Microbiology Exam 2 Flashcards
(166 cards)
1
Q
Bacterial chromosome
A
Has a circular chromosome
Supercoiled
2
Q
Archean chromosome
A
Negative supercoiling
3
Q
How do bacteria compact their DNA into the cell?
A
The DNA is supercoiled (twisted) and stabilized by proteins
4
Q
E. Coli chromosomes
A
~100 supercoiled domains which are stabilized by proteins
Has DNA gyrase
5
Q
What is DNA gyrase?
A
Type of topoisomerase that makes a ds break in the DNA to create supercoils.
Ds DNA passes through the break where it is then religated back together
6
Q
How does bacterial DNA respond to environmental signals?
A
Regulation of gene expression
Regulation of protein activity which is:
- faster, why?
- covalent modification, P and de P
- Feedback inhibition
7
Q
How do proteins bind to specific DNA sequences?
A
Nitrogenous bases are exposed in major and minor grooves
Each base pair is a unique set of contacts for binding proteins
8
Q
Contact sites proteins bind to on DNA
A
G-C
C-G
A-T
T-A
9
Q
Inverted repeat sequences
A
Many binding sites have these
Protein repeats (each binds to DNA) are bound by protein dimers
DNA binding domain fits in major groove and along sugar-phosphate backbone
10
Q
Helix turn helix motif
A
Present in many DNA binding proteins
Alpha helix can fit in major groove
Amino acid side chains can bind nitrogenous bases (N-bases)
11
Q
E. Coli genome
A
88% of it is protein encoding genes (gene dense genome)
70% of the genes are single genes (one gene for mRNA molecule)
Other genes are cotranscribed into a single mRNA molecule (one promoter for multiple genes. Therefore these genes are part of an operon. 6% of operons - 4 or more genes)
12
Q
Operon
A
a functioning unit of DNA containing a cluster of genes under the control of a single promoter.
13
Q
How does sigma subunit work with RNA polymerase?
A
Initiates txn.
Sigma subunit is required for RNA polymerase to bind to promoter to initiate txn.
14
Q
sigma subunit 70 in bacterial cells
A
Default for house keeping genes of E. Coli
For normal growth
15
Q
E. Coli regulation
A
Regulation by repressor or activation
can grow in a glucose, minimal salt media
Glucose, ammonia, salts is what E. Coli needs to grow
16
Q
How is arginine regulated in E. Coli?
A
When arginine is absent the gene to make it needs to be expressed therefore RNA polymerase binds at promoter which means the default is gene is expressed
Repressor is not bound to operator sequence.
If arginine is present it is a waste of energy to make more and is therefore not going to express the gene
A repressor binds the DNA and blocks gene expression
Does not bind to DNA in the absence of arginine
Does because excess arginine binds to the arginine repressor which then makes the repressor bind to the operator sequence.
17
Q
When does the Arg repressor protein bind to DNA?
A
When Arg levels are high and the protein binds Arg
Arg is A.A. required for growth
P-promoter -> size- RNA polymerase binding
O-operator- regulatory sequence (Arg repressor protein binds at operon)
18
Q
Repressor proteins
A
Bind to regulatory seq. near the promoter to regulate gene expression
19
Q
What happens when there are high levels of Arg?
A
Any repressor protein binds to Arg (corepressor)
Conformational change in the repressor protein
Now binds to DNA at operator sequence
Represents txn.
20
Q
Lactose Operon
A
Lactose metabolism
-disaccharide, sugar.
-E. Coli uses it for energy
-Will be catabolized to provide energy
-Broken down to be glucose
Has genes that encode proteins for lactose catabolism
21
Q
Lac repressor protein
A
Binds to DNA when lactose is absent
txn. is repressed (very low level of txn. does occur)
22
Q
Beta-galactosidase
A
Breaks bond to make galactose and glucose
23
Q
For Lac operon regulation in E. Coli, when lactose is present
A
A repressor protein no longer binds to the regulatory region of the gene
Because if you make more while you have some, you are wasting energy
24
Q
What happens to Lac operon when lactose is present?
A
Lactose is cleaved by beta-galactosidase to get galactose and glucose by enzyme
Some lactose is converted to allolactose and acts as inducer and allows gene expression
25
What binds to Lac repressor?
Allolactose
Get change conformation of the repressor protein so that it no longer binds to DNA
Therefore txn. occurs
26
How will E. Coli metabolize glucose and lactose when both are present?
It will metabolize the glucose first
Then lactose second
Do this because lactose is used to make glucose
Therefore if is already has glucose, then it will use that first to make energy and the lactose after glucose has been depleted
Called graph-diauxic growth
27
Graph-diauxic growth
There is a lay period after one energy source is depleted
28
Regulation of the lac operon?
2 proteins important in regulation:
-Lac repressor
-CRP-catabolite responsive protein (cAMP receptor protein):
-DNA binding protein
-Promotes gene expression
-Binds to cAMP=change conformation of protein = binds DNA = promotes gene expression
29
Adenylate cyclase
Inhibited by glucose
Turns ATP into cAMP and PPi
30
CRP-cAMP Complex
Binds DNA when there is no glucose
Binds and bends DNA
Changes DNA shape
Therefore RNA pol. can bind to promoter
Get txn.
31
C site
cAMP binds
32
P site
RNA pol. binds
33
O site
lac repressor
34
Study how Lac operons are regulated
Day 13!
Good Job
35
For lac operon regulation in E. coli when lactose is present
A repressor protein no longer binds to the regulatory region of the gene
36
How does blue-white screening?
IPTG:
Chemical analogy of allolactose
Synthetic/not degraded
Binds lac repressor protein.
Therefore beta-galactosidase syn. is not repressed
Becomes white
X-Gal:
Substrate for Beta-galactosidase
Becomes blue
37
Maltose is a disaccharide that can be that can be catabolized by E. Coli
How is the expression of maltose operon regulated?
An activator protein only binds to DNA in the presence of maltose
There is no repression when maltose is not absent
38
Maltose operon
Regulated by an activator protein
-Only binds DNA when maltose is present
-Maltose is an inducer
Net result: gene not transcribed. Only transcribed when maltose is present
39
When glucose levels are low?
cAMP levels are high, CRP does not bind
40
RNA polymerase of bacterial vs. archaeal?
bacterial RNA-P
sigma factor directs RNA-P to promoter
archaeal RNA-P
similar to eukaryote RNA-P
Has between 11-13 subunits
41
TATA box
Regulating sequence for archaeal genes
Is bound by TATA binding protein (TBP)
BRE-B recognition element in which it is bound by transcription factor B (TFB)
When these two proteins bind the DNA, they promote the binding of RNA-P
42
An example of a gene that is regulated in Archaea
Genes involved in nitrogen fixation
(In the Methanococcus genus)
43
NrpR-repressor protein
Represses expression of genes for nitrogen fixation and glutamine synthesis
44
What happens when N levels are low regarding N-fixation genes?
alpha ketoglutarate accumulates and binds to NprR protein
This causes a change in conformation in the protein which then no longer binds to DNA
This causes N-fixation genes to be expressed and ammonia is synthesized to turn alpha ketoglutarate to form glutamate
This is because when NprR is releases TBP and TFB can bind to allow DNA-P to bind to DNA
45
Bacterial genetics format for gene and protein?
Gene: lacZ will be italicized
Protein: LacZ
46
How is translation initiated in bacteria?
Ribosome binds to the 5' ribosome binding sites in the start codons
Complementary binding between nucleotides between mRNA & the rRNA molecules
47
Start codon
AUG
Specifies A.A.: Met
Bacteria: modifies Met as incorporated into the start codon
-formyl-Met: f-Met
Only for start codon
Met is formulated after added onto the tRNA
48
Attenuation
Transcription regulation-premature termination of transcription
-transcription is initiated but is not completed
Operons that have this (attenuation) have a leader sequence (is before start codon of the first gene) in the mRNA molecule
49
Leader Sequence
Is translated
Contains codons for the A.A.
Operon codes genes for the biosynthesis
50
Trp Operon
Leader peptide has 2 trp codons
Are expressed when trp levels are low b/c genes encode synthesis of trp
51
What happens to Trp operon when trp levels are low?
Not enough trp. low levels of tRNA
leader peptide is not translated and ribosome pauses at Trp codons
Ribosome pauses at the Trp codons
Base pairing at regions 2&3 on the mRNA--> transcription proceeds. Genes expressed so cells can make trp
52
What happens to Trp operon when trp levels are high?
Trp mRNA has 2 different conformations
Leader peptide is translated because there's acetylacyl trp for this to occur. Get base pairing between regions 3 & 4 in the mRNA.
Causes termination of transcription. RNA pol. does not transcribe rest of the gene. Can happen because txn. and trans. are coupled and happen simultaneously. Get a loop that forms for it to stop
Transcription stops as the ribosome is able to completely translated to the leader peptide
Get hairpins between groups 3&4 mRNA
This will cause attenuation
53
Bacterial proteins
Targeted for CM, cell wall or secretion
Their genes code signal sequence = Direct proteins to where to go in cell
54
Typical signal sequence
15-20 A.A.'s
Located at amino terminus of proton as well
Will have a few basic A.A.
Central region: nonpolar A.A.'s
Followed by polar A.A.'s
55
Transcription/translation in bacteria
Occurs simultaneously
mRNA molecules can be translated by multiple ribosomes at the same time
56
Bacteria translation
Slower process
Source 5-50 A.A's per second in terms of incorporation into a protein
Potential increase for incorrect folding interactions to occur during translation
57
Molecular chaperones
Proteins that assist the folding and/or prevent the misfolding of other proteins
58
Which proteins have signal sequences
Proteins that target the cell membrane
In E. Coli the Sec system helps with protein secretion
59
What does SecA do?
Binds to the signal sequence in the cytoplasm
Delivers protein to a protein complex in the cell membrane
Protein will pass through the membrane in an unfolded state
After it is secreted the signal sequence is removed and the protein folds
60
Signal recognition particle (SRP)
Binds to proteins that are targeted to cell membrane
targeting of signal peptide‐bearing proteins to the prokaryotic plasma membrane or the eukaryotic endoplasmic reticulum membrane for secretion or membrane insertion.
61
Protein kinases P other proteins on which amino acids?
Histidine, Serine, Threonine, Tyrosine and aspartic acid in bacteria cells
They gain histidine and aspartic acid which is not in humans
62
What do protein kinases do?
They P other proteins
This is reversible and causes immediate change in activity
63
Where can you find E. Coli?
Intestinal tract
Following a storm, beaches have high levels of E. Coli. Therefore can also be found in the sand
Water
64
2 component signal pathways
Used by microbes to respond to the environment
E. Coli has over 50 alpha component system
65
What is needed in a 2 component signal pathway?
2 proteins are involved: the sensor kinase and the response regulator
66
Sensor kinase
Cell membrane
Will respond/react to environmental signal
67
What happens if signal is present for a 2 component signal pathway?
The sensor kinase auto phosphorylates on His. which causes a change in conformation of the protein
The P from the histidine will then be transferred to the Regulator in the cytoplasm.
68
Response regulator
In cytoplasm
Frequently DNA binding proteins that regulate gene expression, activate gene expression and repress gene expression
69
What happens when PhoR is P?
PhoR is a signaling molecule, sensor kinase in the membrane
It is active when phosphate levels are low
P is transferred to PhoP which is the response regulator
This increases phosphorus metabolism and represses gene expression for nitrogen metabolism and antibody synthesis
70
What is Vibrio fischerii
It is a model organism
Sense numbers of other microorganisms
71
What is quorum sensing?
Regulating system
It monitors population levels of bacteria and controls gene expression dependent on cell density
72
Signaling molecules (talk about auto inducers)
There are different types based on the organism
In Gr + bacteria they are often acyhomoserine lactones
In Gr - bacteria they are often short peptides
73
Why is quorum signaling important for pathogenesis? Use Pseudomonas aeruginosa as an example in cystic fibrosis patients.
In Pseudomonas aeruginosa (secondary pathogen)
Does not cause disease in normal people
Attacks people with cystic fibrosis and individuals with a compromised immune system
Secretes virulence factors to attack host individual
Will degrade the lung tissue
Released only when cell density is high which is why quorum signaling is important for pathogenesis
74
Natural environment for bacteria
rarely single species present
75
Culturing organisms
Requires right nutrients and conditions
76
Biofilms
Complex communities of micro organisms
Attachment matrix of polysaccharides, proteins and/or nucleic acids to attach to surfaces
Community develops within a sticky matrix
Can be multilayered (will have diff. species in different layers
77
Benefits of biofilms
self defense in living in biofilm environment
Matrix prevents penetration by chemicals and predation by protists
Remain in favorable niche with nutrients
Can be chemical gradients (O2 gradients)
Close proximity facilitates chemical signaling (so close you have cell-cell communication)
78
How do biofilms form?
Cells attach to surface (can be protein appendages (pili and flagella), can be surface proteins)
Expression of biofilm specific genes when they attach to surface (intracellular signaling molecules and production of extracellular polysaccharides and other molecules to form a matrix)
79
Health related concerns with biofilms
Pseudomonas- lungs in people with cystic fibrosis, forms homogenous biofilm (in which there are only one type of bacteria)
Tooth decay (heterogenous biofilm with multiple types of bacteria present)
Catheters, kidney stones, consumption
80
Microbial mats
Very thick biofilms that can be found at the edges of hot springs
Can be different layers in the mats for different types of organisms
Layers are dependent on light, nutrients and O2
81
Cyanobacteria mats
Carbon fixation
Carry out aerobic oxygenic photosynthesis which makes O2
Other organisms consume nutrients from C atoms fixed from cyanobacteria
82
What was life prior to modern plants and animals?
Microbial mats
Still seen in places like hot springs where the temperature blocks grazing animals and plants
83
Pace's research
Identified organisms that had not/could be cultured
84
Why couldn't the organisms be cultured in Pace's research?
The growth requirements are not known
Organisms that require other species for growth. Could be symbiosis... Could be other organism are producing molecules required for growth...
85
Virus
Particles that are obligate intracellular parasites
Lack the ability to replicate independently
Require a host cell for ATP, ribosomes, resources to replicate
86
Smallest characterized DNA was
175 kbp
87
Largest known viral genome
2.5 mbp
88
Who devised the classification system for viruses?
David baltimore
89
ds DNA
most bacterial viruses
90
ssDNA
+ strand --> transcription of the + strand does not yield mRNA
Infect a cell: complementary DNA strand is synthesized-cDNA --> transcribed --> mRNA
91
ss DNA strand
Only one is known according to book
92
RNA viruses enzymes
enzyme: RNA replicate RNA dependent RNA polymerase
93
RNA viruses ds RNA?
ss (+) RNA in which RNA genome is also the mRNA
ss(-) RNA in which RNA replicate synthesizes mRNA from genome
94
Retroviruses
RNA genome - DNA is synthesized from the RNA genome by reverse transcriptase
RNA dependent DNA polymerase ej. HIV
95
Hep B
DNA virus
Replicated with an RNA intermediate and the RNA intermediate is used as a template for RNA transcriptase
Genome is replicated
96
What type of virus is COVID?
RNA virus + strand
97
Viral structure components
Genome in the center with DNA or RNA
Capsid which is a protein coat that protects nucleic acids. Important for binding to host cells
Enveloped viruses contain phospholipids from the host cell
98
Basic viral lifecycle
Virus binds to host cell
Nucleic acids are inserted into the host cell
Expression of viral genes and synthesis of new virus particles
Lysis of the host cell and release of viral particles
99
The regulation of viral gene expression
First genes to be expressed are viral enzymes.
Other proteins may inhibit or inactivate host cell transcription and translation
Later gene expression are genes encoding capsid proteins
Structural proteins necessary for assembly for the virus
Synthesized in higher amounts
100
Virus receptors on host cells
Proteins on cell surface
Have specific function for cell
virus envolved to bind to the protein
101
Viral evolution
Evolved early or later than cellular life?
Teacher believes earlier because of RNA replication
102
How does one study viral evolution?
Need to study the structural domains of viral proteins to see when viruses evolved
This points to early origin of viruses
103
Did viruses evolve before or after LUCA?
Most likely before LUCA
pre-cells would have segmented RNA genomes
Early viruses also would have been RNA genomes
Therefore evolved could have lost RNA genes from their genome and came dependent on cells for replication
Could have been some overlap with pre-cells and early viruses???
104
What would be the earliest viruses?
dsRNA
105
Phi-X174
E. Coli virus with small genome (ssDNA) 5386 nt.
Is a bacterial virus called a phage
Overlapping genes and overlapping coding sequences
ej. gene B is within gene A, gene K overlaps genes A and C
106
Replication of ssDNA
Host proteins turns ssDNA into dsDNA called the replicative form
This is replicated in semi-conservative method to create more ds DNA molecules
Are txn so viral genes are txn and translation to make viral proteins
new copies of ss genome are synthesized by rolling circle replication
107
Things that DNA polymerase needs to do their job
3' OH primer
Template
dNTPs
Semi-conservative replication
Double helices with one parental strand and one daughter strand
108
Rolling circle replication
Does not require a primer
Not semi-conservative
Requires 3' hydroxyl group
109
Phi-X174
Life cycle forms dsDNA molecule in replicative form
The + strand is nicked (cleaved) by a protein
Free 5' end and free 3' end
110
What does DNA polymerase do in rolling replication?
Adds nucleotides to the 3' end, replicating genome, 5' end is displaced
When the entire chromosome is replicated protein cleaves new chromosome and chromosome is released
The process is repeated and another protein 5' and 3' ends of the chromosome
111
Temperate phage
Can carry a lytic infection
Sometimes lysogenic pathway
112
Lysogenic pathway
Viral DNA is integrated into host DNA
Viral DNA is replicated with host DNA at cell division
113
Example of temperate phage?
E. Coli and lambda phage infection
Is a very well studied cloning vector
114
When lambda phage infects E. Coli is it lytic or lysogenic?
Two proteins are responsible for this answer: Cro and lambda repressor protein (cI)
Most of the time it is a lytic infection
When Cro is present the lytic cycle happens because Cro inhibits/represses the synthesis of cII which activates synthesis of lambda repressor protein cI
115
cII levels
dependent on Cro
Dependent on proteolysis
In nutrient favorable conditions, cII is cleaved by a protease
116
When does the lytic cycle happen?
Under favorable nutrient conditions (story is more complex)
cII is cleaved by a protease in these conditions
117
Lysogeny conditions
Poor nutrient conditions
proteolysis of cII is inhibited
Causes an increase of cII expression
cI --> lysogeny
118
If multiple lambda phage infect one cell what happens?
cII levels increase which leads to an increase in cI which leads to lysogeny
cI represses the txn. of Cro which leads to lysogeny and blocks the lytic cycle
119
Phrophage
Virus is not active; viral genes are not expressed
DNA is incorporated into the host cell chromosome
120
When would a lysogenic phage enter the lytic cycle?
When a bacteria is stressed because it wants to survive
In good conditions more DNA can be synthesized
121
Relationship of cI and Cro
cI and Cro are DNA binding proteins
cI represses synthesis of Cro
Cro represses synthesis of cI
cI binds DNA as a dimer
lambda repressor is cI
cI binds to Or1 highest affinity which blocks synthesis of Cro
Then the lambda repressor binds Or2 which helps RNA polymerase bind at the promoter for the cI gene
Excess cI binds Or3 and represses transcription of cI gene
122
What happens in a lysogenic infection when there is damage to the host cell DNA?
Activates signaling pathway mechanism within cells
Proteases are activated in response to DNA damage
This protease cleaves the lambda repressor
Cro is expressed; Cro expresses the synthesis of cI; viral genes are expressed and the cell is lysed
123
Animal viruses
Most cause cell lysis (most common)
Some have latent infections where virus is integrated into host cell genome (ej. chicken pox when activated causes shingles)
Persistent infections-slow release of viral viruses that do not kill host cell
124
HPV virus has been show to cause what?
Cancer
125
What is the most effective treatment against or preventative measure against viral diseases?
Vaccines prevent them
Protease and reverse transcriptase inhibitors
126
Retroviruses
Have an RNA genome
RNA genome is copied into DNA by reverse transcriptase (RNA dependent DNA polymerase
Class of viruses with some variation
127
What makes up retroviruses?
Three proteins that are present in the virus particle
Enzymes are the protease, reverse transcriptase and integrate
Enzymes have to be present for the life cycle for viral genes to be expressed and to have replication proceed
128
RNA transcriptase
Take RNA genome and make complementary DNA molecule from this
129
Integrate
Allows complementary ds DNA molecule to be incorporated into the host cell genome
130
Retrovirus genes
Three genes encode multiple proteins:
- gag
- pol
- env
All three genes encode polyprotiens
131
Polymerase gene in retrovirus
Encodes reverse transcriptase and integrase
Is cotranscribed with the gag genes
What rarely happens:
Translation of the pol genes requires the ribosome to continue through a stop codon or switch to another reading frame
This is a regulatory mechanism because it is going to express more gag genes than pol to not make too much reverse transcriptase
This is because the virus only needs low amounts of reverse transcriptase and integrase
132
env gene in retroviruses
Encodes structural proteins for the virus particle
133
Something unique about retrovirus genes
The genes encode poly proteins
Different than bacteria, eukarya and archea
Genes are expressed, Cotranslated peptides are translated that are cleaved by the protease that is present in the viral particle. Then we get active proteins
134
What does gag gene encode in retroviruses
Structural proteins
135
Retrovirus life cycle
1. Entry and uncoating of the retrovirus
2. Reverse transcriptase activity to make ds DNA
3. Viral DNA enter nucleus and integrates into the host genome
4. Transcription by host RNA polymerase forms viral mRNA and genome copies to make ssRNA
5. Translation of mRNA forms viral proteins; new nucleocapsids assembled and released by budding
136
How does GAG-POL become reverse transcriptase or integrase?
Are translated to polyprotiens, then protease cleaves the polyprotiens into the individual subunits/polypeptide chains necessary for the virus to function and be able to replicate
137
HIV
Human immunodeficiency virus
Retrovirus
First appeared in early 1980s
Primarily affected gay men
People who were infected developed the disease AIDs and there was no treatment for this
Low life span
Focus of research back then were drugs to block viral replication
Vaccines have failed against HIV
138
Protease inhibitors and HIV
First HIV drugs developed
139
HIV preventions
Drug cocktail
Consists of two to three pharmaceutical compounds
Have been very effective for people with virus to live a normal life
Have 2-3 because of virus is resistant to one then maybe one of them will work
They target reverse transcriptase
140
Two types of HIV drugs that target reverse transcriptase
1. MRTI Inhibitors: nucleotide molecules that reverse transcriptase. Bind to the active site of reverse transcriptase that inhibits production of complementary DNA molecule
2. NNRTIs: non nucleoside reverse transcriptase inhibitors. Non-competitive inhibitors. Bind to the second site on reverse transcriptase to inhibit the enzyme
141
Influenza
High mutation rate with different strains
Easily transmissible, airborne, respiratory
Viral particles remain viable on surfaces
Has a segmented RNA genome (dangerous)
142
Hosts for influenza
Humans, birds, pigs
Different strains than why infect humans (birds and pigs)
143
Why is segmented RNA genome in influenza dangerous?
Has eight RNA molecules
Virus mutates year to year. Result from genetic drip
Each molecule is a gene that encodes one of the proteins
Key proteins: hemagglutinin, neuramindase which are on the outside and are the antigens
144
Genetic drip
Point mutations that occur randomly through the genome
145
Pandemic flu
Genetic shift: Major changes in the flu that arise from H or N proteins from either birds or pigs being present in viruses that impact people
Happens when pig or bird viruses affect people because we have not have any prior exposure to the antigens.
We do not have the immunity
Or
Can have recombinant viruses
146
Recombinant viruses
Have mixture of human, pig, bird RNA segments in the flu
Happens when human and animal virus that are separate infect the same cell and when budding happens it takes in random viral particles
147
Influenza 1918
Killed twenty to forty million people worldwide
Population targeted the most were twenty to forty year olds
Was better on the younger and older people
148
HPV
Human papilloma virus
Can cause cervical cancer
Vaccine available against several HPV strains which prevents cancer by preventing the infection
Have genes that encode proteins that impact cell division (increase it)
149
What is the role of cyclic AMP (cAMP) in the regulation of the lac operon in E. coli?
cAMP is produced when glucose levels are low and this binds to the cAMP receptor protein (CRP) so that this protein can now bind to the regulatory sequences of the lac operon
Genes can be expressed
Mechanism in which when glucose levels are high the lac operons are not expressed because that carbon source is present
150
How do microbes reproduce
Asexually
Binary fission, budding, or another process so daughter cells are the same as mother cells genetically
151
Vertical gene transfer
Genome replication and cell division
Generation to generation
152
Horizontal gene transfer
or Lateral gene transfer
One cell to another to acquire DNA
Cells of the same species or different species
Mechanism in which microbes can acquire new DNA
Without this mechanism bacteria and microbes would be limited with the ability to acquire new properties
153
How can horizontal gene transfer happen?
Transformation, transduction and conjugation
154
How can one detect if the genes in an organisms genome arose from horizontal gene transfer?
Looking at the GC content of the genes
Different species have different percentages of GC content
Can compare homologues from different species and are the genes more similar to other types of bacteria than that family?
Start, stop, codons, regulatory sequences
Codon bias. Are the codon bias similar to other genes within the organism or compared with other organisms?
155
Core genome
Genes shared by all strains of the species
156
Pan genome
Core genome plus the genes not shared by all the strains
Much larger than the core genome
157
What happens to the DNA that is acquired by microbe?
It may be degraded by the cell
It may be replicated independently from the chromosome (Example are plasmids)
It may be incorporated into the host cell chromosome
158
How to study horizontal gene transfer?
Complementation studies
159
Complementation studies
Test to see if a bacteria will take up a DNA donor strain
Can mutate a bacteria and make the donor strain the WT to see if it can pick up the WT strain
Therefore the cells that would grow in this situation would acquire the donor DNA strain
Aka one strain is providing something the other is missing
Example is lysine with E. coli from March 14th lecture.
160
What requires direct contact for the transfer of DNA from one bacterium to another?
Conjugation
161
Transformation
Lysis of donor cell, DNA is released
Bacteria taking up DNA by environment
Blue-white screening
162
Transduction
Gene transfer is mediated by a virus
Virus injected, chromosome disruption
Virus takes in DNA and infects the recipient cell and injects the donor DNA
163
Conjugation
Chromosome transfer and plasmid transfer
Chromosome transfer- donor cell with integrated plasmid
Plasmid transfer- plasmid containing donor cell
164
If one wanted to study the transfer of DNA from one bacterium to another, what would be the easiest way?
The easiest mechanisms would be if you have a marker to study
Having many things you can trait and easily select for and test without having to break the cells open, get the DNA, or do other studies
Something you can detect by growing bacteria on plate and see if the transfer occurred
Donor and recipients are different based on the conditions you are using
People usually use temperature
165
Specialized transduction
Happens with lysogenic phage
The prophage is in the host cell chromosome
When the prophage is activated (lambda) the virus, the transducing particles, contain viral and host cell DNA
This is relatively rare
Sometimes the virus particles will contain some viral DNA and some host cell DNA
The genomic DNA and the transducing phage is whatever DNA is physically next (at site of integration site of prophage will be transduced) to the site of where it was integrated
166
Generalized transduction
Random transduction
