VCE Biology Question Thread

[cosine]

for photosynthesis, do we need to know about the details of and differences between cyclic and non-cyclic phosphorylation?

also, since the study design only states for the main inputs and outputs of each phase, does this mean that we do not need to learn the actual steps of photosynthesis?

Nah no need for the phosphorylation, not in the study design.
What do you mean by actual steps? You should obviously know the two main stages: Light-dependent and independent, but not the exact steps that occur within them. (Except maybe that electron transport chain exists also in light independent, seen this one on a MC before).

[tashhhaaa]

Nah no need for the phosphorylation, not in the study design.
What do you mean by actual steps? You should obviously know the two main stages: Light-dependent and independent, but not the exact steps that occur within them. (Except maybe that electron transport chain exists also in light independent, seen this one on a MC before).

yeah that's what I meant, steps as in Calvin cycle, electron transport chain etc

so that would mean we don't need to know anything about stuff like RuBP or photosystems yeah? (I've been learning this -.-)

[cosine]

yeah that's what I meant, steps as in Calvin cycle, electron transport chain etc

so that would mean we don't need to know anything about stuff like RuBP or photosystems yeah? (I've been learning this -.-)

I learnt it too ages ago, but now forgot about it because its probably useless, not on the study design, nor have I ever seen a question regarding it. The closest thing I have seen is 'describe the events that occur during the electron transport chain and list the final acceptor molecule' which was on the I think 2007 or 06 U3 exam. But yah, no need to learn the specifics about it, just main inputs, outputs, the whole point of photosynthesis, and their locations.

[cosine]

Is it true that meiosis II can work if a chromosome is missing because there is no homologous line up in the middle, but meiosis I, if there is a chromosome missing then meiosis I cannot occur?

Cans anyone answer this for me, please?

[winchesteraddict]

Could someone summarise DNA sequencing for me?

Since no one replied;
Didioxyribonuceic acids (ddNPT) are used (nucleotides with didioxyribose sugar instead of dioxyribose).
What ddNPTs do is bind to a growing strand on DNA and stops the extension (of nucleotides [like in replication])

ok, so the process:
1) Four different test tubes are prepared, each containing DNA strands (disassociated, after being denatured), free nucleotides (A,T,G and C), Taq DNA polymerase and primers.
2) A type of ddNPT is also added (either ddA, ddT, ddC or ddG)
3) Test tubes are cooled and replication is allowed to proceed. Complementary DNA strands are formed in each tube.
4) Occasionally, a ddnucleotide is incorporated into a growing DNA chain and replication stops
5) Length of each DNA chain indicates where the particular nucleotide occured
6) At the end of replication, each test tube contains a number of DNA fragments of different lengths.
7)Tubes are heated again to produce single strands of DNA
These are placed in gel electrophoresis
9) Shortest will move the furthest distance and longest the shortest distances
10) Gel is exposed to X-ray film which photographs radioactive primers

[Biology24123]

Since no one replied;
Didioxyribonuceic acids (ddNPT) are used (nucleotides with didioxyribose sugar instead of dioxyribose).
What ddNPTs do is bind to a growing strand on DNA and stops the extension (of nucleotides [like in replication])

ok, so the process:
1) Four different test tubes are prepared, each containing DNA strands (disassociated, after being denatured), free nucleotides (A,T,G and C), Taq DNA polymerase and primers.
2) A type of ddNPT is also added (either ddA, ddT, ddC or ddG)
3) Test tubes are cooled and replication is allowed to proceed. Complementary DNA strands are formed in each tube.
4) Occasionally, a ddnucleotide is incorporated into a growing DNA chain and replication stops
5) Length of each DNA chain indicates where the particular nucleotide occured
6) At the end of replication, each test tube contains a number of DNA fragments of different lengths.
7)Tubes are heated again to produce single strands of DNA
These are placed in gel electrophoresis
9) Shortest will move the furthest distance and longest the shortest distances
10) Gel is exposed to X-ray film which photographs radioactive primers

You don't need to know the stages of DNA sequencing

[vox nihili]

Since no one replied;
Didioxyribonuceic acids (ddNPT) are used (nucleotides with didioxyribose sugar instead of dioxyribose).
What ddNPTs do is bind to a growing strand on DNA and stops the extension (of nucleotides [like in replication])

ok, so the process:
1) Four different test tubes are prepared, each containing DNA strands (disassociated, after being denatured), free nucleotides (A,T,G and C), Taq DNA polymerase and primers.
2) A type of ddNPT is also added (either ddA, ddT, ddC or ddG)
3) Test tubes are cooled and replication is allowed to proceed. Complementary DNA strands are formed in each tube.
4) Occasionally, a ddnucleotide is incorporated into a growing DNA chain and replication stops
5) Length of each DNA chain indicates where the particular nucleotide occured
6) At the end of replication, each test tube contains a number of DNA fragments of different lengths.
7)Tubes are heated again to produce single strands of DNA
These are placed in gel electrophoresis
9) Shortest will move the furthest distance and longest the shortest distances
10) Gel is exposed to X-ray film which photographs radioactive primers

I'm with Biology24123 on this; you don't need to know the stages of DNA replication.

Your explanation is close, winchesteraddict, but it appears to have melded a few methods together in one. The big difference between your explanation and how Sanger sequencing actually takes place is about how the tubes are set up. For those interested:



You put your DNA sample into a normal PCR tubes and do all the normal PCR stuff to those tubes. To sequence, some fluorescently tagged ddNTPs are also added to the tube. These are nucleotides that can be added to a strand but to which no nucleotides can be added. They are therefore called chain terminators, because once a ddNTP is added, the chain will stop. In the reaction mixture, these are far outnumbered by dNTPs (i.e. normal nucleotides).

When new strands are made, a ddNTP will be added every so often. This will end the strand. After a number of rounds of PCR, you get a stack of DNA strands (from the template) of different lengths. They are different lengths because the incorporation of the chain terminator determines the length. When a chain terminator is incorporated is essentially random, hence, strands of different lengths.

Then what you do is take all of these strands and separate them out on a gel (in reality there are other ways to do this, but let's not go there). By electrophoresis, the length of the strands obtained can be determined. Using a laser, you then determine what "colour" the strand is (i.e. what chain terminator has been added to the last position). By comparing with the length of the strand, you can then determine what nucleotide—because each is coloured differently—has been added to the strand. For instance, if you have a strand of 176 bp and it's red, then the 176th nucleotide in your sequence is whatever red corresponds to (let's say adenine). If the next strand is 177 bp, and it's green, then the 177th nucleotide is whatever green corresponds to (let's say G). This way you can start building your sequence.

[cosine]

Is it true that meiosis II can work if a chromosome is missing because there is no homologous line up in the middle, but meiosis I, if there is a chromosome missing then meiosis I cannot occur?

[grindr]

You don't need to know the stages of DNA sequencing

You do need to know the stages...

[mahler004]

I'm with Biology24123 on this; you don't need to know the stages of DNA replication.

Your explanation is close, winchesteraddict, but it appears to have melded a few methods together in one. The big difference between your explanation and how Sanger sequencing actually takes place is about how the tubes are set up. For those interested:



You put your DNA sample into a normal PCR tubes and do all the normal PCR stuff to those tubes. To sequence, some fluorescently tagged ddNTPs are also added to the tube. These are nucleotides that can be added to a strand but to which no nucleotides can be added. They are therefore called chain terminators, because once a ddNTP is added, the chain will stop. In the reaction mixture, these are far outnumbered by dNTPs (i.e. normal nucleotides).

When new strands are made, a ddNTP will be added every so often. This will end the strand. After a number of rounds of PCR, you get a stack of DNA strands (from the template) of different lengths. They are different lengths because the incorporation of the chain terminator determines the length. When a chain terminator is incorporated is essentially random, hence, strands of different lengths.

Then what you do is take all of these strands and separate them out on a gel (in reality there are other ways to do this, but let's not go there). By electrophoresis, the length of the strands obtained can be determined. Using a laser, you then determine what "colour" the strand is (i.e. what chain terminator has been added to the last position). By comparing with the length of the strand, you can then determine what nucleotide—because each is coloured differently—has been added to the strand. For instance, if you have a strand of 176 bp and it's red, then the 176th nucleotide in your sequence is whatever red corresponds to (let's say adenine). If the next strand is 177 bp, and it's green, then the 177th nucleotide is whatever green corresponds to (let's say G). This way you can start building your sequence.

Although T-Rav is entirely correct, there's a couple of (very minor) points I'd like to make:

• Really old fashioned DNA sequencing used radioactively labelled nucleotides - that's probably what winchesteraddict was talking about when he spoke about imaging the gel on an autoradiograph. These days when Sanger sequencing is done it's done with fluorescently labelled nucleotides. It probably just depends on how old your textbook is.
• Again, a gel is rarely (if ever) used these days for separating the nucleotides after you've run the sequencing PCR reaction.
  Spoiler

  You use a capillary electrophoresis instrument - basically gel electrophoresis in a glass tube.
• This 'classical' Sanger sequencing has fallen out of favour compared to more modern methods, which are much higher-throughput, cheaper and easier to automate. Sequencing whole genomes with Sanger chemistry is really, really expensive. That said, Sanger is still used all the time, and it's easier to understand then the newer techniques.

Sanger, by the way, was the only person to win the Nobel Prize for Chemistry twice (for both DNA sequencing and being the first person to find the sequence of a protein.)

[warya]

But meiosis I has to occur before II?

Is it true that meiosis II can work if a chromosome is missing because there is no homologous line up in the middle, but meiosis I, if there is a chromosome missing then meiosis I cannot occur?

[sunshine98]

You don't need to know the stages of DNA sequencing

But the study design says - DNA tools and techniques: gel electrophoresis; DNA amplification; DNA sequencing; making a recombinant plasmid; bacterial transformations; DNA profiling; gene cloning; and using plasmids as gene delivery systems

[cosine]

But meiosis I has to occur before II?

Meiosis I will occur with the normal number of chromosomes, but non-disjuntion occurs, this is what I am trying to find out, is it true or?

[Biology24123]

But the study design says - DNA tools and techniques: gel electrophoresis; DNA amplification; DNA sequencing; making a recombinant plasmid; bacterial transformations; DNA profiling; gene cloning; and using plasmids as gene delivery systems

You need to know what it is and how it is used but not the specific steps involved. But you do need to know PCR

[vox nihili]

You need to know what it is and how it is used but not the specific steps involved. But you do need to know PCR

Second this.

Meiosis I will occur with the normal number of chromosomes, but non-disjuntion occurs, this is what I am trying to find out, is it true or?

Non-disjunction means that the homologues haven't separated, so no, this won't be the case. Meiosis I and meiosis II would occur as normal if you start off with one less chromosome, you'd just end up with two daughter cells without that chromosome and two with a full set.

Although, the reality of the matter is that if someone were missing one chromosome, they wouldn't be able to grow to a point whereat meiosis would even be relevant. In other words, lose a chromosome, and you'll probably die. So, theoretically, yes, both stages of meiosis could occur. Practically, however, the organism would be so buggered meiosis wouldn't occur.