BIO1337 Microbiology

Bacterial genomes are ________ compared to eukaryotes, the genes are ________ packed, there are no ________, genes with related functions are grouped together in ________, and the genomes couple ________ and translation

Bacterial genomes are small compared to eukaryotes, the genes are densely packed, there are no introns, genes with related functions are grouped together in operons, and the genomes couple transcription and translation

Bi-directional replication occurs during ________ and during replication of some ________

Bi-directional replication occurs during cell division and during replication of some plasmids

Rolling circle replication occurs during replication of some ________ and during ________

Rolling circle replication occurs during replication of some plasmids and during conjugation

Transformation: 1. DNA binds to a ________ on the recipient cell 2. ________ is taken up by the recipient cell 3. RecA-mediated ________ allows free DNA to integrate into the recipient cell

Transformation: 1. DNA binds to a DNA-binding protein on the recipient cell 2. Single-stranded DNA is taken up by the recipient cell 3. RecA-mediated homologous recombination allows free DNA to integrate into the recipient cell

In generalised transduction ________ from any part of the donor can be transferred

In generalised transduction donor DNA from any part of the donor can be transferred

In specialised transduction a specific ________ of the donor is transferred, this can ________ in the recipient cell, the bacterial gene is transferred during release from the ________ cycle

In specialised transduction a specific DNA region of the donor is transferred, this can replicate in the recipient cell, the bacterial gene is transferred during release from the lysogenic cycle

Generalised transduction: 1. A phage attaches to a ________ on a bacterial cell 2. ________ is released into the cell 3. Phage DNA ________ and breaks down the host DNA 4. The ________ is formed inside the cell, some containing the ________ 5. The cell ________ releasing normal phage and ________ - phage that contain host DNA 6. The transducing particle attaches to a receptor on a ________ 7. ________ DNA is inserted into the cell 8. This DNA inserts into the recipient cell’s ________ by homologous recombination

Generalised transduction: 1. A phage attaches to a receptor on a bacterial cell 2. Phage DNA is released into the cell 3. Phage DNA replicates and breaks down the host DNA 4. The phage is formed inside the cell, some containing the host DNA 5. The cell lyses releasing normal phage and transducing particles - phage that contain host DNA 6. The transducing particle attaches to a receptor on a recipient cell 7. Transduced DNA is inserted into the cell 8. This DNA inserts into the recipient cell’s plasmid by homologous recombination

Specialised transduction (normal event): 1. Phage DNA circularises and ________ from host DNA 2. This phage DNA ________ 3. Phage synthesis is completed 4. The cell ________ and releases normal phage

Specialised transduction (normal event): 1. Phage DNA circularises and detaches from host DNA 2. This phage DNA replicates 3. Phage synthesis is completed 4. The cell lyses and releases normal phage

Specialised transduction (rare event): 1. A portion of host DNA is ________ for phage DNA 2. This defective phage is ________ 3. Phage synthesis is completed 4. Cell ________ and releases defective phage that can ________ genes

Specialised transduction (rare event): 1. A portion of host DNA is exchanged for phage DNA 2. This defective phage is replicated 3. Phage synthesis is completed 4. Cell lyses and releases defective phage that can transduce genes

Conjugation involves ________ contact, it is a ________ encoded mechanism, it requires ________, it is an example of ________ replication that is initiated by the enzyme ________

Conjugation involves cell-cell contact, it is a plasmid encoded mechanism, it requires DNA synthesis, it is an example of rolling circle replication that is initiated by the enzyme Tral

Presence of F plasmids leads to an ability to synthesise the ________, it causes the ________ of DNA for transfer to another cell, and alters ________ receptors

Presence of F plasmids leads to an ability to synthesise the F pilus, it causes the mobilisation of DNA for transfer to another cell, and alters cell surface receptors

Conjugation of F plasmids: 1. An F+ cell attaches it’s ________ to an F- cell 2. The pilus ________ 3. The cell pairs ________ and the F plasmid is nicked in one strand 4. This strand is transferred from the ________ to the F- cell and the ________ is simultaneously replicates in the F+ cell 5. The synthesis of a ________ begins in the recipient cell 6. There is the completion of DNA transfer and ________ and the cells separate

Conjugation of F plasmids: 1. An F+ cell attaches it’s pilus to an F- cell 2. The pilus retracts 3. The cell pairs stabilise and the F plasmid is nicked in one strand 4. This strand is transferred from the F+ cell to the F- cell and the F plasmid simultaneously replicates in the F+ cell 5. The synthesis of a complementary strand begins in the recipient cell 6. There is the completion of DNA transfer and synthesis and the cells separate

Cells with an integrated F plasmid are known as ________

Cells with an integrated F plasmid are known as Hfr

Conjugation of a Hfr cell: 1. The Hfr attaches it’s ________ to an F- cell 2. The pilus ________ 3. The cell pairs stabilise and the ________ is nicked in one strand 4. There is the transfer of ________ followed by chromosomal DNA 5. A second strand is ________ in the recipient cell

Conjugation of a Hfr cell: 1. The Hfr attaches it’s pilus to an F- cell 2. The pilus retracts 3. The cell pairs stabilise and the integrated F plasmid is nicked in one strand 4. There is the transfer of F followed by chromosomal DNA 5. A second strand is synthesised in the recipient cell

Abiogenesis is the idea of ________ generation

Abiogenesis is the idea of spontaneous generation

Spontaneous generation is where ________ organisms can originate from non-living ________

Spontaneous generation is where living organisms can originate from non-living matter

Pasteur’s experiment to disprove ________: 1. Placed a bacterial broth in two ________ flasks 2. The flasks were heated to boil and then ________ which allowed dusk particles to get ________ in the swan-neck 3. One of the flasks was ________, this flask grew ________ whilst the other remained sterile

Pasteur’s experiment to disprove spontaneous generation: 1. Placed a bacterial broth in two swan-necked flasks 2. The flasks were heated to boil and then cooled which allowed dusk particles to get trapped in the swan-neck 3. One of the flasks was tipped, this flask grew microbes whilst the other remained sterile

Koch’s postulates: 1. The suspected ________ organism must always be present in animals suffering from the ________ and should not be present in healthy individuals 2. The organisms must be cultivated in ________ away from the animal body 3. Cells from a pure culture of the suspected organism should cause ________ in a healthy animal 4. The organism should be ________ and shown to be the same as the original

Koch’s postulates: 1. The suspected pathogenic organism must always be present in animals suffering from the disease and should not be present in healthy individuals 2. The organisms must be cultivated in pure culture away from the animal body 3. Cells from a pure culture of the suspected organism should cause disease in a healthy animal 4. The organism should be re-isolated and shown to be the same as the original

With Koch’s postulates it is not always possible to ________ all postulates for every infected ________, and animal models are not always ________

With Koch’s postulates it is not always possible to satisfy all postulates for every infected disease, and animal models are not always available

Robert Hooke invented the ________ microscope

Robert Hooke invented the compound microscope

Antonie van Leeuwenhoek invented the ________ microscope

Antonie van Leeuwenhoek invented the simple microscope

Martinus Beijerinck isolated the N2-fixing bacterium ________

Martinus Beijerinck isolated the N2-fixing bacterium Azotobacter

Alexander Fleming discovered that ________ prevented growth of Staphylococcus aureus

Alexander Fleming discovered that Penicillium notatum prevented growth of Staphylococcus aureus

Edward Jenner’s discovery of vaccines: 1. In 1788 an epidemic of ________ hit Gloucestershire 2. Jenner noted that milkmaids with ________ did not become infected 3. Jenner took material from ________ of milkmaids and inoculated a child

Edward Jenner’s discovery of vaccines: 1. In 1788 an epidemic of smallpox hit Gloucestershire 2. Jenner notes that milkmaids with cowpox did not become infected 3. Jenner took material from pustules of milkmaids and inoculated a child

Classification of microorganisms: 1. DNA is ________ 2. PCR is used to ________ the DNA 3. The sequence of DNA is analysed to generate the ________ tree

Classification of microorganisms: 1. DNA is isolated 2. PCR is used to amplify the DNA 3. The sequence of DNA is analysed to generate the phylogenetic tree

Microorganisms are classified into ________ and prokaryotes, prokaryotes are further divided into bacteria and ________

Microorganisms are classified into eukaryotes and prokaryotes, prokaryotes are further divided into bacteria and archaea

The most common bacteria are classified into ________, gram +ve bacteria, and cyanobacteria

The most common bacteria are classified into proteobacteria, gram +ve bacteria, and cyanobacteria

Normal microbial flora are ________ usually found associated with human body ________

Normal microbial flora are microorganisms usually found associated with human body tissues

Microbial pathogenicity is the ________ mechanisms whereby microorganisms cause ________

Microbial pathogenicity is the biochemical mechanisms whereby microorganisms cause disease

Pathogenicity is an observation of ________ a disease is caused

Pathogenicity is an observation of how a disease is caused

An ________ is a successful persistence or multiplication of a pathogen on or within the ________

An infection is a successful persistence or multiplication of a pathogen on or within the host

A disease is an interaction which causes significant ________ to the host

A disease is an interaction which causes significant damage to the host

Process of infection: 1. Exposure to ________ 2. Adherence to skin or ________ 3. Invasion through ________ 4. Multiplication of ________ and toxins

Process of infection: 1. Exposure to pathogens 2. Adherence to skin or mucosa 3. Invasion through epithelium 4. Multiplication of virulence factors and toxins

Process of disease: 1. Toxin effects are ________ or systemic 2. Further growth at original and ________ sites 3. Tissue or ________ damage

Process of disease: 1. Toxin effects are local or systemic 2. Further growth at original and distant sites 3. Tissue or systemic damage

A disease with low virulence doesn’t cause a ________

A disease with low virulence doesn’t cause a major disease

Factors that influence the severity of the disease: Host, ________ or physiological status, ________ makeup, route of ________, and dose

Factors that influence the severity of the disease: Host, immunological or physiological status, genetic makeup, route of infection, and dose

A pathogen has to: Colonise ________ tissues, ________ within host tissues, avoid host ________, and cause damage to the ________

A pathogen has to: Colonise host tissues, grow within host tissues, avoid host defence mechanisms, and cause damage to the host

How pathogens damage their host: They produce ________ which damage host tissues, and they evoke profound ________ which cause disease

How pathogens damage their host: They produce effectors which damage host tissues, and they evoke profound immune responses which cause disease

Neurotoxins cause ________

Neurotoxins cause paralysis

Enterotoxins cause sickness and ________

Enterotoxins cause sickness and diarrhoea

Cytotoxins cause ________

Cytotoxins cause cell death

AB toxins: B portion binds to ________ and facilitates translocation of A portion which possesses ________

AB toxins: B portion binds to cell and facilitates translocation of A portion which possesses catalytic activity

Cytolytic toxins damage ________ membrane

Cytolytic toxins damage cytoplasmic membrane

An endotoxin is a ________

An endotoxin is a pyrogen

An endotoxin causes the production of ________ from immune cells upon binding to ________

An endotoxin causes the production of cytokines from immune cells upon binding to cell surface receptors

Innate immunity: ________, immediate response, and no immunological ________

Innate immunity: Non-specific, immediate response, and no immunological memory

Adaptive immunity: Specific to ________, lag time from exposure to ________, and immunological memory after ________

Adaptive immunity: Specific to antigen, lag time from exposure to response, and immunological memory after exposure

What is the humoral response of innate immunity?

Complement. enzymes, and cytokines

What is the cellular response of innate immunity?

Phagocytes, natural killer cells, and pattern receptors

What is the humoral response of adaptive immunity?

Antibodies, and cytokines

What is the cellular response of adaptive immunity?

T and B cells

With first antigen exposure, the _________ of antigen-reactive cells are induced resulting in ________

With first antigen exposure, the antigen-reactive cells are induced resulting in clones

With antigen re-exposure to the same antigen, the immune response is ________ and stronger due to the large number of ________

With antigen re-exposure to the same antigen, the immune response is faster and stronger due to the large number of responding cells

The IgA antibody is found in the ________, saliva, tears, and breast milk, and it protects against ________

The IgA antibody if found in the mucous, saliva, tears, and breast milk, and it protects against pathogens

The IgD antibody is part of the ________, and it activates basophils and ________

The IgD antibody is part of the B cell receptor, and it activates basophils and mast cells

The IgE antibody protects against _________, and is responsible allergic reactions

The IgE antibody protects against parasitic worms, and is responsible allergic reactions

The IgG antibody is secreted by ________ in the blood, and able to cross the placenta into the ________

The IgG antibody is secreted by plasma cells in the blood, and able to cross the placenta into the foetus

The IgM antibody may be attached to the ________ of a B cell or secreted into the ________, and it is responsible for early stages of ________

The IgM antibody may be attached to the surface of a B cell or secreted into the blood, and it is responsible for early stages of immunity

Antibodies recognising foreign ________ are said to opsonise them. This aids their ________ by Fc receptors on phagocytes, leading to their eventual ________

Antibodies recognising foreign pathogens are said to opsonise them. This aids their uptake by Fc receptors on phagocytes, leading to their eventual destruction.

T cells are required for the ________ against intracellular pathogens, they bind to the ________, perforin makes holes in the infected cell’s ________, and the infected cell ________

T cells are required for the protection against intracellular pathogens, they bind to the infected cell, perforin makes holes in the infected cell’s membrane, and the infected cell lyses

The seven types of vaccination: Toxoid, live, ________, subunit, inactivated, ________, DNA, and ________ vaccines

The seven types of vaccination: Toxoid, live, attenuated, subunit, inactivated, conjugate, DNA, and recombinant vector vaccines

Subunit vaccines: The pathogen can be ________, chemicals are used to break it apart and gather the ________, antigen molecules from the pathogen can be used using ________

Subunit vaccines: The pathogen can be grown, chemicals are used to break it apart and gather the important antigens, antigen molecules from the pathogen can be used using recombinant DNA technology

Conjugate vaccines: A ________ linked to a toxoid binds to a B cell with an anti-polysaccharide ________, conjugate antigen is taken in and ________ by the B cell, the polysaccharide cannot be presented to ________ by B cells but peptides from the toxoid are presented, interaction with the toxoid peptide from the B cell ________ the Th2 cell, the activated Th2 cell makes ________ that drive the B cell to make ________, plasma cells make the antibodies to the ________, the antibodies bind to the capsule and ________ the pathogen

Conjugate vaccines: A polysaccharide linked to a toxoid binds to a B cell with an anti-polysaccharide antibody, conjugate antigen is taken in and digested by the B cell, the polysaccharide cannot be presented to Th2 cells by B cells but peptides from the toxoid are presented, interaction with the toxoid peptide from the B cell activates the Th2 cell, the activated Th2 cell makes cytokines that drive the B cell to make plasma cells, plasma cells make the antibodies to the polysaccharide, the antibodies bine to the capsule and opsonise the pathogen

Fungi can be used as recyclers, ________, material for packaging and ________, medicines, enzymes, and ________, they can also be used as a ________ for crops, and they cause allergy and ________ diseases

Fungi can be used as recyclers, food, material for packaging and clothes, medicines, enzymes, and model organisms, they can also be used as a disease for crops, and they cause allergy and human diseases

Confocal microscopy has ________, a high resolution and can be used in ________ imagery

Confocal microscopy has specificity, a high resolution and can be used in live cell imagery

Autoclaves sterilise organisms using high ________ and temperature

Autoclaves sterilise organisms using high pressure and temperature

Koch’s postulates demonstrate the ________ of a microorganism

Koch’s postulates demonstrate the pathogenicity of a microorganism

Morphological diversity is sufficient for distinguishing ________ and some obvious prokaryotic differences, it is insufficient to distinguish ________

Morphological diversity is sufficient for distinguishing prokaryotic/eukaryotic and some obvious prokaryotic differences, it is insufficient to distinguish microbe types

Metabolic diversity analyses _________ differences, it determines whether an organism uses energy or ________

Metabolic diversity analyses biochemical differences, it determines whether an organism uses energy or carbon

Ecological diversity analyses the _________ the microbes can survive in

Ecological diversity analyses the environmental conditions the microbes can survive in

Carl Woese knew that all organisms contain ________, rRNA is an excellent chronometer as it is highly ________ and functionally constant, Woese sequenced the ________ from a broad array of microorganisms

Carl Woese knew that all organisms contain ribosomes, rRNA is an excellent chronometer as it is highly conserved and functionally constant, Woese sequenced the 16s rRNA from a broad array of microorganisms

Ribosomal gene sequencing and phylogeny: 1. Pure culture cells ________ and DNA isolated 2. Gene-encoding rRNA is ________ and amplified by PCR 3. Amplified rRNA gene is ________ 4. Obtained sequences aligned by ________ 5. Tree depicts difference in ________ between organisms analysed

Ribosomal gene sequencing and phylogeny: 1. Pure culture cells lysed and DNA isolated 2. Gene-encoding rRNA is isolated and amplified by PCR 3. Amplified rRNA gene is sequenced 4. Obtained sequences aligned by computer 5. Tree depicts difference in rRNA sequence between organisms analysed

Other data that supports rRNA from 3 domains: transcription, ________, and membranes

Other data that supports rRNA from 3 domains: transcription, translation, and membranes

Fundamental differences in archaeal membranes: linkage of ________, and type of side chain

Fundamental differences in archaeal membranes: linkage of hydrophobic side chain, and type of side chain

Fungi are neither plants nor ________ but they are more ________ to animals than plants

Fungi are neither plants nor animals but they are more closely-related to animals than plants

Fungi are ________ diverse and ancient, they might have diverged from ________ organisms

Fungi are ethnically diverse and ancient, they might have diverged from aquatic organisms

Fungi can be used as ________ in brewing, baking, and cheese, drugs like b-lactam antibiotics, ________, and anti-cholesterol, ________ like citric acid, itaconic and gluconic acids, and as ________

Fungi can be used as enzymes in brewing, baking, and cheese, drugs like b-lactam antibiotics, immunosuppressants, and anti-cholesterol, organic acids like citric acid, itaconic and gluconic acids, and as biofuels

Mycorrhizae are fungi that live on ________, they are involved in stress tolerance and ________

Mycorrhizae are fungi that live on land plants, they are involved in stress tolerance and nutrient supply

Fungi are major ________ of organic matter, and recycle carbon and ________

Fungi are major decomposers of organic matter, and recycle carbon and nitrogen

Fungi can grow in very ________ conditions

Fungi can grow in very toxic conditions

In humans: Fungi are a threat to the ________, but they are a less than a threat than bacteria and ________

In humans: Fungi are a threat to the immuno-compromised, but they are less than a threat than bacteria and viruses

In plants: Fungi are a greater threat than ________, bacteria, and viruses

In plants: Fungi are a greater threat than nematodes, bacteria and viruses

Fungal features: Eukaryotic, ________ growth e.g. yeasts, filamentous growth e.g. ________, some are dimorphic so they change from ________ to yeast, heterotrophs, absorb externally digested ________, secrete ________ through wall, fungal wall made of ________ and glucans, fungal cell membrane of ________, storage compounds are mannitol, ________ and glycogen, have ________ nuclei, produce sexual and ________ spores, have plastic ________, and metabolic ________

Fungal features: Eukaryotic, unicellular growth e.g. yeasts, filamentous growth e.g. hyphae, some are dimorphic so they change from filamentous to yeast, heterotrophs, absorb externally digested nutrients, secrete enzymes through wall, fungal wall made of chitin and glucans, fungal cell membrane of ergosterol, storage compounds are mannitol, trehalose and glycogen, have haploid nuclei, produce sexual and asexual spores, have plastic genomes, and metabolic flexibility

Heterotrophs are organisms which ________ carbon from inorganic substrates but use ________ for growth

Heterotrophs are organisms which cannot fix carbon from inorganic substrates but use organic carbon for growth

Opisthokonts are organisms that have developed a ________

Opsithokonts are organisms that have developed a single flagellum

The last common ancestor of the fungal and ________ kingdoms are unicellular, ________, and motile

The last common ancestor of the fungal and animal kingdoms are unicellular, aquatic, and motile

The earliest fungi evolved roughly ________ ago, they were single-celled, ________, motile, and asexual spoores

The earliest fungi evolved roughly 1 billion years ago, they were single-cells, water living, motile, and asexual spoores

Higher fungi have ________ in their walls, whereas the lower fungi do not have them

Higher fungi have septa in their walls, whereas the lower fungi do not have them

Lower fungi: Microsporidia, ________, Chytridiomycota, Zygomycota, and ________

Lower fungi: Microsporidia, Cryptomycota, Chytridiomycota, Zygomycota, and Glomeromycota

Higher fungi: Ascomycota, ________, and Lichens

Higher fungi: Ascomycota, Basidiomycota, and Lichens

Phylum 1: ________, e.g. Nosema ceranae that cause ________ collapse

Phylum 1: Microsporidia, e.g. Nosema ceranae that cause bee hive collapse

Phylum 2: Cryptomycota, e.g. ________ that live within a host

Phylum 2: Cryptomycota, e.g. Rozellida that live within a host

Phylum 3: ________, e.g. Batrachochytrium that kills ________

Phylum 3: Chytridiomycota, e.g. Batrachochytrium that kills amphibians

Phylum 4: Zygomycota, e.g. ________ that infects immuno-compromised patients

Phylum 4: Zygomycota, e.g. Mucormycosis that infects immuno-compromised patients

Phylum 5: ________, e.g. Arbuscular mycorrhizal fungi that form ________ in plant roots

Phylum 5: Glomeromycota, e.g. Arbuscular mycorrhizal fungi that form arbuscules in plant roots

Phylum 6: Ascomycota, e.g. ________ a human pathogen

Phylum 6: Ascomycota, e.g. Candida albicans a human pathogen

Phylum 7: ________, e.g. Puccinia graminis which damages ________ plants

Phylum 7: Basidiomycota, e.g. Puccinia graminis which damages wheat plants

Phylum 8: ________

Phylum 8: Lichens

Nobel prizes for fungal research: ________ for penicillin, Dorothy Hodgkin for penicillin’s ________, Beadle and Tatum for the ________ hypothesis, and Hartwell and Nurse for the dissection of the ________

Nobel prizes for fungal research: Fleming for penicillin, Dorothy Hodgkin for penicillin’s crystal structure, Beadle and Tatum for the one gene-one enzyme hypothesis, and Hartwell and Nurse for the dissection of the yeast cell cycle

Heterothalic fungi require two compatible partners to produce ________, from homothalic ones, which are capable for ________ from a single organism

Heterothalic fungi require two compatible partners to produce sexual spores, from homothalic ones, which are capable for sexual reproduction from a single organism