IMAT Biology · Formula sheet
Microorganisms and Biotechnology formulas
4 formulas, 19 reference tables and 30 common traps for IMAT Biology Microorganisms and Biotechnology, grouped by subtopic.
Bacteria: Structure, Growth and Gene Transfer
Learn this subtopic in the notesBinary fission and the bacterial growth curve
Number of bacteria after n doublings
- number of cells at the start
- number of cells after time t
- number of generations (doublings)
- doubling (generation) time, in the same units as t
The prokaryotic cell and its structures
| 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 shapes
| 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 transfer
| 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) |
Common traps
Circular DNA is not only in prokaryotes
Mitochondria and chloroplasts carry their own circular DNA, and yeast often carries a small circular plasmid too. So a human, plant or yeast cell also contains circular DNA. What only prokaryotes have is a circular main chromosome lying free in the cytoplasm.
Prokaryotic DNA has no chromatin, introns or meiosis
Any feature borrowed from our own nuclei describes a eukaryote, not a bacterium. Bacterial DNA is circular, lies in the cytoplasm, is not packed on histones into chromatin, mostly lacks introns, and is shared out by binary fission.
Flagella move the cell; pili attach it
The flagellum is for movement and nothing else. Sticking to surfaces and joining to another cell for conjugation are jobs of the pili.
Gram-negative does not mean no wall
Gram-negative bacteria still have a peptidoglycan wall; it is just thin, with an outer membrane around it. Their extra outer membrane makes them harder for many antibiotics to enter, not easier.
Bacterial growth multiplies, it does not add
After n generations the population is times bigger, not n times bigger. Eight doublings give 256 times the starting number, not 8 times. Also count generations, not hours: with a 30 minute doubling time, 4 hours is 8 generations.
A transformed bacterium has taken up foreign DNA
In bacteria, transformation means a cell has taken up DNA from its surroundings and now carries the new genes. It needs no virus and no contact with another cell. It is not a mutation, which changes the cell's own DNA. (In animal cell biology, transformation can also mean a cell becoming cancerous, a different use of the word.)
Viruses: Structure, Life Cycles and HIV
Learn this subtopic in the notesVirus structure: genome, capsid and envelope
| 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 bacteriophage
| 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 HIV
| 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.
Common traps
The envelope is lipid, the capsid is protein
An enveloped virus is wrapped in a phospholipid bilayer, so its envelope contains fatty acids (plus glycoproteins). The capsid is protein, made of amino acids. Glycogen and other polysaccharides are not structural parts of either, and phosphodiester bonds belong to the genome.
Viral nucleic acid comes in every form
Viruses can carry double-stranded DNA, single-stranded DNA, double-stranded RNA or single-stranded RNA. An option saying viruses contain only RNA, or only double-stranded DNA, is wrong. What is true is that one particle carries one kind of nucleic acid, not both.
Lysogenic does not mean harmless for ever
During lysogeny the host is not killed and keeps dividing, but the prophage can be induced at any time to start the lytic cycle and burst the cell. The two cycles are two routes of the same virus, not two kinds of virus.
The HIV particle contains RNA, not DNA
HIV's genome is RNA. DNA is made from it only after infection, inside the host cell. So DNA is not a component of the virus particle, but RNA, phospholipids (in the envelope) and reverse transcriptase are.
HIV and AIDS are not the same thing
HIV is the virus. AIDS is the late stage of the disease, when so many helper T cells are lost that opportunistic infections take hold. A person can carry HIV for years without having AIDS, especially with treatment.
Fungi, Protists, Pathogens, Antibiotics and Vaccines
Learn this subtopic in the notesFungi and protists in outline
| 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 cause
| 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 resistance
| 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 immunity
| 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) |
Common traps
Fungi are not plants, and yeast is not a prokaryote
Fungi have walls but no chlorophyll; the wall is chitin and the stored sugar is glycogen. Yeast is a single cell, but it is a eukaryote with a nucleus, mitochondria and 80S ribosomes.
The mosquito is the vector, not the cause, of malaria
Malaria is caused by the protist Plasmodium. The Anopheles mosquito only carries it. Malaria is not caused by a bacterium or a virus, so antibiotics against bacteria are not the treatment; antimalarial drugs are.
Antibiotics select resistance; they do not cause it
The resistance allele already exists by random mutation. The antibiotic removes the competitors, so the resistant bacteria take over. Options saying the bacteria 'adapt', 'become immune' or are made to mutate by the drug are wrong, and so is any option where the patient becomes resistant.
Passive immunity has no memory
Received antibodies work at once but are gone within weeks or months, and they leave no memory cells. Only active immunity, after infection or a vaccine, produces memory cells and lasting protection.
Recombinant DNA: Cutting, Joining and Cloning Genes
Learn this subtopic in the notesRestriction enzymes, sticky ends and counting fragments
Fragments from n cuts
- number of cut sites (at least 1)
Ligase, reverse transcriptase and vectors
| 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 organism
| 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.
Common traps
Restriction enzymes break phosphodiester bonds
The cut goes through the sugar-phosphate backbone, so the bonds broken are phosphodiester bonds. The few hydrogen bonds between the bases of a staggered cut simply come apart on their own. An enzyme that only broke hydrogen bonds would separate the strands without cutting anything.
Restriction enzymes are endonucleases, which are hydrolases
The six enzyme classes are oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases. A restriction enzyme hydrolyses bonds inside the DNA chain, so it is an endonuclease, one kind of hydrolase. Ligase is the enzyme that joins DNA, the opposite job.
A circle with n cuts gives n pieces
Do not add the extra piece you would get on a straight molecule, and do not forget the piece that crosses the plasmid's starting point. The sizes must add up to the plasmid's full length.
Ligase makes phosphodiester bonds, not hydrogen bonds
Complementary sticky ends find each other and pair by hydrogen bonds without any enzyme. Ligase then forms the phosphodiester bonds that close the backbone. Options saying ligase forms hydrogen bonds, or breaks phosphodiester bonds, swap the jobs.
A transformed cell is not necessarily recombinant
A bacterium that has taken up a plasmid is transformed, but the plasmid may have closed up without the gene. That is why a second, screening step (such as blue and white colonies) is needed after the antibiotic selects for any plasmid.
Join before you insert
Ligation happens in the test tube, before the plasmid goes into the host, and the recombinant plasmid is checked before it is used to modify a plant or animal. An order that puts ligase after insertion into the host, or selection before the cutting, is wrong.
PCR, Gel Electrophoresis, Probes and Sequencing
Learn this subtopic in the notesThe polymerase chain reaction (PCR)
Copies after n cycles (ideal)
- number of double-stranded copies at the start
- number of cycles
- number of copies after n cycles
Complementary base pairing, probes and microarrays
Base pairing
Gel electrophoresis and DNA profiling
| 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 outline
| 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 |
Common traps
PCR needs no helicase, and its primers are DNA
In PCR, heat separates the strands, so no helicase is added. The primers are short pieces of DNA made in the laboratory, whereas in a living cell the primers for replication are RNA made by primase. And annealing, not extension, is the lowest temperature in the cycle.
DNA runs to the positive electrode, smallest first
DNA is negative, so it moves to the anode (positive), away from the wells at the cathode. The shortest fragments go furthest. Options with DNA moving to the negative electrode, or large fragments moving fastest, are wrong.
A DNA probe or sticky end contains T, never U
Uracil is found only in RNA. When asked for the bases of a DNA sticky end or a DNA probe, any answer containing U is wrong, even if the pairing is otherwise right. Work out each base by pairing with the opposite strand: A with T, G with C.
Sanger sequencing reads the new strand
The labelled fragments are copies made against the template, so the colours give the complementary strand. To get the template sequence, pair each base back.
GM Organisms, Gene Therapy, Stem Cells, Cloning and CRISPR
Learn this subtopic in the notesGenetically modified organisms and their products
| 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 germline
| 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 potency
| 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 animal
| 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 outline
| 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 |
Common traps
Transgenic DNA can cross any kingdom
There is no rule limiting gene transfer to related species. Invertebrate genes in mammals, bacterial genes in plants and plant genes in animals have all been made. Options that allow only one direction, or only prokaryote to eukaryote, are wrong.
The added allele is dominant, and it fades with the cells
The working allele added in gene therapy is the dominant one, which is why one copy helps. The effect is short-lived because treated cells are replaced by new ones made from untreated stem cells, not because genes break down on their own in a cell.
Pluripotent is one step below totipotent
Only the zygote and the cells of the first few divisions are totipotent: they can also form the placenta. Embryonic stem cells from the inner cell mass are pluripotent: any body cell, but not the placenta.
A clone is not a perfect copy of the nucleus donor
A cloned animal has the donor's nuclear DNA but the egg donor's mitochondrial DNA, and it grows up in a different environment. So it can differ from the donor in small ways, including its appearance and behaviour. The surrogate mother gives it no DNA at all.
The guide RNA aims; Cas9 cuts
Apart from needing a short PAM beside the target, Cas9 has no fixed target sequence, unlike a restriction enzyme. The guide RNA chooses the site by base pairing, so one Cas9 can be sent to almost any gene just by changing the guide.