IMAT Biology · Free notes

Microorganisms and Biotechnology: Microbes, Viruses and Gene Technology

Microorganisms and Biotechnology has 19 past questions since 2011, and the ministry papers from 2023 on have asked 5 of them. Almost all of them test recall: one fact about a bacterial cell or a virus, or which enzyme does which job, often in a 'which statements are correct' format. The ministry papers have so far kept to single facts about prokaryotic cells and the enzymes of gene technology. The few calculations (fragments of a cut plasmid, doubling of bacteria and of PCR copies) are short but trap-laden: a circle cut n times gives n pieces, and growth multiplies by powers of two.

The handout has every subtopic, worked example, formula and trap with answers shown. The formula sheet is the chapter’s formulas and traps alone, on one page.

IMAT home All formulas on one page

Subtopic notes

Formula & revision sheet

4 formulas · 19 reference tables · 30 gotchas across all subtopics — the exam-eve cheat-sheet

Bacteria: Structure, Growth and Gene Transfer

Formulas (1)

Binary fission and the bacterial growth curve · Number of bacteria after n doublings $N = N_0 \times 2^{n} \qquad n = \frac{t}{t_d}$

Reference tables (3)

The prokaryotic cell and its structures8 rows

Structure	What it is	Job
Nucleoid	Region holding the circular chromosome, no membrane around it	Carries the genes the cell needs to live
Plasmid	Small circle of DNA, copied independently of the chromosome	Extra genes, for example antibiotic resistance; can pass to other bacteria
Ribosomes (70S)	rRNA and protein, free in the cytoplasm	Protein synthesis (translation)
Cell wall	Peptidoglycan (murein): sugars cross-linked by short peptides	Keeps the shape and stops the cell bursting by osmosis
Capsule (slime layer)	Polysaccharide layer outside the wall, in some species	Protects from drying and from being engulfed by white cells
Flagellum	Long protein filament turned by a motor in the membrane	Movement (swimming)
Pili and fimbriae	Short, thin protein hairs	Sticking to surfaces and cells; the sex pilus links two cells in conjugation
Endospore (some species)	Tough dormant form with a thick coat	Survives heat and drying; it is not a way of reproducing

Every bacterium has a membrane, cytoplasm, ribosomes and a nucleoid; capsule, flagella, pili, plasmids and spores are found only in some.

Gram staining and bacterial shapes6 rows

Feature	Gram-positive	Gram-negative
Peptidoglycan layer	Thick	Thin
Outer membrane (with lipopolysaccharide)	Absent	Present, outside the thin wall
After the alcohol wash	Keeps the crystal violet	Loses the crystal violet
Colour seen	Purple	Pink or red
Examples	Staphylococcus, Streptococcus, Bacillus, Clostridium	E. coli, Salmonella, Vibrio cholerae, Neisseria
Penicillin	Usually more sensitive	Usually less sensitive: the outer membrane keeps many drugs out

Plasmids and bacterial gene transfer4 rows

Process	How the DNA moves	What it needs
Transformation	A cell takes up naked DNA directly from its surroundings, for example from a dead cell	A competent cell; no contact with another cell, no virus
Transduction	A bacteriophage carries a piece of bacterial DNA from one bacterium to the next	A virus as the carrier
Conjugation	DNA, usually a plasmid copy, passes from a donor to a recipient through a sex pilus	Direct contact between two living cells
Binary fission	A full copy of the DNA goes to each daughter cell	Cell division (this is vertical transfer)

Watch out for (6)

Circular DNA is not only in prokaryotes
→ The prokaryotic cell and its structures
Prokaryotic DNA has no chromatin, introns or meiosis
→ The prokaryotic cell and its structures
Flagella move the cell; pili attach it
→ The prokaryotic cell and its structures
Gram-negative does not mean no wall
→ Gram staining and bacterial shapes
Bacterial growth multiplies, it does not add
→ Binary fission and the bacterial growth curve
A transformed bacterium has taken up foreign DNA
→ Plasmids and bacterial gene transfer

Viruses: Structure, Life Cycles and HIV

Reference tables (3)

Virus structure: genome, capsid and envelope4 rows

Part	Made of	Building blocks and bonds
Genome (DNA or RNA)	Nucleic acid, single- or double-stranded	Nucleotides joined by phosphodiester bonds; bases (A, G, C, and T or U)
Capsid	Protein subunits (capsomeres)	Amino acids joined by peptide bonds
Envelope (some viruses only)	Phospholipid bilayer from the host, with viral glycoproteins	Fatty acids and glycerol in the lipids; peptide bonds in the proteins
Viral enzymes (some viruses)	Proteins carried inside the capsid, such as reverse transcriptase	Amino acids joined by peptide bonds

Lytic and lysogenic cycles of a bacteriophage4 rows

Stage	Lytic cycle	Lysogenic cycle
Viral DNA after entry	Stays separate and is used straight away	Inserted into the host chromosome as a prophage
Host cell meanwhile	Makes viral DNA and proteins, not its own	Lives and divides normally, copying the prophage each time
New virus particles	Many, assembled inside the cell	None while the prophage stays dormant
End of the cycle	Lysis: the cell bursts and dies	Induction by a trigger, then the lytic cycle

Retroviruses and HIV6 rows

Part of HIV	Made of	Role
Genome	Two copies of single-stranded RNA	Carries the viral genes
Reverse transcriptase	Enzyme (protein)	Copies the RNA genome into DNA
Integrase	Enzyme (protein)	Inserts the viral DNA into a host chromosome
Protease	Enzyme (protein)	Cuts long viral proteins into working pieces
Capsid	Protein	Encloses the RNA and the enzymes
Envelope	Phospholipid bilayer from the host, with glycoproteins gp120 and gp41	Attachment to CD4 and fusion with the host cell

HIV has no ribosomes, no cytoplasm and no DNA in the particle itself.

Watch out for (5)

The envelope is lipid, the capsid is protein
→ Virus structure: genome, capsid and envelope
Viral nucleic acid comes in every form
→ Virus structure: genome, capsid and envelope
Lysogenic does not mean harmless for ever
→ Lytic and lysogenic cycles of a bacteriophage
The HIV particle contains RNA, not DNA
→ Retroviruses and HIV
HIV and AIDS are not the same thing
→ Retroviruses and HIV

Fungi, Protists, Pathogens, Antibiotics and Vaccines

Reference tables (4)

Fungi and protists in outline4 rows

Group	Cells and wall	Nutrition	Examples
Yeasts (fungi)	Single eukaryotic cells, chitin wall	Heterotrophic; respire aerobically or ferment	Saccharomyces cerevisiae (baker's yeast), Candida
Moulds and mushrooms (fungi)	Hyphae forming a mycelium, chitin walls	Saprotrophic or parasitic	Penicillium, Rhizopus (bread mould), field mushrooms
Protozoa (protists)	Single eukaryotic cells, no wall	Heterotrophic, take in food	Amoeba, Paramecium, Plasmodium, Trypanosoma
Algae (protists)	Single or many cells, usually cellulose walls	Photosynthetic (autotrophic)	Chlamydomonas, diatoms, seaweeds

Pathogens and the diseases they cause7 rows

Disease	Pathogen	Type	How it spreads
Tuberculosis	Mycobacterium tuberculosis	Bacterium	Airborne droplets
Cholera	Vibrio cholerae	Bacterium	Contaminated water
Influenza	Influenza virus	RNA virus	Airborne droplets
COVID-19	SARS-CoV-2	RNA virus (coronavirus)	Droplets and aerosols
AIDS	HIV	Retrovirus	Blood, sex, mother to baby
Malaria	Plasmodium	Protist	Bite of an infected female Anopheles mosquito
Athlete's foot, ringworm	Several skin fungi	Fungus	Direct contact, shared surfaces

Antibiotics and antibiotic resistance4 rows

Antibiotic	Target in the bacterium	Why human cells are spared
Penicillin and other β-lactams	Block cross-linking of peptidoglycan as the wall is built; the cell bursts by osmosis	Human cells have no cell wall
Tetracycline, streptomycin, erythromycin	Bind 70S ribosomes and block protein synthesis	Human cytoplasm has 80S ribosomes
Ciprofloxacin (quinolones)	Block DNA gyrase, so DNA cannot be copied	Human enzymes of this kind are different
Sulfonamides	Block the bacterium's synthesis of folic acid	Humans take folic acid from food

Vaccines and types of immunity5 rows

Vaccine type	What it contains	Examples
Live attenuated	A weakened living pathogen	Measles, mumps and rubella (MMR); oral polio
Inactivated	Killed pathogen	Injected polio, most flu vaccines
Toxoid	A bacterial toxin made harmless	Tetanus, diphtheria
Subunit (recombinant)	One purified antigen, often made by genetically modified yeast	Hepatitis B, HPV
mRNA	mRNA coding for one viral protein, inside lipid droplets	The first COVID-19 vaccines (2020)

Watch out for (4)

Fungi are not plants, and yeast is not a prokaryote
→ Fungi and protists in outline
The mosquito is the vector, not the cause, of malaria
→ Pathogens and the diseases they cause
Antibiotics select resistance; they do not cause it
→ Antibiotics and antibiotic resistance
Passive immunity has no memory
→ Vaccines and types of immunity

Recombinant DNA: Cutting, Joining and Cloning Genes

Formulas (1)

Restriction enzymes, sticky ends and counting fragments · Fragments from n cuts $\text{linear DNA: } n + 1 \text{ fragments} \qquad \text{circular DNA: } n \text{ fragments}$

Reference tables (2)

Ligase, reverse transcriptase and vectors7 rows

Tool	What it does	Point to remember
Restriction enzyme	Cuts DNA at a specific sequence	Breaks phosphodiester bonds; same enzyme gives matching sticky ends
DNA ligase	Joins DNA fragments	Forms phosphodiester bonds; uses ATP
Reverse transcriptase	Makes cDNA from an mRNA template	From retroviruses; the cDNA has no introns
Plasmid vector	Carries a gene into bacteria	Origin of replication, marker genes, restriction sites
Ti plasmid of Agrobacterium tumefaciens	Carries a gene into plant cells	The bacterium supplies the vector; in nature its genes make plant cells divide
Viral vector	Carries a gene into animal or human cells	Modified so that it cannot multiply
Liposome	Lipid sphere that fuses with the cell membrane	Non-viral vector, used in gene therapy

Making and selecting a recombinant organism6 rows

Step	What is done	Tool
1. Obtain the gene	Cut it out of DNA, make it as cDNA from mRNA, or copy it by PCR	Restriction enzyme, reverse transcriptase or PCR
2. Open the vector	Cut the plasmid with the same restriction enzyme	Same enzyme, so the sticky ends match
3. Join	Mix gene and plasmid; sticky ends pair; seal the backbone	DNA ligase
4. Insert into the host	Bacteria take up the plasmid (transformation)	Heat shock in calcium chloride, or electroporation
5. Select	Grow on a medium where only cells with the recombinant plasmid survive or show a colour	Marker genes
6. Use	Grow the chosen bacteria in a fermenter, or deliver the checked plasmid to plant or animal cells	Fermenter; Agrobacterium or other vector

Steps 1 and 2 can be done in either order; joining must come after both, and selection after insertion into the host.

Watch out for (6)

Restriction enzymes break phosphodiester bonds
→ Restriction enzymes, sticky ends and counting fragments
Restriction enzymes are endonucleases, which are hydrolases
→ Restriction enzymes, sticky ends and counting fragments
A circle with n cuts gives n pieces
→ Restriction enzymes, sticky ends and counting fragments
Ligase makes phosphodiester bonds, not hydrogen bonds
→ Ligase, reverse transcriptase and vectors
A transformed cell is not necessarily recombinant
→ Making and selecting a recombinant organism
Join before you insert
→ Making and selecting a recombinant organism

PCR, Gel Electrophoresis, Probes and Sequencing

Formulas (2)

The polymerase chain reaction (PCR) · Copies after n cycles (ideal) $N = N_0 \times 2^{n}$
Complementary base pairing, probes and microarrays · Base pairing $A \leftrightarrow T \quad (\text{RNA: } A \leftrightarrow U) \qquad G \leftrightarrow C$

Reference tables (2)

Gel electrophoresis and DNA profiling5 rows

Feature	What happens	Why
Direction of movement	Towards the positive electrode	Phosphate groups make DNA negative
Distance travelled	Short fragments travel furthest	The gel slows long molecules more
Fragment nearest the wells	The largest one	It is held back most by the gel
Size of an unknown band	Read against the DNA ladder	Same gel, same conditions
Child in a paternity test	Each band matches the mother or the father	Half of each person's DNA comes from each parent

DNA sequencing in outline4 rows

Method or project	Key idea	What to remember
Sanger sequencing	Chain termination by ddNTPs	ddNTPs lack the 3'-OH; fragments sorted by size
Next-generation sequencing	Millions of fragments read at the same time	Whole genomes quickly and cheaply
Human Genome Project	First full human genome sequence, 2003	About 3 billion base pairs, about 20,000 protein-coding genes
Bioinformatics	Computers store and compare sequences	Finds genes, mutations and relationships between species

Watch out for (4)

PCR needs no helicase, and its primers are DNA
→ The polymerase chain reaction (PCR)
DNA runs to the positive electrode, smallest first
→ Gel electrophoresis and DNA profiling
A DNA probe or sticky end contains T, never U
→ Complementary base pairing, probes and microarrays
Sanger sequencing reads the new strand
→ DNA sequencing in outline

GM Organisms, Gene Therapy, Stem Cells, Cloning and CRISPR

Reference tables (5)

Genetically modified organisms and their products6 rows

Product or organism	Gene added	Host	Purpose
Human insulin	Human insulin gene (as cDNA)	E. coli or yeast	Treat type 1 diabetes
Bt cotton, Bt maize	Toxin gene from the bacterium Bacillus thuringiensis	Plant, using Agrobacterium	Kills insect larvae that eat the crop
Golden Rice	Genes for making β-carotene	Rice	Reduces vitamin A deficiency
Herbicide-tolerant soya	A bacterial gene the herbicide cannot block	Soya	Weeds can be sprayed without harming the crop
Hepatitis B vaccine	Gene for a viral surface protein	Yeast	A safe vaccine antigen
Transgenic goats	Human antithrombin gene, active in the udder	Goat	A human medicine collected from the milk

Gene therapy: somatic and germline4 rows

Feature	Somatic gene therapy	Germline gene therapy
Cells changed	Body cells, such as airway or blood cells	Eggs, sperm or early embryo
Passed to children	No	Yes
How long it lasts	Only as long as the treated cells live	Every cell of the new person carries it
Status	Approved treatments exist	Banned in most countries

Stem cells and potency4 rows

Potency	Can become	Examples
Totipotent	Every cell type, including the placenta	The zygote and the cells of the first few divisions
Pluripotent	Any cell of the body, but not the placenta	Embryonic stem cells from the inner cell mass; iPS cells
Multipotent	Several cell types of one family	Bone marrow stem cells, which make all blood cells
Unipotent	Only one cell type	Muscle satellite cells, which make muscle fibres

Cloning: natural, plant and animal5 rows

Type of cloning	How it is done	Example
Natural cloning	Asexual reproduction, or splitting of an early embryo	Bacteria, strawberry runners, identical twins
Plant cloning	Cuttings, or tissue culture of small pieces of tissue	Mass production of identical crop plants
Reproductive cloning (SCNT)	Body-cell nucleus into an enucleated egg; embryo into a surrogate	Dolly the sheep, 1996
Therapeutic cloning	SCNT embryo grown only to a blastocyst	Embryonic stem cells matched to a patient
Gene cloning	Many copies of one gene made in bacteria or by PCR	Bacteria carrying a recombinant plasmid

CRISPR-Cas9 gene editing in outline5 rows

Component	What it is	Job
Cas9	A nuclease enzyme (protein)	Cuts both strands of the target DNA
Guide RNA	About 20 nucleotides matching the target	Leads Cas9 to the right place by base pairing
PAM	A short DNA sequence beside the target	Must be present for Cas9 to cut
End-joining repair	The cell rejoins the cut ends, often imperfectly	Small insertions or deletions knock the gene out
Template repair	The cell copies a DNA template supplied with Cas9	A precise change or an inserted sequence

Watch out for (5)

Transgenic DNA can cross any kingdom
→ Genetically modified organisms and their products
The added allele is dominant, and it fades with the cells
→ Gene therapy: somatic and germline
Pluripotent is one step below totipotent
→ Stem cells and potency
A clone is not a perfect copy of the nucleus donor
→ Cloning: natural, plant and animal
The guide RNA aims; Cas9 cuts
→ CRISPR-Cas9 gene editing in outline

PYQ weightage by concept

23 concepts · 0 PYQs — where the marks actually sit, so you know what to drill first

Bacteria: Structure, Growth and Gene Transfer0 PYQs · 0%

Concept	PYQs	Share
The prokaryotic cell and its structuresfoundation	—	—
Gram staining and bacterial shapesfoundation	—	—
Binary fission and the bacterial growth curvefoundation	—	—
Plasmids and bacterial gene transferfoundation	—	—

Viruses: Structure, Life Cycles and HIV0 PYQs · 0%

Concept	PYQs	Share
Virus structure: genome, capsid and envelopefoundation	—	—
Lytic and lysogenic cycles of a bacteriophagefoundation	—	—
Retroviruses and HIVfoundation	—	—

Fungi, Protists, Pathogens, Antibiotics and Vaccines0 PYQs · 0%

Concept	PYQs	Share
Fungi and protists in outlinefoundation	—	—
Pathogens and the diseases they causefoundation	—	—
Antibiotics and antibiotic resistancefoundation	—	—
Vaccines and types of immunityfoundation	—	—

Recombinant DNA: Cutting, Joining and Cloning Genes0 PYQs · 0%

Concept	PYQs	Share
Restriction enzymes, sticky ends and counting fragmentsfoundation	—	—
Ligase, reverse transcriptase and vectorsfoundation	—	—
Making and selecting a recombinant organismfoundation	—	—

PCR, Gel Electrophoresis, Probes and Sequencing0 PYQs · 0%

Concept	PYQs	Share
The polymerase chain reaction (PCR)foundation	—	—
Gel electrophoresis and DNA profilingfoundation	—	—
Complementary base pairing, probes and microarraysfoundation	—	—
DNA sequencing in outlinefoundation	—	—

GM Organisms, Gene Therapy, Stem Cells, Cloning and CRISPR0 PYQs · 0%

Concept	PYQs	Share
Genetically modified organisms and their productsfoundation	—	—
Gene therapy: somatic and germlinefoundation	—	—
Stem cells and potencyfoundation	—	—
Cloning: natural, plant and animalfoundation	—	—
CRISPR-Cas9 gene editing in outlinefoundation	—	—