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3.1 Essential ideas

3.1.1 Genes
3.1.2 Chromosomes
3.1.3 Meiosis
3.1.4 Inheritance
3.1.5 Genetic modification and biotechnology

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Book: 3.1 Essential ideas
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Date: Tuesday, 22 September 2020, 11:57 PM

3.1.1 Genes

Figure 3.1.1a – Relationship of chromosomes to genesFigure 3.1.1a – Relationship of chromosomes to genes

  • A gene is a heritable factor located at a specific position, or locus, on a chromosome.
  • A gene consists of a length of DNA. The sequence of bases in the DNA influences a specific characteristic.
  • Each gene codes for one polypeptide during translation (see 2.1.7).
  • Most characteristics are influenced by more than one gene at different loci.
  • The number of genes varies between species, but not between members of the same species. For example, all normal and healthy humans have the same number of genes.
  • The table below compares total amount of DNA, the number of chromosomes, and the number of genes in different organisms. 



Estimated size of genome (DNA base pairs)

Number of chromosomes

Estimated number of genes



(Homo sapiens)

3 billion


23 000

(Oryza sativa)

4.2 million


41 000



Yeast (eukaryote)
(Saccharomyces cerevisiae)

12 million



Bacterium (prokaryote)
(Escherichia coli)

4.6 million




  • There are usually two or more forms of a gene. The various forms of a gene are called alleles.
  • Alleles differ from each other by one or only a few base pairs.
  • Alleles that differ by only one base pair are more accurately named single-nucleotide polymorphisms, or SNPs (pronounced ‘snips’).

Figure 3.1.1b – Three SNP alleles resulting in three variations of a traitFigure 3.1.1b – Three SNP alleles resulting in three variations of a trait

  • These small differences result in variations in the amino acid sequence of the resulting polypeptide, and eventually to differences in the overall characteristic.

New alleles are formed by mutation

  • Mutations are random changes to the DNA sequence. They can be caused by errors during DNA replication, or by external agents, called mutagens.
  • Most mutations are either lethal or neutral, meaning they have no effect on the characteristic.
  • Some mutations form new alleles. In order for the mutation to be passed on to the next generation, it has to be present in the gametes.
  • If the mutation is beneficial, it will be maintained in a population by natural selection.
  • There are many different kinds of mutation; one important type is called a ‘base substitution’, in which one of the four bases – A, T, C or G – is substituted for another.

Figure 3.1.1c – Base substitution in hemoglobinFigure 3.1.1c – Base substitution in hemoglobin

  • A single base substitution (dark blue in Figure 3.1.1c) in the human hemoglobin gene causes glutamic acid to be substituted by valine as the sixth amino acid in the resulting polypeptide.

A genome includes extra-chromosomal DNA

  • In addition to the DNA in chromosomes, there is also DNA in mitochondria, as well as in the chloroplasts of plants.
  • The word ‘genome’ refers to the whole of the genetic information of an organism, including extra-nuclear DNA.
  • In the case of prokaryotes, which have no nucleus, the genome consists of the main chromosome ring (nucleoid) and any plasmids that are present.

The Human Genome Project

  • The original aims of the Human Genome Project were to sequence the entire human genome and to create maps of human chromosomes.

Figure 3.1.1d – Map of the human X chromosome showing loci (left) and associated genes (right)Figure 3.1.1d – Map of the human X chromosome showing loci (left) and associated genes (right)

  • The genomes of other species useful for medical research were also sequenced (e.g. mouse and fruitfly).
  • The project began in the 1990s and involved cooperation between public institutions around the world, including Japan, France, Germany, the UK, USA and China.
  • Due to improvements in gene sequencing technology, the original aims were reached earlier than expected.
  • The entire base sequence of human genes was sequenced in the Human Genome Project.

Figure 3.1.1e – DNAFigure 3.1.1e – DNA

Essential idea

Every living organism inherits a blueprint for life from its parents.

Key questions

  • Define genome, gene, allele and mutation.
  • Outline one example of a base pair substitution.
  • Discuss the relevance of the Human Genome Project to themes in the Nature of Science.

Figure 3.1.1f – UV lightFigure 3.1.1f – UV light
UV light is a mutagen that causes changes in the DNA sequence.

Concept help

  • SNPs are found in genes, but they are also found in non-coding sequences of DNA. For example, there are approximately 10 million SNPs in the human genome, but only 25 000 genes!
  • There are many loci on chromosomes that do not contain genes.

Figure 3.1.1g - DNA sequencing machineFigure 3.1.1g - DNA sequencing machine
DNA sequencing machine: developments in research follow improvement in technology.

Course links

Figure 3.1.1h – Rice in handFigure 3.1.1h – Rice in hand

Food for thought

Do more ‘complex’ organisms have larger genomes? More genes? Discuss your ideas with a classmate.

Further reading

Details about the Human Genome Project goals, accomplishments and methods can be found at the National Library of Medicine website:

3.1.2 Chromosomes

  • All chromosomes are made of a single DNA molecule, but the number and structure of prokaryotic and eukaryotic chromosomes differ.

Figure 3.1.2a – Chromosomes in prokaryotes and eukaryotesFigure 3.1.2a – Chromosomes in prokaryotes and eukaryotes




Number of chromosomes


  • Circular
  • Linear

Association with proteins

  • Histone proteins (for organisation and packaging of DNA)

Presence of plasmids

  • No plasmids
  • Plasmids are a unique feature of prokaryotes. A plasmid is a small piece of circular DNA which codes for additional genes that are not needed for normal growth or development.

Figure 3.1.2b – Bacterial plasmids are not chromosomesFigure 3.1.2b – Bacterial plasmids are not chromosomes

  • For example, genes for antibiotic resistance are usually located on plasmids.

Figure 3.1.2c – Conjugation involves replication and transfer of plasmid DNAFigure 3.1.2c – Conjugation involves replication and transfer of plasmid DNA

  • DNA replication in plasmids occurs independently of the bacterial chromosome. Plasmids can be transferred between bacterial cells, or even between different species.

Features of eukaryotic chromosomes

Figure 3.1.2d – Karyograms for human female (left) and male (right)Figure 3.1.2d – Karyograms for human female (left) and male (right)

  • Homologous chromosomes are identical in shape and structure and carry the same sequence of genes.
  • One chromosome is inherited from the mother and the other is inherited from the father, so that although they carry the same sequence of genes, the alleles of genes on homologous chromosomes may differ.
  • In humans, there are 23 pairs of chromosomes.
  • Chromosomes that determine an individual’s sex are called sex chromosomes.
  • In humans, females have a pair of X chromosomes, and males have one X and one Y chromosome. The Y chromosome is much smaller than the X chromosome, as you can see from Figure 3.2.1d.
  • Chromosomes that do not determine sex are called autosomes.
  • In humans, there are 22 pairs of autosomes, numbered from 1 to 22. The sex chromosomes are the 23rd pair.

Haploid and diploid nuclei

Figure 3.1.2e – Haploid and diploid nucleiFigure 3.1.2e – Haploid (N) and diploid nuclei (2N)

Application: Haploid and diploid numbers

Copy the table and fill in the missing numbers.

Latin binomial

Common name

Number of chromosomes in somatic cells

Number of chromosomes in gametes

Homo sapiens




Pan troglodytes




Canis familiaris




Oryza sativa




Parascaris equorum

Horse threadworm



Key idea

Chromosomes carry genes in a linear sequence that is shared by members of a species.

Figure 3.2.1f – GametesFigure 3.2.1f – Gametes
Gametes have haploid nuclei. The nuclei of haploid cells contain only one chromosome from each homologous pair.

Figure 3.2.1g – X and YFigure 3.2.1g – X and Y
Electron micrograph of human X chromosome (left) and Y chromosome (right).

Food for thought

Are the sex chromosomes in a human male, X and Y, a homologous pair?

International mindedness

Sequencing of the rice genome involved cooperation between biologists in 10 countries.

Figure 3.2.1h – MicrographFigure 3.2.1h – Micrograph
Micrograph showing that transfer of plasmids can be transferred between cells.

Course links

  • Populations of bacteria quickly become resistant to antibiotics because plasmids are easily transferred between cells – see 5.1.2.
  • Plasmids are used to insert genes for the purpose of genetic modification of organisms – see 3.1.5.
  • HL students will learn more about the function of histones in 7.1.1 and 7.1.2.

3.1.3 Meiosis

  • Meiosis is a form of nuclear division in which one diploid nucleus divides to produce four genetically different haploid nuclei.

Figure 3.1.3a – Comparing meiosis (left) and mitosis (right)Figure 3.1.3a – Comparing meiosis (left) and mitosis (right)

  • Mature haploid cells are called gametes. When gametes fuse during sexual reproduction, the result is a diploid zygote.
  • Halving the number of chromosomes through meiosis allows organisms to have a sexual life cycle.

Figure 3.1.3b – Meiosis is necessary to conserve chromosome number in a sexual life cycleFigure 3.1.3b – Meiosis is necessary to conserve chromosome number in a sexual life cycle

  • Sexual reproduction, via the fusion of gametes from different parents, promotes genetic variation.

Meiosis results in genetic variation

  • Meiosis is a single process. However, there are two separate division events: meiosis i and meiosis II.
  • During the first division, the chromosome number is halved and homologous chromosomes separate randomly.
  • During the second division, sister chromatids are separated, resulting in four genetically unique haploid daughter cells.

Crossing over and random orientation

  • DNA replication occurs before the start of meiosis, so that all chromosomes consist of two sister chromatids.

Figure 3.1.3c – Sister chromatids and homologous chromosomesFigure 3.1.3c – Sister chromatids and homologous chromosomes

Figure 3.1.3d – Crossing over occurs between non-sister chromatids during prophase I of meiosisFigure 3.1.3d – Crossing over occurs between non-sister chromatids during prophase I of meiosis

  • Crossing over occurs at points called chiasmata (singular chiasma).
  • The result of crossing over is that sister chromatids can have different combinations of alleles. Some of the alleles from the maternal chromosome become part of the paternal chromosome and vice versa.
  • Crossing over results in genetic recombination.
  • During metaphase I, homologous chromosomes line up as bivalents at the equator of the cell.
  • The pairs line up randomly, meaning that each chromosome in the pair has an equal chance of travelling to either pole during anaphase I.

Figure 3.1.3e – Four possible orientation patterns for three pairs of homologous chromosomesFigure 3.1.3e – Four possible orientation patterns for three pairs of homologous chromosomes

  • The result of random orientation is that each daughter cell will inherit an unpredictable combination of paternal and maternal chromosomes.
  • Crossing over and random orientation of homologous chromosomes prior to separation ensure that there is genetic variation in the cells resulting from meiosis.

Skill: The stages of meiosis

Figure 3.1.3f – The stages of meiosis I (images 1–5), and meiosis II (images 6–10) in a plant cellFigure 3.1.3f – The stages of meiosis I (images 1–5), and meiosis II (images 6–10) in a plant cell





Meiosis I


Prophase I


Metaphase I


Anaphase I

3 + 4

  • Homologous pairs are separated, one of each pair moves to opposite poles

Telophase I


  • Nuclear membrane reforms around two haploid nuclei

Meiosis II

Prophase II


Metaphase II


Anaphase II

8 + 9

  • Sister chromatids separate and move to opposite poles

Telophase II


  • Nuclear membrane reforms around four haploid nuclei

Figure 3.1.3g – Stages of meiosis in an animal cellFigure 3.1.3g – Stages of meiosis in an animal cell

Watch the video to review how a diploid cell divides to form four genetically unique haploid cells during meiosis.

This video will help you understand how random orientation of chromosomes in metaphase I leads to genetic variation in daughter cells.

Essential idea

New genetic combinations result from segregation of alleles during meiosis.

Food for thought

  • Without meiosis, the chromosome number would double with each generation!
  • Why is meiosis I sometimes called the ‘reduction division’?
  • Which of the two divisions is most like mitosis, meiosis i or meiosis II?
  • Why is genetic variation useful for the survival and success of a species?

Concept help

DNA replication occurs during interphase before prophase of meiosis I. There is a short interphase between meiosis I and meiosis II, but there is no further DNA replication.

Course link

Review the stages of mitosis in 1.1.6.

3.1.4 Inheritance

Mendelian inheritance

  • Gregor Mendel discovered the principles of inheritance while studying the characteristics of pea plants over many generations.
  • He had no knowledge of genes or chromosomes, but he predicted the existence of heritable factors and his work disproved the theory of ‘blended inheritance’.

Genotype and phenotype, dominant and recessive alleles

  • The combination of alleles present at locus on homologous chromosomes is the genotype.
  • The genotype is represented by a pair of letters, as shown in the figure below:

Figure 3.1.4a – The relationship of alleles to genotypeFigure 3.1.4a – The relationship of alleles to genotype

Figure 3.1.4b – The relationship of genotype to phenotypeFigure 3.1.4b – The relationship of genotype to phenotype

ABO blood groups: an example of codominance

  • Most traits are influenced by multiple alleles, and often one allele is not completely dominant over the other.

  • In cases of codominance, both alleles in the heterozygote affect the phenotype. An example is ABO blood groups.

  • ABO blood type is determined by the type of antibodies present on the surface of red blood cells.

Figure 3.1.4c – ABO blood groups are an example of codominanceFigure 3.1.4c – ABO blood groups are an example of codominance
  • Notice that there are three different alleles (IA, IB, and i), but there are four different phenotypes, because IA and IB are codominant.


Phenotype (blood group)









Colour blindness: An example of sex linkage

  • Unlike the 22 pairs of autosomes, the human sex chromosomes, X and Y are not homologous. The X chromosome is much larger and contains more genes.

Figure 3.1.4d – Human sex chromosomes, X and YFigure 3.1.4d – Human sex chromosomes, X and Y
  • Genes that occur on the X chromosome and not the Y chromosome are called sex-linked, or X-linked, genes.

Figure 3.1.4e – Patterns of inheritance in sex-linked genes are different from those in autosomal genesFigure 3.1.4e – Patterns of inheritance in sex-linked genes are different from those in autosomal genes
  • Red-green colour blindness (Xb) is a recessive sex-linked trait.

  • Males (XbY) who inherit the recessive allele will always show the trait, while females (XBXb) who are heterozygous for the trait are called ‘carriers’.

Genetic diseases can be autosomal or sex-linked

  • Thousands of genetic diseases have been identified in humans but most are very rare.

  • Many genetic diseases are due to recessive alleles, but some are due to dominant or codominant alleles. An example of each is listed in the table below.



Inheritance pattern

Cystic fibrosis

1 in 2000 born with CF in Europe

Autosomal recessive allele (chromosome 7)

Huntington’s disease

1 in 20 000 affected worldwide

Autosomal dominant allele (chromosome 11)

Sickle cell anemia

1 in 10 000 worldwide (most common in people with African/South American ancestry)

Autosomal recessive allele (chromosome 11)


1 in 5000 males

1 in 12 000 females

Sex-linked recessive allele

Mutation rates and cancer
  • Mutation is a natural, random process that affects the structure of DNA.
Figure 3.1.4f – Mutations in the germline cause heritable diseasesFigure 3.1.4f – Mutations in the germline cause heritable diseases
  • Radiation and mutagenic chemicals increase the mutation rate and cause cancer and genetic disease.

  • When mutations occur in germline cells (gametes), it can cause heritable genetic diseases.

Watch Hank Green explain the Gregor Mendel controversy.

Essential idea

Genetic inheritance follows patterns.

Figure 3.1.4g – Gregor MendelFigure 3.1.4g – Gregor Mendel
Gregor Mendel (1822–84) made quantitative measurements with many replicates. He was able to perform statistical tests that helped him to discover mathematical relationships between heritable ‘factors’.

Figure 3.1.4h – Red-green colour blindnessFigure 3.1.4h – Red-green colour blindness
8% of men and 0.5% of women can’t see the butterfly in this picture. Why is red-green colour blindness more prevalent in males?

Food for thought

Are dominant traits more prevalent than recessive traits? Discuss your ideas and then do some research into factors that affect allele frequencies.

Course links

  • Review the role of mutagens and oncogenes in the development of cancer in 1.2.6.
  • Recall that new alleles are formed by mutation in 3.1.1.
  • HL students will learn more about ABO blood groups in 11.1.1.
  • Learn more about colour blindness in 12.2.3.

3.1.5 Genetic modification and biotechnology

Biologists have developed techniques that allow for the artificial manipulation of DNA, cells and organisms.

Polymerase chain reaction

  • The polymerase chain reaction (PCR) is a technology used to amplify small quantities of DNA into large samples that can be further analysed.

Figure 3.1.5a – PCR amplifies small amounts of DNAFigure 3.1.5a – PCR amplifies small amounts of DNA

  • Sequences of DNA are targeted using DNA primers that bind by complementary base pairing to initiate DNA replication.
  • Millions of copies of the targeted DNA sequence can be made within hours.

Gel electrophoresis

  • Gel electrophoresis is used to separate charged molecules (proteins or fragments of DNA) according to their size.
  • The technique uses a gel, immersed in a conducting fluid onto which an electrical field is applied.

Figure 3.1.5b – Gel electrophoresisFigure 3.1.5b – Gel electrophoresis

  • DNA fragments of varying lengths are loaded into wells on the gel at the negative electrode.
  • DNA fragments, being slightly negatively charged, move through the gel towards the positive electrode.
  • Smaller fragments move faster and travel further down the gel than larger fragments.

DNA profiling

  • DNA profiling involves comparing samples of DNA.
  • Every individual has a unique pattern of DNA fragmentation (like a fingerprint), so this technique is useful for forensic investigations, and in cases of unknown paternity.
  • A DNA profile is made by:
    • obtaining a sample of DNA (i.e. from a crime scene)
    • using PCR to amplify the amount of DNA in the sample
    • cutting the DNA into fragments using restriction enzymes that target specific sequences (the resulting fragments will be different lengths)
    • separating the fragments of DNA sample by gel electrophoresis.
    • When samples from different individuals are loaded on the same gel, banding patterns can be compared.

Skill: Analysing DNA profiles

The DNA of two men (F1 and F2) who claim to be the father of a child is compared to the DNA of the mother (M) and the child (C) in the DNA profile below.

Figure 3.1.5c – DNA profiles for determining paternityFigure 3.1.5c – DNA profiles for determining paternity

Source: Griffiths et al, Introduction to Genetic Analysis, 6th edition

  1. Print the profile. Label the negative electrode and the positive electrode.
  2. Circle the longest DNA fragment on the image.
  3. Account for the bands in C by indicating whether the band is common between mother and child, or between father and child.
  4. Determine whether F1 or F2 is the father of C. Explain your choice.
    (Scroll over image for answers.)

Genetic modification

  • Genetic modification, or genetic engineering, involves gene transfer between species.
  • Genes may be transferred to bacterial plasmids, restriction endonucleases and DNA ligase.
  • The bacterial plasmids are then used as vectors to deliver new genes into organisms. Other vectors might be viruses or a recombinant cell.

Figure 3.1.5d – Gene transfer using a plasmid vector in the production of human insulinFigure 3.1.5d – Gene transfer using a plasmid vector in the production of human insulin

  • Restriction endonucleases are enzymes that digest DNA strands at specific sequences, leaving behind single-stranded ‘sticky ends’.

Figure 3.1.5e – Sticky ends bind by complementary base pairingFigure 3.1.5e – Sticky ends bind by complementary base pairing

  • The desired gene is mixed with bacterial plasmids that have been cut with endonucleases. The sticky ends bind by complementary base pairing to the inserted gene. DNA ligase enzyme joins the DNA backbones to produce a recombinant plasmid.
  • The recombinant is cloned in small populations and then on a larger scale to produce the desired gene product.

Figure 3.1.5f – Thermal cyclerFigure 3.1.5f – Thermal cycler
Care must be taken to ensure that samples loaded into a PCR thermal cycler are not contaminated.

Figure 3.1.5g – Industrial fermentation insulinFigure 3.1.5g – Industrial fermentation insulin
Industrial manufacture of insulin at Novo Nordisk, Inc. (Denmark).


The use of DNA evidence in legal cases is well-established. What criteria are necessary for establishing the reliability of evidence?

Figure 3.1.5h – ElectrophoresisFigure 3.1.5h – Electrophoresis
Agarose gels can be used to perform simple electrophoresis in schools.

Figure 3.1.5i – FluorescentFigure 3.1.5i – Fluorescent
DNA is colourless so fluorescent dyes are used to detect DNA in electrophoresis.

Course links

  • More information on PCR and plasmid gene transfer for the production of human insulin is available in 2.2.7.
  • HL: Details on the specific sequences used in DNA profiling and the role of electrophoresis in genetic sequencing are in 7.2.1.