Genetics Semester 2 Flashcards
When a virus is in it’s extracelluar state what is it called?
Viron.
When a virus is in its intracellular state what is it called?
Replicative state.
What do viruses use from the host?
Metabolic and Replicative machinery.
What size can a genome be?
0.5kb-1000kb.
What are all virus genomes to small for?
Independent life.
How many proteins make up the capsid in TMV?
7.
Why is the coat of a virus being able to self assemble a good thing?
It means less genes are required.
What sort of genetic material is found in TMV?
ssRNA.
What shape is TMV?
Rod.
What do capsomers make up?
The capsid.
What is an isoheadron made up of?
20 identical triangular faces.
What symmetry does a isoheadron have?
2,3 and 5 fold symmetry.
What does not have the isoheadron structure?
Flu and phage viruses.
What are the most numerous microorganisms?
Viruses.
What are the 5 steps of a viral infection?
- Attachment
- Penetration
- Synthesis of nucleic acid.
- Maturation
- Release.
Does the virus have all the machinery needed to assemble the coat?
No. It may have some though.
What type of nucleic acids do the bacterial virus T4 phage have?
Double stranded DNA.
How many proteins does the T4 virus encode for?
Around 250.
What is the structure of the T4 genome?
Circularly permuted.
What is added to the end of the genome sequence in the T4 phage to ensure the genome is the correct size to fit the head?
Terminal repeats.
What is the time course between infection and lysis in a T4 phage?
25 minutes.
What do early proteins encode for?
Nucleases, DNA polymerase, sigma factors.
What do late proteins encode for?
T4 lysosomes and structural proteins.
What mechanisms are in place to ensure that the T4 genes are transcribed and not the hosts?
- Sigma factors to confer specificity.
- Phage promoters modify host RNAP
- Anti sigma factors.
What does the T4 pages anti sigma factor bind to?
Sigma 70 preventing host transcription.
What happens to allow the synthesis of middle proteins?
Early phage proteins modify host RNAP alpha subunits so middle promotes are recognised.
Does T4 encode it’s own RNA polymerase?
No.
What guides RNAP to middle promotor sites?
MOTA.
How are late proteins transcribed?
A new sigma factor is encoded for.
<p>What is the prophage form of the virus?</p>
<p>When the viralDNA is integrated into the host.</p>
A trigger brings about what to change the pathway from lysogenic to lytic?
Induction.
Is all the viral DNA integrated into the host DNA during the lysogenic pathway?
No. Some can remain as the plasmid.
What needs to be turned off in order to enter the lytic pathway?
The repressor to switch of viral protein synthesis.
What does a bacteriophage infect?
E.coli.
<p>What type of nucleic acid does the bacteriophage have?</p>
<p>dsDNA (linear).</p>
What is the attachment site that the bacteriophage integrates into?
Att lambda.
What enzyme is needed to allow the bacteriophage to infect ecoli?
Lambda intergrase.
What happens to the bacteriophage DNA once it has been injected?
It becomes circular.
<p>What type of replication is in the lytic pathway of bacteriophage?</p>
<p>Rolling circle replication.</p>
What happens in rolling circle replication?
A strand of the circular genome is nicked. The single stranded concatomer is then used as a template.
The cos site is cut.
How does intergrase get into the host genome?
Productions of specific late proteins.
<p>What does the lambda repressor repress (in ecoli) ?</p>
<p>Synthesis of all other lambda proteins.</p>
What does the cro repressor repress?
Expression of CIII and CI/ CI Synthesis. These commit the cell to lysis.
What is an example of a (+) strand RNA virus?
Polio, rhinovirus, hepatitis A.
These are all very small.
Capping does not occur in the poliovirus. What happens instead?
The RNA folds into stem loops to mimic the cap with VPG.
How many bases does poliovirus have?
7433.
In the polio virus where does replication occur?
The cytoplasm.
How is the host RNA synthesis inhibited with the poliovirus?
The host cap binding protein is destroyed.
What enzyme allows the synthesis of a - strand then a + strand with poliovirus?
RNA replicase. This is encoded for by the poliovirus polyprotein.
If you have ss (+) RNA what can it also act as?
A messenger.
The combination of the messenger property and the VPG cap mean it can be mistakes as host RNA.
What does destruction of the hosts cap binding protein result in?
Host RNA synthesis being switched off.
is ssRNA (-) the same as mRNA?
No. This means it is not recognised by the host.
What are examples of ssRNA (-) viruses?
Rabies, influenza, Ebola.
Do (-) ssRNA have a enveloped or capsid structure?
Enveloped.
The transcription of what is essential in (-) RNA viruses?
A virus encoded RNA replicase or polymerase.
When the rhabdovirus and the influenza virus leave the host what do they take with it?
A piece of the membrane.
How many classes of RNA are transcribed from (-) RNA viruses such as the rhabdovirus?
- This is because + strands need to be encoded so that the virus can be transcribed.
How many ssRNA molecules are in influenza?
8.
Does the influenza virus have it’s own RNA replicase?
Yes.
What is the role of RNA endonuclease in the influenza virus?
It removes the primer from host capped mRNA precursors.
What are Neurominidase and Hemagglutinin?
They are found on the surface of the influenza virus and are recognised by the hosts immune system.
Neuramindase breaks down in the respiratory tract and Heamglutin allows the virus to bind.
What activates the RNA replicase in influenza?
Uncoating.
What is added to the viral RNA in influenza?
A polyA tail. It is already capped.
What causes antigenic drift?
A fragmented genome.
<p>What is antigenic drift?</p>
<p>A change to the proteins surface on the virusbut not the active site.</p>
How does a fragmented genome cause antigenic drift?
It allows more that one infection at a time.
What does antigentic drift cause?
Antigentic shift.
What is the only DNA eukaryote virus not to replicate in the nucleus?
Pox.
<p>What can the polyomavirus: SV40 do?</p>
<p>Induce tumours.</p>
<p>What does SV40 not have?</p>
<p>Any virally encoded proteins.</p>
What is SV40 regularly used as?
a vector.
The dark gene is found in the SV40 genetic map. What does this encode?
Small and large T antigens. These are involved in binding to the origin of replication.
How are the genes arranged in the SV40 genome?
They overlap. This saves space.
How is DNA converted into RNA in the SV40 virus?
Host cellular RNA is used to make the transcript of early genes.
What happens to the RNA made by cellular RNA from the early region?
It is split into 2 capped MRNAs.
Why can’t SV40 encode it’s own RNA polymerase?
The genome is too small.
How is the late MRNA synthesised in SV40?
From the complementary strand used in early synthesis.
Is the SV40 genome bidirectional?
Yes.
Late RNA in the SV40 virus is processed normally to correspond to what?
The VP1 and VP2 coat proteins.
What happens to the MRNA encoding coat proteins VP1 and VP2 in SV40?
It leaves the nucleus to be translated and re enters to be assembled into the coat.
What do non permissive cells allow?
DNA integration and not normal viral replication. This will cause cancer.
What two viruses use reverse transcriptase?
Retrovirus (RNA) hepadnavirus.
What type of RNA strand does the retrovirus have and how many off them?
2 (+) strands.
What is the correct order for the pol gag env genes in the reterovirus?
Gag pol env.
What does the gag gene code for in the reterovirus?
Structural/ coat proteins and proteases.
What does the pol gene code for in the reterovirus?
Reverse transcriptase and intergrase.
What does the env gene encode for in the reterovirus?
Envelope proteins.
<p>Where does reverse transcriptase get its primer from?</p>
<p>It steals it from a previous host.</p>
<p>What type of molecule is the reverse transcriptase primer?</p>
<p>tRNA.</p>
What are the 8 steps of reverse transcriptase?
Entrance, uncoating, reverse transcription, traveling to nucleus and integrated into host DNA, transcription, encapsidation, budding, release.
What does encapsidation consist of?
The viral RNA has two paths, it can either be re used as a messenger or packed by viral proteins to form genomic RNA in a capsid. This second process is encapsidation.
What does activation of promoters in the LTR repeat regions lead to?
Capped and polyadenylated mRNA.
What is the gene organisation in the hepadnavirus virus?
The genes overlap.
What type of nucleic acid is in the hepadnavirus?
Partial dsDNA.
How does the hepadnavirus replicate?
Through an RNA intermediate.
Uses the hosts machinery for DNA to RNA then it’s own reverse transcriptase for RNA to DNA.
What happens to the virus particles in a persistent infection?
They are slowly released.
What checkpoint does the anaphase promoting complex as a ubiquitin ligase on?
Metaphase checkpoint.
If the kinetochores are not attached to the microtubules what can this inhibit?
The anaphase promoting complex.
What must the activated anaphase promoting complex include?
CDC20 protein.
What can the cdc20 protein in the APC bind to?
Mad/bun protein complex.
When will the mad/bub protein complex form?
When kinetochores are not bound to the the microtubules.
When the anaphase protein complex is bound to the mad/bub complex is it active or inactive?
Inactive. Securin is not broken down.
What do cell cycle arrest and apoptosis both depend on?
C53 protein.
What does the presence of transcription factor P53 allow?
The transcription of p21.
What does p21 inhibit?
CDK cyclin activity.
What happens when P53 is phosphorylated?
It is active.
What type of molecule is mdm2? What is it’s role?
It is a ubiquitin ligase which degrades P53.
What prevents the degradation of P53 by mdm2?
The fact that it is phosphorylated.
Why do all organism have to go through a bottleneck?
As at one point they are only one cell.
What does the Antemepeadia mutation in drosophila result in?
Legs where the antenna should be.
What happens when the ‘dorsel lip of the blastopore’ is transplanted into a different place?
A whole new embryo forms.
What did Hans Spearman do?
Found that an organiser induced formation of another embryo.
What is a tetragen?
An agent which causes birth defects eh thalidomide.
What is phocomelia?
Limb shortening.
What type of organism is C. elegans?
A nemotode worm.
How many adult somatic cells are in C. elegans?
954 (it is very small) .
Who got a Nobel prize for their work on C. elegans?
Brenner, Sulston and Howitz.
What organism was early work on apoptosis done on?
C. elegans.
Does Drosphila melangastor have mitotic cell division?
No. There is no G phase so the cycle is greatly accelerated.
How long is D. melangastor a embryonic development?
A day.
What does D. melangastors embryo run from?
Anterior to posterior.
What cells in DM form first and give rise to the germline?
Posterior cells.
Once the first few cells in DM have gained a membrane what sort of structure is formed?
A hollow one.
In DM developed cells move from P to A to P. What is also formed?
Layers of cells called blastomyces.
What is formed at the Anterior end in DM?
Head.
What is the first movement that DM experiences?
The trachea filling with air.
What type of organism is Xenopus laevis?
An African clawed toad.
What is Arabidopis thaliana?
A model organism plant.
What happens in mosaic development?
Organisation is maintained.
What happens in regulative development?
There is no information on organisation.
Laser ablation has an effect on which development form?
Mosaic.
Transplantation has an effect on which development form?
Mosaic.
What sort of development is present in DM and the nemotoad?
Mosaic.
What sort of development is used by humans and sea urchins?
Regulative.
Where does the frog develop?
On top of the yolk.
What are the 5 steps in the frog life cycle?
- Fertilisation
- Cleavage/ Blasulation
- Gastulation
- Organogenesis
- Cell differentiation.
What is the purpose of cleavage/ Blasulation?
Produces a large number of cells.
What is the purpose of gastulation?
Allows rearrangement of cells.
What develops in the ectoderm?
Nervous system and skin.
What cells development in the mesoderm?
Heart, muscles, skeleton, kidney.
What develops in the endoderm?
Lungs, liver, gut.
What do morphogens do?
Create asymmetry and patterns.
When was DMs genome sequenced?
1997.
How long is the life cycle of DM?
12 days. It is only larva for 24 hours allowing quick observations.
What does DM start of as?
A maggot that feeds ok yeast.
What does an oocyte have at fertilisation?
Polarity.
<p>What is the purpose of nuse cells?</p>
<p>To support the oocyte.</p>
Proteins and mRNA are held in the Nurse cells in what state up until fertilisation?
Untranslational.
After the fertilisation only the nuclei divide for the first 9 times. What does this result in?
A syncytium.
Where do nuclei migrate to after fertilisation to form a blastoderm?
The eggs surface.
What does the morphogenetic gradients of bicos and nanos genes help the cell know?
Where it is in the embryo.
What recognises gene products to allow the concentrations to be seen on morphogenetic gradients with a densitrometric scanner?
Antibodies.
What are early segments called?
Parasegments.
What does the modified ring, also know as the halotere allow DM to do?
Balance.
How many segments are in the abdomen?
8.
Where are maternal effect genes active?
Maternal cells.
What do maternal effect genes control?
mRNA tethering to A and P.
Where are zygotic genes active?
In the mother.
What are the two types of zygotic genes?
Segmentation and homeotic selector genes.
What do segmentation genes do?
Divide the embryo up via division of Parasegments.
What do geographical selector genes control?
Control other banks of genes to allow development of specialised structures including legs.
What does the posterior end of the cell contain?
Posterior pole plasm.
Where do the nuclei move to give rise to the germline?
The posterior pole plasm.
Wha determines fertility in DM?
The genotype of the mother.
What are the three classes of segmentation genes?
Gap, pair rule and segment polarity genes.
What is ‘hunchback’ and example of?
A gap gene.
What pattern is the hunchback gene expressed in?
Broad bands in the central. Other gap genes express similar bands in slightly different positions.
What regulates pair rule gene expression?
Combination of gap gene expression.
What are ‘eve’ and ‘runt’ examples of?
Pair rule genes.
What are the bands like expressed by pair rule genes?
Narrower bands. Expressed in alternative parasegments.
What controls the expression of segmentation genes?
The combination of pair rule genes expressed.
What is ‘fushi tarazu’ an example of?
Segmentation gene.
How many parasegments do the segment polarity genes organise?
14.
When are homeotic selector genes activated?
Once segmentation has been established by the segmentation genes.
What do homeotic selector genes do?
Specify the identity of each segment.
How are related genes in DM organised in it’s genome?
They are clustered on one chromosome.
What does the order of genes in DM correspond to in DM?
Spatial organisation.
What can homeotic selector genes signal?
Changes in gene expression.
What are the two clusters of genes called in DM?
The Antennepeadia complex and the Bithoroax complex.
Are mammals segmented during embryonic development?
No.
How big is the homeobox DNA binding domain?
180bp.
What does an abnormality in the HOXD13 gene cause?
The wrong number of toes.
Nb there is also a PAX6 gene that also causes inherited development.
What does a mutation in the hox gene cause?
A lip mutation.
What do segmentation genes in early mammalian development control formation of?
Bone, blood and gentiles.
What does a mutation in the runt gene cause?
Skeletal defects.
What is the definition of epigenetics?
Heritable changes in gene expression associates with unchanged DNA sequence.
What bases pair is methylated in mammals?
CG.
What position does methylation occur?
5 position of cytosine ring.
What enzyme adds the methyl group to the CG base pair?
Methyl transferase.
Are genes expressed when they are methylated?
Generally not
What type of regulation is methylation?
Long term.
How many histones make up the core that DNA can wind round?
8.
How many times does DNA wind around the histone?
Twice.
What happens to hemi methylated DNA?
The other strand is then methylated.
What structure is the histone when in when transcription is occurring?
Open.
When open are nucleosomes acetates or deacylated?
Acylated.
What type of modification is more rigid, methylation or acetylation?
Methylation.
What happens to the chromosomes when they are between acylation states?
The chromatin can be remodelled.
When do nucleosomes need to be briefly disassembled?
When the replication fork reaches the nucleosome.
When the nucleosome is reassembled is it made of new histones, old histones or both?
Both.
What is RNA induced transcriptional silencing?
When the RNA transcript regulates gene activity. It can also influence to structure.
When the RNA transcript regulates gene activity what does it interact with?
The chromatin.
Is X activation rare in mammals?
No it happens in almost all mammals.
In a human roughly how many genes are found on the X chromosome?
1000.
There are regions that are homologous on the sex chromosomes to allow pairing. How big are these regions?
They are small.
