Week 1

Question 1

How do light microscopes work?

Answer 1

1. Visible light is passed through the specimen and then through glass lenses, the lenses bend the light so that the image is magnified
2. Quality of image depends on:
   a) Magnification: the ratio of image size to actual size
   b) Resolution: clarity of image or minimum distance between two distinguishable points
   c) Contrast: visible differences in parts of the sample

Question 2

How do electron microscopes work?

Answer 2

1. Use magnets to focus an electron beam on or through a specimen, resulting in resolving power a thousand times greater than LM
   a) Scanning electron microscope: uses a beam of electrons to scan the surface of a sample to study the details of its topography
   b) Transmission electron microscope: passes an electron beam through a very thin section and is primary used to study the internal ultrastructure of cells

Question 3

What are the different types of microorganisms and cell types?

Answer 3

1. Domain bacteria:
   a) Prokaryotes
   b) Small single cells
   c) Inhabit broad environmental range - including humans
2. Domain Archaea:
   a) Prokaryotes
   b) Distinct from “bacteria” by distinct rRNA sequence
   c) Can survive broad environmental range - such as in humans or in extreme environments
3. Domain Eykarya:
   a) Animals, plants, and other eukaryotic microorganisms e.g. Helminths, algae, protists, and fungi
   b) Usually larger than bacteria and archaea
   c) Single and multicellular
   d) Linear DNA (chromosomes) contained in nucleus with a nuclear membrane
   e) Contain membrane-bound organelles

Question 4

What do all cells have in common?

Answer 4

1. Cytoplasmic (cell) membrane: barrier that separates the inside of the cell from the outside environment
2. Cytoplasm: aqueous mixture of macromolecules, small organics, ions, and ribosomes inside cell
3. Ribosomes: protein-synthesising structures
4. Cell wall: present in some microbes - confers structural strength

Question 5

What are the properties of cells?

Answer 5

1. All cells:
   a) Metabolism
   b) Growth
   c) Evolution
2. Some cells:
   a) Differentiation
   b) Communication
   c) Genetic exchange
   d) Motility

Question 6

What are bacteria?

Answer 6

1. Single celled prokaryotes
2. Many different shapes - cocci, bacillus, spirals, spirochete, curved rod, coryneform (club), pleomorphic
3. Arrangement: pairs, chains, clusters
4. Fast growing - reproduce via binary fission
5. Rigid cell wall composed of peptidoglycan
6. High metabolic diversity - ubiquitous
7. Accessory structures - endospores, capsule, flagella, pili

Question 7

What are archaea?

Answer 7

1. Prokaryotes
2. Diverse unicellular shapes (similar to bacteria) - some form filaments
3. Lack a cell wall composed of peptidoglycan
4. Divide by binary fission, can also bud and fragment
5. Differ metabolically to bacteria
6. Have distinctive rRNA sequences
7. Different cell wall to bacteria
8. Can be found everywhere including extreme environments

Question 8

What are fungi?

Answer 8

1. Eukaryotic - non-photosynthetic
2. Single celled (yeast) or multicellular (moulds/mushrooms)
3. Multicellular have branched filaments of cells called hyphae
4. Have cell walls made of complex sugar chitin (polysaccharide) or cellulose
5. Reproduce sexually and asexually
6. Can grow in harsh environmental conditions - absorb nutrients from environment
7. Heterotopic (uses carbon as a food source) - saprophytic (decaying/dead matter), mutualistic, parasitic

Question 9

What are protozoa?

Answer 9

1. Eukarya
2. Mostly unicellular animal-like, many are motile, free living, or parasitic
3. Microscopic algae - photosynthetic
4. Eukaryotic, unicellular, lack tissue organisation
5. Highly diversive - confusing taxonomy
6. Heterotrophs or photosynthetic
7. Ubiquitous
8. Are symbiotic - mutualists, commensals, parasitic
9. Can reproduce asexually (mostly) or sexually
10. Can have pigments

Question 10

What are helminths?

Answer 10

1. Eukarya

2. Parasitic worms which range in size from microscopic forms to adult tapeworms (over 7 m in length)

Question 11

What are viruses?

Answer 11

1. Acellular
2. Obligate parasites that can only replicate within host cell
3. Do not carry out metabolism - take over other metabolic systems to replicate
4. Have small genomes of double-stranded or single-stranded DNA or RNA
5. Very diverse - classified based on structure, genome composition, and host specificity

Question 12

What is a microenvironment?

Answer 12

1. The immediate environmental surroundings of a microbial cell or group of cells
2. Soil particles contain many microenvironments

Question 13

What is a biofilm?

Answer 13

1. Biofilms are an aggregate group of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells
   a) Examples of biofilms include plaque on teeth
2. The matrix is typically a mixture of polysaccharides
3. Biofilm formation is initiated by attachment of a cell to a surface followed by expression of biofilm-specific genes
   a) Genes encode proteins that synthesise intercellular signalling molecules and initiate matrix formation

Question 14

Why do bacteria form biofilms?

Answer 14

1. Self defence
   a) Biofilms resist physical forces that sweep away unattached cells, phagocytosis by immune system cells, and penetration of toxins (e.g. antibiotics)
2. Allow cells to remain in a favourable niche
3. Allow bacterial cells to live in close association with one another

Question 15

What is a microbiome?

Answer 15

1. A functional collection of different microbes in a particular environmental system (e.g. the human microbiome)

Question 16

Describe the normal flora of the skin and its microbiome:

Answer 16

1. Three main microenvironments:
   a) Dry skin
   b) Moist skin
   c) Sebaceous skin
2. Composition of the microbes of the skin is influenced by:
   a) Environmental factors (e.g. weather)
   b) Host factors (e.g. age - puberty, personal hygiene)
3. Each microenvironment shows a unique microbiota

Question 17

Describe the normal flora of oral cavity and airways and their microbiome:

Answer 17

1. Oral cavity is a complex, heterogeneous microbial habitat
   a) Saliva contains antimicrobial enzymes
   b) High concentrations of nutrients near surfaces in the mouth promote localised microbial growth
   c) The tooth consists of a mineral matrix (enamel) surrounding living tissue, the dentin, and pulp
2. Microenvironments of the respiratory tract:
   a) Microbes thrive in the upper respiratory tract - bacteria constantly enter respiratory tract from air in breathing but most of this is trapped in mucus of nasal and oral passages to be expelled or swallowed into stomach for destruction
   b) Lower respiratory tract however has no normal microbiota in healthy adults

Question 18

Describe the normal flora of the GIT and its microbiome:

Answer 18

1. Microbes in gut affect early development, health, and predisposition to disease - colonisation of gut begins at birth
2. The acidity of the stomach and duodenum (~pH 2) prevent many organisms from colonising the GI tract - however there is a rich microbiome in the healthy stomach
   a) Firmicutes, Bacteroidetes, and Actinobacteria are common in the mucus layer of the stomach
   b) Firmicutes and proteobacteria are common in the mucus layer of the stomach
   c) Helicobacter pylori is present in the gastric mucosa
3. The intestinal microorganisms of the large intestine carry out a variety of essential metabolic reactions that produce various compounds

Question 19

Describe the normal flora of urogenital tracts and their microbiome:

Answer 19

1. Very specific microenvironment
2. Altered conditions can cause potential pathogens in the urethra (such as Escherichia coli and Proteus mirabilis) to multiply and cause disease
3. E. coli and P. mirabilis frequently cause urinary tract infections in women
4. Lactobacillus acidophilus, a resident organism in the vagina, ferments glycogen to produce lactic acid
   a) Lactic acid maintains a local acidic environment

Question 20

How do microbial interactions transition to disease?

Answer 20

1. Entry/penetration due to invasion from surfaces into tissues
   a) e.g. actively by producing enzymes
2. Passively through wounds/injury
3. Increase in virulence due to:
   a) Multiplication/increase in numbers
   b) Ability to survive extreme conditions increases
   c) Ability to overcome host immune system develops - kills host

Question 21

What virulence factors in microbes can develop?

Answer 21

1. Capsules - extra protective coating (slime) to avoid immune attack or desiccation
   a) Also promotes adhesion
2. Flagella, cilia - increase motility
3. Pili, flagella - aid attachment to a surface/body site
4. Glycocalyx/ECM of biofilm - barrier/coating for protection from host immune system
5. Endospores - ability to endure times of limited nutrients
6. Enzymes - degrade surfaces to assist with attachment e.g. streptokinase, proteases
7. Toxins - exotoxins (TSST) and endotoxins (LPS) can hyperstimulate immune response causing pathology

Question 22

What are the types of microbial transition to disease?

Answer 22

1. Obligate infections - microorganisms that are always pathogenic and never normal flora
2. Opportunistic infections - caused by normal flora that take advantage of disorder (e.g. immunosuppresion due to another infection/disease) or lack of competition (e.g. vaginal thrush) by moving from its normal habitat
3. Nosocomial infections - hospital/healthcare facility-acquired (HAI) e.g. ventilator-associated pneumonia from Klebsiella pneumoniae