Lectures 6-10 Flashcards Preview

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Flashcards in Lectures 6-10 Deck (63):
1

Virus classification

Baltimore method - Based on replication and genome type
There are 7 different types
I, II, VII All start with DNA
The rest all start with RNA

2

Virus Biology

Non- living entities
Infect all kingdoms
Utilise host proteins upon infection
Extracellularly exist as inert virions
Naked virus or enveloped virus
5kb to 1.2Mbp genome size
Virus that infects mimivirus - virophage

3

Viruses of bacteria - Bacteriophages

Complex structures. Most ds genomes
T4 - 200 nm long and 80-100nm wide

4

Temperate lifestyle - Bacteriophage lambda

Can take Lytic pathway - Viral DNA replicates and viral particles break out
Lysogenic pathway - Viral genes not expressed, the genome (prophage) integrates into host chromosome. (Is replicated)

5

Control of Pathways

If cI gene dominates, phage will go into lysogenic pathway
If cro gene dominates, lytic pathways

6

Lytic Pathway

Transcription begins at Pl and Pr (promoter Left/right).
The polymerases stop transcription after a few genes.( N and cro)- They are then translated.
N protein blocks action of termination sequences.
RNA polymerase transcribes cII and cIII genes (these are transcribed)
Q protein is also transcribed - blocks termination region.
N and Q allow Pr to go around chromosome

7

Lysogenic

Same until cII and cIII made
cI is transcribed, this competes with cro proteins

8

I, II VII types

dsDNA (+) - I, V
ssDNA (+) - II , Synthesis of other strand, ds DNA intermediate
dsDNA - VII - Reverse transciptase

9

III, IV, V, VI

dsRNA (+) - III - Transcription of minus strand
ssRNA (+) - IV - Used directly as mRNA
ssRNA (-) - V - Transcription of minus strand
ssRNA (+) - VI - Reverse transcription, dsDNA intermediate, transcription of minus end

10

Bacterial growth

Binary fission - Cell elongation, septum formation, septum completed, formation of walls, cell separation

B. Subtilis - No cell wall constriction
Caulobacter - No septum

11

Bacterial growth (continued)

Segregation of Genome
Faciliated by proteins MinC, D and E
MinE pushes C and D to the poles and acts as signal for FtsZ (ring)

Protein called MreB essential in morphology (part of cytoskeleton)
Coccoid cells don't have MreB, so thats default shape.

12

Phases of growth

Lag, Exponential, Stationary, Death

13

Different type of oxygen levels

Obligate aerobes - Only oxygen
Aerotolerant anaerobes- Can grow in both oxic and anoxic
Facultative aerobes - Grows more in oxic but can grow in anoxic
Microaerophiles - Grow in oxic, or just at top of anoxic
Anaerobes - Only anoxic

14

Temperature as most important factor

Pscyhrophile - Low Temp - 4- (Polaromonas vacuolata)
Mesophile - Mid temp - 39 - E.coli
Thermophile - Mid high - 60 - Geobacillus stearothermophillus
Hyperthermophile - 88 and 106 - Thermococcus celer and pyrolobus fumaril.

15

Sources of Carbon, Energy and E-

Energy - Phototrophs or chemotrophs
Electron - Lithotrophs or organotrophs
Carbon - Autotrophs or heterotrophs ( Pyruvate is key molecule)

16

Denitrification

Similar to oxidative phosphorylation but Nitrate reductase is the final protein

17

Fermentation

Organic compound is both the electron donor and acceptor
Pyruvate reduced by NADH
Substrate level phosphorylation
If no ETC, reduced NADH is oxidised back to NAD+

If lactate produced, homofermentative
Others = Heterofermentative

18

Nitrogen cycle

1) Uptake of NH4 or NO3 by organisms
2) Release of NH4 by decomposition
3,4) Microbial oxidation of NH4
5) Denitrification in anaerobic
6) Nitrogen fixation
7) Nitrate leaching from soil

19

Chemolithotrophy

Oxidation of inorganic materials - Autotrophs
Nitrofying bacteria - grow like this at expensive of inorganic nitrogen compounds, found in proteobacteria

20

Nitrifying bacteria

Ammonia monooxygenase - Oxidizes NH3 to NH2OH
Nitrite oxidase - Oxidizes NO2- to NO3-
Nitrosomas
Nitrobacter

21

Denitrification

When nitrate is electron acceptor - Dissimilative metabolism

22

N2 fixation

Performed by nitrogenase complex
Dinitrogenase and dinitrogenase reductase
Nitrogenase inhibited by oxygen - Protected by Leghemoglobin that binds and protects

23

Bacterial genomes

Smalled compared to eukaryotes
Genese densely packed
No introns
Genes with related functions grouped together (operons)
Coupled transcription and translation

Plasmids - Replicate independently - Can be integrated into chromosomal DNA (episome)

24

Plasmids

Vary in Copy number
Classed into incompatibility groups (INC) based on replication control or partitioning functions
R100 is resistance

25

Bacterial DNA replication

Bi- Directional replication - Occurs during cell division and during replication of some plasmids
Reolling circle replication - Replication of some plasmids and during conjugation

26

Bi- directional

Normal way, 5 to 3, 1000 nucleotides a second , semi conservative. Has a replication fork

27

Gene transfer

Horizontal gene transfer by
Transformation
Transduction
Conjugation

28

Transformation

Extracellular binding,
Converstion to single stranded DNA
Stabilisation
Homologous recombination

They break out and are naturally taken up

29

Transduction

Donor DNA from any part of donor can be transferred
Specific DNA region of donor transferred
Can replicate in recipient cell
Occurs via viruses which will inject and put the DNA in
Generalised occurs in lytic
Specialised in lysogenic

30

Conjugation

Cell to cell contact
Plasmid encoded mechanism
Conjugative plasmids, could involve pilli
F Plasmid(episome) leads to -
F pilus created
Mobilisation of DNA for transfer
Alteration of cell surface receptors.
Requires DNA synthesis, rolling circle, initiated by enzyme TraI
Cells integrated with F plasmid are Hfr

31

Human - Microbial interactions

Most micro-organisms are benign, there is a normal microbial flora.
Found in human body tissue

32

Pathogen

Microbial pathogenicity - Biochemical mechanisms whereby microogranisms cause disease
Not all have equal probability

33

Infection

Successful persistence or multiplication of a pathogen

34

Disease

Interaction which causes significant overt damage to the host

35

Pathogenicity

Describes the way in which microorganism causes disease

36

Virulence

Relative term - Pathogenic potentials

37

Factors influencing severity of disease

Host
Immunological status
Physiological status
Genetic makeup
Route of infection
Dosage

38

Infectious dosage

Francisella tularensis is the most infectious
Salmonella is the worst

39

Attenuation

Decrease or loss of virulence

40

How pathogens cause disease

Colonise host tissues
Grow within host tissues
Avoid host defence mechanisms
Cause damage

41

How do they damage?

2 mechanisms( Virulence factors)
Produce effectors which damage host tissues
Evoke profound immune responses which cause damage

42

Toxins are effectors (Exotoxins)

Neurotoxins - Cause paralysis
Enterotoxins - Cause sickness and diarrhoea
Cytotoxins - Cause cell death

43

Toxins mode of action

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

44

Endotoxins

LPS or endotoxin is a pyrogen
Causes cytokines from immune cells upon binding to cell surface receptors

45

Innate immunity

Non - specific, general. Immediate response. No immunological memory

46

Humoral innate

Complement
enzymes
Cytokines

47

Cellular Innate

Phagocytes
Natural killer cells
Pattern receptors

48

Adaptive immunity

Specific to antigen
Lag time from exposure to response
Immunlogical memory after exposure

49

Humoral adaptive

Antibodies
Cytokines

50

Cellular Adaptive

T and B cells

51

Innate cells

Myeloid precuror
Monocyte --- Dendritic or macrophage
Granulocytes (Neutrophil or mast cells)

52

Adaptive cells

Lymphoid precursor
T cells (Thymus maturation)
B cells (Bone marrow maturation) ---- Plasma cell

53

Antibodies

IgG made of four polypeptide chains- 2 heavy and 2 light chains
IgM - Longer heavy chains
Can circulate as pentamer or on surface of B cells

54

Responses from these antibodies

Primary response is mostly IgM and secondary response is mainly IgG

55

Other types of antibodies

IgA - Found in mucous, saliva. Protects against pathogens. Dimer of two antibodies
IgD - Part of B cell receptor. Acivates basophils and mast cells. - Normal antibody
IgE - Protects against parasitic worms, responsible for allergic reactions. Normal antibody

56

Adaptive immune response

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

57

T cells

Required for protection against intracellular pathogens. - They bind, then release perforin - makes holes in cells membranes. Causes Lysis

58

Vaccination

Antibodies are required for protection against toxins and extracellular bacteria. Primary response needs to be with a non active toxin or attenuated strain.

59

Types of vaccination

Toxoid
Live, attenuated
Subunut
Inactivated
Conjugate
DNA
Recombinant vector

60

Subunit Vaccines

Can contain 1 to 20 antigens
Pathogen can be grown and then use chemicals to break it apart and gather the antigens
Antigen molecules from the pathogen can be using recombinant DNA.

Foreing DNA usually tagged with a gene encoding a tag that will facilitate purification of recombinant antigen
Controlled expression of foreign genes. If IPTG not added, no expression of the correct antibody.

61

Live Attenuated Vaccines

Hard to identify which genes to knockout if no obvious virulence factors
Good targets are those involved in amino acid metabolism

62

How to Knockout genes

Use of homologous recombination
Cut with EcoRI and ligate. Cut with Bam HI and transform into cell with wild type

63

If you delete genes involved in virulence and leave those who products elicit an immune response the vaccine is

Attenuated