F215 - Revision thread 13th June 2011
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Original post by ManPowa
Who else is finding this exam difficult? I absolutely hate revising for it.. Although i got a very high B in Jan for F214, i think im going to end up with a U or an E for this exam. I cant doooo ittt.. !!!
im in same position as you...but i need at least a C in this exam....its not that had if you look at it... unit 3 and 4 are easy.. and 2 is al right as well....... how much have u revised for this
Original post by wilsea05
Original post by wilsea05
rhizobium fixes Nitrogen gas in air
Nitrosomonas converts NH4+ to NO2-
Nitrobacter converts NO2- to NO3-
thats pretty much it tbh
Nitrosomonas converts NH4+ to NO2-
Nitrobacter converts NO2- to NO3-
thats pretty much it tbh
so does rhizobium convert N2 into only NH4+ ?
These are the notes I've written for this bit of the spec:
(a) outline the steps involved in sequencing the genome of an organism;
Genomes are mapped to identify which part of the genome that they come from. Information that is already known is used, for example using the location of microsatellites.
Samples of the genome are mechanically broken into small sections of around 100,000 base pairs.
These sections are placed into separate bacterial artificial chromosomes (BACs) and transferred to E.coli (bacterial) cells. As the cells grow in culture, many copies of the sections are produced – referred to as clone libraries.
IN ORDER TO SEQUENCE A BAC:
Cells containing specific BACs are taken and cultured. The DNA is extracted from the cells and restriction enzymes used to cut it into smaller fragments. The use of different restriction enzymes on a number of samples gives different fragment types.
The fragments are separated using electrophoresis.
EACH FRAGMENT IS SEQUENCED USING AN AUTOMATED PROCESS:
The many copies of the fragments are put in a reaction mixture containing DNA polymerase, free DNA nucleotides and primers, with some of the nucleotides containing a fluorescent marker.
The primer anneals to the 3’ end of the template strand, allowing DNA polymerase to attach.
DNA polymerase adds free nucleotides. If a modified nucleotide is added, DNA polymerase is thrown off and the reaction stops on that template strand.
As the reaction proceeds, many molecules of DNA are made. The fragments generally differ in size, as different numbers of nucleotides will have been added.
As the strands run through a machine, a laser reads the colour sequence. The sequence of colours, and therefore the sequence of bases, can then be displayed.
Computer programmes then compare overlapping regions from the cuts made by different restriction enzymes in order to reassemble the whole BAC segment sequence.
Finally, the DNA fragments from all the BACs are put back in order, by computers, to complete the entire genome.
______________________
I understand that you need single stranded DNA for the automated sequencing so I'm just wondering where in that process the DNA strands become single stranded? Surely they are double stranded when in the BAC?
(a) outline the steps involved in sequencing the genome of an organism;
Genomes are mapped to identify which part of the genome that they come from. Information that is already known is used, for example using the location of microsatellites.
Samples of the genome are mechanically broken into small sections of around 100,000 base pairs.
These sections are placed into separate bacterial artificial chromosomes (BACs) and transferred to E.coli (bacterial) cells. As the cells grow in culture, many copies of the sections are produced – referred to as clone libraries.
IN ORDER TO SEQUENCE A BAC:
Cells containing specific BACs are taken and cultured. The DNA is extracted from the cells and restriction enzymes used to cut it into smaller fragments. The use of different restriction enzymes on a number of samples gives different fragment types.
The fragments are separated using electrophoresis.
EACH FRAGMENT IS SEQUENCED USING AN AUTOMATED PROCESS:
The many copies of the fragments are put in a reaction mixture containing DNA polymerase, free DNA nucleotides and primers, with some of the nucleotides containing a fluorescent marker.
The primer anneals to the 3’ end of the template strand, allowing DNA polymerase to attach.
DNA polymerase adds free nucleotides. If a modified nucleotide is added, DNA polymerase is thrown off and the reaction stops on that template strand.
As the reaction proceeds, many molecules of DNA are made. The fragments generally differ in size, as different numbers of nucleotides will have been added.
As the strands run through a machine, a laser reads the colour sequence. The sequence of colours, and therefore the sequence of bases, can then be displayed.
Computer programmes then compare overlapping regions from the cuts made by different restriction enzymes in order to reassemble the whole BAC segment sequence.
Finally, the DNA fragments from all the BACs are put back in order, by computers, to complete the entire genome.
______________________
I understand that you need single stranded DNA for the automated sequencing so I'm just wondering where in that process the DNA strands become single stranded? Surely they are double stranded when in the BAC?
Original post by lola1993
These are the notes I've written for this bit of the spec:
(a) outline the steps involved in sequencing the genome of an organism;
Genomes are mapped to identify which part of the genome that they come from. Information that is already known is used, for example using the location of microsatellites.
Samples of the genome are mechanically broken into small sections of around 100,000 base pairs.
These sections are placed into separate bacterial artificial chromosomes (BACs) and transferred to E.coli (bacterial) cells. As the cells grow in culture, many copies of the sections are produced – referred to as clone libraries.
IN ORDER TO SEQUENCE A BAC:
Cells containing specific BACs are taken and cultured. The DNA is extracted from the cells and restriction enzymes used to cut it into smaller fragments. The use of different restriction enzymes on a number of samples gives different fragment types.
The fragments are separated using electrophoresis.
EACH FRAGMENT IS SEQUENCED USING AN AUTOMATED PROCESS:
The many copies of the fragments are put in a reaction mixture containing DNA polymerase, free DNA nucleotides and primers, with some of the nucleotides containing a fluorescent marker.
The primer anneals to the 3’ end of the template strand, allowing DNA polymerase to attach.
DNA polymerase adds free nucleotides. If a modified nucleotide is added, DNA polymerase is thrown off and the reaction stops on that template strand.
As the reaction proceeds, many molecules of DNA are made. The fragments generally differ in size, as different numbers of nucleotides will have been added.
As the strands run through a machine, a laser reads the colour sequence. The sequence of colours, and therefore the sequence of bases, can then be displayed.
Computer programmes then compare overlapping regions from the cuts made by different restriction enzymes in order to reassemble the whole BAC segment sequence.
Finally, the DNA fragments from all the BACs are put back in order, by computers, to complete the entire genome.
______________________
I understand that you need single stranded DNA for the automated sequencing so I'm just wondering where in that process the DNA strands become single stranded? Surely they are double stranded when in the BAC?
(a) outline the steps involved in sequencing the genome of an organism;
Genomes are mapped to identify which part of the genome that they come from. Information that is already known is used, for example using the location of microsatellites.
Samples of the genome are mechanically broken into small sections of around 100,000 base pairs.
These sections are placed into separate bacterial artificial chromosomes (BACs) and transferred to E.coli (bacterial) cells. As the cells grow in culture, many copies of the sections are produced – referred to as clone libraries.
IN ORDER TO SEQUENCE A BAC:
Cells containing specific BACs are taken and cultured. The DNA is extracted from the cells and restriction enzymes used to cut it into smaller fragments. The use of different restriction enzymes on a number of samples gives different fragment types.
The fragments are separated using electrophoresis.
EACH FRAGMENT IS SEQUENCED USING AN AUTOMATED PROCESS:
The many copies of the fragments are put in a reaction mixture containing DNA polymerase, free DNA nucleotides and primers, with some of the nucleotides containing a fluorescent marker.
The primer anneals to the 3’ end of the template strand, allowing DNA polymerase to attach.
DNA polymerase adds free nucleotides. If a modified nucleotide is added, DNA polymerase is thrown off and the reaction stops on that template strand.
As the reaction proceeds, many molecules of DNA are made. The fragments generally differ in size, as different numbers of nucleotides will have been added.
As the strands run through a machine, a laser reads the colour sequence. The sequence of colours, and therefore the sequence of bases, can then be displayed.
Computer programmes then compare overlapping regions from the cuts made by different restriction enzymes in order to reassemble the whole BAC segment sequence.
Finally, the DNA fragments from all the BACs are put back in order, by computers, to complete the entire genome.
______________________
I understand that you need single stranded DNA for the automated sequencing so I'm just wondering where in that process the DNA strands become single stranded? Surely they are double stranded when in the BAC?
If they're double stranded then how come we get numerous,small dna fragments? at the beginning when DNA polymerase,primers areadded to the buffer solution ,that instant is when two dna molecules are split up to make numerous copies.
Original post by lola1993
These are the notes I've written for this bit of the spec:
(a) outline the steps involved in sequencing the genome of an organism;
Genomes are mapped to identify which part of the genome that they come from. Information that is already known is used, for example using the location of microsatellites.
Samples of the genome are mechanically broken into small sections of around 100,000 base pairs.
These sections are placed into separate bacterial artificial chromosomes (BACs) and transferred to E.coli (bacterial) cells. As the cells grow in culture, many copies of the sections are produced – referred to as clone libraries.
IN ORDER TO SEQUENCE A BAC:
Cells containing specific BACs are taken and cultured. The DNA is extracted from the cells and restriction enzymes used to cut it into smaller fragments. The use of different restriction enzymes on a number of samples gives different fragment types.
The fragments are separated using electrophoresis.
EACH FRAGMENT IS SEQUENCED USING AN AUTOMATED PROCESS:
The many copies of the fragments are put in a reaction mixture containing DNA polymerase, free DNA nucleotides and primers, with some of the nucleotides containing a fluorescent marker.
The primer anneals to the 3’ end of the template strand, allowing DNA polymerase to attach.
DNA polymerase adds free nucleotides. If a modified nucleotide is added, DNA polymerase is thrown off and the reaction stops on that template strand.
As the reaction proceeds, many molecules of DNA are made. The fragments generally differ in size, as different numbers of nucleotides will have been added.
As the strands run through a machine, a laser reads the colour sequence. The sequence of colours, and therefore the sequence of bases, can then be displayed.
Computer programmes then compare overlapping regions from the cuts made by different restriction enzymes in order to reassemble the whole BAC segment sequence.
Finally, the DNA fragments from all the BACs are put back in order, by computers, to complete the entire genome.
______________________
I understand that you need single stranded DNA for the automated sequencing so I'm just wondering where in that process the DNA strands become single stranded? Surely they are double stranded when in the BAC?
(a) outline the steps involved in sequencing the genome of an organism;
Genomes are mapped to identify which part of the genome that they come from. Information that is already known is used, for example using the location of microsatellites.
Samples of the genome are mechanically broken into small sections of around 100,000 base pairs.
These sections are placed into separate bacterial artificial chromosomes (BACs) and transferred to E.coli (bacterial) cells. As the cells grow in culture, many copies of the sections are produced – referred to as clone libraries.
IN ORDER TO SEQUENCE A BAC:
Cells containing specific BACs are taken and cultured. The DNA is extracted from the cells and restriction enzymes used to cut it into smaller fragments. The use of different restriction enzymes on a number of samples gives different fragment types.
The fragments are separated using electrophoresis.
EACH FRAGMENT IS SEQUENCED USING AN AUTOMATED PROCESS:
The many copies of the fragments are put in a reaction mixture containing DNA polymerase, free DNA nucleotides and primers, with some of the nucleotides containing a fluorescent marker.
The primer anneals to the 3’ end of the template strand, allowing DNA polymerase to attach.
DNA polymerase adds free nucleotides. If a modified nucleotide is added, DNA polymerase is thrown off and the reaction stops on that template strand.
As the reaction proceeds, many molecules of DNA are made. The fragments generally differ in size, as different numbers of nucleotides will have been added.
As the strands run through a machine, a laser reads the colour sequence. The sequence of colours, and therefore the sequence of bases, can then be displayed.
Computer programmes then compare overlapping regions from the cuts made by different restriction enzymes in order to reassemble the whole BAC segment sequence.
Finally, the DNA fragments from all the BACs are put back in order, by computers, to complete the entire genome.
______________________
I understand that you need single stranded DNA for the automated sequencing so I'm just wondering where in that process the DNA strands become single stranded? Surely they are double stranded when in the BAC?
Eek I've neva come across BAC's or most of anything you say! All I got told you needed to know for sequencing of the genome is the automated termination method :s what the hell!
Eek I've neva come across BAC's or most of anything you say! All I got told you needed to know for sequencing of the genome is the automated termination method :s what the hell!
Tbh, I'm pretty confused about what we do/don't have to know when it comes to sequencing the genome... ffs, I bet it's going to come up in the exam and all!
If they're double stranded then how come we get numerous,small dna fragments? at the beginning when DNA polymerase,primers areadded to the buffer solution ,that instant is when two dna molecules are split up to make numerous copies.
Hi, can anyone answer the following questions (I'm sorry if any have already been posted, I couldn't be bothered reading through the 20 pages):
1. What do we need to know in relation to homeobox genes? (2.1.6)
So far I've just got the definitions of 'homebox genes', 'morphogens', 'transcription factors' 'maternal effect genes' and 'segmentation genes'. I remember my teacher talking about something being 'conserved', can anyone explain this?
2. Can someone explain what translocation mutations are?
I was making notes on 2.1.9 - The significance of meiosis and in the key defintion box it talks about mutations to chromosomes such as inversion, deletion, translocation and non-disjunction. I went on youtube and I found some videos that explained them, but I don't really understand translocation mutations.
http://www.youtube.com/watch?v=XAGxp9j5rtc&feature=channel_video_title
In this video (from 2:20) it shows a balanced translocation mutation. I can't tell the difference between this and the crossing over of alleles at prophase 1, but the book specifically says 'The shuffling of alleles in prophase 1 is not an example of a mutation'. Is the book suggesting that translocation mutations are only mutations when they are unbalanced? Or is there something more specific about a balanced translocation mutation that I have missed?
3. Are all primary consumers herbivores? Because, not all producers are plants, some are protoctists/bacteria? Does anything eat them?
1. What do we need to know in relation to homeobox genes? (2.1.6)
So far I've just got the definitions of 'homebox genes', 'morphogens', 'transcription factors' 'maternal effect genes' and 'segmentation genes'. I remember my teacher talking about something being 'conserved', can anyone explain this?
2. Can someone explain what translocation mutations are?
I was making notes on 2.1.9 - The significance of meiosis and in the key defintion box it talks about mutations to chromosomes such as inversion, deletion, translocation and non-disjunction. I went on youtube and I found some videos that explained them, but I don't really understand translocation mutations.
http://www.youtube.com/watch?v=XAGxp9j5rtc&feature=channel_video_title
In this video (from 2:20) it shows a balanced translocation mutation. I can't tell the difference between this and the crossing over of alleles at prophase 1, but the book specifically says 'The shuffling of alleles in prophase 1 is not an example of a mutation'. Is the book suggesting that translocation mutations are only mutations when they are unbalanced? Or is there something more specific about a balanced translocation mutation that I have missed?
3. Are all primary consumers herbivores? Because, not all producers are plants, some are protoctists/bacteria? Does anything eat them?
Original post by kej817
Hi, can anyone answer the following questions (I'm sorry if any have already been posted, I couldn't be bothered reading through the 20 pages):
1. What do we need to know in relation to homeobox genes? (2.1.6)
So far I've just got the definitions of 'homebox genes', 'morphogens', 'transcription factors' 'maternal effect genes' and 'segmentation genes'. I remember my teacher talking about something being 'conserved', can anyone explain this?
2. Can someone explain what translocation mutations are?
I was making notes on 2.1.9 - The significance of meiosis and in the key defintion box it talks about mutations to chromosomes such as inversion, deletion, translocation and non-disjunction. I went on youtube and I found some videos that explained them, but I don't really understand translocation mutations.
http://www.youtube.com/watch?v=XAGxp9j5rtc&feature=channel_video_title
In this video (from 2:20) it shows a balanced translocation mutation. I can't tell the difference between this and the crossing over of alleles at prophase 1, but the book specifically says 'The shuffling of alleles in prophase 1 is not an example of a mutation'. Is the book suggesting that translocation mutations are only mutations when they are unbalanced? Or is there something more specific about a balanced translocation mutation that I have missed?
3. Are all primary consumers herbivores? Because, not all producers are plants, some are protoctists/bacteria? Does anything eat them?
1. What do we need to know in relation to homeobox genes? (2.1.6)
So far I've just got the definitions of 'homebox genes', 'morphogens', 'transcription factors' 'maternal effect genes' and 'segmentation genes'. I remember my teacher talking about something being 'conserved', can anyone explain this?
2. Can someone explain what translocation mutations are?
I was making notes on 2.1.9 - The significance of meiosis and in the key defintion box it talks about mutations to chromosomes such as inversion, deletion, translocation and non-disjunction. I went on youtube and I found some videos that explained them, but I don't really understand translocation mutations.
http://www.youtube.com/watch?v=XAGxp9j5rtc&feature=channel_video_title
In this video (from 2:20) it shows a balanced translocation mutation. I can't tell the difference between this and the crossing over of alleles at prophase 1, but the book specifically says 'The shuffling of alleles in prophase 1 is not an example of a mutation'. Is the book suggesting that translocation mutations are only mutations when they are unbalanced? Or is there something more specific about a balanced translocation mutation that I have missed?
3. Are all primary consumers herbivores? Because, not all producers are plants, some are protoctists/bacteria? Does anything eat them?
1. I thought we dont need to know THAT much about them.. I think its literally that they determine the gene plan of an organism and determine the polarity of a body. Segmentation genes determine the order of segments in an insect. What are morphogens??
2. Translocation simply is the swapping of a section of a chromosome with a homologous pair of chromosome so for example as you know there are 23 pairs of chromosome. Pair 23 determines the sex and all the others are autosomal chromosomes.
A section of a chromosome from pair 1 might get swapped with pair 3
3. It's better to call primary consumers, primary consumers as like you said but to the level we need to know producers are plants but its better to refer to them as autotrophs
Original post by sportycricketer
1. I thought we dont need to know THAT much about them.. I think its literally that they determine the gene plan of an organism and determine the polarity of a body. Segmentation genes determine the order of segments in an insect. What are morphogens??
2. Translocation simply is the swapping of a section of a chromosome with a homologous pair of chromosome so for example as you know there are 23 pairs of chromosome. Pair 23 determines the sex and all the others are autosomal chromosomes.
A section of a chromosome from pair 1 might get swapped with pair 3
3. It's better to call primary consumers, primary consumers as like you said but to the level we need to know producers are plants but its better to refer to them as autotrophs
2. Translocation simply is the swapping of a section of a chromosome with a homologous pair of chromosome so for example as you know there are 23 pairs of chromosome. Pair 23 determines the sex and all the others are autosomal chromosomes.
A section of a chromosome from pair 1 might get swapped with pair 3
3. It's better to call primary consumers, primary consumers as like you said but to the level we need to know producers are plants but its better to refer to them as autotrophs
1. A morphogen is a substance that governs the pattern of tissue development by activating the homeobox genes (e.g. retinoic acid). I'm pretty sure we had to know something about things being conservative....
2. So it's sort of like, swapping alleles that don't actually code for the same gene (whereas crossing over in prophase 1 is shuffling alleles that do code for the same gene)?
3. Er, Right :P
Original post by kej817
1. A morphogen is a substance that governs the pattern of tissue development by activating the homeobox genes (e.g. retinoic acid). I'm pretty sure we had to know something about things being conservative....
2. So it's sort of like, swapping alleles that don't actually code for the same gene (whereas crossing over in prophase 1 is shuffling alleles that do code for the same gene)?
3. Er, Right :P
2. So it's sort of like, swapping alleles that don't actually code for the same gene (whereas crossing over in prophase 1 is shuffling alleles that do code for the same gene)?
3. Er, Right :P
1. ohh yeahh that rings a bell :P.. it activates the homeobox genes right? and I dont think we do
2. well first part is right. Second one no they code for different things cos remember they are NON-sister chromatids, does that make sense?
Original post by J DOT A
Is a Homologous pair of chromosomes a bivalent? Or is it 2 maternal chromatids joined together at centromere?
Homologous pair of chromosomes
Original post by sportycricketer
1. ohh yeahh that rings a bell :P.. it activates the homeobox genes right? and I dont think we do
2. well first part is right. Second one no they code for different things cos remember they are NON-sister chromatids, does that make sense?
2. well first part is right. Second one no they code for different things cos remember they are NON-sister chromatids, does that make sense?
1. Yeah. We do we do! my teacher kept talking about it, when I find out, I will post it :P
2.
in the book it specifically says 'this leads to similar sections of non-sister chromatids being swapped over. These sections contain the same genes but, often, different alleles'Can someone explain the types of mutation to me? Thanks 
please 
please Original post by kej817
1. Yeah. We do we do! my teacher kept talking about it, when I find out, I will post it :P
2. in the book it specifically says 'this leads to similar sections of non-sister chromatids being swapped over. These sections contain the same genes but, often, different alleles'
2.
in the book it specifically says 'this leads to similar sections of non-sister chromatids being swapped over. These sections contain the same genes but, often, different alleles'1. It might be something your teacher said that isnt in the spec? :P
2. i think they're similar in the sense they're on the same locus and yh thats right as well sorry, didnt read it through properly the first time
Original post by slacker07906
Can someone explain the types of mutation to me? Thanks please
please Point - a base is substituted with another one. This may not do anything as it may be a silent mutation i.e. the triplet code codes for the same amino acid. Or as it may change the sequence of amino acids, which leads to the tertiary structure of the protein being changed
Insertion/Deletion of bases - this may cause a frame shift and will change the sequence of the amino acids and codes for a completely different protein which might be advantageous/harmful depending on the environment
Original post by slacker07906
Can someone explain the types of mutation to me? Thanks please
please Types of DNA mutation:
Point/Substitution mutation -Base pair is replaced e.g. the sequence ..AGT AGT... may change to ATT AGT
Insertion/deletion mutations -Base pair(s) inserted or deleted e.g. the sequence ...AGT AGT... may change to ...AGA GT...and this would cause a framshift because every base would move along one, so all of the triplet codons after the mutation would be different and possibly code for different amino acids
There are also chromosomal mutations (see key definition, pg 121): I found that these videos explained it well alongside a re-read of the text in the little box
http://www.youtube.com/watch?v=XAGxp9j5rtc&feature=channel_video_title
– Explains the chromosomal mutations: inversion, deletion and translocation.
http://www.youtube.com/watch?v=yP4ZItCHouU&feature=related
– Explains the chromosomal mutation ‘non disjunction’.
The second one is a bit longwinded and cheesy, but meh.
Hope that helps.
What is the behaviour of centrioles in meiosis? Its so frickin confusing!!! I'm going through each specification point and this has left me a little confused :s
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