.
    • (convection currents carry contaminants away)

1

Soak paper discs in antibiotics of the same concentration.

2

Spread diluted bacterial broth (about 1 × 10⁸ CFU mm^-3) over sterile agar to make a lawn.

3

Place discs evenly, away from the edge and each other.

4

Incubate overnight.

5

Measure the clear zones of inhibition and compare areas using area = πr².

Interpretation

• Interpretation larger clear zones mean more effective antibiotic; no zone means resistance.

MIC

• MIC the minimum inhibitory concentration is the lowest concentration that inhibits microbial growth.

Section 18 of 29Courtship and species

Species

• Species organisms that interbreed in nature to produce fertile offspring.

Courtship behaviour

Courtship behaviour precedes mating and aids species recognition, so it increases the probability of successful mating.

• Can be simple (a few visual, chemical or sound signals) or complex (birds of paradise).
• Drosophila species look alike but each has a distinct, genetically controlled courtship dance.

Section 19 of 29Phylogenetic classification and the hierarchy of taxa

Phylogenetic classification

Phylogenetic classification groups organisms by evolutionary origin, using a hierarchy of non-overlapping taxa.

• Uses DNA, RNA and protein similaritiesmore similar means a more recent common ancestor.
• It helps communication, allows predictions (medicinal properties may be shared) and gives accurate species counts for conservation.

Domains

• Bacteria, Archaea and Eukarya; RNA analysis shows archaea are closer to eukaryotes than to bacteria.

Hierarchy

• Hierarchy domain, kingdom, phylum, class, order, family, genus, species.
• MnemonicKings Play Chess On Fancy Gold Squares.

Binomial

• Binomial genus (capital) and species (lower case) in italics or underlined, for example Homo sapiens.

Section 20 of 29Evolutionary relationships from molecules

Genome sequencing

• Genome sequencing compare DNA, mRNA or amino acid sequences, even from extinct species.
• More similar sequences mean more closely related species that diverged more recently.
• Use proteins found in many organisms with enough variation, for example cytochrome c.

Immunological comparison

• Immunological comparison albumin from different species is injected into rabbits; the antibodies are mixed with albumin samples and the mass of precipitate shows similarity.
  • (heavier precipitate means closer relationship)

Why proteins

• Why proteins easier to isolate, and amino acid sequences are more conserved than DNA.

Section 21 of 29Biodiversity, species richness and index of diversity

Biodiversity

• Biodiversity variation in genes, species and habitats; ecosystem diversity is the variety of habitats.
  • (a coral reef is high; a sandy desert is low)

Species richness

• Species richness the number of species in a community; it ignores abundance.
• Habitat A with 10 species of one individual each is richer than habitat B with 7 species of 20 individuals, but B has more evenness.

Index of diversity

Index of diversity d = N(N – 1) ÷ Σ n(n – 1).

• N is the total number of organisms and n the number of each species.
• Larger d means greater diversity.
• Insects
  • N = 202, so N(N – 1) = 40 602;
    • Σ n(n – 1) = 6884;
    • d = 5.90.

Section 22 of 29Conservation and farming

Modern farming

• Modern farming monoculture, larger fields, drained wetlands, more pesticides and fertilisers, and autumn sowing,
  • (hedgerow removal)
• which reduce habitats and biodiversity.
  • (for example bumblebee decline)

Why conserve

• Why conserve wild species may have future value, ecosystem stability, ethical and cultural reasons, and carbon storage in woodland and peatland.

Practice	Benefit
Maintain hedgerows	Habitats and wildlife corridors
Wildflower strips	Pollinators and natural pest predators
Crop rotation	Less soil depletion, more soil biodiversity
Organic fertilisers	Less eutrophication, healthier soil
Agri-environment schemes	Financial incentives for wildlife-friendly farming

• Conflict
  • conservation can reduce yield and profit, so subsidies and grants offset the loss.
    • (avoiding pesticides helps bumblebees but allows pests)

Section 23 of 29Measuring genetic diversity

1Species

• Species members interbreed and are reproductively isolated from others.
  • (mules are sterile hybrids)

2Characteristics

• Characteristics measurable and observable (colour, patterns); quick but unreliable because phenotype depends on genes and environment.
  • (legs, petals, seeds)

3DNA analysis

• DNA analysis extract DNA, sequence it and compare;
  • fewer differences mean closer relationship, and trees can be built.

4mRNA analysis

• mRNA analysis easier to obtain; reverse-transcribed into cDNA containing exons only; compare the same mRNA using primers.
  • (for example cytochrome c)

5Amino acid sequences

• Amino acid sequences easier to isolate and evolve more slowly, but less precise than DNA because of degeneracy and silent mutations.
• Methodalign the sequences, count identical positions for each pair, and the pair with most identical positions is most closely related.
• Always check whether you are comparing bases (A, T, C, G) or amino acids (Met, Ala, Val).

Section 24 of 29Random sampling and calculating abundance

Sampling

• Sampling used because complete counts are impractical in large ecosystems.
• Random sampling uses a random number generator to avoid bias.
• Systematic sampling at set intervals can be biased if easy areas are chosen.

Population density

• Population density place quadrats at random coordinates, count individuals, use a running mean until it stabilises,
  • then multiply the mean per quadrat by habitat area.

Percentage cover

• Percentage cover a grid quadrat of 100 squares;
  • count squares where the species covers more than half;
  • use one assessor for consistency.

Frequency

(quadrats with the species ÷ total quadrats) × 100.

• 18 of 50 gives 36%.

Density

Density individuals ÷ total quadrat area: 107 bluebells in 50 quadrats of 1 m² is 2.14 per m².

Limitations

• Limitations quadrats suit sessile or slow-moving organisms; frequency gives no population size.

Section 25 of 29Mean and standard deviation

Mean

Mean sum ÷ number of values; extreme values distort it.

• 15 maze times totalling 226 s gives 15.1 s.

Standard deviation

Standard deviation measures spread around the mean (small = values close to mean).

1

Calculate the mean.

2

Subtract the mean from each value.

3

Square each difference.

4

Add the squares.

5

Divide by n – 1.

6

Take the square root.

Mean and standard deviation

Example

• Example rabbit ear lengths with mean 59 mm and sum of squares 36: 36 ÷ 14 = 2.571;
  • square root = 1.60 mm, a small spread.

Comparing groups

• Comparing groups groups with the same mean can differ in spread.
  • (Groups A and B both have mean 13)
• If mean ± SD ranges overlap, the difference is probably not significant.
• Artery lumen example: experimental 0.71 to 0.77 mm overlaps its before value and the control, so the diet had no significant effect.

Section 26 of 29Interpreting sequence data

1Alignments

• Alignments count differences: ATGCCCGAT vs ATGCCTGAT has one.

2Comparison tables

• Comparison tables fewer differences between a pair means closer relationship.

3Phylogenetic trees

• Phylogenetic trees closer branches mean fewer differences; branch length may show genetic change or time.

4Molecular versus observable methods

• Molecular versus observable methods phenotypes depend on genes and environment,
• so DNA and amino acid sequence comparison is more accurate;
  • amino acid comparisons are less precise than DNA because of degeneracy.

Section 27 of 29Worked examples

1. A gene has 150 coding nucleotides including the stop codon. How many amino acids does it code for? [2]2 marks

   Show mark scheme

2. Describe the effect of a deletion mutation compared with a substitution. [3]3 marks

   Show mark scheme

3. A species has 2n = 12. Calculate the possible chromosome combinations from meiosis (no crossing over) and after random fertilisation. [3]3 marks

   Show mark scheme

4. A habitat has species counts 10, 5, 5 (N = 20). Calculate the index of diversity. [3]3 marks

   Show mark scheme

5. Explain how directional selection led to antibiotic resistant bacteria. [4]4 marks

   Show mark scheme

Section 28 of 29Key terms

Term	Meaning
Locus	The position of a gene on a chromosome.
Degenerate code	More than one triplet can code for the same amino acid.
Splicing	Removal of introns and joining of exons in pre-mRNA.
Non-disjunction	Failure of chromosomes to separate during meiosis.
Fitness	The ability to survive and pass on alleles.
Stabilising selection	Selection against extreme phenotypes that keeps the mean constant.
Binomial	A two-part Latin name consisting of genus and species.
Index of diversity	A measure of species diversity that includes richness and evenness.
Standard deviation	A measure of the spread of data around the mean.

Section 29 of 29Exam technique

1

Confusing DNA polymerase (replication) and RNA polymerase (transcription).

2

Writing DNA triplets where mRNA codons are needed — convert to complementary bases with U.

3

Calling cytokinesis part of meiosis or mitosis stages — it follows telophase.

4

Using species richness alone to compare diversity — evenness also matters, so use the index of diversity.

5

Saying overlapping standard deviations show a significant difference — overlap suggests it is not significant.