Biology SL/HL help

[ILM]

Im Stuck on a lab here!

Everyone says that i need 'literature values' to compare in my lab for my conclusion,

I cant find any in both my study guides and textbooks for chemistry and Biology

Ive already tried looking for lit. values for my experiment on google scholar, no luck there though!

is there any website where i can search for lit. values and data?

EDIT: in case anyone was wondering, the experiment was to test the 'sensitivity' of Benedict's solution on glucose, we measured the time taken for the solution to turn brown on varied concentrations of glucose.

You can ask your teacher, he can find it to you from the source that he got the lab from.

[dhabyahalk]

Im Stuck on a lab here!

Everyone says that i need 'literature values' to compare in my lab for my conclusion,

I cant find any in both my study guides and textbooks for chemistry and Biology

Ive already tried looking for lit. values for my experiment on google scholar, no luck there though!

is there any website where i can search for lit. values and data?

EDIT: in case anyone was wondering, the experiment was to test the 'sensitivity' of Benedict's solution on glucose, we measured the time taken for the solution to turn brown on varied concentrations of glucose.

See the quote below v

Try and get your hands on a CRC Handbook of Chemistry and Physics, it has (I feel like I'm not even exaggerating here) EVERY literature value you could ever need

Our chem teacher showed us her own copy (only the 77th edition though) and all 5 of us kind nerded over it for a good 20min, stupid bell rang and ended the fun

It was for Chem and Physics, though..but apparently Google just told me that there is CRC Handbook of Biochemistry and Molecular Biology so you may want to get it, or ask the school to get one(s) so you can just go to the library whenever you need any lit value

ARGH

ITS $159

Omg. i'll try to get the school to get it , but they take YEARS

Thank you though!!

that would be a big help to people in my school in the future

INM :

My teacher is the Vague-i-want-you-to-find-your-own-way-so-run-off-and-dont-ask-me-again kind of teacher... it sucks when you're IB

Edited December 31, 2010 by dhabyahalk

[Hinuku]

Could You tell me what I have to know about pigments.

Also, does IB require me to learn all the enzymes and reactants of those cycles? Our teacher says it's obligatory for her class but I don't see any sense in learning a bunch of meaningless names ;p

Also, I read that the porphyrin ring is hydrophylic and the hydrocarbon tail hydrophobic. Doesn't this make the whole molecule of chlorophyll polar? that's what I deduce, however - in martin,solomon,berg biology - it is written that the long hydrocarbon tail makes the molecule extremely non-polar. How is that correct?

Thanks again anyways ^^

Another question - do light dependent reactions take place on the chloroplast membrane or on the thylakoid membrane? I thought that on the latter is correct, but now I'm reading a different book so..

[Mahuta ♥]

Could You tell me what I have to know about pigments.

Also, does IB require me to learn all the enzymes and reactants of those cycles? Our teacher says it's obligatory for her class but I don't see any sense in learning a bunch of meaningless names ;p

Also, I read that the porphyrin ring is hydrophylic and the hydrocarbon tail hydrophobic. Doesn't this make the whole molecule of chlorophyll polar? that's what I deduce, however - in martin,solomon,berg biology - it is written that the long hydrocarbon tail makes the molecule extremely non-polar. How is that correct?

Thanks again anyways ^^

Another question - do light dependent reactions take place on the chloroplast membrane or on the thylakoid membrane? I thought that on the latter is correct, but now I'm reading a different book so..

Simply, you do not need to know about any pigments or their structures. You just have to know the most common one is Chlorophyll.

IB does not require you to learn all the enzymes, just the ones mentioned in the syllabus.

Don't worry about molecular structure of chlorophyll, you don't need to know that.

Light dependent reaction takes place in the thylakoid membranes of the chloroplast. Chloroplasts contain thylakoids:

Here's a tip:

Download the syllabus from here. Follow that syllabus, point by point. Anything you can't find in the syllabus, just ignore! I mean it, the IBO will not get questions outside the syllabus,except paper 2 section A.

The photosynthesis part on the syllabus tells you exactly what you need to know, follow that and throw behind you everything else you read.

If there's anything unclear about the syllabus, we're here to help.

[Hinuku]

Could You tell me what I have to know about pigments.

Also, does IB require me to learn all the enzymes and reactants of those cycles? Our teacher says it's obligatory for her class but I don't see any sense in learning a bunch of meaningless names ;p

Also, I read that the porphyrin ring is hydrophylic and the hydrocarbon tail hydrophobic. Doesn't this make the whole molecule of chlorophyll polar? that's what I deduce, however - in martin,solomon,berg biology - it is written that the long hydrocarbon tail makes the molecule extremely non-polar. How is that correct?

Thanks again anyways ^^

Another question - do light dependent reactions take place on the chloroplast membrane or on the thylakoid membrane? I thought that on the latter is correct, but now I'm reading a different book so..

Simply, you do not need to know about any pigments or their structures. You just have to know the most common one is Chlorophyll.

IB does not require you to learn all the enzymes, just the ones mentioned in the syllabus.

Don't worry about molecular structure of chlorophyll, you don't need to know that.

Light dependent reaction takes place in the thylakoid membranes of the chloroplast. Chloroplasts contain thylakoids:

Here's a tip:

Download the syllabus from here. Follow that syllabus, point by point. Anything you can't find in the syllabus, just ignore! I mean it, the IBO will not get questions outside the syllabus,except paper 2 section A.

The photosynthesis part on the syllabus tells you exactly what you need to know, follow that and throw behind you everything else you read.

If there's anything unclear about the syllabus, we're here to help.

Would You have any 64 bit version available? ^^ I managed - thanks

Edited January 30, 2011 by Hinuku

[parth patel]

Heyy can you please help me with option C.....i really dont get it and im like really dead for the test coming up....please would be really helpful

Edited February 7, 2011 by Mahuta ♥
No text speak please!- Maha

[Mahuta ♥]

*C.1.1--Protein Structures*

Levels/Structures of Proteins and significance:

This is basically the different structures protein can be found in.

Primary

This is the simplest structure and it shows the number of amino acids in their sequence. In another words, if you have a protein in the primary structure, you are most likely to see a sequence of amino acids. Primary structure proteins are found in every other structure. Therefore the significance of this structure is that it determines other ones. If you have a short primary structured protein, you can really have a large secondary structured.

Strcictly speaking, this structure is the structure of a single polypeptide

Secondary

The secondary structure is just as simply as the primary one. Only that the secondary structure includes a group of polypeptides, that are held together by Hydrogen Bonds(very strong intermolecular bond).

This group of polypeptides could either be beta-pleated sheet or Alpha helices.

Beta Pleated sheet is the structure where H-bond forms between the N-H and C=O in polypeptides.

Alpha Helices is when the polypeptide forms a helix and H-bonds form between the sides, keeping the helix stable

You dont really need to know much about alpha and beta.

This type of strucutre is found alot in fibrous proteins.

Tertiary

This is a very common structure and it is the 3D protein structure. Unlike the secondary structure, the tertiary structure is when polypeptides fold up in a globular shape. This shape is help by 3 different intermolecular forces:

1)Ionic Bond between atoms of R-group

2)Disulfide Bridges/covalent bonds between the sulphurs

3)Hydrogen Bonds between two R-groups

This structure determine all globular proteins such as Haemoglobin and insulin.

An easier way to think about this is if you have a primary structured protein that goes like A-B-D-C-A-D-B-C-A-B-D

If you imagine this sequence folded up so that the first A and the last D held together by one of the bonds, you get a 3D shape. Thats exactly what the tertairy structure is about.

Queternary

This is the most advanced structure. It invloves the linkage of 2 or more poly peptides. Take the example I just gave above. think of 4 of those 3D structures held together into a one protein, thats the queternary structure.

One main feature of this structure is that it allows the binding of prosthetic group. It is a non-polypeptide substance, forming a conjugated protein.

A very good example is Haemoglobin. It consists of 4 polypeptides and the haem(iron) as the prosthetic group.

*C.1.2--Fibrous and Globular*

Globular Protein:

Tertiary or Queternary structure of protein, so irregular a.a sequences with à rounded irregular structure. They are mostly soluble in water. You can say main function is metabolic, such as enzymes and hormone.

Eg. Hemoglobin and Insulin

Fibrous Protein:

Secondary structure protein, long strands. Most of them are insoluble in water. Main function, structures: such as collagen (found in hair) and myosin & Actin (in muscles)

Eg. Collagen and Myosin. Do NOT say fibrinogen.

*C.1.3--Polar and Non-polar Amino acids*

Having polar and non-polar amino acids:

1) Their positions determine the structure of the protein.

2) In membrane channels, the one exposed to elements entering or existing the cell are polar, therefore, moving ions and and polar substances is easier. Imagine if you have hydrophobic amino acids in contact with everything, it will never happen.

3) Also, A.A on the outer and inner layers of the membrane are hydrophilic because they’re in contact with water, whereas the inner part of the membrane is made if of hydrophilic aminos acids. They are trying to get away from the water, so they will maintain that structure. 

*C.1.4-Functions of Proteins*

4 functions of proteins, I think you know this already, but I will mention it anyway:

1)Transport: Hemoglobin

2)Hormones: Insulin.

3)Receptors: neurotransmitter

4)Defence: Antibodies

5)Facilitated diffusion and Active transport channels

6)Structure: actin and myosin in muscles.

7) Enzymes: choose any enzyme.

Others to come...

[Mahuta ♥]

C.2.1, C.2.2 and C.2.3:

I assume you know, if not let me know.

*C.2.4--Competitive and Non-competitive

Inhibition*

1)Competitive inhibition:

Competitive inhibition is the type of inhibitionwhere the inhibitor inhibits/takes over the active site. It is competing for the active site.

To be able to compete for the active site, theinhibitor has to be similar, chemically, to the substrate.

Since the inhibition is due to the competitionover active site, the higher the concentration of the substrate, the lower theeffect of the inhibitor, because there is less chance of the inhibitor takingover the active site.

2) Non-competitive inhibition:

Non-competitiveinhibition as the name suggests, is the type of inhibition where the inhibitoris not competing for the active site.

The only thing that this inhibitor does is that it binds to another site, notthe active site but the allosteric site. Binding to the allosteric sitecauses a change in the shape of the active site. A change in shape of theactive site stops the substrate from binding to the active site.

The problem with this is, that even if you increase the concentration of thesubstrate, the inhibitor will still have the effect as its not a matter of'competition'.

Since this inhibitor is not competing for the active site, it doesn't have tohave a similar structure, thus, the non-competitve inhibitor is not chemicallysimilar to the substrate.

*C.2.5--End product inhibition*

End product inhibition:

This could be put under uncompetitive inhibition.

When you have a metabolic pathway, whether cyclical or non-cyclical.

This is when the last product inhibits the enzyme thatcatalyzes the first reaction at the allosteric site.

The significance of this inhibition is to stop the build-up of the products ifthere is too much of it. This is an example of negative feedback.

[Mahuta ♥]

*C.3.2: Glycolysis*

Takes place in the cytoplasm

1)Phosphorylation:

Glucose (6C) -----------(2 ATP---->2 ADP+Pi)------------------------------->Hexose Bisphosphate

Basically, you have the sugar you start with and it is turned into another form by adding 2 phosphates. Why? Because that reduces the energy of activation for the next reaction.

2) Lysis:

Hexose Bisphosphate -----------------------------------------------------------> 2 Triosphosphate.

Lysis obviously means breaking down. So we have a 6 carbon sugar that has been split into two others with 3 carbons and PO4 each.

3) Oxidation:

It's loss of electron or Hydrogen and gain of oxygen.

2 Triosphosphate -------------(NAD⁺----->NADH+H⁺)----------------------------------->2 Pyruvate (3C)

The NAD⁺ took 2H from the 2 Triosphosphate (from the PO₄ specifically)

4)ATP Formation:

This happens with the previous step.

4ADP+Pi ------------------------->4ATP.

So, glycolysis used 2 ATP and produce 4.

If you were asked about the yield:

2 ATP, 2 NADH+H⁺, 2 Pyruvate.

*C.3.4-Link Reaction, Kreb's Cycle and Transport Chain*

Link Reaction:

Pyruvate (3C)----(NAD⁺-->NADH+H⁺)-------------(CO₂ released)----------------------------------> Acetyl Coenzyme A (2C)

This is just turning 3C to 2C by taking away 2H (oxidation) and 1CO₂ (Decarboxylation). Therefore, this step is called oxidative decarboxylation.

Kreb's Cycle: (Put the diagram in front of you before you read the next)

• After the link reaction, you have acytelcoA, a 2 Carbon molecule with the coA enzyme.
  
• The Cycle starts with a 4carbon.
  
• The 2carbon is added to it so: 2+4=6 we get a 6 carbon molecule.
  
• The 6 carbon is changed into 5 carbon. Therefore, we must reduce the carbon number by removing CO₂, so CO₂ is lost. Everytime a CO₂ is lost, a H₂ is lost as well. So you have the NAD⁺ + H₂----> NADH⁺ + H⁺.
  
• The 5 carbon is changed into 4carbon by the exact same process, CO₂ and NADH⁺ + H⁺ formed.
  
• The 4 carbon formed isnt the same as the one we started with, so to get it back to the first one, we remove 2H_2. One is taken by the NAD⁺ and the other by FAD.
  
• ATP is formed as well in this process.
  
• So to sum up the krebs cylce produces the following: 1 ATP, 1 FADH₂, 3NADH⁺ + H⁺, 2CO₂
  

*C.3.5--Oxidative phosphorylation.*

Oxidative phosphorylation.

Takes place on the electron carrier chain located on cristae or the folds of the mitochondria.

Okay I am going go try and explain this the best I can:

NAD+H⁺ we had earlier is going to come along and give an electron to a protein in the chain, and the electron will go from one protein to another Every time that happens, 2H go from the matrix to the inter-membrane space.

You will have that space filled with H⁺ (protons). At the end of the chain, there's an enzyme called ATP synthase, the H⁺s will be pumped back to the matrix, with every H⁺, you have an ATP made.

The movement of H⁺ down the concentration gradient is called chemiosmosis.

Now, the O₂ we breath in is only used now:

the electrons that have been passed along from one protein to another are released back to the matrix and taken by the the H⁺. 1 electron + 1 proton will give you a hydrogen. 2 of those are combined with the O₂, which will give you water.

*C.3.6-Structure and Function of Mitochondria*

Mitochondria:

1)The cristae give the largest possible surface area for the chemiosmosis to take place, therefore more ATP formation.

2) Inter-membrane space is very small, so it's filled easily, which will form the gradient quickly.

3)The matrix has all the enzymes used in the krebs cycle.

[Hinuku]

I have this question my friend came up with: where from does the RuBP in the Calvin Cycle come from? Any help would be appreciated

[Mahuta ♥]

RuBP, Ribulose Bisphosphate is..as you know the 5 carbon sugar you start the cycle with.

Where it originally came from..no idea. But where it normally comes from...

It's a cycle remember? You end up with a 6 molecules of trios phosphate. 5 of which will be regenerated back in to RuBP and 1 is transformed to glucose phosphate.

Here's the calvin cycle

[Hinuku]

Could you help with this? :

Why is the correct summary of photosynthesis written like this:

6 CO2 + 12 H2O ----> C6H12O6 + 6 O2 + 6 H2O

Why is the water present on both sides?

[Drake Glau]

Because all in all, by the time it's all said and done, 6 CO2 are used with 12 waters to make a single glucose, 6 oxygen and 6 water

[Hinuku]

Because all in all, by the time it's all said and done, 6 CO2 are used with 12 waters to make a single glucose, 6 oxygen and 6 water

Hey - that actually makes sense

Another question: Why is there no Atp produced in the second ETC in the non cyclic ET? Is it because if the electrons would lose more energy they wouldn't be enough to supply for a NADP?

[Drake Glau]

The whole point of photosynthesis is to make glucose O.o I haven't studied this in a year so I can't really give you much of answer other than that, sorry =/

[Mahuta ♥]

What are you exactly talking about?

The ETC from the Photosystem 1 to the ATP Synthase or what exactly?

Either way you do not have to know this, you just have to know:

1)Light dependent reaction starts by the photoactivation of PII, which releases electrons.

2)Electrons are replaced by photolysis.

3)Electrons are transported from one protein to another.

4)Every time it passes from one protein to another there is H+ pumped inside.

5)If this is non-cyclic, there is photoactivation of PI, electron released.

6)Elecrtons are replaced by photolysis at PII that passes them onto PI.

7)That electron (the one released by PII) will combine with NAPD+ and H+ to give NADPH.

8)In cyclic: their job is to make more ATP and stop the production of NADP. The plant needs to ensure that there is the correct amount of NADP for the Calvin Cycle.

This is all you have to know really, but explain your question more maybe it's something else.

Here's a video that might answer your question:

Photosynthetic Electron Transport Chain

[Drake Glau]

I'd suggest making a new thread with this also in the chem forum. This sounds like a really overcomplicated lab and I have no idea either

[Mahuta ♥]

Ok he already posted it in chem help, though we can't give IA help on these topics.

Hinuku, I really want to know why you are doing that lab..

[Hinuku]

Ok he already posted it in chem help, though we can't give IA help on these topics.

Hinuku, I really want to know why you are doing that lab..

I have no idea it's my assignment - do you know maybe why pheophytin appears grey? is it siomply because it reflects grey light or can more be said to it?

[Hinuku]

Hello,

I have a question - is it possible for dry pea seeds to be as much as 2 times lighter than turgid ones? I know that there is much more water in the second ones but I still think that twice as heavy is a bit harsh

Anyways, thanks for help