VCE Biology Question Thread

[HighTide]

Is this a sufficient explanation of DNA sequencing:

A DNA sample is mixed with primers, DNA polymerase, nucleotides and fluorescently marked dideoxynucleotides.
PCR is performed. When a fluorescently marked nucleotide is added this terminates polymerisation, subsequently this results in many fragments differing by a single nucleotide base.
Gel electrophoresis is performed on this sample separating these fragments by the number of base pairs, the end nucleotides are tagged with a fluorescent dye and are read as peaks on a chromatogram.

And a few questions;
Why is it DNA polymerase not Taq polymerase for Dna sequencing?

In PCR are the primers/nucleotides/Taq polymerase added after heating to 95C or before? I believe it is after but textbooks explain it as a mixture before heating. My thinking is that heating to 95C would denature Taq polymerase.

Just a dot point summary:
-That is Sanger Sequencing or Chain Termination sequencing
-DNA is obtained from a sample of hair, blood etc.
- It is heated to high temperatures to separate into two single strands of DNA.
- Four flasks are set up with each base dideoxynucleotides (ddATP, ddCTP, ddGTP, ddTTP). DNA Polymerase is added not Taq DNA Polymerase because it's commercially available and you don't need Taq Polymerase as this part of Sanger sequencing doesn't occur under high heat.
- Free nucleotides are added for replication and primers for initiating replication.
- When the strand of DNA is run through each flask, each time, the DNA will keep replicating using the free nucleotides until the specific dideoxynucleotide comes up. I.e. In the flask with ddATP, it will continue to replicate until A comes up. When A does come up, the ddATP will attach to the single strand complementary and terminate the sequence.If you repeat this four times for each base, you eventually will get the exact sequence of nucleotides in the desired gene.
-When the strands are run through electrophoresis, the exact sequence of bases can be determined from the tagged ones

PCR:
Everything is added initially, but the role of primers and nucleotides are only in annealing and extension. It won't denature the enzyme. Thermus aquaticus lives in hot springs at about that temperature of 95°C (thermophile). Therefore, its enzymes have a tolerance to heat and so, won't denature at that temperature.

You seem to be on the right track Sine. I don't know how much detail is needed but yeah that's correct. 

[Sine]

Just a dot point summary:
-That is Sanger Sequencing or Chain Termination sequencing
-DNA is obtained from a sample of hair, blood etc.
- It is heated to high temperatures to separate into two single strands of DNA.
- Four flasks are set up with each base dideoxynucleotides (ddATP, ddCTP, ddGTP, ddTTP). DNA Polymerase is added not Taq DNA Polymerase because it's commercially available and you don't need Taq Polymerase as this part of Sanger sequencing doesn't occur under high heat.
- Free nucleotides are added for replication and primers for initiating replication.
- When the strand of DNA is run through each flask, each time, the DNA will keep replicating using the free nucleotides until the specific dideoxynucleotide comes up. I.e. In the flask with ddATP, it will continue to replicate until A comes up. When A does come up, the ddATP will attach to the single strand complementary and terminate the sequence.If you repeat this four times for each base, you eventually will get the exact sequence of nucleotides in the desired gene.
-When the strands are run through electrophoresis, the exact sequence of bases can be determined from the tagged ones

PCR:
Everything is added initially, but the role of primers and nucleotides are only in annealing and extension. It won't denature the enzyme. Thermus aquaticus lives in hot springs at about that temperature of 95°C (thermophile). Therefore, its enzymes have a tolerance to heat and so, won't denature at that temperature.

You seem to be on the right track Sine. I don't know how much detail is needed but yeah that's correct. 

Nice, from memory I don't think VCAA has ever asked for a full explanation of the process (maybe this year) but I think all the knowledge is relevant and needs to be understood as they will examine a specific part of the process..

[BakedDwarf]

what plant defences (both physical and chemical) are we required to know for the exam? If a question asked to list a few physical and chemical plant defences, what could you say?

[heids]

what plant defences (both physical and chemical) are we required to know for the exam? If a question asked to list a few physical and chemical plant defences, what could you say?

*pulls out VCAA definitions and processes document*

(surprisingly, it's really handy for myself too ) So these are answers from past questions they've asked:

Barriers in plants:
•   Waxy layers on outside surface
•   Intact or thick cuticle
•   Chemicals that repel potential pathogen vectors such as insects
(Not from the exam report but my own knowledge: another could be thorns and hairs to deter vectors, or excreting nasty chemicals that kill pathogens - no need to be specific)

And if infection does occur in plants:
•   Grow ‘gall’ tissue round area containing infective agent to prevent spread to other areas
•   Produce chemicals e.g. tannins
•   Produce ‘gum’ to seal off wounded area
•   Drop infected leaf to inhibit spread to other areas

[vox nihili]

Is this a sufficient explanation of DNA sequencing:

A DNA sample is mixed with primers, DNA polymerase, nucleotides and fluorescently marked dideoxynucleotides.
PCR is performed. When a fluorescently marked nucleotide is added this terminates polymerisation, subsequently this results in many fragments differing by a single nucleotide base.
Gel electrophoresis is performed on this sample separating these fragments by the number of base pairs, the end nucleotides are tagged with a fluorescent dye and are read as peaks on a chromatogram.

And a few questions;
Why is it DNA polymerase not Taq polymerase for Dna sequencing?

In PCR are the primers/nucleotides/Taq polymerase added after heating to 95C or before? I believe it is after but textbooks explain it as a mixture before heating. My thinking is that heating to 95C would denature Taq polymerase.

Pretty sure sequencing isn't even part of the course? If it is, all of that's right expect for the gel electrophoresis part. If you're going to read it on a chromatogram, it's capillary electrophoresis.

Taq polymerase is DNA polymerase from Thermus aquaticus. They don't use Taq pol in sequencing because it's too error prone.

Taq polymerase is used because it's thermostable. It's added at the start of PCR and can be heated up to 95°C without being denatured.

[heids]

I don't think VCAA has ever asked for a full explanation of the process

Can confirm that they haven't.

Pretty sure sequencing isn't even part of the course?

Can confirm that it is.  (Listed in SD).

[vox nihili]

Can confirm that they haven't.
Can confirm that it is.  (Listed in SD).

It's been in the study design since '08 though and they've never once asked about the way it's achieved.

My advice would be that people need to understand what sequencing is and what it's useful for, but beyond that, I highly doubt anybody needs to know the process, not least because there are a variety of means by which DNA can be sequenced and the study design doesn't specify any particular method of sequencing.



Gotta admit, kind of wished it were expected in detail... I've got a lecture coming up and was really excited about the prospect of having to talk about sequencing :p

[Sine]

Just to clarify a few things that I found whilst doing Trial Exams:

We don't need to know about:
 Water balance
specific types of regulation e.g An appropriate response for an endotherm whose cored body termperature decreased are?
Again, Water balance in plant roots(ion concentration in root hairs)
About metabolic waste products question attached.

[Biology24123]

Just to clarify a few things that I found whilst doing Trial Exams:

We don't need to know about:
 Water balance
specific types of regulation e.g An appropriate response for an endotherm whose cored body termperature decreased are?
Again, Water balance in plant roots(ion concentration in root hairs)
About metabolic waste products question attached.

Depends if appropriate information is provided in the question. I'd say you need to know the question attached but not sure about the res of it

[KingDrogba]

Just wondering, with one sac to go i've dropped only 2 marks for the year, hoping that nothing drastic happens i should finish on about 197-198/200, what exam score would i need to obtain a high end 40?

[Biology24123]

Just wondering, with one sac to go i've dropped only 2 marks for the year, hoping that nothing drastic happens i should finish on about 197-198/200, what exam score would i need to obtain a high end 40?

So you've gotten 100% on every SAC?

[KingDrogba]

So you've gotten 100% on every SAC?

Not on all, but majority yes, i was just wondering at what exam score i'd need to get that 48-50 score i really want!

[Biology24123]

Not on all, but majority yes, i was just wondering at what exam score i'd need to get that 48-50 score i really want!

Are the sacs really easy then

[StupidProdigy]

I've got no idea where to even start (see attachment). Any hints please?

[BakedDwarf]

I've got no idea where to even start (see attachment). Any hints please?

Perform a dihybrid cross between the parents: HHGG x hhgg