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Biology SL/HL help


Mahuta ♥

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*TOPIC 4 (4.4.8)---Genetic engineering (reverse transcriptase)*

Genetic engineering is another word for genetic modification.

This is basically the new technology of taking certain bits of DNA of an organism and putting it into the gene of another.

Main example you have to know:

Genetic modification that is used in the production of human insulin.

  1. mRNA coding for insulin is taken from the pacreatic cells that produce it.
  2. Reverse transcriptase is used to make DNA from this mRNA.
  3. 'G' nucelotides are added to each end to allow it to stick.
  4. Now the insulin gene is read.
  5. A plasmid (small hoop of DNA in bacteria) is extracted from the bacteria and opened using restricting enzymes
  6. C nucleotides are added to each side of the plasmid(to stick to the 'G' added on to insluin gene).
  7. The insulin gene and the plasmid are stuck together, however, they leave nicks in between.
  8. DNA ligase(also used in replication) heals these nicks by adding sugar-phosphate bond.
  9. The plasmid witht the insulin gene is called 'recombinant'. It is inserted into the bacteria.
  10. The bacteria/host cell normally used is the E.Coili bacteria and it starts producing human insulin.

That's all you have to know about gene modification. A definition and a use.

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Can some one please explain this:

Explain photophosphorylation in terms of chemiosmosis.

Mark scheme Answer:

electron transport causes proton/hydrogen ion pumping;

protons inside thylakoids;

accumulation of protons / H+ / drop in pH;

protons leave through proton channel (to stroma);

ATP synthetase / enzyme catalyses phosphorylation of ADP;

I usually come across this question and always find it hard to understand it. Can you please explain about it. The answer scheme provided doesn't really help me.

Thanks in advance.

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*TOPIC 8 (8.2.4)---Photophosphorylation in terms of chemiosmosis*

Ok, no worries, it's easy. Just understand it:

This follows the same principal as oxidative phosphorylation in respiration.

1)When light is absorbed by the photosystem (2), electrons are excited and released into the electron carrier chain(which consists of proteins).

2) Everytime electrons move from one carrier to another, a Hydrogen ion is pumped across the thylakoid membrane into the thylakoid space.3)So, you will have a high concentration of protons(hydrogen ions), therefore, you have a concentration gradient.

4)Hydrogen ions are pumped out of the thylakoid through the ATP Synthase, causing it to spin, this spinning generates energy.

5)electrons are accepted by the NADP+.

You have to remember that the hydrogen ions come from the photolysis of water that produce protons as well as electrons(which replace the ones accepted by the NADP+).

Chemiosmosis refers to the diffusion of protons, so basically, they wanted you to explain this by mentioningand referring to chemiosmosis.

I know I just gave the whole light dependent process here, but I personally write all this to garuntee that I dont miss any marks.

If there's anything else unclear, feel free to ask. :ot:

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  • 2 weeks later...

Rather than 'concentration gradient', I'd say an 'electrochemical gradient' which may be easier to visualise. Since the protons are building up, it's more the change in potential rather than concentration that causes the proton pumping through ATPase

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*OPTION F (F.4.1)---Use of SACCHAROMYCES in BEER and WINE production*

Well this is an objective 3 and it says 'explain' so you need to understand it carefully.

So basically they want you to know how mircobes( saccharomyces specifically) are used in wine and beer production along with bread.

Saccharomyces are basically yeast(as far as we'r concerned for this part). So for:

Wine:

1-Wine is made from grape juice. Grape uis crushed into juice in a large container.

2-Yeast are naturally growing in the juice. So when the juice is made, yeast starts carrying out aerobic respiration and using up all the oxygen.

3-Once no oxygen is available, they switch to anaerobic respiration which produces ethanol. This is called fermentation.[/b]

4-Fermentation keeps going on until: a) all glucose(sugars) in juice used up(no more respiration) or b)ethanol content become 15%.

Thats all for wine.

Beer:

1-Beer production doesnt use sugars, it used starch which yeast cells cant use.

2-To fix this, barley seed are wetted with water and kept to initiate germination, which produces amyalse.

3-Amylase breaks down starch into maltose and seeds are dried to kill them off preserving the enzyme.

These seeds are called 'malted barley'.

4-Malted barley is mixed with starch sources and some yeast types and water.

5-Amylase in the seeds break down starch into maltose which the yeast cells use for anaerobic respiration producing ethanol.

6-Hops are added for the flavor.

Anything else, feel free to ask.

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Rather than 'concentration gradient', I'd say an 'electrochemical gradient' which may be easier to visualise. Since the protons are building up, it's more the change in potential rather than concentration that causes the proton pumping through ATPase

Well I would personally suggest the use of concentration gradient since its what given by IB, in other words, to stay on the safe side. Also some people may find it hard seeing it as a potential and electricity matter.

But I do see your point and probably would make sense more to people who have that electrical terms' ability. I personally don't. I am more of a bio-chem person. SO yeah, I was just using what i learnt. :P

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*OPTION F (F.2.8)---METHANE GENERATION*

This process, also called methanogenisis, is used to replace the biomass fuel by converting it into an organic fuel (eg, ethanol and methane). Methane is naturally produced in animals in anaeroibic respirations using 'feedstock' in animals' alimentary canel. Therefore, for industrial methane generation, these conditions have to be found in the bioreactors.

Organic substance is normally used for 'feedstock' provided for the respiration. Organic substances used could be 'manure' and cellulose.

Feedstock is put in the bioreactor providing the anaerobic condition.

This condition enhances the growth of three main groups of bacteria.

1) First group converts: organic matters ---------> organic acids and alcohols.

2) Second group convets: organic acids and alcohol -----------------> Carbon Dioxide + Hydrogen + acetate.

3)Third group, the most important one, generates methane from carbon dioxide, hydrogen and acetate. This group contains methanogenic archaea.

The reaction equation for this part is required:

CO2 + 4H2 ------------------> CH4 + 2H2O

CH3COOH -------------------> CH4 + CO2

All the gas that is normally produced in bioreactors is called biogas. It contains about 40-70% methane gas.

The syllabus requires you to know:

  • Conditions needed.
  • organisms used, in other words, groups of bacteria.
  • Chemical reactions involved.

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*TOPIC 6 (6.5)---NERVES AND IMPULSES*

Ok, so:

Neurons

  • Nerves have different functions of sending impulses to do, therefore have more than one type.
  • The first type is the 'motor' neuron, the most important one. This neuron carries the impulse from the CNS to the effector. It is taking the order for actions of muscles and its normally urgent. Think about it this way: urgency needs high speed so, we're using a motor. If that helps.
  • The second type is the sensory neurons. It is where the impulse, or 'request of action' comes from. Sensory neurons are more or less 'sensing' what happened. The only way I remembered this was this way: When you hurt yourself, the message is delivered to the CNS and then back to the muscle by the sensory neuron. You wont feel that pain if the message didn't go back to the muscle to produce that feeling. It's not an accurate example, but I always relate sensory and sensing in my head to remember that sensory neurons are the what take the message back to the effector.
  • The third one, is the relay neuron which carries the impulse within the CNS itself. A way of remembering this is normal relay races where runner 2 for example is connecting the path of runner 1 and runner 4, just as the relay neuron is doing.

Potentials (depolarization)

This is a very important part of the nerves part and I strongly advise you not to go to synapses unless you get this.

  • A nerve cell membrane has 2 types of channel that are concerned with this: Na+/K+ pump and Na+ pump.
  • There is a certain charge across the membrane when the membrane is at rest (no impulse passing), this is caused by Na+ moving out of the cell and K+ into the cell through the same channel. Some K+ can move back out but Na+ can't. So, you have a net negative charge inside the cell and net positive charge outside.(This is really stupid but I remember it this way: Outside= You think outside the box, therefore you think positively). This is Resting membrane potential.
  • When an impulse hits the dendrites, Na+ channels (for Na+ ONLY) open up causing Na+ to start moving in, while K+ are still in. So, you will have a positive charge inside the cell and a negative outside. This is called depolarization (change in charge).
  • When one Na+ pump opens and a certain amount of ions get in, the neighbooring channels start opening (Like dominoes). So you have a series of 'Na+ channel opening down the membrane', this is Action Potential moving down. (the charge changing and ions are in action)
  • When the potential becomes 30+mV (you dont have to know the number, but it helps.), Na+ pumps close (They got too tired of remaining open) and K+ pumps open (They take over). So K+ starts coming out of the cell.
  • This sets the potential back again to normal, with -ve charge inside and +ve charge outside. this is Repolarization.

Ok, if this didn't make any sense to you try this:

http://highered.mcgraw-hill.com/sites/0072...ve_impulse.html

It is very clear and makes absolute sense. I wouldnt try understanding it from any of the books.

Synapses

Synapse is the space between each neuron and its neighboor.

I just mentioned how impulses is passed in terms of neurons. Synapses is all about how the impulse is passed exactly form neuron to neuron, or more specifically, from the presynaptic neuron to the post synaptic. we know it passes, but how. Very simple.

  1. Ca2+ enters the presynaptic. This causes vesicles that contain neurotransmitters ( they are the impulse it self) to move towards the membrane.
  2. As it gets there, the vesicle fuses with the membrane, exocytosis. Neurotransmitters diffuse out in to the synapse(synaptic cleft).
  3. On the post synaptic membrane there is a channel for Na+. Neurotransmitters go and bind to a certain place on the channel, this makes the channel open.(think about it as a button pressed). This causes depolarization ( because Na+ are starting to come in, remember that part about depolarization?)
  4. The Ca 2+ that went in the presynaptic moves out again. (It's job is done and its getting ready to repeat it for the next impulse).
  5. Neurotransmitters is broken down and they are reabsorbed into the vesicles. (Once again, their job is over and they're preparing them selves to do it again.)

If there is anything missing or unclear ask.. biggrin.gif

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Hey Mahuta, I'm having a hard time with the HL part of the DNA processes (Chapter 7). I would really appreciate it if you could explain (or summarise) each of the different processes referring to what the IB expects me to know for HL. Thanks in advance!

Regards.

Edited by Hedron123
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*TOPIC 7 -- DNA replication, transcription and mRNA translation*

Alrighty, if you understand the SL then there isn't much more, but I'll go over both together.

DNA Replication- 7.2.1-2:

  1. DNA Helicase enzyme uncoils DNA double helix by breaking hydrogen bonds between bases. The seperated strands are called template strands.
  2. Since Replication normally happen in 5' to 3' direction, DNA POLYMERASE IIIstarts adding nucleotides*(with complementary bases) in that direction, which is towards the replication fork(another name for the point at where helicase is working).
  3. On the other strand, which is 3' to 5', the replication process can't take place normally, as it needs to go in the opposite direction (to work 5' to 3').
  4. RNA PRIMASE starts binding some lengths of RNA (with complementay bases) in that strand.
  5. These lengths are called 'primers' and they give the starting point for DNA POLYMERASE III to bind to it and be able to work 5' to 3' (opposite direction).
  6. Once it binds, DNA Polymerase III starts the replication from the primers(adding nucleotides).
  7. As DNA POLYMERASE IIIreplicates the strand, DNA POLYMERASE I works on removing the primers and replacing them with nucleotides.
  8. On this strand, with all the different things happening to it, there will be small gaps(nicks) between the section replicated. (a gap of 2 nucleotides).
  9. To fix this, DNA Ligase puts a sugar-phosphate bond in between to fill the gap.

*The cell always produces nucleotides that are free floating in the cell. They are usually triphosphates. When replication starts, 2 phosphates are removed in order to release energy.

So the enzymes used are:

  • DNA polymerase III: carries out replication.
  • DNA polymerase I: Replaces RNA primers with DNA molecules.
  • RNA Primase: as the name suggests, it adds the primers on the 3' to 5' strand.
  • DNA Ligase: Seals up the gaps left on the 3' to 5' strand.
  • DNA helicase: unwinds helix.

DNA TRANSCRIPTION- 7.3.1-3:

You know that this is the process by which mRNA is produced from the DNA so it is translated into a protein.

  1. RNA polymerase bind on DNA on the 'promoter region' and unwinds the double helix into two strands. One is called sense strand and the other anti-sense strand. the anti-sense strands is the template by which mRNA is going to be formed.
  2. Free floating complementary nucleosides(with triphosphates) are added onto the anti sense strand by RNA polymerase.
  3. Once the nucleosides are added, two phosphates are removed and we have a nucleotide instead. It forms covalent bonds between the nucleotides.
  4. RNA polymerase works on this in a 5'-3' direction.
  5. After the required region is transcribed, the end of the RNA polymerase rewinds the helix.

The mRNA produced here is sometimes called 'pre mRNA'. This because it contains introns which are interveing sequence of nucleotides that dont seem to have a reason why they'er there just yet. These introns are removed are the pre mRNA is now called mRNA or mature mRNA.

TRANSLATION- 7.4.3

Translation consists of:

Initiation:

  • First tRNA is bound to the small ribosome subunit in the A site. This tRNA has the complementary base to the start codon (AUG).
  • The small sub unit then binds to the mRNA and move along in 5' to 3' direction until it reaches AUG.
  • At that point, the large sub unit binds.
  • A second subunit with codon complementary to the second codom on the mRNA binds in the P site.

Elongation:

  • The two tRNA with the amino acid on each allow a peptide bond to form between the two amino acids.
  • The amino acids then break their bond with the tRNA.
  • As this happens, the first tRNA moves along to the E site of the ribosome and the second to the P site and so allowing a third one to bind.
  • Once the third one binds, the first is immediatly released. And so on.
  • As the ribosome slides along the mRNA and the peptide bonds forming between amino acids, the polypeptide chain is growing.

Termination:

  • When the ribosome reaches the codon UGA on the mRNA, translation stops.
  • This is because there isn't a tRNA with the complementary codon, so the two subunits seperate.
  • This causes the last tRNA to detach from the ribosome along with the polypeptide chain breaking off it.

Note that there are two different types of ribosomes:

  1. One that is found free, in which case it forms polypeptides to be used inside the cell it self.
  2. The other is bound on the Endoplasmic Reticulum which forms polypeptides that will be exported out of the cell or used by the lysosomes.

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Ok, I have some questions about the syllabus.

Firstly, what does starch break down into? Maltose? Glucose? Sucrose? Galactose? There was a multiple question on that and I have no idea.

Secondly, 6.1 Digestion, 6.1.3 State the source, substrate, products and optimum pH conditions for one amylase, one protease and one lipase.

Do I need names for the amylase enzyme and others that I pick? Or is it enough to say "Amylase, source: salivary glands, substrate: polysaccharides (starch), products: monosaccharides (maltose and galactose, whatever starch breaks down into) and optimum pH 6.0-7.0?" Or does the enzyme I pick need a specific name?

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*TOPIC 6 (6.1.3)---Digestive Enzymes*

I would say that starch breaks down to give maltose. Because what IB says is that: polysaccharides break down to give disaccharides, hence maltose. Logically it cant be anything but glucose or maltose. But since the IB states that, it is maltose.

*TOPIC 6 (6.1.3)---Digestive Enzymes*

It says one amylase...etc..so this is what you should have:

Salivary Amylase: salivary glands, substrate;starch, product: maltose/glucose..Optimum pH: 6.9.

Pepsin/any other protease: stomach wall, substrate;proteins, product: amino acids..Optimum pH: 2

Pancreatic lipase(for example):pancreas, substrate;lipid, product: fatty acids and glycerol..Optimum pH: 6.9

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Thanks.

And anyone who's doing Neurobiology as an option, can you explain this: Outline the role of inheritance and learning in the development of birdsong in young birds. I have a short part on it in my book but it's an inquiry (so it says "What do you notice about the role of learning in birds?") Essentially useless.

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Thanks.

And anyone who's doing Neurobiology as an option, can you explain this: Outline the role of inheritance and learning in the development of birdsong in young birds. I have a short part on it in my book but it's an inquiry (so it says "What do you notice about the role of learning in birds?") Essentially useless.

So it is about that some of the features of a bird song are innate and some are learned from other bird of the same species. In my book the example is the chaffinch. They compared the song that a, from birth onwards, isolated chaffinch sings to the song free chaffinches sing (- the song varies a bit between the free male chaffinches because that allows identification of individuals). They used soundproof boxes to ensure the birds don't hear any other bird sing. The song of the isolated birds will still have features of the song free birds sing: the isolated bird's song had the correct length and the correct number of notes - these are innate. It had however a narrower range of frequencies and as they call it, fewer distinctive phases - these are learned from other chaffinches.

That's it. :)

(I recommend the IB study guide for biology.)

Edited by remy
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By the way, my friend who went to Oxford Revision Courses was told to expect evolution and classification to feature largely in the exam, because apparently it's Darwin's 100th birthday this year or something with 100 years and him anyways.

Another question, this time about the general syllabus: what are the identifying features for bryophyta, coniferophyta, filicinophyta and angiospermophyta? My book has this nowhere.

Also, are we required to know an entire food web (for ecology) and dichotomous key (for classification) by heart?

So it is about that some of the features of a bird song are innate and some are learned from other bird of the same species. In my book the example is the chaffinch. They compared the song that a, from birth onwards, isolated chaffinch sings to the song free chaffinches sing (- the song varies a bit between the free male chaffinches because that allows identification of individuals). They used soundproof boxes to ensure the birds don't hear any other bird sing. The song of the isolated birds will still have features of the song free birds sing: the isolated bird's song had the correct length and the correct number of notes - these are innate. It had however a narrower range of frequencies and as they call it, fewer distinctive phases - these are learned from other chaffinches.

That's it. :)

(I recommend the IB study guide for biology.)

Thank you for answering. I read some stuff online about white-crowned sparrows, similar stuff. Now I know what to say.

Edited by Vvi
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