Login

Welcome, Guest. Please login or register.

March 30, 2024, 01:53:11 am

Author Topic: VCE Biology Question Thread  (Read 3571856 times)  Share 

0 Members and 6 Guests are viewing this topic.

PhoenixxFire

  • VIC MVP - 2018
  • Honorary Moderator
  • ATAR Notes Legend
  • *******
  • Posts: 3695
  • They/them/theirs
  • Respect: +3102
Re: VCE Biology Question Thread
« Reply #11460 on: November 26, 2018, 02:04:41 pm »
+3
hey! i'm going into bio 3&4 next year and i'm wondering if it's worth it to get the A+ notes? i'm talking about in terms of revision or as some kind of summary. thanks in advance.
Hey! Welcome to AN ;D

I don't know much about the A+ notes specifically but I wouldn't bother. Because bio is such a big subject there's heaps and heaps of resources available for free online (including free notes here) and if you're having trouble with a specific topic there's lots of explanations available online (or you can ask here), so I don't think it's worth buying summary notes - I doubt you'll end up using them much.
2019: B. Environment and Sustainability/B. Science @ ANU
2020: Just Vibing
2021: B. Paramedicine/B. Nursing @ ACU Canberra

DBA-144

  • MOTM: APR 19
  • Forum Obsessive
  • ***
  • Posts: 211
  • Respect: +35
Re: VCE Biology Question Thread
« Reply #11461 on: December 12, 2018, 05:13:27 pm »
+2
Hey ATARNotes, I promise I will not be learning all of Unit 3 or do anything crazy, I am just trying to reduce the workload for when I get bombarded with work in the first 2 weeks of school. I am mostly aware of the importance of taking a break.

If there are questions that you think are silly, or could be easily googled, please call me out for it. A lot of this is just for determining how much I need to know and get a feel for what's required. 

Does translation occur inside the rER? I believe that only protein modification would occur in the rough endoplasmic reticulum, given that there are ribosomes that would be translating the mRNA strand into amino acids on the exterior surface of the rER.

Thus, would we be required to say that translation occurs in the cytosol, as saying cytoplasm would then also include inside organelles? I understand Google says that it would occur in the cytoplasm, but, if it does not occur inside the rER, would this be incorrect, given that translation does not occur in any other organelle? 

Also:
2. What exactly would tertiary structure be? Is it just the overall 3D structure of the protein, i.e going beyond just the secondary structure, but now including the 'deliberate' folds of the protein made in the rER? This seems really confusing as various sources are saying that the tertiary structure is the 3D shape- yet even the molecules that make up the primary and secondary structure (which is just if there are alpha helices and beta pleated sheets present) are 3 dimensional.

3. With DNA and RNA, is it sufficient to know the similarities and differences, what they are made up of, their condensation polymerisation reactions and that the RNA polymerase binds to the promoter region at the 3' to start reading the DNA template strand? How granular do we need to get regarding the structure of these nucleic acids? (Do we need to know about the diagrammatic representation of nucleosomes to chromosomes and is it required that we understand what distinguishes uracil from thymine? Is this too much?)
 
4. What might we be required to know about the upstream/downstream regions- is knowing that they do not include the stop and start codons, if mutated can change the structure of the protein fine?

Sorry for asking so many questions :(   
 
« Last Edit: December 12, 2018, 05:19:10 pm by DBA-144 »
PM me for Methods (raw 46) and Chemistry (raw 48) resources (notes, practice SACs, etc.)

I also offer tutoring for these subjects, units 1-4 :)

PhoenixxFire

  • VIC MVP - 2018
  • Honorary Moderator
  • ATAR Notes Legend
  • *******
  • Posts: 3695
  • They/them/theirs
  • Respect: +3102
Re: VCE Biology Question Thread
« Reply #11462 on: December 12, 2018, 05:40:16 pm »
+6
Hey ATARNotes, I promise I will not be learning all of Unit 3 or do anything crazy, I am just trying to reduce the workload for when I get bombarded with work in the first 2 weeks of school. I am mostly aware of the importance of taking a break.


1. Does translation occur inside the rER? I believe that only protein modification would occur in the rough endoplasmic reticulum, given that there are ribosomes that would be translating the mRNA strand into amino acids on the exterior surface of the rER.

Thus, would we be required to say that translation occurs in the cytosol, as saying cytoplasm would then also include inside organelles? I understand Google says that it would occur in the cytoplasm, but, if it does not occur inside the rER, would this be incorrect, given that translation does not occur in any other organelle? 

Also:
2. What exactly would tertiary structure be? Is it just the overall 3D structure of the protein, i.e going beyond just the secondary structure, but now including the 'deliberate' folds of the protein made in the rER? This seems really confusing as various sources are saying that the tertiary structure is the 3D shape- yet even the molecules that make up the primary and secondary structure (which is just if there are alpha helices and beta pleated sheets present) are 3 dimensional.

3. With DNA and RNA, is it sufficient to know the similarities and differences, what they are made up of, their condensation polymerisation reactions and that the RNA polymerase binds to the promoter region at the 3' to start reading the DNA template strand? How granular do we need to get regarding the structure of these nucleic acids? (Do we need to know about the diagrammatic representation of nucleosomes to chromosomes and is it required that we understand what distinguishes uracil from thymine? Is this too much?)
 
4. What might we be required to know about the upstream/downstream regions- is knowing that they do not include the stop and start codons, if mutated can change the structure of the protein fine?
1. If you get asked where translation occurs then your answer should normally be at a ribosome or occasionally (depending on context) the roughER.
I would say that translation occurs at the rough ER, not in it. Translation occurs and then the peptide enter the rough ER (or at least that's what I got taught - you don't need to know exactly though). But yeah, don't say cytosol or cytoplasm - the correct answer is ribosome.

2. Yep it's the 3D shape. Technically everything is 3D, but for the sake of describing it, it's the functional 3D shape of a protein.

3. You need to know everything you mentioned up to RNA polymerase. You don't need to know about nucleosomes or chromosomes (that's 1/2 content). You don't need to know much about the bases - just which ones can bind to each other and whether they're found in DNA or RNA.

4. What exactly are you referring to when you say upstream and downstream regions? (Just saying upstream and downstream is sort of like saying left or right - it doesn't define a specific section). There's an area upstream and downstream called the non-coding regions, mutations there won't matter because they don't get synthesised into the protein.

If there are questions that you think are silly, or could be easily googled, please call me out for it. A lot of this is just for determining how much I need to know and get a feel for what's required.
So long as you've given them some thought and are genuinely confused or stuck (which you've clearly demonstrated by showing your thinking) then there's no issues - we just don't want to be doing people's homework for them.

Sorry for asking so many questions :(   
Don't be - It's why this thread exists :)
« Last Edit: December 12, 2018, 05:42:08 pm by PhoenixxFire »
2019: B. Environment and Sustainability/B. Science @ ANU
2020: Just Vibing
2021: B. Paramedicine/B. Nursing @ ACU Canberra

Bri MT

  • VIC MVP - 2018
  • Administrator
  • ATAR Notes Legend
  • *****
  • Posts: 4719
  • invest in wellbeing so it can invest in you
  • Respect: +3677
Re: VCE Biology Question Thread
« Reply #11463 on: December 12, 2018, 05:43:44 pm »
+5
snip 


1. Translation occurs in the ribosomes. Ribosomes are located in the RER but also other places, such as floating freely in the cytosol
Cytosol is too vague for VCAA purposes - you're better off specifically referring to the ribosomes

2. The tertiary structure is the 3D shape. I understand your confusion with alpha helices & beta pleated sheets - think of it as further folding. Another way you can distinguish the two (I'm not saying this as a guide for what to refer to in your answers) is that secondary structure is the result of hydrogen bonding, whereas teritiary structure results from a range of different attractions.

3. That is too much - you definitely don't need to understand why/how uracil and thymine are different. In general, you are not expected to know the structure of nitrogenous bases.

4. I'll double check the study design and edit if I find anything, but you don't need to know much about upstream & downstream regions


No need to apologise for asking questions! That's what this thread is for :)


Edit: beaten by PF but hopefully having multiple perspectives helps :)

Erutepa

  • VIC MVP - 2019
  • Forum Leader
  • ****
  • Posts: 721
  • evenin'
  • Respect: +775
Re: VCE Biology Question Thread
« Reply #11464 on: December 12, 2018, 06:08:49 pm »
+1
Hey ATARNotes, I promise I will not be learning all of Unit 3 or do anything crazy, I am just trying to reduce the workload for when I get bombarded with work in the first 2 weeks of school. I am mostly aware of the importance of taking a break.

If there are questions that you think are silly, or could be easily googled, please call me out for it. A lot of this is just for determining how much I need to know and get a feel for what's required. 

Does translation occur inside the rER? I believe that only protein modification would occur in the rough endoplasmic reticulum, given that there are ribosomes that would be translating the mRNA strand into amino acids on the exterior surface of the rER.

Thus, would we be required to say that translation occurs in the cytosol, as saying cytoplasm would then also include inside organelles? I understand Google says that it would occur in the cytoplasm, but, if it does not occur inside the rER, would this be incorrect, given that translation does not occur in any other organelle? 

Also:
2. What exactly would tertiary structure be? Is it just the overall 3D structure of the protein, i.e going beyond just the secondary structure, but now including the 'deliberate' folds of the protein made in the rER? This seems really confusing as various sources are saying that the tertiary structure is the 3D shape- yet even the molecules that make up the primary and secondary structure (which is just if there are alpha helices and beta pleated sheets present) are 3 dimensional.

3. With DNA and RNA, is it sufficient to know the similarities and differences, what they are made up of, their condensation polymerisation reactions and that the RNA polymerase binds to the promoter region at the 3' to start reading the DNA template strand? How granular do we need to get regarding the structure of these nucleic acids? (Do we need to know about the diagrammatic representation of nucleosomes to chromosomes and is it required that we understand what distinguishes uracil from thymine? Is this too much?)
 
4. What might we be required to know about the upstream/downstream regions- is knowing that they do not include the stop and start codons, if mutated can change the structure of the protein fine?

Sorry for asking so many questions :(   
1.   Agree with PF and miniturtle, best just refer to translation as occurring in the ribosome at the rER. You don’t need to overcomplicate it.

2.   The 3D shape of the protein is a combined result of the secondary, tertiary and quaternary structures. Some proteins have a 3D structure composed of essentially only alpha helixes, and some multiple polypeptide chains, therefore I don’t think it is accurate to say that the tertiary structure is the 3D structure – there’s more to it then that. Instead I would say:
a.   Primary structure = the linear sequence of amino acids
b.   Secondary structure = Folding due to hydrogen bonds between amino acid backbone (alpha helix + beta pleated sheets)
c.   Tertiary structure = Folding due to interactions between variable side chains (interactions can be hydrophobic/hydrophilic sidechains interacting with water, ionic, covalent, or hydrogen again)
d.   Quaternary structure = Interaction of multiple polypeptide chains

I know this kinda disagrees with what has been said, so I would be keen to hear others opinions. :D

3.   I agree with everything miniturtle and PF have written about this. I will just add that for the structure of a nucleotide, you should now the three main components: a phosphate group, deoxyribose/ribose (5 carbon) sugar and a variable nitrogenous base. You should know that the phosphate of the next nucleotide is added onto the 3’ of the previous and that the strands run antiparallel. You should probably understand that DNA forms chromatin and can form more tightly packed chromosomes and that it has associated proteins, but not too much detail is here needed.

4.   It is probably good to know that directly upstream and directly down stream of each gene there are untranslated regions (UTRs) referred to as the 3’ UTR and the 5’ UTR. I am not sure what you mean when walking about mutations here. Further clarification would be nice.

« Last Edit: December 12, 2018, 06:11:10 pm by Erutepa »
Qualifications
 > Have counted to 227
 > Can draw really good spiders
 > 2 Poet points
 > 6.5 insanipi points
 > 1 Bri MT point

vox nihili

  • National Moderator
  • Great Wonder of ATAR Notes
  • *****
  • Posts: 5343
  • Respect: +1447
Re: VCE Biology Question Thread
« Reply #11465 on: December 12, 2018, 10:54:23 pm »
+4
2.   The 3D shape of the protein is a combined result of the secondary, tertiary and quaternary structures. Some proteins have a 3D structure composed of essentially only alpha helixes, and some multiple polypeptide chains, therefore I don’t think it is accurate to say that the tertiary structure is the 3D structure – there’s more to it then that. Instead I would say:
a.   Primary structure = the linear sequence of amino acids
b.   Secondary structure = Folding due to hydrogen bonds between amino acid backbone (alpha helix + beta pleated sheets)
c.   Tertiary structure = Folding due to interactions between variable side chains (interactions can be hydrophobic/hydrophilic sidechains interacting with water, ionic, covalent, or hydrogen again)
d.   Quaternary structure = Interaction of multiple polypeptide chains

I know this kinda disagrees with what has been said, so I would be keen to hear others opinions. :D

Your definitions of the structures are all correct, but I think you've taken this far beyond VCE here. To say that tertiary structure is the 3D structure of the protein is perfectly reasonable in the context of VCE

Quote
The 3D shape of the protein is a combined result of the secondary, tertiary and quaternary structures. Some proteins have a 3D structure composed of essentially only alpha helixes, and some multiple polypeptide chains, therefore I don’t think it is accurate to say that the tertiary structure is the 3D structure

Be careful with this too. I think you've tried to be a bit too smart for your own good here! :p
2013-15: BBiomed (Biochemistry and Molecular Biology), UniMelb
2016-20: MD, UniMelb
2019-20: MPH, UniMelb
2021-: GDipBiostat, USyd

Erutepa

  • VIC MVP - 2019
  • Forum Leader
  • ****
  • Posts: 721
  • evenin'
  • Respect: +775
Re: VCE Biology Question Thread
« Reply #11466 on: December 12, 2018, 11:38:17 pm »
0
Be careful with this too. I think you've tried to be a bit too smart for your own good here! :p
I probably have, but I am unreasonably stubborn and now need to get my knowledge fixed up. :D
I know this is definitely not of concern to VCE biology, but where would you say I perhaps strayed from the path of truth.

I have done some quick extra research, although have not been overly successful (just some uni powerpoints and a nature article). Nonetheless, I have not had my mind changed. I still would say that the functional 3D shape of a protein is a result of protein folding/interactions, whether it be that of the secondary, tertiary or quaternary.
I don't mean to sound argumentative (sorry if it comes across that way), and I am genuinely appreciative of your polite criticisms, but I can't leave in doubt.
Qualifications
 > Have counted to 227
 > Can draw really good spiders
 > 2 Poet points
 > 6.5 insanipi points
 > 1 Bri MT point

vox nihili

  • National Moderator
  • Great Wonder of ATAR Notes
  • *****
  • Posts: 5343
  • Respect: +1447
Re: VCE Biology Question Thread
« Reply #11467 on: December 13, 2018, 07:27:08 pm »
+3
I probably have, but I am unreasonably stubborn and now need to get my knowledge fixed up. :D
I know this is definitely not of concern to VCE biology, but where would you say I perhaps strayed from the path of truth.

I have done some quick extra research, although have not been overly successful (just some uni powerpoints and a nature article). Nonetheless, I have not had my mind changed. I still would say that the functional 3D shape of a protein is a result of protein folding/interactions, whether it be that of the secondary, tertiary or quaternary.
I don't mean to sound argumentative (sorry if it comes across that way), and I am genuinely appreciative of your polite criticisms, but I can't leave in doubt.

No no, you're fine. No need to apologise—I, like everyone on this thread, am really grateful for your contributions here!

EVERYONE ELSE IGNORE, BEYOND VCE

It's really nitpicky. Your descriptions of all the levels of structures are completely correct as above. I wonder whether you understand how each level interacts with the other. Ultimately, the configuration that a protein takes on is the product of its primary structure. Because it has amino acid residues in that order, it folds in a particular way. You change the primary structure, the following levels of structure are also destablised.
You can say the same about secondary structure. The way the secondary structures are configured helps to determine tertiary structures, as well. [above you said that secondary structures are alpha helices and beta-sheets, and said implied that those sections where the residues do not form a helix or a sheet have a "primary structure"—this is not entirely correct; we'd call these "random coils", as all of the protein has a primary structure].

The overall shape of the protein as you've described it above is essentially correct. It probably is a little bit of a lie to say that tertiary/quarternary structure determines the overall shape, as you've pointed out. Really the shape of the protein is just its topography, which is determined by all of the interactions between amino acid residues in the protein. You might find the program  "pymol" (you can get a free copy) a nice way of visualising different levels of structure; I've used this before in my lectures and I find that it often helps.
2013-15: BBiomed (Biochemistry and Molecular Biology), UniMelb
2016-20: MD, UniMelb
2019-20: MPH, UniMelb
2021-: GDipBiostat, USyd

Erutepa

  • VIC MVP - 2019
  • Forum Leader
  • ****
  • Posts: 721
  • evenin'
  • Respect: +775
Re: VCE Biology Question Thread
« Reply #11468 on: December 13, 2018, 10:49:27 pm »
+1
No no, you're fine. No need to apologise—I, like everyone on this thread, am really grateful for your contributions here!

EVERYONE ELSE IGNORE, BEYOND VCE

It's really nitpicky. Your descriptions of all the levels of structures are completely correct as above. I wonder whether you understand how each level interacts with the other. Ultimately, the configuration that a protein takes on is the product of its primary structure. Because it has amino acid residues in that order, it folds in a particular way. You change the primary structure, the following levels of structure are also destablised.
You can say the same about secondary structure. The way the secondary structures are configured helps to determine tertiary structures, as well. [above you said that secondary structures are alpha helices and beta-sheets, and said implied that those sections where the residues do not form a helix or a sheet have a "primary structure"—this is not entirely correct; we'd call these "random coils", as all of the protein has a primary structure].

The overall shape of the protein as you've described it above is essentially correct. It probably is a little bit of a lie to say that tertiary/quarternary structure determines the overall shape, as you've pointed out. Really the shape of the protein is just its topography, which is determined by all of the interactions between amino acid residues in the protein. You might find the program  "pymol" (you can get a free copy) a nice way of visualising different levels of structure; I've used this before in my lectures and I find that it often helps.
Thank you, and consider myself enlightened.
It seems I had here fallen for the far too common problem of misrepresenting through oversimplifying.

As for pymol, I will definitely look into finding a free copy. I was actually just looking for a program that could 3D model different biomolecules, but all that I found were research tools that spat out boring numbers, so this seems rather more interesting.
Qualifications
 > Have counted to 227
 > Can draw really good spiders
 > 2 Poet points
 > 6.5 insanipi points
 > 1 Bri MT point

Evolio

  • MOTM: MAY 20
  • Forum Leader
  • ****
  • Posts: 604
  • Respect: +485
Re: VCE Biology Question Thread
« Reply #11469 on: December 14, 2018, 12:20:50 pm »
0
Hi guys.
I have two questions.
1. Is a coenzyme temporary?
2. Is this statement true or false?. 'Enzymes change the activation energy of a reaction by providing a different reaction pathway'. I put true but the answer is false. Is it false because it's supposed to be 'enzymes provide a different reaction pathway by changing the activation energy of a reaction'?
Taken from the Nature of Biology: Book 2, 5th Edition

darkz

  • Forum Obsessive
  • ***
  • Posts: 413
  • Respect: +154
Re: VCE Biology Question Thread
« Reply #11470 on: December 14, 2018, 12:31:27 pm »
+1
Hi guys.
I have two questions.
1. Is a coenzyme temporary?
2. Is this statement true or false?. 'Enzymes change the activation energy of a reaction by providing a different reaction pathway'. I put true but the answer is false. Is it false because it's supposed to be 'enzymes provide a different reaction pathway by changing the activation energy of a reaction'?
Taken from the Nature of Biology: Book 2, 5th Edition

I'm pretty sure that a constant supply of coenzymes is required for the correct functioning of the enzyme, so I would not necessarily describe it as being 'temporary'

Well in my opinion, this is rather pedantic and I doubt you really need to know about it for bio 3/4 since it's slightly leaning towards chemistry. However, enzymes, which are biological catalysts, cause a reaction to occur more quickly because they provide a new reaction pathway, which causes the activation energy barrier of the overall reaction to be reduced. (This definition is taken from the Heinemann Chem 3/4 textbook)
2018: Biology [50 + Prems]
2019: English [46], Latin [45], Chemistry [41], Mathematical Methods [48], Specialist Mathematics [41]
ATAR: 99.95

2020: BMedSci, M.D. @ Monash Uni

VCE Biology Units 1&2 and 3&4 Tutoring for 2021

PhoenixxFire

  • VIC MVP - 2018
  • Honorary Moderator
  • ATAR Notes Legend
  • *******
  • Posts: 3695
  • They/them/theirs
  • Respect: +3102
Re: VCE Biology Question Thread
« Reply #11471 on: December 14, 2018, 12:34:02 pm »
+1
Hi guys.
I have two questions.
1. Is a coenzyme temporary?
2. Is this statement true or false?. 'Enzymes change the activation energy of a reaction by providing a different reaction pathway'. I put true but the answer is false. Is it false because it's supposed to be 'enzymes provide a different reaction pathway by changing the activation energy of a reaction'?
Taken from the Nature of Biology: Book 2, 5th Edition
1. I don't like this question at all haha. Conenzymes (e.g. ATP, NADH, NADPH) are changed in the reaction (e.g. ATP is converted into ADP), however these can then be changed back into the useable form. So I suppose they're temporary in that they have to be replaced and/or 'repaired' but that's a weird question.

Edit: Beaten by darkz but going to post this for Q1 anyway
2019: B. Environment and Sustainability/B. Science @ ANU
2020: Just Vibing
2021: B. Paramedicine/B. Nursing @ ACU Canberra

Erutepa

  • VIC MVP - 2019
  • Forum Leader
  • ****
  • Posts: 721
  • evenin'
  • Respect: +775
Re: VCE Biology Question Thread
« Reply #11472 on: December 14, 2018, 12:38:26 pm »
+1
Hi guys.
I have two questions.
1. Is a coenzyme temporary?
2. Is this statement true or false?. 'Enzymes change the activation energy of a reaction by providing a different reaction pathway'. I put true but the answer is false. Is it false because it's supposed to be 'enzymes provide a different reaction pathway by changing the activation energy of a reaction'?
Taken from the Nature of Biology: Book 2, 5th Edition
1. As far as I am aware, coenzymes are 'used-up' in a reaction but are being constantly cycled back into a loaded form within the cell. Think about the cycling of ATP and ADP.

2. Enzymes don't just lower activation energy by providing alernate pathways as described by darkz, but enzymes can also catalyse reactions by placing stresson/distoring the chemical bonds of the substrate such to essentially nudge it in the direction of the reaction (closer to what is called the transition state), thereby reducing the energy needed for the reaction to occur.
Edit: As PF says below this explanation is probably a bit beyond VCE biology and should be disreguarded. sorry :)

also congradulations darkz on your 50 in bio!!!  :o
« Last Edit: December 14, 2018, 12:42:02 pm by Erutepa »
Qualifications
 > Have counted to 227
 > Can draw really good spiders
 > 2 Poet points
 > 6.5 insanipi points
 > 1 Bri MT point

PhoenixxFire

  • VIC MVP - 2018
  • Honorary Moderator
  • ATAR Notes Legend
  • *******
  • Posts: 3695
  • They/them/theirs
  • Respect: +3102
Re: VCE Biology Question Thread
« Reply #11473 on: December 14, 2018, 12:39:24 pm »
+4
2. Enzymes don't just lower activation energy by providing alernate pathways as described by darkz, but enzymes can also catalyse reactions by placing stresson/distoring the chemical bonds of the substrate such to essentially nudge it in the direction of the reaction (closer to what is called the transition state), thereby reducing the energy needed for the reaction to occur.
For anyone else reading - you don't need to know this much detail for bio
2019: B. Environment and Sustainability/B. Science @ ANU
2020: Just Vibing
2021: B. Paramedicine/B. Nursing @ ACU Canberra

Evolio

  • MOTM: MAY 20
  • Forum Leader
  • ****
  • Posts: 604
  • Respect: +485
Re: VCE Biology Question Thread
« Reply #11474 on: December 14, 2018, 12:51:18 pm »
0
Hi guys.
I have two questions.
1. Is a coenzyme temporary?
2. Is this statement true or false?. 'Enzymes change the activation energy of a reaction by providing a different reaction pathway'. I put true but the answer is false. Is it false because it's supposed to be 'enzymes provide a different reaction pathway by changing the activation energy of a reaction'?
Taken from the Nature of Biology: Book 2, 5th Edition
Sorry about my phrasing for the first question. I meant in the sense that the binding of coenzymes to the enzymes is temporary since they have weak bonds ,as opposed to prosthetic groups which are permanent in enzymes since they have really strong bonds with the enzyme.