Introduction to Microbiology

Question 1

overview of earth formation

Answer 1

1. 4.5Gy = supernova created the sun and planets
2. 4.0Gy = apparition of water and atmosphere
3. 3.9Gy = earth cooled down and water condensed to form oceans
   
   • oldest sedimentary rocks formed
4. 3.5Gy = stromatolites were formed
   
   • bacterial communities lived in sediment layers
5. Microfossils
   
   • first experimental evidence that life started around 3.5Gy

Question 2

what is the prebiotic soup model?

Answer 2

This model suggests that the chemically reducing atmosphere of the earth produced simple organic monomers. These monomers accumulated in a ‘soup’, producing complex polymers, and eventually life

all building blocks of life can be produced from the same pool of compounds under certain conditions;

• hydrogen cyanide (HCN)
• hydrogen sulphide (H2S)

Question 3

What was Miller’s experiment?

Answer 3

An atmosphere that mimicked the atmosphere of early earth was produced by mixing water vapour, methane, molecular hydrogen and ammonia with electrical discharges.

A week later, organic compounds like amino acids were produced

limitations: no evidence of amino acids present in sediments, and the atmosphere had a higher H2 concentration than what was used in the experiment

Question 4

what is the RNA world hypothesis

Answer 4

RNA could have been the first macromolecule encoding complex info:

• requires less energy than DNA to form/degrade as unwinding isnt required
• some viruses use ssRNA as genetic material
• RNA have have catalytic properties - ribozymes = splicing

Question 5

How did compartmentalisation lead to LUCA? (apparition of cellular life)

Answer 5

Hypothesis 1: surface origin

• primitive cells were formed spontaneously on earth from prebiotic soup
• natural selection led to optimise metabolic process

Hypothesis 2: subsurface origin

• life appeared in hydrothermal mounds on ocean floor
• geothermally heated water from fissure, and cool ocean water formed montmorillonite clays
• H2 and H2S provided electrons to form organic molecules

Question 6

what is the panspermia theory?

Answer 6

life originated from space and that evolution is driven by viruses from space e.g. spanish flu

Question 7

who introduced the nomenclature for the 3 domains of life?

Answer 7

Carl Woese: he intoduced Bacteria, Archaea and Eukarya, defining a new taxon

Question 8

How does gene plasticity cause microbial diversity?

Answer 8

Haploid genome creates diversity:
- bacteria only have one chromosome, so mutations are easily passed on

Rapid multiplication means population can double within 20 minutes
- 10 hours -> 1 billion cells

Gene transfer: transformation, transduction, conjugation

Question 9

what is taxonomy?

Answer 9

discipline which deals with classification of organisms

• species are defined according to a taxonomic hierarchy + common phenotypes
• uses binomial nomenclature

Question 10

Describe phenotypic analyses used in taxonomy:

Answer 10

1. morphology/staining
   - direct observations
   - limited as morphology can change depending on environment
2. metabolic properties
   - biochemical tests on unknown bacteria produce an ID value after incubation which can be compared to a computerised list to identify the bacteria
3. phage typing
   - phages identify species by targeting specific organisms on agar plate
   - lysis plaques are zones of bacteria which have been lysed by phages
4. fatty acid profiles
   - fatty acids are extracted from bacterial culture and gas chromatography forms peaks which can be compared on database
5. mass spectrometry
   - surface proteins produce a finger print of molecules associated with that organism which can be compared on database

Question 11

describe genotypic analyses used in taxonomy:

Answer 11

1. DNA hybridisation
   - comparision of 2 species by seeing hoe much their DNA can hybridise by denaturing them and mixing them together
   - no. H bonds formed indicates how closely they are related
2. FISH
   - gene is labelled and hybridised with DNA in sample, and can see which organisms have that gene
3. MLST/fingerprinting
   - housekeeping genes are selected and sequenced to compare alleles of different genes
   - barcode is formed which can be compared with other species
4. whole genome sequencing
   - samples are prepared and sent to a company

Question 12

what is phylogeny?

Answer 12

studies evolutionary history and relationships of organisms

• achieved by comparing DNA and using rRNA sequences called molecular clocks
• housekeeping genes are required across many organisms for comparison
• forms phylogenetic trees which is based on a comparative analysis of the rRNA gene sequence

Question 13

name some unicellular eukaryotes:

Answer 13

Fungi:
- yeasts = unicellular
- molds = filamentous
- basidiomycetes = mushrooms
can be multicellular 

protists:

• unicellular algae (plant-like)
• protozoa (animal-like)
• slime molds

Question 14

General properties of fungi:

Answer 14

• cell walls made of chitin, mannans and/or glucans
• most form multicellular filaments called hyphae (pleiomorphic)
• 2 phases in life cycle involving asexual and sexual reproduction to form spores (resistant)
• undergo transitions between unicellular and multicellular forms

Question 15

why are fungi important?

Answer 15

• contribute to carbon cycle as they are decomposers
• can be plant pathogens and spoil 10-30% of crops
  
  • loss of £150 billion/year
• penicillin is extracted from mold
• fungal infections cause over 1.5 million deaths per year

Question 16

what are molds?

Answer 16

filamentous fungi e.g. bread mold

• vegetative form = coenocytic hyphae
• absorption and nutrient growth occur at tip of hyphae which secretes material via vesicles
• hyphae drive symbiosis and pathogenesis

Question 17

what are basidiomycetes and their life cycle?

Answer 17

• live in symbiosis with plants/trees
• form huge mycelium networks in association with roots of trees
• provide plant with nutrients in return for amino acids

life cycle:

• haploid mycelium undergoes cytoplasmic fusion to form secondary mycelium
• gametes fuse nuclei to form diploid zygote

Question 18

what are yeasts?

Answer 18

• unicellular fungi
• used in brewery and bakery industries (S. cerevisiae)
• cause opportunisitic infections of humans (crytpococcus and candida)
• used as a model organism for apoptosis, cell cycle, mitochondira and oxidative stress, lysosomal/peroxisomal function and vesicular trafficking

Question 19

what is the life cycle of yeast?

Answer 19

• multiplies by budding or asymmetric binary fission
• cell expands to form progeny cell (bud scar is left)
• form unicellular but become hyphae under specific conditions (dimorphism)
• haploids germinate and multiply in mitosis to form new progeny
• haploids mate and fuse genetic material to form diploids which multiply by mitosis
• diploid phase forms sporangium which produce spores to start cycle again

Question 20

what are the two types of unicellular algae?

Answer 20

primary endosymbiotic algae (Chlamydomonas reinhardtii):

• autotrophs
• match structure of chloroplasts
• true algae resulting from ancestral endosymbiosis

secondary endosymbiotic algae (diatoms):

• result from protists that engulfed primary endosymbiont
• mixotrophs
• structure of chloroplasts have extra set of membranes (2 engulfments occured)
• envelope with 4 different membranes
• nucleus is engulfed and degenerates

Question 21

why are unicellular algae important?

Answer 21

• components of phytoplankton so produce 50-80% of atmos oxygen
  -key food item in ocean food web
• model organism:
  
  • photosynthesis, motility, cell cycle
    oxidative stress etc
  • doubling time 6-8 hours
  • swims using 2 flagella
  • contains chloroplast with 2
    membranes
  • vacuole for osmoregulation
  • cell wall made of hydroxyproline
    glycoproteins (NO CELLULOSE)

Question 22

what is the life cycle of unicellular algae?

Answer 22

• haploid asexual reproduction (binary fission)
• meiosis to form gametes
• haploid cells form opposite mating types that fuse to form zygote

colonial life style:

• colonies within colonies made of linked cells with shared cytoplasm
• contains specialised cells which undergo sexual/asexual cycle

Question 23

what are diatoms?

Answer 23

• mot abundant organisms in phytoplankton
• produces 20% of the oxygen on earth
• large morphological diversity
• mobile by sliding on mucus using actin and myosin (don’t use appendeges)
• mixotrophs: photosynthesis and metabolism (not just reliant on one process)
• chloroplasts have 4 membranes
• cell wall called frustule , which is made of silica (crosslinked silicon oxide)

have treatments against fleas/red mites

Question 24

what are the two types of diatoms?

Answer 24

1. radial symmetry = centric diatoms

2. bilateral symmetry = pennate diatoms

Question 25

what is the life cycle of diatoms?

Answer 25

- frustules sediment at bottom of ocean - cell walls are rigid, so division is unusual - frustules have 2 valves, with one overlapping the other - each daughter cell inherits half of the frustule and is smaller than the parent cell - when critical size is reached, the cell undergoes meiosis to form gametes - zygote is formed which forms a frustule the same size as the parental diatom

Question 26

what are coccolithophores?

Answer 26

a form of secondary endosymbiotic algae | their frustules are made of calcium carbonate, meaning they have key role in carbon cycle

Question 27

what are alveolates (protozoa)?

Answer 27

- contain alveoli - motile organisms due to cilia - mainly aquatic 3 types: 1. ciliates - predatory protists - key role in food web (zooplankton) 2. apicomplexans - parasites - major impact on human health e.g. malaria parasite 3. dinoflagellates - predatory algae - key role in carbon cycle

Question 28

what are ciliates?

Answer 28

- contain 2 micronuclei with germline material - contain a macronucleus with metabolic functions and polyploid genome - cilia are used for motility to capture prey - prey is phagocytosed in vacuole

Question 29

what are the two ways in which ciliates multiply?

Answer 29

1. Binary fission - macronucleus elongates and divides into 2 macronuclei, each inherited by 2 daughter cells 2. conjugation - 2 protozoa establish physical contact and macronucleus disintegrates - mitosis/meiosis produces 4 daughter cells - micronuclei degenerate - exchange of genetic info produces diploid micronuclei that divide by mitosis

Question 30

what are apicomplexans (parasitic protozoa)?

Answer 30

- spore-forming parasites, lacking flagella, cilia or pseudopods - contain apical complex to enter host cell - contain apoplast which degenerates into chloroplast to carry out fatty acid metabolism - micronemes and rhoptries secrete enzymes for metabolism

Question 31

how do apicomplexans multiply?

Answer 31

uses a vector for host infection e.g. mosquito - sporozoite is infectious form - these multiply by mitosis in schizont ruptures to release merozoites which invade red blood cells - merozoites form male/female gametocytes which go into mosquito - in mosquito, gametes fuse to form zygote that invades cells and undergoes meiosis to produce sporozoites

Question 32

what are dinoflagellates?

Answer 32

- photosynthetic aquatic organisms - mixotrophs: use sources of energy that aren't light - responsible for algae blooms which can be toxic to fish - mobile predatory algae which feed on bacteria, diatoms, ciliates and other algae - involved in symbiotic and parasitic interactions - cell walls made of cellulose plates called thecae, and chloroplasts have complex membranes

Question 33

what is the life cycle of dinoflagellates?

Answer 33

- vegetative reproduction - can exist as dormant (cysts) - little is known about their life cycle - hypnozygote enables cell to exist as both diploid or haploid

Question 34

what are parasitic protozoa?

Answer 34

- mobile parasites that cause common diseases in humans e.g. diarrhoea - mostly harmful, but sometimes symbionts - can be transmitted via vectors or direct contact between individuals example: metamonads

Question 35

what are examples of metamondads?

Answer 35

Mixotricha paradoxa: - found in gut of termites - lives in symbiosis with other bacteria - 1 endosymbiotic bacterium degrades cellulose - 2 ectosymbiotic bacteria provide motility in form of spirochetes Giardia lamiblia: - human parasite causing diarrhoea - contains 2 nuclei and divides by binary fission - use adhesive discs to adhere to epithelial cells Trypanosoma brucei: - transmitted through a fly - causes fever, headaches, and can invade the CNS, causing sleep cycle disruption

Question 36

what are slime molds and amoebas?

Answer 36

- predatory organisms found in damp environments - differentiate to multicellular reproductive stage when food supply is low - amoebas cause human diseases via contaminated water

Question 37

How do pseudopods aid amoeba motility?

Answer 37

- amoeba cell shape is variable - motility/predation is conferred by pseudopods created by actin polymerisation/diassembly - actin assembly pushes the membrane to form pseudopods - same mechanism as human phagocytes

Question 38

Give an example of a cellular slime mold:

Answer 38

Dictyostelium discodeum: - grows as an amoeboid, unicellular organism that divides by binary fission - produces cAMP metabolite when starved that drives aggregation to form slug - slug differentiates to a fruiting body (sporangium + stalk) - spores are released to start new cycle

Question 39

give an example of a plasmodial slime mold:

Answer 39

Physarum polycephalum: - grows and divides by binary fission as an amoeboid single cell - individual cells can aggregate to form plasmodium - single cell and single cytoplasm with several nuclei - plasmodium forms a fruiting body - spores are released to initiate a new cycle