Module 4: Microbiology Flashcards

1
Q

Microbes make up ____ the biomass on Earth

A

half

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2
Q

Where is the chromosome of a prokaryotic cell found

A

Nucleoid

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3
Q

What is the order of layers of a prokaryotic cell (inside to out)

A

Plasma membrane, cell wall, glycocalyx

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4
Q

What shapes can bacteria be

A

Cocci, rods, spirals

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5
Q

What is the function of a prokaryotic cell membrane

A

Cell regulation

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6
Q

What is the function of a prokaryotic cell wall

A

Cell integrity, shape, strength, prevent desiccation, osmotic lysis

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7
Q

What is the purpose of the glycocalyx

A

Extracellular: cell protection

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8
Q

Do archaea have peptidoglycan cell walls

A

No

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9
Q

Describe the bacterial genome and its location

A

One circular chromosome restricted to an area known as the nucleoid, and plasmids in the cytosol

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10
Q

What are plasmids

A

Small circular self replicating DNA molecules found in the cytosol

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11
Q

What are prokaryotes that lack cell walls called

A

Mycoplasmas (group of pathogenic bacteria)

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12
Q

Describe the structure of peptidoglycan

A

NAM-NAG sugar chains cross linked laterally by amino acid chains and vertically by amino acid side chains

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13
Q

What is the enzyme that cross links NAM-NAG sugar chains and amino acid chains

A

Transpeptidase

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14
Q

What are the most common gram stain reference bacteria

A

Staphylococcus aureus (gram positive) and escherichia coli (gram negative)

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15
Q

What colour are gram positive bacteria stained

A

Purple

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16
Q

What colour are gram negative bacteria stained

A

Red/pink

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17
Q

What are the four steps of the gram stain procedure

A

Application of crystal violet (purple dye), application of iodine (mordant), alcohol wash (decolourisation), application of safranin (counterstain)

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18
Q

Describe the structure of a gram positive bacterial cell wall

A

Thick peptidoglycan layer makes up the cell wall, plasma membrane underneath

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19
Q

Why do gram positive bacterial cells retain the crystal violet

A

Peptidoglycan traps violet, masks red

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20
Q

How thick is the peptidoglycan layer of gram positive bacteria

A

THICK: 20-80 nm

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21
Q

Describe the structure of a gram negative bacterial cell wall

A

Thin peptidoglycan layer and outer membrane make up the cell wall, plasma membrane underneath

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22
Q

Why do gram negative bacterial cells not retain the crystal violet

A

It is easily rinsed away, revealing red safranin dye

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23
Q

How thick is the peptidoglycan layer of gram negative bacteria

A

THIN: 5-10 nm (between two plasma membranes)

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24
Q

What does the gram negative bacterial outer membrane have that gram positive doesn’t

A

Carbohydrate portion: lipopolysaccharide

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25
Q

What are flagella made of

A

Flagellin protein

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26
Q

What is the diameter of flagella

A

10-20 nm

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27
Q

How many flagella per cell

A

5-10

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28
Q

How do flagella work

A

Act like propeller, cell rotates them to move through liquid medium

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29
Q

Chemotaxis

A

Bacteria move along a concentration gradient towards a chemical attractant (positive) or away from a chemical repellent (negative)

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30
Q

Function of fimbriae (can also be called adherence pili or adhesins)

A

Structures with adhesive properties that cause bacteria to stick/adhere to surfaces

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31
Q

What is the diameter of pili

A

2-8 nm

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32
Q

How long are pili

A

1µm

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33
Q

How many pili per cell

A

100-1000

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34
Q

Difference between fimbriae and pili

A

Fimbriae are for adhesion to surfaces, pili are for attachment to other bacteria

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35
Q

Purpose of a sex pilus

A

Horizontal gene transfer (conjugation)

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36
Q

What are the two forms of glycocalyx

A

Capsule (organised), slime layer (disorganised without cell shape, attached loosely to cell wall)

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37
Q

What is the glycocalyx

A

A gelatinous polysaccharide and/or polypeptide outer covering of a bacteria

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38
Q

Function of capsules

A

Virulence factors: evade immune system, protection from phagocytosis and engulfment by immune cells. Prevent cell from drying out (desiccation)

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39
Q

What is a bacterial endospore

A

Highly differentiated cells resistant to heat, harsh chemicals, antibiotics, disinfectants and radiation. Enable bacteria to stay dormant for a very long time

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40
Q

What cells have endospores

A

Some types of gram positive bacteria

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41
Q

Why do bacterial endospores form

A

Formed during unfavourable growth conditions to protect cells from stress, germinate under favourable conditions

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42
Q

Why are prokaryotes so dominant

A

Because they evolve so fast due to fast growth rate (exponential), have existed for so long so colonised most habitats resulting in extreme ecological and metabolic diversity

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43
Q

What does colonially pure mean

A

All cells identical

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44
Q

What is binary fission

A

The process of one cell becoming two (asexual)

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45
Q

Outline the process of binary fission

A

DNA replication (one origin of replication), two origins move to cell poles, two cells differentiate

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46
Q

What is a closed batch culture system

A

Defined (limited) supply of nutrients provided, once used cells cannot proliferate

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47
Q

What are the 4 stages of microbial growth in a closed batch system

A

Lag, exponential, stationary, death

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48
Q

Describe the lag phase

A

Time taken to get biosynthetic reactions running

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49
Q

Describe the log phase

A

Cells are actively dividing and nothing is limiting for growth. Population is doubling in a constant time interval under ideal conditions

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50
Q

Describe the stationary phase

A

Cells stop growing and cryptic growth is observed, equilibrium between growing and dying cells

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51
Q

What is cryptic growth

A

When organisms survive by consuming lysed cell constituents of other dead cells within the culture

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52
Q

Describe the death phase

A

Equilibrium between growing and dying cells is skewed toward death

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53
Q

What do batch culture assays measure

A

The average behaviour of cells

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54
Q

What do prokaryotes need to multiply

A

Carbon source, energy source (electrons to power anabolic and catabolic reactions), reducing power (carriers of electrons (NAD+, NADP+))

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55
Q

Catabolism

A

Breakdown: energy generation

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56
Q

Anabolism

A

Build up: energy consumption

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57
Q

Photoautotroph (plants, algae, cyanobacteria, green and purple sulfur bacteria)

A

Light energy source, inorganic carbon source

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58
Q

Photoheterotroph (green and purple non sulfur bacteria)

A

Light energy source, organic carbon source

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59
Q

Chemoautotroph (hydrogen, sulfur and nitrifying bacteria)

A

Chemical energy source, inorganic carbon source

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60
Q

Chemoheterotroph (animals, fungi, protozoa)

A

Chemical energy source, organic carbon source

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61
Q

What is a wild type strain

A

Bacteria with all essential genes, can grow by itself and be isolated in pure culture

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62
Q

What is an auxotroph (98% of microorganisms sequenced lack essential pathways for synthesis of amino acids)

A

Bacteria lacking or defective in one or more essential genes, cannot grow unless missing factor supplied

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63
Q

What is cross feeding (also known as syntrophy)

A

When one species gains metabolic products of another species. Can benefit one or both species

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64
Q

Microbiome definition

A

The complete collection of microorganisms and their genes within a particular environment

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65
Q

Microbiota definition

A

Individual microbial species in a biome- bacteria, fungi, archaea and viruses

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66
Q

Opposite of being dependent on others

A

Autonomy

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67
Q

Culture dependent methods pros

A

Access to phenotype, can study one organism at a time, can manipulate conditions to see response of organism

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68
Q

Culture dependent methods cons

A

Not all organisms can be cultured, too many species to grow them all, culturing requires precise conditions to match microbes needs, doesn’t match real world conditions

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69
Q

Culture independent methods pros

A

Allows access to genotype, can study many organisms at a time, shows communities as they are in nature, can target non-culturable organisms, provides access to unknown information/species

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70
Q

Culture independent methods cons

A

No pure culture so no ability to manipulate, expensive and complex

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71
Q

What is a culture dependent method

A

Culturing of microbes in lab, uses pure cultures or simple (reduced diversity) enrichments

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72
Q

What is a culture independent method

A

Relies on nucleic acid based methods, uses sequencing or metabolic profiling to study all microbes in a sample

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73
Q

What is microbial ecology

A

The field of study focused on the relationship between microbes and their environment (interrelationships among organisms and their environment)

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74
Q

What is a microbial population

A

Individual microbial cells of a species proliferated

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75
Q

What is a microbial community

A

Interaction of populations of microbes

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76
Q

Anabolism and catabolism must be

A

Coupled (harvesting of building blocks = harvesting of energy)

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77
Q

For every oxidation reaction in the body there must be

A

An equal and opposite reduction

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78
Q

What are the electron carriers in the body

A

NAD+ and NADP+ (NADH and NADPH when they have electrons)
Facilitate redox reactions without being consumed

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79
Q

Photoautotroph

A

Light energy source, inorganic carbon source
e.g plants

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80
Q

Chemoautotroph

A

Chemical energy source, inorganic carbon source
e.g hydrogen, sulfur and nitrifying bacteria

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81
Q

Photoheterotroph

A

Light energy source, organic carbon source
e.g green and purple non sulfur bacteria

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82
Q

Chemoheterotroph

A

Chemical energy source, organic carbon source
e.g animals, fungi, protozoa

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83
Q

Decomposers are

A

Heterotrophs (reliant on primary producers)

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84
Q

Primary producers are

A

Autotrophs (fix CO2)

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85
Q

Chemical energy source examples

A

Glucose: organic, H2S: inorganic

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86
Q

How can so many different microbes share the same metabolisms?

A

Evolve to require very specific resources (e.g absorption of wavelength of light)

87
Q

How can a microbe live in an anoxic place if it requires oxygen to live?

A

Cables (shuttle electrons from anoxic to oxic zone: oxygen terminal electron acceptor) (gram negative: 2 membranes)

88
Q

What is metabolism

A

2 linked but different process (anabolism and catabolism)

89
Q

What was the aim of the human microbiome project? (2008)

A

Characterise microbial communities found at multiple human body sites and look for correlations between changes in the microbiome and human health

90
Q

How was the human microbiome project undertaken

A

Culture-independent methods of microbial community characterisation as well as whole genome sequencing of individual bacterial species

91
Q

What parts of the body did the human microbiome project put emphasis on

A

Oral, skin, vaginal, gut, nasal/lung

92
Q

How many microbial species are in the the human microbiome

A

10000

93
Q

How many microbial species are in the human gut

A

500-1000

94
Q

What were the goals of the HMP

A

Develop a reference set of microbial genome sequences and perform preliminary characterisation of the human microbiome. Explore the relationship between disease and changes in the human microbiome. Develop new technologies and tools for computational analysis, establish a resource repository, study the legal, ethical and social implications of human microbiome research

95
Q

Is there diversity within and among individual microbiomes

A

Yes

96
Q

How much more genetic diversity does an individual’s gut bacteria have compared to the human genome

A

50 times

97
Q

Why might the HMP not be representative of all people

A

Most information came from healthy Western people

98
Q

Everyone’s microbiome has around ___ species

A

160, 57 very common

99
Q

A person’s microbiome community can change, but its _____ will not much

A

Function

100
Q

What are the functions of the human microbiome

A

Prevent pathogens from being successful, block colonisation niches, competing for nutrients, modifying environment to change virulence factor expression, making environment actively hostile, lowering pH, cause host to thicken mucus layer, cause host to upregulate antimicrobial peptides (defensin, IgA), primes host neutrophils and macrophages

101
Q

What do microbes produce to make an environment actively hostile

A

Bacteriocins (antimicrobial) and short chain fatty acids (SCFAs)

102
Q

How many phylum groups dominate human microbial communities

A

4 (firmicutes, bacterioidetes, actinobacteria, proteobacteria)

103
Q

What percent of human associated microbes are thought to have eluded cultivation so far

A

20-80%

104
Q

The human microbiome is undiverse in _____ but very diverse in ______

A

Phyla, species, strains (can be as unique as a fingerprint)

105
Q

What is the purpose of SCFAs that gut microbiota produce

A

Modulate our metabolisms and affects our defence against pathogens

106
Q

What vitamins can the human microbiome synthesise

A

Many B vitamins and vitamin K

107
Q

What is a functional food

A

A food claimed to have a health promoting or disease preventing property beyond the basic function of providing nutrients

108
Q

What are probiotics

A

Live microorganisms (most commonly lactic acid bacteria (LAB) and bifidobacteria)

109
Q

What are prebiotics

A

An ingredient that beneficially nourishes the good bacteria already in the large bowel or colon (e.g body doesn’t digest some plant fibres (oligosaccharides) but they promote growth of bacteria)

110
Q

What is the problem with broad spectrum antibiotics

A

If you clear out all your commensal microbes you may be colonised by pathogenic microbes

111
Q

What does C.difficile do to the gut

A

Heterotroph that uses sialic acids from mucins (main structural component of mucus layer in gut) as carbon/energy source, speed of growth and presence of accessory genes make it pathogenic: cause damage to cells and inflammation and fluid build up. Flushed out by diarrhea

112
Q

What is the purpose of faecal matter transplants

A

Provide healthy bacteria to outcompete pathogenic. Highly successful in mutliple recurrences of C.difficile

113
Q

What are the 4 groups of bacteria that dominate the human microbiome

A

Firmicutes, bacteroidetes, actinobacteria, proteobacteria

114
Q

What host processes do the microbiome affect

A

Digestion, immune system, pathogen susceptibility, neurology

115
Q

What is the genetically most diverse biological entity on earth

A

Viruses

116
Q

What are viruses

A

Acellular organisms with no metabolic abilities of their own (rely entirely on biosynthetic machinery of host to multiply)

117
Q

What is the most abundant biological entity on eath

A

Viruses

118
Q

How do viruses vary in size

A

10-400 nm

119
Q

What is a capsid

A

Protein coat made of capsomers

120
Q

What is an envelope

A

Envelope of lipids surrounding capsid when outside cell

121
Q

What is the function of the capsid

A

Protect viral genome

122
Q

What are the three types of capsid symmetry

A

Helical, icosahedral (20 faced polyhedron, each face an equilateral triangle), complex

123
Q

How do nucleic acids vary between viruses

A

Can be RNA or DNA, linear or circular, segmented or not, and single or double stranded. Can be 4000 to >1 million nucleotides

124
Q

How are viruses classified?

A

Nucleic acid -> capsid symmetry -> naked or enveloped -> genome architecture

125
Q

What do viruses infect

A

All cell types and all forms of life

126
Q

What are bacteriophages

A

Viruses that infect and replicate in bacteria

127
Q

What is a lytic (virulent) cycle

A

Using a host cell to manufacture more viruses and results in destruction of the host cell

128
Q

What are the 5 stages of the lytic cycle of bacteriophages (takes 20-30 minutes)

A

Attach, penetrate, uncoat (expose genetic material), genome replication and gene expression, assembly, release (likely destruction of cell)

129
Q

What are the 6 stages of viral infection

A

Attachment, penetration, uncoating to expose genetic material, gene expression and genome replication, assembly, release

130
Q

Describe the SARS-CoV-2 virus

A

Enveloped ssRNA linear non segmented virus with spikes and nucleocapsid protein

131
Q

How are virus variants generated

A

D/RNA polymerase making errors

132
Q

What is the purpose of a virus spike (vaccines target the spike)

A

Bind to a receptor protein to infect a cell (ACE2 for SARS-CoV-2)

133
Q

What are the 6 stages of the SARS-CoV-2 replication cycle

A
  1. Spike binding to ACE2 receptor
    2/3. Cell entry/fusion
  2. Genome translation replication module only
    Viral RNA synthesis
    Viral mRNAs and genome
    Translation
  3. Assembly
  4. Exocytosis
134
Q

Describe the HIV virus

A

RNA enveloped retrovirus that causes AIDS

135
Q

What are the 6 stages of the HIV replication cycle

A

1/2/3. HIV fuses with cell membrane and digestion of capsid
4. Reverse transcriptase converts ssRNA to dsDNA (mistakes), incorporated into host genome. DNA replicated and viral proteins and glycoproteins synthesised (sent to membrane in vesicles)
5. Assembly (enveloped as exocytosed)
6. Release (with viral envelope glycoproteins)

136
Q

What are two important attributes transferred by horizontal gene transfer

A

Virulence and drug resistant factors

137
Q

What is horizontal gene transfer

A

The ability of one mature organism to pass its DNA directly to another mature organism

138
Q

What is vertical gene transfer

A

Passing DNA from a parent to an offspring

139
Q

Why did heat treated cells and harmless cells result in the death of the mouse

A

Horizontal gene transfer of pathogenic genes by transformation

140
Q

What are virulence factors

A

Attributes that help bacteria survive in the host, sometimes at a cost to the host (e.g capsules which prevent phagocytosis). May help with adherence, invasion, proliferation, survival and disease causing

141
Q

What is antibiotic resistance

A

Attributes of bacteria that reduce the effectiveness of antibiotics (e.g beta lactamase enzyme which inactivates penicillin)

142
Q

What is transformation

A

Form of horizontal gene transfer involving the uptake of short fragments of naked DNA by naturally transformable bacteria (dead or dying release genetic material)

143
Q

What is transduction

A

Form of horizontal gene transfer from one bacterium to another via bacteriophages (accidentally will package plasmid from within bacteria and form new type of phage, instead of killing next bacteria will form new type of phage)

144
Q

What is conjugation

A

Form of horizontal gene transfer involving a sexual pilus (cell to cell contact) Doesn’t have to be between same bacteria

145
Q

What is a sex pilus

A

Long tube through which unwound plasmids are transferred

146
Q

What are the features of a bacteriophage

A

Icosahedral head, helical tail, sheath, base plate, tail fibres with very specific ligands to attach to specific bacterial cell membrane

147
Q

What is phage therapy

A

The therapeutic use of bacteriophages to treat pathogenic bacterial infections

148
Q

Are fungi pro or eukaryotic

A

Eukaryotic

149
Q

Are protozoa pro or eukaryotic

A

Eukaryotic

150
Q

Are helminths pro or eukaryotic

A

Eukaryotic

151
Q

Are bacteria pro or eukaryotic

A

Prokaryotic

152
Q

What are Koch’s postulates

A

Guidelines used to demonstrate that a specific pathogen causes specific disease symptoms

153
Q

Outline Koch’s postulates

A

Pathogen must be present in every individual with the disease, sample of microorganism taken from diseased host can be grown in pure culture, sample of pure culture causes same disease when injected into healthy host, microorganism can be recovered from experimentally infected host

154
Q

What are the exceptions to Koch’s postulates

A

Microbes that can’t be cultured, pathogens that can also be found in healthy subjects

155
Q

What are the 4 stages of microbial pathogenesis

A
  1. Adherence to host cells
  2. Invasion of host tissues
  3. Replication within host tissues
  4. Disease causing damage to host tissues (pathology)
156
Q

What is a virulence factor

A

Something that enables a microbe to be pathogenic, protect bacteria from phagocytosis and engulfment by immune cells, prevent cell from drying out (desiccation)

157
Q

What is the virulence factor associated with the adherence stage of microbial pathogenesis

A

Fimbriae

158
Q

What are the virulence factors associated with the invasion stage of microbial pathogenesis

A

Flagella, internalin-related proteins

159
Q

What are the virulence factors associated with the replication stage of microbial pathogenesis

A

Siderophores, capsules

160
Q

What are siderophores

A

Scavenge iron from blood by solubilising and binding, and taking back to bacteria

161
Q

What are the virulence factors associated with the pathology stage of microbial pathogenesis

A

Exotoxins and endotoxins (toxic virulence factors)

162
Q

What are endotoxins

A

Lipopolysaccharides (LPS) components found in the outer membrane of gram negative bacteria, and elicit strong immune responses

163
Q

What effect do endotoxins have

A

Inflammation (, fever, blood clotting, shock) I.e causes our immune system to be overworked, immune system causes the pathology, not LPS itself

164
Q

What are the tree types of exotoxins

A

Cytotoxins, neurotoxins and enterotoxins

165
Q

What are exotoxins

A

Proteins produced within living bacteria and then released into the surrounding medium

166
Q

What do cytotoxins do

A

Destroy cells (e.g beta haemolysis)

167
Q

What do neurotoxins do

A

Destroy the brain (e.g cause paralysis)

168
Q

What do enterotoxins do

A

Harm the digestive system (e.g cause dysentery)

169
Q

What is selective toxicity

A

Finding a way to kill pathogenic cells and not host cells

170
Q

How did the idea of selective toxicity originate

A

Methylene blue stained microbes better than host cells

171
Q

How was penicillin discovered

A

A fungi that prevented bacterial growth (zone of inhibition created)

172
Q

How does penicillin work

A

Interferes with the formation of the host cell wall by inhibiting the formation of peptidoglycan cross links

173
Q

What bacterial cell components can antibiotics target

A

Cell wall synthesis, protein synthesis, cytoplasmic membrane, general metabolic pathway, inhibition of DNA or RNA synthesis, inhibition of pathogen’s attachment or entry into host cell

174
Q

What is the most important cause of genetic diversity in microbial populations

A

Mutation

175
Q

What is the enzyme produced by penicillin resistant bacteria called

A

Beta lactamase

176
Q

How does beta lactamase work

A

Breaks a bond in the beta lactam ring of penicillin to disable the molecule

177
Q

What gene causes the production of beta lactamase on penicillin resistant bacteria

A

blaZ gene

178
Q

How can we reduce the development of antibiotic resistance

A

Decrease antibiotic utilisation, improve diagnostics, identify new targets, combination therapies

179
Q

What are antibiotic combination therapies

A

Traditional antibiotics combined with molecules that block resistance mechanisms

180
Q

What are the five stages of an infectious disease

A

Incubation period, prodromal period, illness, decline, convalescence

181
Q

What characterises the incubation period

A

Infected but no signs and symptoms

182
Q

What characterises the prodromal period

A

Vague, general symptoms

183
Q

What characterises the illness period

A

Most severe signs and symptoms, most amount of microbe so most infectious

184
Q

What characterises the decline period

A

Declining signs and symptoms

185
Q

What characterises the convalescence period

A

No signs or symptoms

186
Q

What is epidemiology

A

The study of disease transmission

187
Q

What are the six parts of the chain of infection

A
  1. Causative agent: pathogenic organism
  2. Reservoir/source (human, animal, water, etc)
  3. Means of exit: way out of the body
  4. Mode of transmission: method of spread
  5. Portal of entry: way into the body
  6. Person at risk (elderly, young, immunocompromised)
188
Q

How can the causative agent stage of the chain of infection be disrupted

A

Rapid detection and treatment

189
Q

How can the reservoir/source stage of the chain of infection be disrupted

A

Good hygiene/sterilisation/disinfection

190
Q

How can the means of exit stage of the chain of infection be disrupted

A

Waste removal/disinfection

191
Q

How can the mode of transmission stage of the chain of infection be disrupted

A

Airflow control/ bed spacing

192
Q

How can the portal of entry stage of the chain of infection be disrupted

A

Aseptic technique catheter/wound care

193
Q

How can the person at risk stage of the chain of infection be disrupted

A

Identifying at risk and targeting them for special care, vaccination and education

194
Q

What is mortality

A

The incidence of death in a population

195
Q

What is morbidity

A

The incidence of cases in a population, fatal and non fatal

196
Q

What is the incidence of a disease

A

The number of new cases of the disease in a given time

197
Q

What is the prevalence of a disease

A

The total number of new and existing cases in a population in a given time

198
Q

What does endemic mean

A

The amount of a disease that is usually present in a community

199
Q

What does sporadic mean

A

A disease that occurs infrequently and irregularly

200
Q

What does epidemic mean

A

An increase, often sudden, in the number of cases of a disease above what is normally expected in that population in that area

201
Q

What does pandemic mean

A

An epidemic that has spread over several countries or continents, usually affecting a large number of people

202
Q

Describe the HIV virus

A

A lentivirus (RNA genome) that causes AIDS, infection through bodily fluids (blood products before recognition), infects and causes failure of the immune system

203
Q

What does sequencing a virus mean

A

Using PCR isolate viral genomes from infected patients

204
Q

What was the key finding of the tree of HIV sequences

A

More variation between patients than within

205
Q

What were the two possible explanations for why there is more HIV variation between patients than within

A

Infections from multiple viruses, viruses are changing

206
Q

What does proximate mean

A

By what mechanism is the change occurring

207
Q

What does ultimate mean

A

What is causing the change

208
Q

Why does HIV change as it proliferates

A

Reverse transcription of RNA genome by reverse transcriptase enzyme which has no proof reading mechanism, resulting in errors

209
Q

Why is HIV mutation classed as evolutionary

A

All variants found encode active working viruses because HIV has variation, inheritance, selection and time

210
Q

What selects for or against HIV variants

A

The immune system, drug regimen, changes in the receptor, tropism in tissues

211
Q

How do we know that HIV evolves (testing)

A

Viruses evolve differently if patient is put on antiretroviral drugs

212
Q

Approximately how many HIV variants could be in a person

A

5x10^10

213
Q

What is a retrovirus

A

A virus that synthesises DNA from its RNA genome (reverse transcription)