Prokaryote and extrachromosomal! Flashcards
(108 cards)
1
Q
What type of inheritance is shown by extrachromosomal DNA?
A
Non-Mendelian
2
Q
Where do maternally inherited diseases map to?
A
Mitochondrial genome
These diseases therefore tend to affect energy production, and damage tissues that are dependent on energy e.g. nerves and mucle
3
Q
How would you describe the mitochondrial and chloroplast genomes?
A
Circular
4
Q
What is the shorthand for DNA found in mitochondria and cholorplasts?
A
- Mitochondrial DNA = mtDNA
- Chloroplast DNA = cpDNA
5
Q
Which parent provides the mitochondrial/chloroplast DNA?
A
Maternal parent
Vachina
6
Q
What is heteroplasmy
A
The possession of a mix of normal and mutated mtDNA leading to variable symptoms
- two or more mtDNA variants exist within the same cell. The mutation can usually be compensated for with healthy copies
The ratio of wild type to mutant mtDNA plays a big role in buffering against harmful mutations, evolution, and the inheritance of mitochondrial conditions
7
Q
How do mitochondria replicate within cells?
A
Randomly - they aren’t like nuclear chromosomes
- little chunks break off and grow into its own structure
8
Q
What does three person IVF prevent?
A
Prevents inheritance of mitochondrial diseases:
- Nucleus is removed from donor egg
- Nucleus is removed from mother’s egg and inserted into the donor egg cell
- Cell is fertilised with father’s sperm
- Healthy zygote produced
- implant into mother to grow as baby
9
Q
What is the endosymbiotic theory?
A
The theory that once, mitochondria and chloroplasts were free-living bacteria that became part of eukaryotic cells
10
Q
What is the evidence that supports endosymbiotic theory?
A
- Own circular DNA
- Replicate independently
- Use bacterial-like (70s) ribosomes
11
Q
What is homoplasmy?
A
All mtDNA copies are all the same - e.g. all mutant or all wild type
- normal genome and normal function
- or all mutant genome - no function
If they are all mutated, this will likely lead to the death of the organism
12
Q
What 2 other forms of extrachromosomal inheritance are there?
A
- Endosymbiotic bacteria e.g. wolbachia
- Infectious prions (cause misfolding of normal proteins)
13
Q
How do prokaryotes introduce genetic diversity?
A
Horizontal Gene Transfer (HGT)
14
Q
What is the mechanism by which bacteria divide?
A
Binary Fission (vertical gene transfer)
- prokaryotes can do too
15
Q
Why do prokaryotes need HGT?
A
Binary fission copies all mutations, including the harmful ones (these become permanent in the genome) so genetic fitness declines over time
- HGT introduced beneficial mutations over time (e.g. antibacterial resistance), increasing adaptability
- Need HGT to shuffle genes and maintain genetic variation
16
Q
What are the three main methods by which prokaryotes perform HGT?
A
- Conjugation: direct transfer of plasmids by cell-to-cell contact
- Transformation: uptake of free DNA from the environment
- Transduction: gene transfer via bacteriophages (viruses)
Increases genetic variation and adaptability in prokaryote populations
17
Q
What are the 2 types of bacteria populations/multicellular aggregates that form?
A
- Biofilms
- Syntrophic consortia
18
Q
What is the difference between a biofilm and a syntrophic consortia?
A
- Biofilm: structures of SAME microbe communities that adhere to surfaces, surrounded by extracellular polymers
- Syntrophic consortia: mutually beneficial interactions between DIFFERENT microbial species, wherein metabolites are shared
19
Q
Compare the sizes of chromosomes and plasmids
A
- Chromosomes are bigger and denser circular genomes, vary between ~2 to 12 Mbp in size, normally only one in a cell
- Plasmids are smaller DNA mols that replicate independently - there can be multiple per cell however
- plasmids are ~2 Kbp – 500 Kbp in size
20
Q
What types of genes do plasmids carry?
A
Non-essential, but beneficial genes for environmental conditions e.g. antibiotic resistance, virulence, metabolism, nitrogen fixation, carb utilisation
21
Q
Explain the process of conjugation
A
- Donor cell extends a pilus that attaches to a recipient cell
- Rolling circle replication copies one strand of plasmid DNA from the oriT part of the plasmid, which transfers to the recipient
- Recipient synthesises a complementary strand, forming a complimentary strand and a complete plasmid
- single strand DNA copied back into dsDNA
- Recipient cell (minus) becomes a donor (plus) and can now transfer the plasmid to others
22
Q
What is oriT? What does it need to be transcribed?
A
- oriT = Origin of transfer
- it is a recognition site for tra/trs gene-encoded enzymes
- Needs transfer machinery encoded by the plasmid to be transcribed
- supports rolling circle DNA replication
23
Q
What do plus and minus mean in the transfer of plasmids?
A
- Plus/positive gene = donor cell (has plasmids)
- Minus/negative gene = recipient cell (plasmids absent)
24
Q
What promotes conjugation?
A
The aggregation of cells (either in a biofilm or a syntrophic consortia) and when environmental conditions change
25
What is a transposable element?
A jumping gene - mobile DNA sequences that can make extra copies of themsleves outside of DNA replication
| Jump like a spring
26
What are the 2 types of transposable elements?
1. Insertion sequences
2. Transposons
27
What is an insertion sequence?
- The simplest transposons
- Small DNA segments (containing only a single gene) encoding only a transposase enzyme
- Flanked by inverted repeats (transposase cuts these and moves the sequence)
28
What is a transposon?
- Larger DNA elements that include functional genes and a **transposase**
- Move between chromosomes and plasmids, increasing genetic diversity
- Also flanked by inverted repeats that the transposase knows to cut
29
What are the 2 mechanisms of transposition?
1. Non-replicative transposition (cut and paste)
2. Replicative transposition (copy and paste)
30
How can prokaryotes shuffle their genes?
- Transposition
- Homologous recombination
- HGT (which further subcategorises into conjugation, transduction, transformation)
31
What is homologous recombination in prokaryotes?
- It occurs when DNA sequences exchange strands, allowing gene shuffling between different DNA molecules
- Similar to crossing over in meiosis
32
What is plasmid integration?
Homologous recombination combines the plasmid and chromosome
- plasmid is integrated into the chromosome
33
What is plasmid excision?
Homologous recombination reverses the process, freeing the plasmid and chromosome from one another
- plasmid is ejected
34
What is the name given to plasmids with sequences homologous to a host cell
chromosome, which exhibit reversible integration and excision?
Episomal plasmids
35
How does plasmid integration work?
Homologous sequences are paired up, crossover reaction occurs, and the plasmid is integrated into the chromosome
## Footnote
The reaction is enzymatic and can be reversed, there is an equilibrium between them being separate and joined together
36
How can an entire chormosome transfer into another cell?
If a conjugatve plasmid (with an oriT/tra gene) integrates into the chromosome, the entire chromosome can be transferred to another cell
| The recipient cell effectively becomes diploid
37
What is a Hfr strain?
High frequency of recombination
A bacterial cell in which the plasmid is integrated into the bacterial chromosome
## Footnote
Allows the recipient cell to try out the other's phenotype effectively
38
What is the process of bacteriophage transduction of bacterial DNA?
- Virus attaches to a bacterial cell
- Viral nuclease chops up host DNA
- Host cell replicates the DNA
- New virus accidentally packages bacterial DNA into new capsid
Now, instead of triggering a lytic infection the injected DNA is now available
to recombine with any homologous sequence in the new host cell
39
What is bacterial cell competence? What is it mediated by?
- The ability of the cell to absorb DNA from its environment (transformation)
- Mediated by specific transport proteins in the membrane which transport ssDNA
40
What can happen to transformed DNA in a bacterial cell if it is homologous with the cell's DNA?
It can be integrated in the genome if they are homologous by homologous recombination
41
How can you induce artificial competence? Why is this important?
- Can be induced using Ca2+ treatment
- This is a key tool in genetic engineering
42
What is a mobilome?
The collection of mobile genetic elements (e.g. plasmids, transposons, phage DNA) that can move within a single genome or between genomes
| Basically the USB stick
43
What is homologous recombination?
Occurs when transferred DNA is integrated into the recipient genome
- shuffling genes
## Footnote
Has to have a homologous sequence for this to occur
44
Explain what quorum sensing is in bacteria
- Detecting presence of other bacterial cells of same species
## Footnote
Works almost like a barcode the competent systems of others in the species recognise
45
What are the 2 examples of extrachromosomal plasmids in eukaryotes?
- Yeast 2-micron plasmid: a parasite that carries no beneficial genes, just those for its own replication (often used as a vector in genetic engineering)
- Double minutes (dmins) in cancer cells: often contain oncogenes that drive cancer progression - infect humans and other animals
46
What is transfection?
Where artificial DNA is inserted into a genome for genetic modification in labs
- uses electroporation
## Footnote
Transfected DNA is often transient and does not integrate into the genome
47
Give an example of transduction in eukaryotes
Retroviruses e.g. HIV
48
what did mendelian rules for eukaryotic genetics emerge from?
from the confinement and processing of chromosomal DNA info within orderly cells e.g obvious phenotypes
49
What did Carl Correns discover?
Genetic contribution (stem and leaf colour) is from maternal line
Various human genetic disease traits are also only inherited from maternal parent (Not X-linked)
50
What are some mitochondrial diseases? What do they cause?
LHON, NARP, MERRF,
- all to do with muscle and eye pigment diseases
- affect energy production and damage tissue
51
How many genes does human mitochondrial DNA encode?
37 genes for mitochondrial function (energy production)
52
How many base pairs are in human mitochondrial circular DNA?
16,500bp
53
How many base pairs are in chloroplast circular DNA? What are they for?
150kbp - for photosynthesis and pigment production
54
Does a copy of every mtDNA get into each daughter cell?
No, division is not as regimented so its more random
55
How can heteroplasmy change phenotype?
Can cause variation in leaf colour in plants and variation in disease severity in humans
56
When did engulfment happen that lead to endosymbiont theory?
About 1.5 billion years ago
57
What are Wolbachia?
Obligate parasites - bacteria
Ongoing endosymbiosis in flies as flies can't live without them and Wolbachia can't live without flies
58
What is the relationship between Wolbachia and flies?
Semi-parasitic and semi-symbiotic
59
Where are prions commonly found?
Fungi, especially yeast
60
What can prions proteins regulate?
Gene expression
61
What can fungi produce in times of environmental stress?
Protein chaperones
62
What do protein chaperones do?
Refold the Prion+ form of the protein aggregates back to the normal state (Prion-)
63
What does a pilus do?
Recognises cells that don't have the plasmid and find and attaches to it so that plasmid can replicate by rolling-circle replication
64
What is a pilus made of?
Pilins
65
What do plasmids replicate by?
Rolling-circle replication
66
What is rolling-circle replication?
- DNA peels off from oriT and transfers into recipient cell
- Single DNA and copied back to dsDNA
- conjugation
67
What happens if transposase enzymes get confused over which pair of inverted repeats to act on?
- Can jump both ISs plus the intervening gene
- This is called a transposon (carries extra genes)
68
Do transmisible elements occur in prokaryotes and eukaryotes?
Yes but more frequent in prokarys
69
What are the steps in prokaryote homologous recombination?
1. Transposable elements, such as IS, provide regions of homology allowing whole
plasmids to recombine INTO the chromosome.
2. Conjugation can transfer large regions of
chromosome between cells.
3. Transfer of chromosomal DNA between cells allows reciprocal DNA exchange by
recombination
70
What does homologous recombination create in prokaryotes?
A co-integrated molecule
- plasmid and chromosome
71
Are recipient cells haploid or diploid after conjugation?
Partially diploid bc have copies of genes
72
Can conjugation transfer a whole chromosome?
Not normally BECAUSE the pili break but can move large amounts
73
Why do prokaryotes use HR with conjugation and transposition?
To fully shuffle genes
74
What infects E.coli?
T4 bacteriophage virus
75
What is a virion?
protein capsid containing nucleic acid genome
76
What are nuclease enzymes? What are they encoded by?
Digest host cell chromosome to provide raw materials for replication of viral genome
- encoded by lytic viruses
77
Why is quorum sensing used in bacteria?
- Ensures that extracellular DNA is from the same species
- Quorum signals are released from one cell to another to let the surrounding bacteria of the same species know that they are competent and ready for gene transfer
78
What do competent haemophilus cells do?
- only take up DNA when they recognise an 11 base ‘signal sequence’ that has evolved to occur frequently in haemophilus genomes
- they have a barcode to detect other haemophilius so only lets its DNA in
79
What are DNA islands?
Areas if DNA with higher % of G and C
80
what are trans-species HGT events?
some leakage of genetic info between species by HGT by prokaryotes forming symbiotic/syntrophic aggregates and biofilms with members of other species and other domain
81
what is double minutes (dmins)?
- cancer cell extra-chromosomal circular DNA fragments
- produce tiny circle called double minute molecules
- encode for oncogenes which drive cancer
e.g MYCK gene
82
What can agrobacterium do?
Form a crown gall when it transfers genes
- Uses conjugative Ti plasmid, some of it transferred into plant cell nucleus and integrates into chromosome
83
How can transduction happen in eukaryotes?
- Retroviruses and retroelements able to copy mRNA molecules into DNA and integrate them into chromosomes, creating and mobilising new genes within eukaryotic genomes
84
how is artificial transduction done?
- Create vectors for genetic manipulation of mammalian cells using modified adenovirus and retrovirus genomes
85
What's the difference between adenovirus and retroviral artificial transduction?
- Adenovirus genomes can be propagated extra-chromosomally in nucleus whereas retroviral genomes are integrated into host cell genomes
86
Mirabilis stem and leaf colour depended ONLY on the genetic contribution from which line
Maternal line
87
Give 3 human genetic diseases that descend from the maternal line
LHON: Leber’s Hereditary Optic Neuropathy
NARP: Neurogenic muscle weakness, Ataxia, and Retinitis Pigmentosa
MERRF: Myoclonic Epilepsy with Ragged Red Fibers
88
What causes plant colour variagation?
Heteroplasmy
89
Describe the Wolbachia infection - what does it infect?
70% of current arthropod species have stable intracellular Wolbachia bacterial “infections” within their cells. Genes encoded in these bacteria control some host phenotypes and the bacteria are transmitted maternally like mitochondria
90
Explain how prions are a form of extra-chromosomal inheritance
In fungi they act like dominant heritable genes
Prion mutations can occur that change the shape of the actual prion protein, which can then go on to change the normal prion-s into prion+ states, and these form a larger aggregate
91
How are fungi able to deal with mutated prions?
In fungi, environmental stress can lead to production of protein ”chaperones” which re-fold [PRION+] aggregates back to their normal state
92
What is a single prokaryotic chromosome called?
Nucleoid
93
What will purely dividing asexually do to the genetic fitness of a species?
Cause it to decline - passing on all the unfavourable mutations
94
What does vertical gene transfer mean?
Genes are transmitted “down” through lineages of cells via the mitotic and meiotic cell cycles
95
What can prokaryotes differentiate their cells to do? Give some examples
Collect and distribute nutrients; adhere to, or penetrate, surfaces; create protective goop; swim; disperse spores… – e.g., Bacillus
96
What is a biofilm?
When AGGREGATES of cells with different mutually supportive functions which resemble complex tissues collect on a surface
97
Give an example of a plasmid
plasmid (pGO1) was identified in pathogenic
Staphylococcus bacteria isolated from drug-resistant hospital infections
98
What are 3 key features of a conjugative plasmid?
tra/trs genes: Encode proteins for forming a pilus and DNA transfer.
oriT (origin of transfer): Site where DNA transfer begins.
Enable conjugation: direct transfer of plasmids between cells
99
What are the cells in conjugation that lack the specific plasmid involved called?
Recipient, or minus
100
What are the cells in conjugation that harbour the specific plasmid involved called?
Donor, or plus
101
What do tra/trs genes code for?
Pilin proteins, which form the pilus
Enzymes that catalyse the rolling circle mechanism
102
What mechanism transfer the plasmid between cells in conjugation?
ROLLING CIRCLE DNA REPLICATION – catalysed by enzymes encoded by the tra/trs genes
103
What happens if an episomal plasmid is also conjugative?
Any plasmid integration event will place an oriT, WITHIN the chromosome
104
What do oriTs support?
Rolling circle DNA replication
105
Define transduction
The movement of chromosomal DNA
segments between cells… but mediated by prokaryotic VIRUSES
106
What is transformation?
The deliberate uptake of DNA from the external environment by a prokaryotic cell - this is then converted back into dsDNA in the bacteria
107
What are most forms of HGT restricted to?
Restricted to being within a prokaryotic species
108
How do prokaryotes use restriction/modification as their immune system?
Cells produce a RESTRICTION ENDONUCLEASE (REase) that cuts
foreign DNA at a commonly occurring short sequence (e.g., GAATTC).
Host cell DNA is PROTECTED from destruction because its equivalent
sequences are MODIFIED by a host DNA methylase (MTase)
