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PH1123 Microbiology > cardiff exam-style questions > Flashcards

cardiff exam-style questions Flashcards

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1
Q

why is the bacterial DNA circular unlike eukaryotic DNA?

A

because in bacterial DNA, the 5’ end is attached to the 3’ end which forms the circular nature of bacterial DNA

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2
Q

what’s the difference between gram negative and positive bacteria

A

compare in terms of cell wall/plasma membrane/gram stain/lipid & protein content

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3
Q

how do you differentiate gram positive and gram negative?

A

via gram staining procedure:

  • Gram-positive, the low lipid concentration is important for the retention of the complex iodine-crystal violet: the cells remain blue
  • In Gram-negative, the high lipid concentration found in the outer layers of the cell wall is dissolved which facilitates the release of the iodine-crystal violet complex leaving the cell colourless.
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4
Q

what are the major amino acids that make up the cell wall of bacteria (peptidoglycan layer)?

A
  • n-acetyl muramic acid
  • n-acetyl glucosamine
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5
Q

how does the cell wall (peptidoglycan layer) form in bacteria?

A

penicillin binding proteins help in the final assembly of the outside membrane via the high molecular weight polymer of (n-acetyl muramic acid/glucosamine) attached to several amino acids attached to n-acetyl muramic acid molecules

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6
Q

what types of chemotherapeutic antibiotics are there?

A
  • intracellular
  • glycopeptides
  • beta lactams (PBP inhibitors)
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7
Q

what are the types of beta lactam antibiotics

A
  • penicillins
  • cephalosporins
  • monobactams
  • penems
  • carbapenems
  • beta lactamase inhibitors
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8
Q

what is the chemical composition of plasma membrane of bacteria

A

40% lipid

60% protein

small amount of carbohydrates with no sterols

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9
Q

what is the function of the cytoplasmic membrane?

A
  • Effective permeability barrier of the cell regulating the inflow and outflow of metabolites to, and from the protoplast.
  • the proton motive force that generates adenosine triphosphate (ATP; energy)
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10
Q

what facilitates the release of iodine crystal violet complex in gram negative during gram procedure?

A

the high lipid concentration in the outer layer of the cell wall

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11
Q

what is the function of efflux proteins in bacteria’s cytoplasmic membrane?

A

use chemical energy to transport molecules

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12
Q

compare and contrast:

bacterial vs eukaryotic ribosomes

A
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13
Q

define plasmid

A

a short length of extrachromosomal DNA, they play an important role in the transfer of genetic material between bacteria.

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14
Q

true or false

The chromosome exists as a closed circle in all bacteria and is not surrounded by a nuclear membrane.

A

true

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15
Q

Many bacteria form and store granules in their cytoplasm in the form of high molecular weight polymers. what are they?

A
  • glycogen: a storage form of both carbon and energy
    • polymer of β-hydroxybutyric acid (storage form of both carbon and energy)
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16
Q

what molecules can be stores as inclusion granules in bacteria?

A
  • phosphate as polymeric phosphate volutin
    • protein crystals such as those of Bacillus thuringiensis
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17
Q

look at the different targets of each antibiotic

A

just look at them again

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18
Q

what is the function of flagella

A

enables movement and chemotaxis

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19
Q

what is Pili (fimbriae)?

A

very fine, hair-like, surface filaments, consist of protein sub-units wound around one another generating a hollow core.

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20
Q

Pili can be separated into a number of types based on their function, list its functions

A
    • adherence: both to one another and to foreign cells (e.g. red blood cells)
  • antigenic
  • genetic exchange (gene transfer) by conjugation:
  • attachment sites for bacteriophages
  • Chemotaxis
  • virulence: toxin
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21
Q

bacteria divide by binary fission in 4 steps

A
  1. elongation and DNA replication
  2. cell membrane and cell wall divide
  3. cross wall forms completely around DNA
  4. cell separation
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22
Q

in binary fission, the daughter cell is identical to ________ cell

A

mother cell

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23
Q

define bacterial growth

A

Change in the population rather than an increase in the size or mass of the individual bacterium

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24
Q

explain what happens in each phase of bacterial growth

A
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25
Q

explain what happens in the exponential growth phase in bacterial growth

A

One cell divides producing 2 (‘daughter’) cells.

Total population b at the end of a given period (starting with 1 cell)

b = 1 x 2n

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26
Q

a bioreactor to which fresh medium is continuously added, while culture liquid is continuously removed to keep the culture volume constant. What is the name of the bioreactor?

A

chemostat

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27
Q

what does a chemostat achieve?

A
  • controlled growth rate
  • optimised production
  • continuous fermentation
  • batch fermentation
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28
Q

what are the chemical and physical requirements for the growth of bacteria?

A

Chemical: oxygen, sulfur, phosphorus, ions,carbon,nitrogen,electrons

Physical: temperature, pH, high water activity

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29
Q

how do you prevent microbial growth

A
  • extreme pH > 8
  • -20C deep freeze of raw materials
    • 8-12 syrups/eye drops
    • 80C for WFI
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30
Q

low pH results in spoilage by ___________ e.g. fruit juice flavoured syrups

A

mould and yeast

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31
Q

Water activity of aqueous formulations can be lowered to decrease microbial growth to ________

A

Aw = 0.86

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32
Q

define sterile pharmaceutical products

A

Preparations required to be sterile on the dosage form and other preparations labelled sterile

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33
Q

what is considered a non-sterile pharmaceutical product

A
  • topical products/resp products
  • oral/rectal administration
  • herbal medicines
  • natural product/raw
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34
Q

what is a viable count?

A

The viable count referred as to the number of colony-forming units (cfu)

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35
Q

list the plate count methods

A
  • pour plate
  • spread plate
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36
Q

what type of filter is used for aqueous, oily and weakly alcoholic solutions in bacterial enumeration?

A

Cellulose nitrate filter (0.45 µm membrane filters)

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37
Q

what filter is used for strongly alcoholic solutions in bacterial enumeration?

A

Cellulose acetate

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38
Q

how do you get the total cell count/mass/density/activity?

A
  • Cell count Directly by microscopy or electronic particle counter
  • Cell mass Directly by weighing, measurement of cell nitrogen; measurement of dry weight (oven)
  • Spectrophotometric measurement Measurements of turbidity, optical density
  • Cell activity Indirectly by relating the degree of biochemical activity to the size of the population
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39
Q

what Rapid Microbiology Methods (RMM) are there?

A
  • growth based methods
  • direct measurement
  • cell component analysis
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40
Q

what are examples of growth based RMM?

A
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41
Q

what are examples of direct measurement RMM

A
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42
Q

what is an example of cell component analysis RMM?

A

nucleic acid amplification technique (NAAT)

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43
Q

why are the classifications of life based on RNA

A

because rRNA is present in all living cells thus they can be classified into similar categories

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44
Q

what are the three domains of life

A
  • eukaryotic
  • prokaryotic
    • archaea
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45
Q

staphylococcus aures

state the genus and the species

A

genus: staphylococcus
species: aures

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46
Q

what are the traditional and newer bacterial identification techniques?

A

traditional:

  • cultivation growth: requirement
  • selective agar
  • biochemical profiling
  • serological testing

New:

  • nucleic acid techniques
  • MALDI TOF
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47
Q

what are the rapid bacterial identification methods?

A
  • serological testing
  • nucleic acid techniques
  • MALDI TOF
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48
Q

what is pure culture?

A

a culture containing a growth of a single kind of organism free from other organisms and is dependent on its growth requirements

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49
Q

what does pure culture help identify?

A
  • Morphological characterisation
  • Shape (cocci, bacilli, etc)
  • Staining characteristics endospore production flagella capsule
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50
Q

what is selective media?

provide an example of a type of selective media

A

suppressing the growth of all bacteria while promoting the growth of only one selected type

e.g. MacConkey agar/ vogel johnson agar

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51
Q

what is biochemical profiling based on?

provide examples of biochemical profiling

A
  • growth requirements of the organism
  • enzymatic activities

e.g. sugar fermentation/oxidase production/hydrogen sulfide production

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52
Q

what are the positives and negatives of cultivation?

A
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53
Q

how does serological testing work? provide an example of a serological test

A

Uses highly specific antibody (Ab) antigen (Ag) interaction

e.g Enzyme Linked Immunosorbent Assay (ELISA)

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54
Q

how does Enzyme Linked Immunosorbent Assay (ELISA) work?

A
  • Sensitive: signal amplified by conjugate enzyme
  • Quantitative (linked to the concentration of antibodies (intensity of colour depend on antibody concentration)
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55
Q

what are the positives and negatives of serological testing?

A
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56
Q

what are Polymerase Chain Reaction (PCR)?

A

Polymerase Chain Reaction (PCR) based techniques allow amplification of a known gene of interest for nucleic acid sequencing, allows accurate identification of genus/species

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57
Q

how do PCRs work?

A
  1. Gene sequence is compared with online database e.g. NCBI (National Center for Biotechnology Information)
  2. BLAST tool finds regions of similarity between your sequence and those identified previously
  3. Gene sequence is then compared with online database e.g. NCBI (National Center for Biotechnology Information)
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58
Q

what are the positives and negatives of pcr tests

A
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59
Q

how do microarrays work in the identification of bacteria?

A
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60
Q

what does whole genome sequencing tell you?

A
  • bacterial identification
  • metabolism
  • growth requirements
  • pathogenecity
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61
Q

what does MALDI-TOF stand for

A

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry

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62
Q

how does MALDI TOF work?

A
  1. bacteria mixed with matrix material
  2. bombarded with laser pulses
  3. Sample is ionised and passed through electrostatic field (acceleration)
  4. Ions pass through flight tube before hitting detector
  5. Generates a unique mass spectrum for different bacteria
  6. check spectrum with database
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63
Q

what are the advantages and disadvantages of maldi tof

A
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64
Q

what species are capable of sporulation?

A

bacillus

clostridium

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65
Q

Spores enable the survival of the bacterium (genetic material) during harsh conditions such as ________

A

lack of food& water

chemical and physical stress

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66
Q

draw an endospore

A
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67
Q

define sporulation

A

the formation of spores

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68
Q

is sporulation a reproductive process?

A

NOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

you’ll remember that for sure

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69
Q

what is germination

A

Germination is the process by which a spore reverts into a (vegetative) bacterium

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70
Q

Germination can be forced to occur using certain chemicals called germinants such as_______

A

D-alanine

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71
Q

talk about the stages of sporulation/germination

A
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72
Q

what are the properties of spores

A
  • highly dehydrated
  • no metabolic activity
  • constituents (e.g. small acid soluble proteins, SASPs; dipicolinic acid)
  • structure (lots of coats)
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73
Q

how are spores eliminated?

A

High-level disinfection: kill (99.999% reduction or 5 log10 reduction in viability) of micro-organisms including spores

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74
Q

what is the function of spore coats in an endospore?

A

barrier to biocides

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75
Q

what are the properties of inner membrane of endospores?

A
  • highly compressed
  • barrier to biocides
  • barrier to rehydration
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76
Q

what does the spore core contain?

A

Small Acid Soluble Proteins (SASPs) that Protect nucleic acid and low water content 10-30%

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77
Q

process that kill all micro-organisms including spores

A

sterilization

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78
Q

The use of broad spectrum chemotherapeutic antibiotics is associated with an increased risk of developing ___________

A

C.diff associated disease (CDAD)

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79
Q

Chlamydia are obligate intracellular bacteria, what does that mean?

A

they lack the metabolic pathway to produce their own high-energy phosphate compounds (“energy parasites”)

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80
Q

what are the forms of chlamidya

A
  • the small (300-400nm) extracellular infectious elementary body (EB)
  • the larger (800-1000nm) intracellular non-infectious reticulate body (RB)
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81
Q

describe the structure of chlamidya

A
  • internal and external membrane similar to Gram-negative bacteria
  • no peptidoglycan layers
  • lipopolysaccharide
  • no flagella and non-piliated
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82
Q

how is chlamidya treated?

A
  • Tetracyclines: doxycycline 100 mg bds; 7 days
  • Macrolides: azithromycin 1g: single dose.
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83
Q

explain how chlamidya infections occur

A
  1. Elementary Body are metabolically inactive and represent the extracellular C. trachomatis growth form. EB are highly infectious
  2. Once ingested into a phagosome, fusion of the phagosome with the host lysosome is prevented
  3. The EB reorganizes within the phagosome into a metabolically active (not infectious) Reticulate body
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84
Q

mycobacteria is a gram positive bacteria

A

remember that

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85
Q

explain and draw the structure of mycobacteria

A
  • highly hydrophobic cell wall (peptidoglycan connected to arabinogalactan) esterfied to mycolic acid structure
  • 25% of the dry weight is free lipids located outside the outer layers
  • cord factor (6,6”-dimycolate of trehalose)
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86
Q

what is mycolic acid found in mycobacteria

A

High-molecular-weight (60-90 carbons) 3-hydroxy fatty acid.

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87
Q

what lipids are there in mycobacteria

A
  • waxes
  • , species-specific mycosides (complex glycolipids and peptidoglycolipids
  • lipopolysaccharides
  • cord factor (6,6”-dimycolate of trehalose)
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88
Q

who are at risk of TB?

A
  • close contact
  • places where TB is common
  • immunocompromised
  • poor lifestyle factors
  • young children/elderly
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89
Q

what are the first line of treatment for TB

A

isoniazid, rifampicin, pyrazinamide, ethambutol

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90
Q

why are Anti-TB drugs always prescribed in combination

A

to reduce the risk of the TB bacilli becoming resistant to one or more of them

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91
Q

why is It vital that TB medication is taken as prescribed

A

. Taking anti-TB medication in the wrong dose, intermittently or for too short a time can result in the development of drug resistance

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92
Q

why is necessary that a course of anti-TB drugs lasts for at least six months?

A

because the medicine is most effective against bacilli that are “awake” and growing.

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93
Q

define Infectious diseases

A

also known as transmissible diseases or communicable diseases comprise clinically evident illness, resulting from the infection, presence and growth of pathogenic biological agents in an individual host organism.

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94
Q

what are the determinant factors of an infectious disease?

A
  • Adhere to colonise or invade the host.
  • Multiply or complete its life cycle on or in the host or the host’s cells.
  • Initially evade the hosts defence mechanism.
  • Possess the mechanical, chemical, or molecular ability to damage the host.
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95
Q

what is an opportunistic pathogen

A

normal flora, able to cause disease at a time of immune compromise

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96
Q

what does asymptomatic carrier mean

A

pathogenic organisms that may be present in a large percentage of the population without causing disease (not microflora)

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97
Q

what bacteria can one be an asymptomatic carrier to

A

clostridium difficile

Methicillin resistant Staphylococcus aureus

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98
Q

the degree or intensity of pathogenicity of an organism is known as

A

virulence

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99
Q

a microbial (bacteria, fungi, protozoa…) product that contributes to virulence is known as

A

virulence factor

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100
Q

what are the virulence factors of E.coli

A
  • Adhesin - colonization factor (CFA1, CFA2)
  • Endotoxin- lipopolysaccharide (pyrogen)
  • Exotoxin - heat-labile (LT) enterotoxin - Vero cytotoxin-producing E. coli (VTEC) e.g. E. coli O157
  • Invasin (uropathogenic E. coli)
  • Capsule - evade phagocytosis
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101
Q

is antibiotic resistance a virulence factor?

A

NOPE NOPE NOPE AND NOPE

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102
Q

define Toxin

A

substance produced by an organism to damage the host

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103
Q

what types of toxins are there and what’s the difference?

A

Exotoxin Usually proteins released by bacteria as it grows and divides. small amounts cause disease,antigenic, unstable

Endotoxin - Bound to bacterium and is released when the bacterium lyses - Gram-negative bacteria; lipopolysaccharide (lipid A)

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104
Q

what bacterial exotoxins are there?

A
  • neurotoxins
  • enterotoxins
  • cytotoxins
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105
Q

how do exotoxins mediate their effects?

A
  • membrane damaging
  • membrane acting
  • intracellular
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106
Q

provide examples of exotoxins and their mechanism of action

A
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107
Q

what are the properties of endotoxins?

A
  • weakly immunogenic
  • stable
  • capable of producing general systemic effects
  • toxic at high doses
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108
Q

what do the lipopolysaccharides of gram-negative bacteria constitute

A
  • lipid A (responsible for toxicity)
  • core polysaccharide (intermediate)
  • o specific side chain (antigenic outermost)
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109
Q

what is capsule in bacteria?

A

Loose-fitting, gelatinous structure that surrounds some bacteria.

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110
Q

what is the function of bacterial capsule?

A
  • prevents phagocytosis
  • water protects against dessication
  • protection against detergents
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111
Q

where are the virulence genes located within the bacteria?

A

chromosomes / plasmids

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112
Q

what is the function of virulence genes in plasmids?

A
  • export of virulence factors directly into cells
  • Confer a variety of virulence traits (e.g. cell adherence, cell entry, toxins)
  • radical changes in bacterial-host interactions
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113
Q

list all 22 antibiotic classes

A
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114
Q

a comparison of the amount of a therapeutic agent that causes the therapeutic effect to the amount that causes death (in animal studies) or toxicity (in human studies)” is known as

A

Therapeutic index/therapeutic dosage level

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115
Q

Therapeutic index = TD50 / ED50

what is td50 and ed50

A

TD50: dose that produces a toxicity in 50% of the population ED50: minimum effective dose for 50% of the population

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116
Q

Higher the therapeutic index, the more effective and less toxic the antibiotic

A

yes

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117
Q

provide examples that are NOT contraindicated in penicillin allergy

A

Amikacin

Minocycline

Azithromycin

Moxifloxacin

Chloramphenicol

Nitrofurantoin

Ciprofloxacin

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118
Q

what antibiotics are high risk of causing CDAD

A
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119
Q

list bacteria that have developed resistance

A
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120
Q

what’s the difference between intrinsic and acquired resistance?

A

intrinsic resistance: natural property of a micro-organism

Acquired resistance: can be transferred between bacteria

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121
Q

what are the mechanisms by which bacteria confer resistance to antibiotics?

A

intrinsic: a natural property of the microorganism

Acquired resistance: can be transferred between bacteria

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122
Q

what are examples of intrinsic bacterial resistance?

A
  • impermeability barrier (change in permeability)
  • efflux
  • enzymatic inactivation
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123
Q

what are examples of acquired bacterial resistance?

A
  • decreased uptake/permeability
  • decreased accumulation (efflux)
  • enzymatic inactivation
  • duplication & overproduction of targets
  • modification of target site
  • bypass of a metabolic pathway/enzyme
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124
Q

which domain of life do fungi belong to

A

eukaryotes

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125
Q

what are the properties of fungi?

A

eukaryotic

spore-bearing

absorptive nutrition

no chlorophyll

reproduce sexually and asexually

cell wall made of chitin (polysaccharide)

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126
Q

what’s the difference between saprophytes and parasites?

A

Saprophytes: live on dead plant and animal material

Parasites: live on/in living material

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127
Q

name 3 types of fungal metabolism

A
  • Aerobic (e.g. generate ATP from glycolysis)
  • Facultative anaerobes-fermentation (make ethyl alcohol from glucose)
  • Obligate anaerobes (rumen of cattle)
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128
Q

90,000 fungal species -only approx. 50 cause human diseases

A

Read that again, 50

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129
Q

define mycoses

A

a disease caused by infection with a fungus, such as ringworm or thrush

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130
Q

who are the risk patients of fungal infections?

A
  • immunocompromised
  • chemotherapy/radiotherapy
  • indwelling catheters
  • corticosteroid treatments
  • surgery
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131
Q

name two opportunistic fungal pathogens

A

aspergillus fumigatus

candida albicans

132
Q

name a systemic fungal disease and its pathogen

A

Blastomycosis caused by → Blastomyces dermatitidis

133
Q

what type of fungal infection is athlete’s foot and what fungus causes it

A

it is a cutaneous fungal infection caused by trichophyton rubrum

134
Q

what causes Black piedra and what type of mycosis is it?

A

superficial, affecting the scalp, and caused by Piedraia hortae

135
Q

what is candidiasis

A

a systemic fungal infection

136
Q

how do fungal infections spread?

A

Fungal spores (moulds) - Inhaled - Cut or wound

Direct contact (yeast)

137
Q

what are mycotoxins?

A

naturally occurring toxins produced by certain moulds (fungi) and can be found in food.

138
Q

what are the outcomes of mycotoxins

A
  • intoxication (digestion)
  • allergies
    • infection
139
Q

provide examples of contagious cutaneous dermatomycoses

and non-contagious subcutaneous dermatomycoses

A

contagious: Tinea pedis, Tinea capitis, Tinea corporis

non-contagious: sporotrichosis, chromomycosis,

140
Q

list some Non-contagious systemic infections

A
  • aspergillosis
  • blastomycosis
  • cryptococcosis
  • histoplasmosis
  • sporotrichosis
141
Q

describe oral thrush

A
  • White deposit on the tongue, oral cavity
  • Most common: acute pseudomembranous candidiasis
  • Asymptomatic lesions
142
Q

how is candida diagnosed

A
  • Identification of clinical signs and symptoms
  • Presence of candida on direct examination
  • Biopsy examination showing hyphae in the epithelium
  • Positive culture
  • Serological tests
143
Q

how is candida albicans cultured?

A

on a Sabouraud glucose agar, 25°C

144
Q

candida albicans is an opportunistic pathogen, what makes it manifest as a disease?

A

disruption of microflora

145
Q

candida albicans is dimorphic, what does that mean?

A

Can change from yeast form to mycelial, depending on environmental factors: nutrients, CO2 ,temperature

146
Q

true or false

candida albicans are strict aerobes

A

true

147
Q

what is chitin (cell wall of fungi)

A

natural polymer of n-acetyl glucosamine

148
Q

how much of the cell wall does chitin make up?

A

80%

149
Q

why is chitin a good antifungal therapy target?

A

because chitin is absent in mammalian cells, meaning the drug (caspofungin) will not be toxic to human cells

150
Q

what is the function of ergosterol in fungal cells?

A

it is synthesized for incorporation in plasma membrane that limits the permeability of the membrane

this makes the cytoplasmic membrane sensitive to antimicrobial agents which either block the synthesis of ergosterol (e.g. azoles) or bind specifically to the ergosterol (e.g. polyene antifungals)

151
Q

how does yeast reproduce?

A

by budding, producing daughter diploid cells that are identical to mother cell with no genetic diversity

152
Q

what species of aspergillus are the most common causes of aspergillosis?

A

aspergillus fumigatus

aspergillus flavus

153
Q

what is pulmonary aspergillosis?

A

opportunistic infection that gains entry through the respiratory tract that may cause an allergic response (mycotoxins), it can spread to other organs

154
Q

who is at risk of aspergillosis

A
  • immunocompromised
  • neutropenia
  • leukemia
  • chemotherapy
  • corticosteroid treatment
155
Q

Hyphae can be _______ or crossed walled-septa

A

continuous

156
Q

define hyphae

A

Long branched thread-like filaments of cells

157
Q

when do yeast reproduce sexually and asexually

A

when starved: sexual (fusion)

when there’s plentiful food supply: asexually (budding)

158
Q

what makes antifungal therapy difficult?

A

Similarity to human

Drugs tend to be more toxic

Repeated applications

Lengthy treatments

159
Q

are the drug targets for antifungals?

A

ergosterol

chitin

b-1,3 glucan synthase

membrane sterols

160
Q

what is the mechanism of action of itraconazole

A

inhibits cytochrome P450 14α-demethylase (P45014DM), Enzyme required in the sterol biosynthesis pathway, prevents lanosterol methylation to ergosterol, thus lessening the amount of ergosterol in cell wall leading to membrane instability, growth inhibition, and cell death

161
Q

what is the mechanism of action of amphoterecin B

A

binds ergosterol, the dominant sterol in fungal cells, increasing membrane permeability by formation of pores allowing escape of intracellular potassium, magnesium, sugars, and metabolites

162
Q

what are the toxicity problems caused by amphoterecin b

A

cardiovascular

renal

hepatic

163
Q

what are the properties of protozoa

A
  • eukaryotic
  • unicellular
  • heterotrophic
  • parasitic (commensal)
  • live in aqueous environments
164
Q

provide 3 examples of protozoal diseases and their pathogenic cause

A

Giardiasis → Giardia intestinalis

Amoebiasis → Entamoeba histolytica

malaria → plasmodium vivax

165
Q

what are the Plasmodium-ameboid intracellular parasites

A

P. vivax, P. falciparum, P. malariae

166
Q

how is malaria prevented?

A
  • mosquito control
  • prophylaxis drugs and exposure
  • rapid identification
167
Q

what drugs can be used for prophylactic treatment of malaria?

A
  • Chloroquine
  • Mefloquine
  • Doxycyline
  • Malarone
168
Q

what types of treatments are there for malaria?

A
  • Artemisinin-based combination therapy (ACT)
  • co-formulated drugs (Malarone or riamet)
169
Q

For P. falciparum two or more drugs with different modes of action in combination are now recommended, why?

A

Combination therapy to prevent malaria parasite’s resistance from developing

170
Q

what are companion drugs of ACT

A

lumefantrine, mefloquine, amodiaquine

171
Q

what do Artemisinin derivatives include

A

dihydroartemisinin

artesunate

artemether

172
Q

define co-formulated drug

A

one in which two different drugs are combined in one tablet

173
Q

what is the mechanism of action of malarone?

A

Proguanil interferes with two different pathways involved in biosynthesis of pyrimidines (cytosine, thymine, uracil) required for nucleic acid replication.

Atovaquone -Inhibit electron transport chain

174
Q

what is the mechanism of action of riamet?

A

Interferes with the ability of the malaria parasites to convert heme into hemozoin.

Causes levels of the toxic heme to rise, which kills the blood stages of the malaria parasites

175
Q

how is Cryptosporidiosis transmitted?

A

fecal-oral route

176
Q

how is Cryptosporidiosis diagnosed?

A

stool sample

177
Q

how do you treat Cryptosporidiosis

A
  • Fluid and electrolyte replacement
178
Q

what are the symptoms of Cryptosporidiosis

A

abdominal pain

diarrhea

nausea

179
Q

what organism causes Cryptosporidiosis

A

Cryptosporidium parvum, hominis

180
Q

who is a risk patient for severe Cryptosporidiosis

A

HIV patients

181
Q

what organism causes Amoebiasis

A

Entamoeba histolytica

182
Q

describe amebiasis

A
  • range from mild diarrhea to dysentery with blood and mucus in the stool.
183
Q

how is Amoebiasis transmitted?

A

fecal-oral route

184
Q

how is Amoebiasis diagnosed

A

stool sample

185
Q

what are the forms of severe Amoebiasis

A
  • Invasion of the intestinal lining causes amoebic dysentery or amoebic colitis.
  • Parasite reaching the bloodstream and becoming systemic, most frequently ending up in the liver where it causes amoebic liver abscesses
186
Q

how do you treat amoebiasis?

A
  • Metrodinazole
  • Tinidazole
  • Diloxanide fluorate (Asymptomatic patients)
187
Q

what are helminths?

A

Parasitic worms

188
Q

what are the transmission routes for helminths

A

Schistosome or hookworm larvae directly penetrate the skin from infected water or soil

Filarial worms (e.g. Onchocerca) transmitted by insect vectors

189
Q

what are examples of helminthic infections

A
  • Schistosomiasis (bilharzia)
  • Cysticercosis
  • Lymphatic filariasis (elephantiasis)
  • Onchocerciasis (river blindness)
190
Q

what is a major risk for developing helminth infections

A

inadequate sanitation

191
Q

what are the general symptoms of helminthic infections

A
  • asymptomatic (a few roundworms). \
  • reduced nutritional uptake
  • intestinal obstruction or bleeding
  • rectal prolapse
  • presence of a worm within vomit or stools.
192
Q

how do tapeworms gain entry to human body

A

ingestion of uncooked meat (eggs)

193
Q

talk about the life cycle of helminths

A
194
Q

name two antihelmintic drugs and their mechanism of action

A

Praziquantel: Increases membrane permeability to calcium ions, paralyzing the parasite

Mebendazole: Inhibits the synthesis of microtubules, glucose uptake

195
Q

true or false

viruses are acellular, they are only carriers of genetic material (RNA/DNA)

A

true

196
Q

how are viruses classified?

A

enveloped

nonenveloped

197
Q

viruses are obligatory intracellular parasites, what does that mean?

A

they require a host for replication

198
Q

true or false

viruses cause diseases in all living organisms, including bacteria

A

true

199
Q

what is the viral envelop?

A

surrounds the viral capsid, derived from portions of the host cell membranes

200
Q

true or false

enveloped viruses can survive longer when mixed with fomites (blood/mucus)

A

true

201
Q

what is the viral capsid

A

s the protein shell that encloses the nucleic acid. It is built of structure units known as capsomeres

202
Q

what forms of capsid are there

A

icosahedral

helical

203
Q

define viral receptors

A

Glycoproteins (virus encoded) on the surface of the envelope or protruding from the capsid serve to identify and bind to receptor sites on the host’s membrane

204
Q

how do viruses gain entry to the host cell

A

endocytosis

fusion

205
Q

describe the properties of the viral genome

A

Either RNA or DNA but can be single or double stranded, circular or linear

206
Q

describe the steps in the virus life cycle

A
  1. attachment and penetration
  2. uncoating and macromolecular synthesis of nucleic acids
  3. assembly of progeny virions and release into host cells
207
Q

define antigenic shift

A

Process by which two or more different strains of a virus, or strains of two or more different viruses, combine to form a new subtype having a mixture of the surface antigens of the two or more original strains

208
Q

what types of influenza reassortment are there

A

antigenic drift

antigenic shift

209
Q

define antigenic drift

A

Small changes (mutations) in the virus that happen continually over time, Difficult to immunise/vaccinate for long term protection

210
Q

what is herpes virus latent infection

A

when it persists in a quiescent but persistent form in the neural ganglia

211
Q

how does HSV infect the mucosal epithelia?

A
  • Productive replication, production of progeny virions and virions spread to infect additional epithelial cells
  • Virus enters innervating sensory neurons, and nucleocapsids are transported to the neuronal cell body
  • Viral DNA is released into the neuronal nucleus and circularizes
    • Circular viral DNA persists in the neuronal cell nucleus
212
Q

how is HSV reactivated

A
  1. Initiation of viral lytic gene expression
  2. Newly formed capsids are transported to the axonal termini
  3. Infectious virus is released from the axon and infects epithelial cells leading to recurrent infection and shedding
213
Q

what type of viruses are coronaviruses

A

Enveloped, positive-sense RNA viruses

214
Q

true or false

coronaviruses are responsible for up to 30% of common colds

A

true

215
Q

Coronaviruses use a viral__________________ enzyme to synthesize mRNA

A

RNA-dependent RNA-polymerase

216
Q

_________ mediates RNA proofreading and regulate replication fidelity

A

Viral RNA exonuclease

217
Q

why are coronaviruses able to produce new strains that often cause pandemics?

A

Combination of RNA recombination, high polymerase error, and regulated replication fidelity appears to favor the generation of recombinant and highly diverse populations of viruses with the potential to cross species and subsequently adapt to new hosts

218
Q

how does RNA-RNA recombination occur?

A

“jump” across an RNA template or between two different templates

219
Q

SARS-CoV is a zoonotic virus likely derived from _____

A

bats

220
Q

what does MERS-COV stand for

A

Middle East respiratory syndrome

221
Q

_____________ may be a major reservoir host for MERS-CoV

A

Dromedary camels

222
Q

SARS-COV-2 resulted in a pandemic in the year of ______

A

r u serious? 2020

223
Q

what are the properties of HIV

A
  • retrovirus
  • infects CD4+ and destroys them
  • severely weakens immune system
224
Q

define AIDS

A

Defined as an HIV infection with either a CD4+ T cell count below 200 cells per µL

or

the occurrence of specific diseases associated with HIV infection

225
Q

how is HIV transmitted

A

Unprotected sex

Sharing needles, syringes or other injecting equipment

Transmission from mother to baby during pregnancy, birth or breastfeeding

226
Q

primary HIV is asymptomatic or associated with _________

A

acute retroviral syndrome

227
Q

describe the stages of HIV

A
228
Q

To design a drug, one needs to understand virus life cycle.

describe the life cycle of HIV

A
229
Q

what do antivirals target

A

virus specific enzymes

life cycle processes

230
Q

what is the aim of HIV antiviral therapy

A

reduce viral levels (viral load < 50copies/ml) and reduce AIDS-related illnesses

231
Q

what is the mechanism of action of zidovudine

A

zidovudine is nucleoside reverse transcriptase inhibitor, which acts as a nucleoside analogue , it prevents any more DNA from being made - by blocking further extension of the growing DNA chain.

it does so by inserts a molecule of zidovudine rather than a nucleoside, This terminates the DNA chain and no more can be appended to

232
Q

what is the mechanism of action of non nucleoside reverse transcriptase inhibitors? provide an example of an NNRTI

A

NNRTIs attach to the reverse transcriptase and affect the activity of the enzyme by restricting its mobility and making it unable to function

Example: Efavirenz

233
Q

what is the function of viral protease

A

an enzyme that cleaves peptide/polypeptide/protein chains

234
Q

what is the mechanism of action of protease inhibitors

A

HIV protease inhibitors binds to enzyme active site. HIV virus is therefore unable to process proteins

235
Q

what is viral integrase

A

an enzyme that allows the transfer of HIV cDNA to cellular DNA

236
Q

what is the mechanism of action of integrase inhibitors?

provide 2 examples of integrase inhibitors

A

Dolutegravir

Raltegravir

237
Q

define Fusion inhibitor, provide an example

A

an enzyme that prevent HIV envelope fusion

Enfuvirtide

238
Q

a protein on the surface of white blood cells that is involved in the immune system as it acts as a receptor for chemokines (chemotactic cytokines.) this is known as

A

C-C chemokine receptor type 5, also known as CCR5 or CD195

239
Q

what is the function of viral DNA polymerase

A

enzyme that creates DNA molecules by assembling nucleotides – essential for viral DNA synthesis

240
Q

what drug is used to treat HSV? and what is its mechanism of action?

A

Acyclovir is converted by viral thymidine kinase to acyclovir monophosphate which is then converted by host cell kinases to acyclovir triphosphate (ACV-TP)

ACV-TP competitively inhibits and inactivates HSVspecific DNA polymerase

241
Q

what is the mechanism of action of Neuraminidase inhibitors

A

prevent the release of the virions

242
Q

what does prodrug mean?

A

an inactive drug that needs to be hydrolysed in the liver to function

oseltamivir → oseltamivir carboxylate

243
Q

what makes viral diagnosis difficult?

A

Viruses have to be cultured in the presence of the host cell

244
Q

how does plaque assay of viruses work

A
  1. Grow a lawn of host cells on dish
  2. Add virus
  3. Virus replicate and lyse host cells
  4. Viral Plaques: cytopathic effect
245
Q

what is plaque forming units (PFU)

A

measure of infectivity not number of viruses

246
Q

what are immunodiagnostics

A

Detection of host antibodies against virus

247
Q

what is hemaegglutination

A

causing red blood cells to stick together

248
Q

Presence of anti-virus _______ in patient serum can inhibit reaction

A

antibodies

249
Q

what does Haemagglutinin Inhibition Assay (HI Test) - Inflluenza do?

A
  • Measure how well antibodies bind to (and thus inactivate) influenza viruses
  • RBCs (turkey, guinea pigs) in a solution will sink to the bottom of the assay well and form a red dot at the bottom
  • When an influenza virus is added to the RBC solution, the virus’ haemagglutinin surface proteins bind to multiple RBC and keep RBCs suspended
250
Q

what methods of molecular biology are used to diagnose viruses

A

o Viral DNA hybridisation with labelled probes

o Sequencing of portions of the viral genome

o Polymerase chain reaction

251
Q

according to the baltimore classification system, list the 6 virus classes

A
  1. Double stranded DNA
  2. Single stranded DNA
  3. Double stranded RNA
  4. Single stranded RNA
  5. Single stranded RNA
  6. Double stranded DNA
252
Q

what are the subviral agents

A

satellites

viroids spongiform encephalopathies

253
Q

list the dsDNA viruses

A

Poxviruses

adenoviruses

Herpes

253
Q

list the dsDNA viruses

A

Poxviruses

adenoviruses

Hepres

254
Q

list ssDNA viruses

A

parvovirus

255
Q

what class of viruses is Rotaviruses

A

dsRNA viruses

256
Q

list ssRNA viruses

A

Togaviruses

Orthomyxoviruses

Rhinoviruses

Paramyxoviruses

Picornaviruses

257
Q

what viruses are considered retroviruses

A

hepatitis B

HIV

258
Q

what are reverse transcriptase viruses

A

there is an RNA intermediate before viral proteins can be manufactured.

259
Q

true or false

Group VII can first transcribe their DNA into RNA, then transcribe it back to DNA (using reverse transcriptase) before it is inserted into the host DNA

A

true

260
Q

what is the function of reverse transcriptase in retroviruses

A

The enzyme is responsible for transcription of the viral RNA to produce a dsDNA that can be inserted into the host genome

261
Q

where is the normal flora located

A

stomach

small intestine

large intestine

urethra

vagina

nasopharynx

262
Q

what is the metabolic function of microbiome

A
  • Provide vital biochemical pathways for the metabolism of non-digestible carbohydrates (cellulose, hemicellulose, pectins, and gums), some oligosaccharides, unabsorbed sugars, alcohols and host-derived mucins
  • Synthesis of vitamins - Enteric bacteria secrete Vitamin K and Vitamin B12
    • Stimulate the development of certain tissues (Caecum; caecum of germ-free animals is enlarged, thin-walled, and fluid-filled)
263
Q

what is the immune function of the microflora

A
  • Produce antimicrobial compounds - Fatty acids and peroxides to highly specific bacteriocins.
  • Compete for nutrients and sites of attachment in the gut lining, preventing colonization by pathogens (barrier or competitive-exclusion effect)
  • intestinal epithelium is the main interface between the immune system and the external environment
  • Exposure to intestinal bacteria is also implicated in the prevention of allergy
  • The normal flora stimulates the production of cross-reactive antibodies.
264
Q

what is the function of the gut brain axis

A
  • Bidirectional communication system that integrates neural, hormonal, and immunological signalling between the gut and the brain.
  • Stress influences the composition of the gut microbiota
  • Stress influences the integrity of the gut epithelium and alter peristalsis, secretions, and mucin production.
265
Q

what is the function of mucins

A

Glycoproteins that are expressed in cells

Signal transduction

Regulation of gene expression

Cell proliferation

Embryogenesis

Cell differentiation

Immunity

Apoptosis

Cancer

266
Q

what is irritable bowel syndrome

A

Gut microbiota alteration linked to low-grade intestinal inflammation (inflammatory Bowel Disease)

267
Q

what is obesity as a metabolic disease

A

alteration of Firmicutes/Bacteroidetes ratio in the gut microbiota

268
Q

true or false

diabetes type 2 impacts the composition of intestinal microbiota

A

true

269
Q

what are probiotics

A

Probiotics are microorganisms that are believed to provide health benefits when consumed.

270
Q

The inflammation of the colon is pseudomembranous colitis and is generally caused by________

A

antibiotic associated diarrhea

271
Q

C. difficile normally are indigenous bacteria, able to proliferate when most of the normal intestinal flora killed by the ________

A

antibiotic

272
Q

why does eukaryotic DNA forms a helix?

A

The nucleobases in DNA have the ability to form hydrogen bonds between themselves, the poly nucleotide chain of DNA coils into a helix, which gets bonded to another helical strand by hydrogen bonds between the appropriate base pairs

273
Q

what are the base pairs of DNA

A

In DNA, the base pairs are A-T (2 hydrogen bonds) and C-G (3 hydrogen bonds)

274
Q

what is DNA made up of

A

long unbranched chain of oligonucleotides, which are linked via a phosphate group that joins the sugar unit with the nucleobase

275
Q

The ester linkage between nucleotides is often a __________

A

phosphodiester bond.

276
Q

phosphate group in nucleotides is attached via a ________

A

phospho ester linkage

277
Q

nucleobase is linked to the sugar unit through an ___________ bond at C1.

A

N-glycoside

278
Q

purines are linked through ______ while pyrimidines are linked through ________

A

N9

N1

279
Q

what are nucleotides?

A

polymers of nucleic acids that are structurally made up of a heterocyclic base, sugar, phosphate

280
Q

what is the most notable difference in DNA & RNA

A

deoxyribose in DNA and ribose in RNA

281
Q

what is a nucleoside?

A

nucleotide lacking a phosphate group

282
Q

what types of bases are there?

A
  • monocyclic pyrimidines: cytosine, thymidine, uracil
    • bicyclic purines: adenine, guanine
283
Q

what type of sugar is the one in DNA/RNA

A

Pentoses

They are D-ribose in RNA and 2-deoxy-D-ribose in DNA

284
Q

describe the structure of DNA

A
  • bases are directed inwards to allow hydrogen bonding (base pairing)
  • sugar units and the phosphodiester bonds will of the main chains form the outside part of the double helix
  • The helix makes a complete turn every 10 bases
  • The chains are antiparallel
285
Q

how do the minor/major grooves form

A

because the glycoside bonds between the sugars and bases of a particular base pair are not directly opposite to each other, grooves along the outside of the double helix array are unequal in with giving rise to what is known as the minor groove and major groove

286
Q

DNA replication proceeds in 3 enzymatically mediated steps known as

A
  • initiation
  • elongation
  • termination
287
Q

DNA replication is initiated in DNA regions known as ______

A

origins

288
Q

what is the function of helicases in DNA replication

A

break the hydrogen bonds that ‘bind’ the DNA stands together

289
Q

DNA synthesis is catalyzed by __________ enzyme

A

DNA polymerase

290
Q

how is termination achieved in DNA replication

A

blocking the replication fork and this is often achieved by DNA replication terminus site binding proteins

291
Q

The precursors for the synthesis of new DNA strands are___________

A

nucleoside triphosphates

292
Q

triphosphate anhydrides are susceptible to nucleophilic attack from _______

A

hydroxyl groups

293
Q

true or false

DNA chain extension is simply an esterification reaction of the 3’-hydroxyls using the triphosphate anhydrides that have the diphosphate as a good leaving group

A

true

294
Q

how does RNA differ from DNA?

A
  • . The sugar in RNA is ribose while in DNA its deoxyribose.
  • Thymine is replaced by uracil in RNA.
  • RNA is usually single stranded.
  • DNA stores genetic information and RNA participate in the processes by which this information is used.
295
Q

what are the three major forms of RNA found in prokaryotic cells

A
  • mRNA
  • tRNA
  • rRNA
296
Q

It’s the sequence of bases along one DNA strand which provides information for the synthesis of proteins in an organism. this is known as?

A

the coding strand

297
Q

what is template strand

A

a complementary strand to the coding strand

298
Q

DNA segment that contains the information necessary for the synthesis of one protein.

who am i?

A

gene

299
Q

a sequence of 3 nucleotides

A

codons

300
Q

true or false

Every amino acid is designated 2 or 3 specific triplet codons

A

true

301
Q

what are stop codons

A

Three different codons which stop the translation process

302
Q

Describe the stereochemistry of amino acids

A

Almost all amino acids contain a chiral centre on the alpha carbon. All naturally occurring amino acids have L-stereochemistry, i.e. they have the same configuration as the reference compound glyceraldehyde. D-amino acids are very rare, and are the product of biosynthesis

303
Q

Explain what is unusual about the stereochemistry of glycine. Explain your answer

A

Glycine has no chiral centre and therefore cannot exist in L/D-forms. The alpha carbon does not have four non-identical groups attached, two are hydrogen (i.e. identical)

304
Q

Provide a concise definition of a peptide

A

A small protein containing 50 or less amino acid residues

305
Q

Briefly describe the nomenclature of peptides

A

. Peptides should be named, using three letter or single letter amino acid abbreviations starting from the N-terminal residue and listing sequentially to the C-terminal. Abbreviations separated by dashes

306
Q

Consider the decapeptide (below) and answer the following questions: Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp

a) Name the N-terminal amino acid.
b) Name the C-terminal amino acid.

A

a) lysine
b) asparatic acid

307
Q

State the side chain property of each amino acid in the peptide

Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp

A

Lys – basic;

Ala, Val, Leu and Ile – hydrophobic;

Ser – polar;

Asp – Acidic

308
Q

Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp

Would you predict this peptide to be water soluble? Briefly explain your answer.

A

Will have some water solubility, although mostly non-polar amino acids there are three polar aa’s, two of which form a salt. OR – will not be soluble in water as 7 non-polar aa’s versus 3 polar.

309
Q

) Describe the structure of a globular protein

A

Compact (tightly folded), roughly spherical, structurally complex, comprised of many elements of secondary structure, e.g. alpha helix, beta sheet, often clearly defined active site / cleft, internal bonding to maintain structure, e.g. disulfide bridges etc etc

310
Q

Give an example of a globular protein.

A

trypsin (any enzyme)

311
Q

Describe the general properties of a globular protein

A

c. Hydrophobic interior, hydrophilic exterior, water soluble, often function as catalysts

312
Q

Describe how the three dimensional structure of a globular protein is maintained

A

ionic interactions, hydrogen bonding, hydrophobic interactions, covalent crosslinks

313
Q

why isn’t the alpha helix considered a double helix?

A

The alpha helix is a single peptide backbone coiled around itself and stabilised by intra-strand H-bonds. [By contrast, DNA is an example of a double helix – two chains stabilised by inter-strand H-bonds]

314
Q

why does the peptide bond usually adopts a trans conformation

A

Cis-amide bonds force unfavourable steric interactions between aa side chains and are not commonly found in proteins

315
Q

why are antiparallel beta sheets more stable than parallel beta sheets

A

because the network of inter-strand H-bonds are better aligned and more stable in the anti-parallel type.

316
Q

what is Native conformation.

A

biologically active form of the protein

317
Q

what are Non-essential amino acids

A

An amino acid that can be biosynthesized with the body and therefore is not essential in the diet. E.g. Ala, Gly, Pro, Ser etc. It requires energy and raw materials to synthesize aa’s so in practice these are obtained from diet whenever possible

318
Q

what is a Cyclic peptide.

A

A polypeptide joined via an amide (peptide) bond between the N and C terminal amino acids creating a continuous cyclic peptide backbone. Have pharmaceutical use. E.g. ciclosporin, a microbial cyclic peptide that contains non-coding biosynthesized amino acids. When non-amino acid groups are incorporated known as a pseudo-peptide

319
Q

. Very briefly describe how enzymes function as catalyst

A

…by lowering the activation energy barrier to the reaction. Achieved by precise orientation of the substrate in the active site in a reactive conformation and provide missing functional groups or cofactors for the reaction. Enzymes provide the reaction ‘template’

320
Q

Briefly describe how enzymes are named and classified. Illustrate your answer with suitable examples

A

Two methods, trivial and systematic. Trivial – name associated with the function or substrate (or both) is suffixed with –ase. E.g. L-dopa decarboxylase or DNA polymerase. Systematic system (enzyme commission: EC) assigns a unique serial number comprised of 4 digits. First digit is one of the six classes (list them) followed by two sets of sub classes and finally the unique identifier, e.g. alcohol dehydrogenase = EC1.1.1.1.

321
Q

Many enzymes require cofactors for their biological function. Discuss this statement using alcohol dehydrogenase and another enzyme of your choice to illustrate your answe

A

. The 20 amino acids that occur naturally in proteins have limited functional groups / chemistry in their side chains. Co-factors, which can be metal ions or organic molecules (co-enzymes) supply this chemistry. Alcohol dehydrogenase uses two co-factors, a zinc ion and a NAD+ coenzyme. The zinc aligns the substrate in the active site to the –OH group. The NAD+ contains a functional group that accepts a proton (i.e. dehydrogenation)

e L-Dopa decarboxylase. The enzyme uses a co-enzyme (pyridoxal phosphate/vitB6) to facilitate the removal of a carboxylic acid. The co-enzyme contains an aldehyde functional group – not found in amino acids – to form an intermediate (imine) with the substrate etc etc.

322
Q

Briefly discuss the importance of metals in protein function. Give one example of a protein that requires a metal atom to function

A

Proteins containing metal ions are known as metalloproteins or metalloenzymes if they have a catalytic function. The 20 amino acids that occur naturally in proteins have limited functional groups / chemistry in their side chains. Co-factors, which can be metal ions or organic molecules (co-enzymes) supply this chemistry. Metals are important in transport proteins (e.g. haemoglobin, Fe required to bind, store then release O2, four Fe atoms held in 4 prosthetic haem groups etc etc). Alcohol dehydrogenase and Zn etc etc

323
Q

mRNA synthesis also known as transcription is mediated by the enzyme _______

A

RNA polymerase

324
Q

The synthesis of mRNA from the DNA template is called _______

A

Transcription

325
Q

Ribosomes are made up of 2 subunits termed S50 and S30, which are combinations of ________and proteins

A

rRNA

PH1123 Microbiology (9 decks)

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