Lecture 4/5 - Microbial Genetics Flashcards
1
Q
What is an immunogen?
A
Any antigen that can elicit an immune response
2
Q
What is an epitope?
A
Part of the antigen that binds to the antigen receptors
3
Q
Where do mutation occur in surface Ag’s of a pathogen?
A
Within the nucleic acids – DNA/RNA
4
Q
What is the results of the a mutation within the surface antigens of a pathogen?
A
Change in the structural proteins
– or –
Enzymes responsible for it’s assembly
5
Q
What is the direct impact of genetic mutations in a pathogen?
A
Host immune response
6
Q
Where is the H antigen found?
A
Flagella
7
Q
Where is the O antigen found?
A
LPS
8
Q
What are three methods to which antigenic mutations occur?
A
Drift + Shift + Switching
9
Q
What are the two subtypes of antigenic switching?
A
Phase variation
– and –
Gene conversion
10
Q
What can undergo antigenic shift?
A
Bacteria + Viruses
11
Q
What can undergo antigenic shift?
A
Viruses
12
Q
What can undergo antigenic switching?
A
Bacteria + Protozoa + Fungi
13
Q
What is the process of antigenic drift?
A
Overtime population accumulates point mutations.
Leads to proteins products being altered causing distinct new strains of the bacteria
14
Q
Where does antigenic drift tend to occur on a flu virus?
A
H antigen
15
Q
What are the two components of the flu virus envelope spikes?
A
Hemaglutttinin
– and –
Neuraminidase
16
Q
What is hemagluttinin?
A
Glycoprotein spike which attaches to the host receptors
17
Q
What is neuraminidase?
A
Enzyme on the glycoprotein spike that releases from virus from the host cell
18
Q
What is the structure of the flu viruses genome?
A
8 segments of ssRNA
19
Q
What is the example of antigenic shift seen in the flu virus, that is given in lecture?
A
Two different strains (ie. human + birds), populate the same cell and undergo reassortment. this creates a whole new subtype of flu virus.
20
Q
What is so dangerous about antigenic shift in the flu virus?
A
Can easily cause a pandemic because no species has been exposed to it. therefore no one has built immunity, leading to quicker spread of the virus.
21
Q
Which genomic mutation is responsible for why we need yearly flu vaccines?
A
Antigenic drift
22
Q
What genomic mutation is responsible for why there are flu pandemics in the world?
A
Antigenic shift
23
Q
What are two important things that a successful pathogen must do?
A
Multiply in host
– and –
Evade the immune system
24
Q
What is the mechanism of phase variation, a type of antigenic switching?
A
The gene is always apart of the cell genes but not always apart of the phenotype, but it is turned on and off depending on the current environment
25
What does phase variation lead to?
Phenotypic variation and therefore surface antigen variation. Go from having no flagella to having one
26
How is phase variation regulated?
Inversion of DNA sequence via recombinase
27
What are the two important components of a bacterial gene?
Promoter + Coding sequence
28
What is another name for gene conversion, a method of antigenic switching?
Gene shuffling
29
What is the mechanism of gene conversion?
Recombination within a specific group of genes. The phenotype is always there but the bacteria can switch through types, like changing a shirt. Biological function remains the same
30
What pathogen causes relapsing fever?
Borrelia recurrenntis
31
Why does relapsing fever occur?
Gene conversion; switches through serotypes causing the immune system to stop being able to recognize it.
32
What is responsible for malaria?
Plasmodium falciparum
33
What method is used by malaria to evade the immune system?
Variable surface glycoproteins aka VSG; does this by avoiding splenic destruction by attaching to endothelium
34
What are mobile genetic elements?
Segments of DNA that encode for enzymes/proteins that mediate movement of DNA within the genome or between cells
35
What are the two groups of MGE?
Replicons
-- and --
No replicons
36
What is the basic method of the replicon?
Replicate DNA/RNA independently of host cell chromosome
37
What is the basic method of cells that are not replicons?
Replicate DNA/RNA as part of cell chromosome or plasmid DNA
38
What is different about a bacteriophage compared to a plasmid genetically?
RNA + DNA (plasmids are DNA only)
39
What do plasmids tend to carry?
Non-essential genetic information
40
What do plasmids allow for in a bacteria?
Selective advantage, especially when an AB is present
41
What are R plasmids?
Resistance plasmids, carry 1+ genes for AB resistance
42
What is special about R plasmids?
They are not genera specific and can be shared amongst any bacteria for the most part
43
What are bacteriophages?
Bacteria viruses
44
What do bacteriophages do?
Inject DNA into bacteria and use the host machinery to copy it's DNA. Then use the lytic or lysogenic cycle to break out of the bacteria
45
Can bacteriophages move amongst genera?
No, they are genera specific.
46
What are the three mechanisms that bacteria user to exchange DNA among bacteria?
Transformation - Conjugation - Transduction
47
In general, what is transformation in regards to genetic exchange?
Incorporation of exogenous (aka naked DNA) into cytoplasm (via plasmid) or chromosome
48
In general, what is conjugation?
Mating leading to exchange of genetic information from one bacterium to another
49
In general, what is transduction?
Transfer of bacterial DNA from one bacterium to another via bacteriophage
50
How is naked DNA, from transformation, incoporated into the genome of the receiving bacteria?
Homologous recombination + Nonhomologous recombination
51
When does invitro competence normally develop in bacteria?
During the log phase of cell culture
52
What does naturally competent mean?
Process of natural transformation, meaning the cells have the ability to undergo this process. Which is not common
53
When does recombination of DNA occur in a bacteria?
When cell takes up new DNA and it does not have a bacterial origin
54
What happens if the DNA is rejected in transformation?
Restriction enzymes cut it up
55
What does homologous recombination require?
Sequence similarity between donor and recipient
56
What does homologous recombination use to be successful?
Recombination gene products (aka Rec proteins)
57
What are the two mechanisms by which nonhomologous recombination can occur?
Random or Site Directed
58
What occurs with random nonhomologous recombination?
Gene is randomly inserted, recombined with host DNA. Can lead to distruption of the genetic makeup of that bacteria. Especially if it is placed within a promoter or coding sequence of a gene
59
What is it call when there is a failed attempt at non-homologous recombination with random insertion?
Null mutaiton
60
How is the site-directed nonhomologous recombination done?
Has a specific sequence - "CATGCAC"
| No REC proteins are needed
61
What is the end result of nonhomologous recombination?
Addition NOT replacement of chromosomal DNA
62
What is the most common method of genetic exchange?
Conjugation
63
What is the pro of conjugation?
Can occur between bacteria of the same species or different ones; depends on the plasma type involved
64
What occurs with conjugation?
One way transfer between donor and recipient bacteria
65
What directs Conjugation?
Genes on the plasmid DNA
66
What type of plasmid carry information for plasmid mobilization?
Conjugative plasmids
67
What can also be carried on conjugative plasmids?
Bacteriocins + AB resistance
68
What genes are important for the conjugative process?
Transfer of plasmid (making the recipient a donor)
Ability to make sex pilus
Initiate plasmid DNA synthesis
69
What system is needed to carry out the DNA transfer in conjugation?
T4SS - Type IV secretory system
70
What bacteria has T4SS been ID'ed in?
Gram-negative, but similar system found in Gram-positive.
71
What designates whether a bacteria is the donor or the recipient?
```
F+ = donor = male
F- = recipient = female
```
72
What is a conjugant cell?
When F+ and F- are attached
73
What determines what mating type a cell is?
Presence of F plasmid
74
What is the result of plasmid transfer?
Plasmid moved as linear ssDNA
-- and --
Rolling circle replication
75
What is rolling circle replication?
Produces dsDNA plasmid in recipient AND DONOR cell
76
Where does mobilization being in rolling circle replication of a plasmid?
Plasmid-encoded protein causing single-stranded, site-specific cleavage at oriT
77
What initiates rolling circle replication?
Nick
78
What is responsible for directing the linear strand of plasmid?
T4SS - In Gram-negative bacteria
79
What is the steps in rolling circle replication?
Transfer of ssDNA + Recircularize/Replication = dsDNA
80
What is an antigen?
Any molecule that can be bound by antibody, T cell receptor, or MHC
81
How does gram-positive conjugation occur?
Adhesion molecules on surface of the donor cells
| NO SEX pilus
82
What occurs with high frequency recombination?
Before conjugation begins - F plasmid intergrats into IS/Tn within host chromosome
83
How does the F plasmid during Hfr intergrate itself within the host chormosome?
Via nonhomologous recombination
84
What is the definition of a Hfr cell?
Host cell with integrated F plasmid
85
What is an episome?
A replicon that can exist either seperate from the host cell chromosome or as part of the chromosome
86
What does Tn stand for?
Transposon
87
What is IS stand for?
Insertion sequence
88
What is an integrated plasmid?
Plasmid that has been integrated into the host cell chromosome
89
What is the order of chromosome transfer when a Hfr cell is involved?
First 1/2 of the F plasmid + Chromosome + Second 1/2 of F plasmid
90
Why is there a chance that conjugation with a Hfr cell might be incomplete?
Cellular connection is fragile and the DNA is long, may break before finished.
91
What is the highest probable ending to conjugation involving a Hfr cell?
Transfer of the first 1/2 of the F plasmid and a portion of the adhacent chromosome. Meaning the F- cell does not become an Hfr cell
92
What occurs with full transfer of the Hfr genome?
Conversion of the F- cell to the Hfr cell
93
What mediates the process of transduction?
Bacterial viruses aka bacteriophages
94
What is the basic process of genetic transfer in regards to transduction?
Phage picks up fragments of bDNA and packages them into virions (phage particles). bDNA is then delivered to infected cell
95
What happens to the bDNA once a bacteriophage introduces it to the infected cell?
Incorporated into bacterial genome via homologous recombination
96
What are the three structural components of a bacteriophage?
Capsid + Tail + Nucleic acid core
97
What are the two mechanisms for escape from the host cell that virulent phages use?
Lytic or/and Lysogenic
98
What are the basic steps that occur in the lytic cycle?
```
Attaches/Absorption
Injection/Penetration
Replication
Assembly
Lysis (once enough are made)
```
99
What is the key to generalized transduction?
The Lytic Cycle
100
What is still present during the phage assembly of the lytic cycle?
bDNA
101
What happens when a viral capsid is packed with bDNA?
becomes a Defective phage and can only attach to a new host cell and inject bDNA, where recombination with host chromosome is carried out
102
Why does a viral capsid sometimes get bDNA?
Doesn't know the difference between bDNA or vDNA
103
What is important about the lytic cycle, in regards to what it involves?
Virulent phages, but if accidentally pick up bacteria this changes
104
What is lysogeny?
Integration of vDNA into bDNA/chromosome
105
How is lysogeny carried out?
via nonhomologous recombination
106
What is formed because of lysogeny?
Latent prophage
107
What is the result of lysogenic conversion?
Bacterial cell becomes lysogen
108
What becomes of a latent prophage?
Replication of this viral DNA with the bacterial host DNA so all the daughter cells carry it
109
What can happen to the latent prophage?
If stress occurs (ie. UV light, temp, nutrients etc.) lytic cycle can be activated. If the prophage has a virulent gene this will then make the bacteria a pathogen.
110
What were three examples of pathogenic lysogens in the lecture?
Hemorrhagic diarrhea
Botulism
Diphtheria
111
What is specialized transduction?
Very rare but during stress-induced lytic cycle prophage is incorrectly excised from bDNA and now has segments of bDNA + vDNA.
112
What is a defective phage?
Machinery packs capsids with vDNA + bDNA
| Lytic cycle releases these and they are spread via nonhomologous recombination
113
What are not replicons?
IS + Tn + PAI
114
What does PAI stand for?
Pathogenicity Island
115
What is the simplest form of MGE?
Insertion sequence
116
What does an IS contain?
Inverted repeats on ends
| Transposase gene for integration into replicon w/ no additional coding
117
How is an IS inserted?
Via nonhomologous method into a specific sequence - creates direct repeats upon insertion
118
Where does a Tn transfer?
transfers DNA within a cell from one position to another
chromosome to plasmid
plasmid to plasmid
119
What is the structure of a Tn?
2 insertion sequences + central region
120
What is contained on the central region of a Tn?
AB resistance + toxin genes
121
What can be the results of the nonhomologous recombination with a Tn?
Can insert into an inactive gene on chromosome or plasmid and aid bacteria in being more virulent or resistant
or can insert into a essential protein and cause cell death
122
What is a PAI?
unusual clusters of genes, that insert tRNA or tRNA-like genes into bacterial chormosome
123
What do PAI encode for?
Virulence factors such as toxins + AB resistance
124
How is a PAI inserted into the genome?
Nonhomologous recombination
125
Why are PAI's unstable?
Different %G+C that parent DNA - implies foreign source to DNA
Overtime breaks down, lost from genome
Not seen in nonpathogenic forms of species
126
What is clinically important to remember about PAI's?
Can cause different pathogens even if the bacteria are from the same species
127
What is structure is adding to the spread of AB resistance?
Integron
128
What is an integron?
Genetic element that allows for efficient capture and expression of exogenous genes
