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VCE Stuff => VCE Science => VCE Mathematics/Science/Technology => VCE Subjects + Help => VCE Biology => Topic started by: Yacoubb on January 20, 2013, 04:00:00 pm

Title: Concept discussion
Post by: Yacoubb on January 20, 2013, 04:00:00 pm
Hey guys I've started this topic where everyone can jump on and we can just discuss some concepts in Bio 3+4, sort of like revision + just so we can learn things/advise others, etc.

Shall we start off by talking about macromolecules? Feel free to start any discussion you like!

:)
Title: Re: Concept discussion
Post by: Bad Student on January 20, 2013, 04:49:18 pm
What makes a macromolecule organic? Does it need to have carbon? Or is it carbon and hydrogen? I haven't been able to find a satisfactory definition because they all have exceptions.
Title: Re: Concept discussion
Post by: alondouek on January 20, 2013, 05:03:51 pm
What makes a macromolecule organic? Does it need to have carbon? Or is it carbon and hydrogen? I haven't been able to find a satisfactory definition because they all have exceptions.

Right, so the broadest definition of an organic molecule is a molecule which has a carbon 'backbone' (where carbon is generally the structural basis of the molecule) bonded to other elements (leading to compounds such as alkanols, amines, etc) or radicals (atoms, molecules, or ions with unpaired electrons - but this is more chemistry).

You may have heard humans referred to as 'carbon-based life-forms' - as science-fictiony as this may seem, it's pretty much correct. All our biological macromolecules have carbon backbones;


As you can tell, carbon is common to all of these biomacromolecules, so they are defined as organic.
Title: Re: Concept discussion
Post by: Bad Student on January 20, 2013, 05:14:00 pm
But if you define organic molecules as carbon based, then carbon dioxide would be organic when its not.
Title: Re: Concept discussion
Post by: alondouek on January 20, 2013, 05:45:26 pm
You're right; I should have been more specific :P

Organic compounds are ones that contain carbon covalently bonded to hydrogen. This is the case with all biomacromolecules.

Any questions?
Title: Re: Concept discussion
Post by: pi on January 20, 2013, 05:50:31 pm
There isn't really a fixed definition for what an "organic compound" is. To see the discussion/exceptions -> http://en.wikipedia.org/wiki/Organic_compound

Quote
most carbon-containing compounds are organic, and most compounds with a C-H bond are organic. Not all organic compounds necessarily contain C-H bonds (e.g., urea).
Title: Re: Concept discussion
Post by: paulsterio on January 20, 2013, 05:56:03 pm
I believe that all carbon containing compounds are organic apart from oxides (i.e. carbon dioxide), cyanides, carbides, diamond and graphite.

And yes, not all organic compounds contain C-H bonds, urea is one, I guess you could have tetra-fluoro-methane and stuff like that as well.
Title: Re: Concept discussion
Post by: Bad Student on January 20, 2013, 06:27:40 pm
So basically, organic compounds:
Title: Re: Concept discussion
Post by: pi on January 20, 2013, 06:36:56 pm
I believe that all carbon containing compounds are organic apart from oxides (i.e. carbon dioxide), cyanides, carbides, diamond and graphite.

Line of wikipedia:

Quote
a few types of carbon-containing compounds such as carbides, carbonates, simple oxides of carbon (such as CO and CO2), and cyanides, as well as the allotropes of carbon such as diamond and graphite, are considered inorganic

...
Title: Re: Concept discussion
Post by: Yacoubb on January 20, 2013, 08:13:06 pm
I agree that carbon is definitely present in all macromolecules, making them organic compounds. :) Remember though that although lipids and polysaccharides are composed of Carbon, Hydrogen and Oxygen, the levels of oxygen in lipids is less than that of polysaccharides. Hence, lipids are more dense than water (ie lipids like oils float on water) and more energy-dense.
Title: Re: Concept discussion
Post by: Yacoubb on January 20, 2013, 08:22:45 pm
What makes a macromolecule organic? Does it need to have carbon? Or is it carbon and hydrogen? I haven't been able to find a satisfactory definition because they all have exceptions.

I think that what VCAA would like you to know is what chemical composition makes up the macromolecules polysaccharides, proteins, lipids and nucleic acid :) an exam question may ask you to say whether C6H12O6 is glucose or the enzyme maltase. By recognising that it is made up of Carbon, Hydrogen and Oxygen, it makes it a monosaccharide, hence glucose. The absence of Nitrogen sufficiently indicates that it is not a protein, or in this case, the enzyme Maltase
Title: Re: Concept discussion
Post by: alondouek on January 20, 2013, 08:26:49 pm
although lipids and polysaccharides are composed of Carbon, Hydrogen and Oxygen, the levels of oxygen in lipids is less than that of polysaccharides. Hence, lipids are more dense than water (ie lipids like oils float on water) and more energy-dense.

haha so many U3 chem lessons, oh the nostalgia

Summarised depiction of the above quote:

Arachidic acid, a saturated lipid has the chemical formula CH3(CH2)18CO2H. Note that there are only 2 oxygen molecule present, despite the relative complexity of the overall molecule.

Conversely, the monosaccharide glucose (C6H12O6) is very simple structurally, yet contains three times the amount of oxygen. Side note - chemical formulae of carbohydrates follow the C:H:O of 1:2:1

Now for a slightly tricky question for anyone keen: Outline the differences between white and brown adipose tissue, and explain why brown adipose tissue is prevalent in thermogenesis. (This is beyond VCAA standards, but it never hurts to have some extra comprehension and knowledge in biol :P )
Title: Re: Concept discussion
Post by: Bad Student on January 20, 2013, 08:37:19 pm
I agree that carbon is definitely present in all macromolecules, making them organic compounds. :) Remember though that although lipids and polysaccharides are composed of Carbon, Hydrogen and Oxygen, the levels of oxygen in lipids is less than that of polysaccharides. Hence, lipids are more dense than water (ie lipids like oils float on water) and more energy-dense.

Did you mean lipids are less dense than water? Why does having less oxygen molecules make it less dense?
Title: Re: Concept discussion
Post by: pi on January 20, 2013, 08:39:37 pm
I think that what VCAA would like you to know is what chemical composition makes up the macromolecules polysaccharides, proteins, lipids and nucleic acid :) an exam question may ask you to say whether C6H12O6 is glucose or the enzyme maltase. By recognising that it is made up of Carbon, Hydrogen and Oxygen, it makes it a monosaccharide, hence glucose. The absence of Nitrogen sufficiently indicates that it is not a protein, or in this case, the enzyme Maltase

VCE Biology isn't really that dense in chemistry. I'm with alondouek on this one.


Hence, lipids are more dense than water (ie lipids like oils float on water)

Check this please :)
Title: Re: Concept discussion
Post by: Yacoubb on January 20, 2013, 09:00:48 pm
VCE Biology isn't really that dense in chemistry. I'm with alondouek on this one.


Check this please :)

Oops gosh how can I do that! Water is more dense than H2O. That is obviously why it floats. Daft moment sorry.
Title: Re: Concept discussion
Post by: alondouek on January 20, 2013, 09:03:19 pm
Water is more dense than H2O. That is obviously why it floats. Daft moment sorry.

Moral of the story; always review what you write; read the above again :P
Title: Re: Concept discussion
Post by: Yacoubb on January 20, 2013, 09:08:42 pm
It's because I'm using my phone + it doesn't show every line until I preview it, and by doing that, my stupid phone freezes lol
Title: Re: Concept discussion
Post by: Bad Student on January 20, 2013, 11:06:51 pm
So... can someone explain why lipids are less dense than water? I can't find anything on da interwebz that explains it in language I can understand.
Title: Re: Concept discussion
Post by: Stick on January 20, 2013, 11:18:54 pm
Using only Chemistry 1/2 knowledge, water is held together quite compactly in liquid form since there are hydrogen bonds between molecules, whereas in lipids (eg oils) the molecules are only somewhat held together by weaker dispersion forces. I'm not sure if this is correct but the explanation seems logical. :)
Title: Re: Concept discussion
Post by: alondouek on January 20, 2013, 11:24:11 pm
To be honest, I would be more concerned about the hydrophobic nature of lipids than their density. Density is something that, IIRC, doesn't factor much into the Biol 3/4 course - it's more chemistry.

Focus more on the fact that lipids are hydrophobic - you'll need to analyse this further when you start learning about the phospholipid bilayer, micelles, etc.
Title: Re: Concept discussion
Post by: Bad Student on January 20, 2013, 11:24:28 pm
Hmmm... makes sense.
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 01:23:56 am
To be honest, I would be more concerned about the hydrophobic nature of lipids than their density. Density is something that, IIRC, doesn't factor much into the Biol 3/4 course - it's more chemistry.

Focus more on the fact that lipids are hydrophobic - you'll need to analyse this further when you start learning about the phospholipid bilayer, micelles, etc.

I think that this is an appropriate assumption merely because the course (i.e. as outlined in the textbook), does not go further to mention anything regarding particular bonds between lipids, except in saturated and unsaturated fats where it discusses the compactness of the fatty acid molecules in determining whether a lipid is saturated (solid) or unsaturation (liquid consistency, e.g. oil).
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 01:34:19 am
Ooh, okay lets discuss proteins. I'll do my little summary and feel free to give me constructive criticism.

Proteins are organic molecules composed of elements Carbon, Hydrogen, Oxygen, Nitrogen and sometimes Sulfur. Proteins are composed of amino acid subunits.

    R group
         |
H2N=C=COOH
         |
         H

The above diagram is of an amino acid. There are 20 known amino acids synthesised by living organisms. The essential difference between amino acids is the composition of the R-group, which varies from amino acid to amino acid. During the condensation reaction, amino acids join by strong, peptide bonds in the free ribosomes / rough endoplasmic reticulum, as two hydrogen atom react with an oxygen atom, forming a H2O molecule that is released for every dipeptide formed. Examples of proteins include enzymes, haemoglobin, keratin.
Title: Re: Concept discussion
Post by: alondouek on January 21, 2013, 01:55:36 am
There are four stages of structure that many proteins go through before they achieve their final product.

The primary structure is the linear sequence of amino acid subunits. These amino acids are joined by covalent bonding.

The secondary structure is the initial 'folding' of the polypeptide sequence. Most commonly, the secondary structures of a protein are categorised as 'alpha-helix', 'beta-pleating' or 'random coiling'. Other, rarer secondary structure can occur, such as the 'pi helix' or the '310 helix' (though this is beyond the realms of VCE biology). Generally, hydrogen bonding is involved in the formation of the protein secondary structure

The tertiary structure arises from further folding of the a series of alpha-helices, beta-pleats and random coils. The tertiary structure refers to the protein's 3D structure, which is held in position by varying degrees of hydrophobic and hydrophilic interactions. Tertiary structures can arise from disulfide bonds between two cysteine amino acids in a polypeptide chain; this causes the sequence to fold in on itself. These disulfide bonds aid in maintaining the protein's shape during transport via endo/exocytosis.

The quaternary structure of a protein is essentially the 'bonded aggregation' of multiple tertiary-structured proteins. Haemoglobin is an example of a quaternary protein, as is DNA polymerase.

That's pretty much all I remember :)
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 02:01:04 am
There are four stages of structure that many proteins go through before they achieve their final product.

I don't know if this is due to your expression being wrong, but not all proteins MUST have this molecular organisation (i.e. having a primary/secondary/tertiary/quaternary). Not all proteins have a quaternary structure when investigating molecular organisation. Other than that, all of the above is spot on.

Just adding to Tertiary structure; this makes the protein critical for its function. The tertiary structure of the protein is actually responsible for the formation of a very specific active site in enzymes complementary to a specific substrate, which together form the lock-and-key model in enzymes.

Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 02:04:28 am
Also thought of addressing Proteomics: the study of the complete array of proteins synthesised by an organism. Proteomics now focusses not only on investigating proteins as single macromolecules, simply because no one protein acts in isolation to another protein. They all interact.

Also, I've heard of marks being deducted for stating Beta-Sheet rather than the official 'beta-pleats or pleated sheet', just to exemplify how meticulous VCAA really is!
Title: Re: Concept discussion
Post by: alondouek on January 21, 2013, 02:09:01 am
There are four stages of structure that many proteins go through before they achieve their final product.

I don't know if this is due to your expression being wrong, but not all proteins MUST have this molecular organisation (i.e. having a primary/secondary/tertiary/quaternary). Not all proteins have a quaternary structure when investigating molecular organisation.

haha yeah, I was trying to imply that not all proteins have a quaternary structure, hence "many proteins".
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 02:24:48 am
I don't know if this is due to your expression being wrong, but not all proteins MUST have this molecular organisation (i.e. having a primary/secondary/tertiary/quaternary). Not all proteins have a quaternary structure when investigating molecular organisation.


haha yeah, I was trying to imply that not all proteins have a quaternary structure, hence "many proteins".

Oh fair enough :) I cannot wait for this year because I am in love with Bio as you can tell ^ Hoping for a 45+. Shall work thy ass off lol!
Title: Re: Concept discussion
Post by: alondouek on January 21, 2013, 02:26:47 am
Oh fair enough :) I cannot wait for this year because I am in love with Bio as you can tell ^ Hoping for a 45+. Shall work thy ass off lol!

You should be in love with it, that's the key to doing well! In my honest opinion, the greatest subject offered by VCAA... shame you don't get to do a U3 mid-year, those are actually a lot of fun.
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 02:31:52 am
You should be in love with it, that's the key to doing well! In my honest opinion, the greatest subject offered by VCAA... shame you don't get to do a U3 mid-year, those are actually a lot of fun.

Yeah I do wish we had mid-years but its kinda better for yr 11 students like me who don't miss out on much when during mid years you'd neglect yr 11 for a momentary period! Hehe
Title: Re: Concept discussion
Post by: slothpomba on January 21, 2013, 03:33:44 am
To be honest, I would be more concerned about the hydrophobic nature of lipids than their density. Density is something that, IIRC, doesn't factor much into the Biol 3/4 course - it's more chemistry.

Focus more on the fact that lipids are hydrophobic - you'll need to analyse this further when you start learning about the phospholipid bilayer, micelles, etc.

This. Honestly, i've studied chem, bio and biochem at VCE (first two anyway) and uni level. You're straying much more towards the chem side of things, VCAA try to make their subject as independent as possible. You probably won't need to know what makes a molecule organic in Bio and you certainly won't need to know about density in the manner you're talking about.

I'm not sure if you guys have someone teaching you or you're just reading through the book on your own. If it's the latter, this is one of the pitfalls of doing it before class actually starts. The course has a disproportionate focus compared to most books. 3 or 4 chapters might brushed over in a week or two. You might spend a good 3 or 4 weeks on a chapter or two in detail.

As suggested above, you'll be much better off learning about membranes.  It extends into a few other topics in the course too. It'll be time well spent.

The essential difference between amino acids i...

I wouldn't use the word essential. It could get confusing.

There are things called essential amino acids, your body cant make them, they have to be taken in through food.  If you misplace the word or the person reading it just gets confused, it might not go so well...

Just adding to Tertiary structure; this makes the protein critical for its function. The tertiary structure of the protein is actually responsible for the formation of a very specific active site in enzymes complementary to a specific substrate, which together form the lock-and-key model in enzymes.

The tertiary structure is pretty much what it *really* is. I mean your table is technically Carbon and whatever else is in there but what gives it its function is its shape and organisation as table.
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 10:12:10 am
So basically can we fairly state that every protein has

a) primary structure - amino acid sequence of the polypeptide.
b) secondary structure - foldings of various amino acid on the polypeptide to form an alpha-helix, beta-pleated sheet or random coil.
c) tertiary structure - the 3d shape of the protein determined by foldings of the chain and formation of linkages between these folded proteins (e.g. disulfide bonds connecting cysteine amino acids together).

Some....
d) quaternary structure: proteins are sometimes made up of more than one amino acid chain.

And thanks for the tip @kingpomba :) I didn't really focus upon the meaning of 'organic' simply because all that we really need to know is the four biomacromolecules Proteins, Lipids, Polysaccharides and Nucleic Acids, and characteristics of each. On a Chem level, I think maybe in some cases the bondings between the sub-unit monomers in addition to the chemical composition of each is probably what will be assessed by VCAA.
Title: Re: Concept discussion
Post by: Russ on January 21, 2013, 10:14:27 am
I doubt you need to worry about random coil for VCE
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 10:17:53 am
I doubt you need to worry about random coil for VCE

You're right, it doesn't delve into too much about random coils, but its worth knowing for some case. But the main focus is upon alpha-helices and the reason it has obtained this name (has a helical structure) and the beta-pleated sheet (the pleats that are joined together by hydrogen bonds).

Hey can someone please go over fibrous + globular proteins and perhaps put down some characteristics of each?!
Title: Re: Concept discussion
Post by: Stick on January 21, 2013, 11:11:45 am
Hmm... If I recall correctly, fibrous proteins have very linear tertiary structures, meaning they cannot be stretched and are generally insoluble in water. Structural proteins (eg keratin) are usually fibrous in nature. Globular proteins, as the name suggests, have spherical patterns in the tertiary structure, meaning they can be stretched and can be soluble in water (hence most enzymes have some globular structure to them). I think proteins can have a combination of both structures as well.

Sorry if it doesn't sound too good; I finished my Biology headstart work ages ago and don't remember it too well. :P
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 11:56:31 am
Hmm... If I recall correctly, fibrous proteins have very linear tertiary structures, meaning they cannot be stretched and are generally insoluble in water. Structural proteins (eg keratin) are usually fibrous in nature. Globular proteins, as the name suggests, have spherical patterns in the tertiary structure, meaning they can be stretched and can be soluble in water (hence most enzymes have some globular structure to them). I think proteins can have a combination of both structures as well.

SO really we can say that fibrous proteins cannot be stretched further due to their linear tertiary structure that is somehow already stretched, wheras globular proteins have a more round, compact structure (e.g. haemoglobin) that can be stretched :) And have you done Bio 1+2?
Title: Re: Concept discussion
Post by: Stick on January 21, 2013, 12:32:34 pm
No, upon consulting my textbook I was getting slightly confused. Everything is correct except that fibrous proteins can be stretched. Sorry about that.

And no, I didn't do Units 1&2.
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 01:41:23 pm
We can reasonably assume that fibrous proteins are tough and insoluble in water because of its linear, stretched,  tertiary structure; wheras, globular proteins tend to be soluble in water because of their compact, round, tertiary structure.

:)

Perhaps some examples of fibrous + globular proteins:

I'll put some I know, feel free to add on :D

The following are globular proteins:
* Enzymes - increasing rate of chemical reactions
* Haemoglobin - transport of O2 and other substances to somatic cells.
* Antibodies - substances that complement antigens after they have been detected as 'non-self'.

The following are fibrous proteins:
* Keratin - structural protein found in nails, claws and hair.
* Collagen - connective tissue in animals.

Title: Re: Concept discussion
Post by: Russ on January 21, 2013, 01:42:48 pm
Redefine antibodies
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 01:55:46 pm
Redefine antibodies

Antibodies are proteins (immunoglobin) produced by animals in response to antigens that specifically react with the antigen that induced their formation.

Sorry I knew that definition was really bad lol!
Title: Re: Concept discussion
Post by: Stick on January 21, 2013, 01:57:29 pm
Hmm... I just spent the last two hours revising chapter 1 from Nature of Biology (gosh there is so much I have forgotten =_=), so allow me to give you a better definition of fibrous and globular proteins. This is my own understanding and wording here, so it may not be 100% perfect.

The tertiary structures of proteins can often be classified under two distinct formations: fibrous and globular. Fibrous proteins consist of only one type of secondary structure (i.e. alpha-helix or beta-pleated sheet, but not both) and consequently can align themselves in a linear fashion using cross-linking bonds. Fibrous proteins are generally quite tough and are insoluble in water. They are useful for structural purposes (e.g. collagen in skin). Globular proteins consist of multiple secondary structures and consequently form spherical shapes in their tertiary structure. Generally, globular proteins are soluble in water and are often useful for catalytic or transport purposes (e.g. the presence of enzymes to increase the rates of metabolic reactions).

To be honest, I'm not sure we need to go to this sort of detail. I think only the basics of chapter 1 are expected of us. :S
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 02:00:53 pm
It would probably be best in the likelihood of a comparison question?

E.g. What are the differences between globular and fibrous proteins? (2 marks)
Globular proteins are made up of more than one polypeptide chain that compacts to form a round, protein, wheras Fibrous proteins are made up of one polypeptide chain that can arrange in a linear-form, which gives it its tough, insoluble composition.

But you are right, I think maybe knowing the general idea that proteins can be classified as Globular or Fibrous, and a few examples of each + their functions should be adequate. :D
Title: Re: Concept discussion
Post by: Stick on January 21, 2013, 02:06:54 pm
Well fibrous and globular tertiary structures are only mentioned in one sentence in Nature of Biology. I had to refer to Biozone to get the information I have provided.

On a sidenote, I don't like Biozone very much. I find Nature of Biology to be a great resource and it frustrates me that the books contain different sets of information. For someone that would rather rely on one good resource compared to multiple sources, it gets very confusing in regards to what I really need to know. Perhaps it will grow on me in time, since I've only explored chapter 1 content of Nature of Biology at this stage. People reckon it is a fantastic resource and I hope it turns out to be the case. :|
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 02:37:44 pm
Well fibrous and globular tertiary structures are only mentioned in one sentence in Nature of Biology. I had to refer to Biozone to get the information I have provided.

On a sidenote, I don't like Biozone very much. I find Nature of Biology to be a great resource and it frustrates me that the books contain different sets of information. For someone that would rather rely on one good resource compared to multiple sources, it gets very confusing in regards to what I really need to know. Perhaps it will grow on me in time, since I've only explored chapter 1 content of Nature of Biology at this stage. People reckon it is a fantastic resource and I hope it turns out to be the case. :|

Stick its because Biozone is for the whole of Australia; each syllabus in every state, VCE, HSC or QSCE, will vary in their Biology content. Therefore, something you may encounter in Biozone may very-well not even be mentioned in Nature of Bio 2. For example, if you look at Carbohydrates in Biozone, it looks almost like Chem where it talks about bondings between monosaccharides, etc. IT is an excellent resource for applying your knowledge and answering questions. Your teacher may specify certain questions that focus mainly on the VCE syllabus, opposed to the Australian, more broad, syllabus. :D Hope that helped.
Title: Re: Concept discussion
Post by: Stick on January 21, 2013, 03:25:34 pm
I guess. I'm glad this thread popped up though - it will help me refresh my knowledge of the macromolecules I covered in chapter 1 for headstart. :)

Here's some more questions I have:
- Do we need to know that adenine and guanine are purines, and that cytosine and thymine are pyrimidines?
- Do we need to know the significance of the 3' and 5' ends of a nucleotide strand?
Title: Re: Concept discussion
Post by: alondouek on January 21, 2013, 03:33:58 pm
Here's some more questions I have:
- Do we need to know that adenine and guanine are purines, and that cytosine and thymine are pyrimidines?

It's good to know, but not necessarily necessary; an easy way to remember is this:

Cytosine and Thymine are Pyramidines - they all have y's; hence guanine and adenine are purines.

- Do we need to know the significance of the 3' and 5' ends of a nucleotide strand?

Absolutely, 100% you need to. This becomes very important when you start doing DNA replication. You may need to identify the directionality of replication of a DNA strand (5' end to 3' end IIRC). You'll also learn about upstream (towards the 5' end) and downstream (towards the 3' end) of a sequence.
Title: Re: Concept discussion
Post by: Stick on January 21, 2013, 03:36:18 pm
Absolutely, 100% you need to. This becomes very important when you start doing DNA replication. You may need to identify the directionality of replication of a DNA strand (5' end to 3' end IIRC). You'll also learn about upstream (towards the 5' end) and downstream (towards the 3' end) of a sequence.

I meant this in terms of early Unit 3 Biology. I'll make sure that when it comes up later in Unit 4 that I take note of it. :)
Title: Re: Concept discussion
Post by: alondouek on January 21, 2013, 03:39:10 pm
Fair enough; my teacher taught us DNA replication in Unit 3, obviously I don't know if it's standard in other schools :P
Title: Re: Concept discussion
Post by: Stick on January 21, 2013, 03:41:26 pm
By early Unit 3, I mean chapter 1 of Nature of Biology. :P
Title: Re: Concept discussion
Post by: alondouek on January 21, 2013, 03:47:21 pm
In which case, the best advice I can offer is this:

(http://www.troll.me/images/x-all-the-things/learn-all-the-things.jpg)
Title: Re: Concept discussion
Post by: Stick on January 21, 2013, 03:48:42 pm
Well it turns out I made a note of both of my questions in my Biology bound reference two months ago without even realising it. I must've known I would forget it. :P
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 03:53:50 pm
Here's some more questions I have:
- Do we need to know that adenine and guanine are purines, and that cytosine and thymine are pyrimidines?
- Do we need to know the significance of the 3' and 5' ends of a nucleotide strand?
[/quote]

1) All you really have to know is that Adenine + Guanine are purines, and that Cytosine and Thymine are pyrimidine. It isn't even in the textbook so that should be adequate, as this sort of stuff is more Chem orientated.

2) Yes. You need to know that DNA always replicates from 5' to 3' in anti-parrallel directions. That is, if one side of the DNA strand is 3' from the top to 5' from the bottom, the other side of the DNA molecule will be 5' from the top to 3'. You don't need to know about that completely now, its more when you do unit 4 genetics and you start to look at Replication Forks + how DNA replicates!

Hope that was somewhat helpful. Lol I'm going through the concepts of the textbook which is why I know that. Don't worry about something that sounds too Chemistry-ish. It is often not relevant. Though a good point to add is that you need to know questions like the one below. This was in the 2012 Bio exam 1.

Question 5
A particular DNA double helix is 100 nucleotide pairs long and contains 25 adenine bases.
The number of guanine bases in this DNA double helix would be
A. 25
B. 50
C. 75
D. 100

Knowing that 100 pairs long = 200 bases is essential. This is because of there are 25 adenine bases, there must be 25 complementary Thymine bases. 200 - (25 adenine + 25 thymine) = 150 bases left. You now know that the remaining bases are made up of Guanine and Cytosine nitrogenous bases. Divide 150 by 2, to get 75 guanine and 75 cytosine. Therefore the answer is C. So it is possible you'll get a question like this that just requires you to dissect it based on your knowledge of complementary base pairs. It may also come as a percentage.

So it says there are 30% guanine bases in DNA. How many adenine (in percentage form).
You just know that 30% guanine equates to 30% cytosine. This means (100 - 60) = 40% made up of Adenine and Thymine. Divide it by 2, and you get 20%.

That is about all you'll need to know. Do some practice where you find complementary base pairs for DNA or RNA sequences, and learn differences between DNA + RNA. :)

Hope that helps.
Title: Re: Concept discussion
Post by: Stick on January 21, 2013, 04:00:28 pm
I like that question. You're right though, it doesn't necessarily have much to do with the Chemistry of DNA, it's more the understanding of how bases work (which is part of chapter 1). Thanks! :)
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 04:07:55 pm
I like that question. You're right though, it doesn't necessarily have much to do with the Chemistry of DNA, it's more the understanding of how bases work (which is part of chapter 1). Thanks! :)

Yeah like in the 2012 Chem Exam there was a DNA molecule that asked what the two types of bonds were: you don't have to know that for Bio because that then investigates the Chemistry component of DNA. So glad that Chem complements Bio in certain things, because its a bit easier I imagine to work through.
Title: Re: Concept discussion
Post by: pi on January 21, 2013, 04:21:41 pm
It's good to know, but not necessarily necessary; an easy way to remember is this:

Cytosine and Thymine are Pyramidines - they all have y's; hence guanine and adenine are purines.

I remember from some podcast as "imagine a glass pyramid that's very pointy, it can CUT you. Hence, pyrimidines are Cytosine, Thymine and Uracil" :)
Title: Re: Concept discussion
Post by: Yacoubb on January 21, 2013, 11:28:41 pm
Let's start with Cell Organelles :)

Okay so we have two main types of cells:
a) Eukaryotic: possess a distinct nucleus housing hereditary information DNA + organelles held in a membrane.
b) Prokaryotic: lack a nucleus [DNA is dispersed in cytosol] and organelles not held in membrane.

Essential difference between animal + plant cells:
Plants cells possess a cell wall, chloroplasts (some) and vacuoles that store cell sap and other dissolved solution. Animals do not possess these distinct structure/organelles respectively.

One thing to note is that mentioning chloroplasts on its own is inaccurate, because not all plant cells on a plant have chloroplasts in them (non-photosynthetic cells). Instead, mentioning a cell wall as the PRIMARY difference between them is correct because even some animal cells possess vacuoles.

Let's begin with organelles and writing their functions:

I'll start:

Plasma membrane: the boundary of all cells that controls the entry and exit of substances into and out of a cell. It is primarily composed of lipids, forming the phospholipid bi-layer, and protein molecules, forming channels for the transport of lipophobic (i.e. substances that are insoluble in the phospholipid bi-layer) across the plasma membrane.

Five main methods of transport of substances include:
a) Diffusion - passive transport
b) Facilitated diffusion or mediated transport - passive transport
c) Osmosis - passive transport
d) Active Transport - active transport
e) Vesicular Transport (endo/exocytosis) active transport.

The difference between active + passive transport is that active transport requires an input of energy to take place, wheras passive transport occurs with the absense of an energy source.
Title: Re: Concept discussion
Post by: Scooby on January 22, 2013, 10:24:02 pm
Okay so we have two main types of cells:
a) Eukaryotic: possess a distinct nucleus housing hereditary information DNA + organelles held in a membrane.
b) Prokaryotic: lack a nucleus [DNA is dispersed in cytosol] and organelles not held in membrane.

I probably wouldn't say that the DNA in prokaryotic cells is dispersed. Most of it is contained within the nucleoid. It's not as if it's all just floating randomly around the cytoplasm

Essential difference between animal + plant cells:
Plants cells possess a cell wall, chloroplasts (some) and vacuoles that store cell sap and other dissolved solution. Animals do not possess these distinct structure/organelles respectively.

One thing to note is that mentioning chloroplasts on its own is inaccurate, because not all plant cells on a plant have chloroplasts in them (non-photosynthetic cells). Instead, mentioning a cell wall as the PRIMARY difference between them is correct because even some animal cells possess vacuoles.

If you're asked to describe a difference between animal and plant cells, mentioning that plant cells contain a large and central vacuole but that animal cells don't is fine. Just make sure you mention that it's large and central  :P

The point you made about chloroplasts is a good one! It's definitely a common mistake

Plasma membrane: the boundary of all cells that controls the entry and exit of substances into and out of a cell. It is primarily composed of lipids, forming the phospholipid bi-layer, and protein molecules, forming channels for the transport of lipophobic (i.e. substances that are insoluble in the phospholipid bi-layer) across the plasma membrane.

Also carbohydrates (eg. glycolipids and glycoproteins)

The difference between active + passive transport is that active transport requires an input of energy to take place, wheras passive transport occurs with the absense of an energy source.

Active transport also allows substances to be moved against the concentration gradient, whereas passive transport doesn't


I'm just being picky though. Good job!  8)
Title: Re: Concept discussion
Post by: Yacoubb on January 23, 2013, 02:06:33 am
Could you kindly tell me what the function of glycolipids and glycoproteins are?!
Title: Re: Concept discussion
Post by: alondouek on January 23, 2013, 02:34:56 am
Glycolipids (lipids with an attached carbohydrate):

Glycoproteins (proteins with glycans that are attached to polypeptide chains) have numerous functions; they can act as structural, immunological, transportational, hormonal and enzymatic molecules (this is not a complete list of functions). Examples of a glycoprotein are collagen (structural), immunoglobins (immunological) and TSH (hormonal - this is an important hormone in VCE-level homeostasis; learn it :P )
Title: Re: Concept discussion
Post by: Yacoubb on January 23, 2013, 09:37:10 am
Thank you very much. I need to make those fine-tuning adjustments for a good result so I appreciate the constructive criticism. :)

So really glycolipids act as signalling molecules for intracellular activity + provide energy for metabolic processes, whereas glycoproteins have diverse structural, immunological, enzymatic or transportational. Thanks so much.

So really if we were asked to draw a plasma membrane, you must include:
* Phospholipid bi-layer
* Protein molecules forming protein channels
* Glycolipids attached to lipid segment of cell membrane
* Glycoproteins attached to the protein molecule
* Fully labelled diagram + a little diagram to demonstrate the hydrophilic phosphate head and hydrophobic fatty acid tails of a phospholipid.

^ That would be sufficient, right?? Unless of course it specifies something like the arrangement of phospholipids in the fluid-mosaic model?

Functions of cholestrol in plasma membrane:
* gives the plasma membranes more flexibility
* promotes more stability
* increases fluidity of plasma membrane in cold environments
* CAN SOMEONE ADD SOME MORE THINGS PLEASE? :) much appreciated.
Title: Re: Concept discussion
Post by: alondouek on January 23, 2013, 12:09:27 pm
glycoproteins have diverse structural, immunological, enzymatic or transportational.

This may just be a type, but it should be: "...glycoproteins have a diverse range of functions; including structural, immunological, enzymatic or transportational roles".

So really if we were asked to draw a plasma membrane, you must include:
* Phospholipid bi-layer
* Protein molecules forming protein channels
* Glycolipids attached to lipid segment of cell membrane
* Glycoproteins attached to the protein molecule
* Fully labelled diagram + a little diagram to demonstrate the hydrophilic phosphate head and hydrophobic fatty acid tails of a phospholipid.

^ That would be sufficient, right?? Unless of course it specifies something like the arrangement of phospholipids in the fluid-mosaic model?

There have been a couple of "diagram the phospholipid bilayer" questions in past VCAA exams; they're never very specific in the given solution, so you could probably get away with a correctly-oriented bilayer with a couple of embedded protein channels. Everything MUST be labelled unless otherwise specified. You can be as detailed as you want, but it's important not to spend too much time on a diagram in the exam.

Functions of cholestrol in plasma membrane:
* gives the plasma membranes more flexibility
* promotes more stability
* increases fluidity of plasma membrane in cold environments
* CAN SOMEONE ADD SOME MORE THINGS PLEASE? :) much appreciated.

A question like this would be a great opportunity to throw in the term 'fluid mosaic model'.

In temperatures that are above the norm for a cellular environment, cholesterol stops fatty acid tails from coming into contact, thereby maintaining the structure of the membrane.
Title: Re: Concept discussion
Post by: Yacoubb on January 23, 2013, 01:57:40 pm
Summary of cholestrol function:
* gives flexibility
* gives stability
* maintains shape of membrane in cold climates by preventing fatty acid tails from becoming compact together.
* fluid-mosaic model is retained

^ would that be sufficient for the functions of cholestrol in the plasma membrane.
Title: Re: Concept discussion
Post by: alondouek on January 23, 2013, 02:09:26 pm
Summary of cholestrol function:
* gives flexibility
* gives stability
* maintains shape of membrane in cold climates by preventing fatty acid tails from becoming compact together.
* fluid-mosaic model is retained

^ would that be sufficient for the functions of cholestrol in the plasma membrane.

These are very general, so you'd need to elaborate on the first two points. My definition of the function of cholesterol would be:

"In the fluid mosaic model of the plasma membrane, cholesterol maintains fluidity and integrity of the phospholipid bilayer. Moreover, cholesterol molecules within the bilayer make it less permeable to water-soluble substances.

Cholesterol keeps the plasma membrane at optimal fluidity. At high temperatures, cholesterol makes the plasma membrane less permeable to small molecules by increasing rigidity. Conversely, at low temperatures, cholesterol makes the bilayer more fluid to prevent damage to the cell from the cold."
Title: Re: Concept discussion
Post by: Yacoubb on January 23, 2013, 03:22:52 pm
Yeah elaboration is essential; I merely placed points for its function. I would then obviously have to elaborate depending in the question. Do I have to include cholestrol in the diagram of plasma membrane or perhaps even mention it?!
Title: Re: Concept discussion
Post by: alondouek on January 23, 2013, 03:31:16 pm
Probably not, it's a bit difficult to accurately represent cholesterol in the bilayer diagrammatically. Here's wikipedia's version, you don't have to be anywhere near this accurate.

(http://upload.wikimedia.org/wikipedia/commons/d/da/Cell_membrane_detailed_diagram_en.svg)
Title: Re: Concept discussion
Post by: Yacoubb on January 23, 2013, 11:43:29 pm
Yeah I thought so. Okay so I'm going to place the definition for my five methods of transport across plasma membranes + please give me constructive criticism.

Diffusion:
The passive transport of a substance across the semi-permeable plasma membranes from an area of high solute concentration to low solute concentration along a plasma membrane.

Facilitated Diffusion
The passive transport of a substance that cannot readily diffuse across phospholipid bi-layer, and is thereby transported by a carrier molecule across the plasma membrane via the protein channel along a concentration gradient (area of high solute concentration to low solute concentration.

Active Transport
The endergonic movement of a substance across the plasma membrane from an area of low solute concentration to an area of high solute concentration, against a concentration gradient.

Osmosis
The net movement of water molecules across the semi-permeable plasma membrane from an area of low solute concentration to high solute concentration.

Endocytosis
The bulk transport of large, solid particles (phagocytosis) or dissolved substances (pinocytosis) into a plasma membrane by engulfment of the material.

Exocytosis
The bulk, vesicular transport of a substance across a plasma membrane by fusing with the membrane and being secreted or voided outside the cell.

Please give me some constructive criticism; my aim is to improve and do so accordingly :) Much appreciated guys!!
Title: Re: Concept discussion
Post by: alondouek on January 23, 2013, 11:59:52 pm
Yeah I thought so. Okay so I'm going to place the definition for my five methods of transport across plasma membranes + please give me constructive criticism.

Diffusion:
The passive transport of a substance across the semi-permeable plasma membranes from an area of high solute concentration to low solute concentration along a plasma membrane.

"Along a plasma membrane"? I think you either mean 'along the concentration gradient' or 'across the plasma membrane'. The first statement is a handy piece of info to mention. Also, when you say "semi-permeable plasma membranes", you can make it singular ('membrane') for the purpose of a definition.

Quote
Facilitated Diffusion
The passive transport of a substance that cannot readily diffuse across phospholipid bi-layer, and is thereby transported by a carrier molecule across the plasma membrane via the protein channel along a concentration gradient (area of high solute concentration to low solute concentration.

Read over to remove typos ([the] phospholipid bilayer). Also consider saying "therefore transported via a carrier molecule (often protein-based) across etc..." - better, briefer and more specific is what examiners like. "via the protein channel" - IIRC not all forms of facilitated diffusion utilise protein channels specifically.

Quote
Active Transport
The endergonic movement of a substance across the plasma membrane from an area of low solute concentration to an area of high solute concentration, against a concentration gradient.

Instead of saying "the endergonic movement", simply begin with "the movement...". You can state that the process is endergonic at the end, and why it is endergonic (an input of energy is required) - you want to be as specific as is reasonably possible. Otherwise this is a pretty good definition.

Quote
Osmosis
The net movement of water molecules across the semi-permeable plasma membrane from an area of low solute concentration to high solute concentration.

Good definition. You might want to mention that osmosis is a form of passive transport, and that no carrier molecules are required (water molecules pass through gaps in the bilayer).

Quote
Endocytosis
The bulk transport of large, solid particles (phagocytosis) or dissolved substances (pinocytosis) into a plasma membrane by engulfment of the material.

You need to mention that bulk transport is a form of active transport, as an energy input is required.

Quote
Exocytosis
The bulk, vesicular transport of a substance across a plasma membrane by fusing with the membrane and being secreted or voided outside the cell.

"Vesicular bulk transport" is better phraseology. Maybe don't mention vesicles so early, leave it for later in the definition when you're discussing the technicalities of exocytosis, i.e. "fusing with the membrane to form a vesicle etc...". Again, mention that exocytosis is a form of active transport.
Title: Re: Concept discussion
Post by: Yacoubb on January 24, 2013, 12:23:57 am
Here are the modified ones:

Diffusion
The passive transport of a substance across a semi-permeable plasma membrane from an area of high solute concentration to an area of low solute concentration, along a concentration gradient.

Facilitated diffusion
The passive transport of a substance across the plasma membrane via the protein channel from an area of high solute concentration to an area of low solute concentration, along a concentration gradient.

Active transport
The transport of substances across a semi-permeable plasma membrane from an area of low solute concentration to an area of high solute concentration against a concentration gradient. Active transport is an energy-requiring (active) form of transport.

Vesicular transport
The bulk transport of a substance into and out of a cell that occurs by the fusion of transport vesciles with the semi-permeable plasma membrane.
Title: Re: Concept discussion
Post by: alondouek on January 24, 2013, 12:38:12 am
Here are the modified ones:

Diffusion
The passive transport of a substance across a semi-permeable plasma membrane from an area of high solute concentration to an area of low solute concentration, along a concentration gradient.

Facilitated diffusion
The passive transport of a substance across the plasma membrane via the protein channel from an area of high solute concentration to an area of low solute concentration, along a concentration gradient.

Active transport
The transport of substances across a semi-permeable plasma membrane from an area of low solute concentration to an area of high solute concentration against a concentration gradient. Active transport is an energy-requiring (active) form of transport.

Vesicular transport
The bulk transport of a substance into and out of a cell that occurs by the fusion of transport vesciles with the semi-permeable plasma membrane.

Ya these are good. One things is, is with the active transport one you're going to want to throw in the word 'endergonic' instead of "(active)" - you don't use part of the word you're defining in the actual definition, ever!

Also, I'm not sure why you suddenly have a definition for "vesicular transport". Keep separate definitions for endo- and exocytosis.
Title: Re: Concept discussion
Post by: Yacoubb on January 24, 2013, 12:59:18 am
These are just handy ones I've constructed just from knowledge of reading through the textbook + looking at the transportation of molecules that can occur in various ways. My next mission is basically to differentiate between which organelles are found in eukaryotes/prokaryotes (e.g. prokaryotes anaerobically respire due to the absence of mitochondria, the organelle where Kreb's Cycle and the Electron Transport chain take place in the complete process of aerobic respiration). Knowing these sort of things (i.e. the organelles in relation to prokaryotes and eukaryotes) is helpful for these sorts of questions. :D

Maybe some assistance?
Title: Re: Concept discussion
Post by: Yacoubb on January 24, 2013, 03:54:58 pm
Okay so I thought that we should start looking at some organelles. I'll start with Mitochondria:

Mitochondria are membrane-bound organelles found exclusively in eukaryotic cells that are the principle site of cellular respiration (specically aerobic respration) and ATP production. The mitochondrion in cells contains cristae and a matrix.

Cristae
Inner-membrane folds that increase the surface area of the mitochondria.

Matrix
Contains fluid that is actually enclosed by the cristae.

It is important than when describing a cell with this organelle found in them, you should emphaise whether it is singular (mitochondrion) or mitochondria They are most abundant in cells that have high enery needs. E.g. kidney tubule cells, muscle cells like the heart, etc.

Feel free to add to that:

Oh, and perhaps let us discuss mitochondria in relation to the endosymbiotic theory of evolution. Things to support that it was once a prokaryotic organism:
* had a plasma membrane, supporting double-membrane in which it is held in within cytosol of eukaryotic cells.
* the presence of ribosomes within the mitochondria.
* mtDNA (mitochondrial DNA) present in them!
Feel free to add
Title: Re: Concept discussion
Post by: Scooby on January 24, 2013, 04:20:06 pm
Cristae
Inner-membrane folds that increase the surface area of the mitochondria.

Matrix
Contains fluid that is actually enclosed by the cristae.

The cristae are the "compartments" created in the intermembrane space by the folding of the inner mitochondrial membrane

The matrix is the space within the inner mitochondrial membrane, and is filled with fluid. It's not really right to say that it's "enclosed by the cristae" though
Title: Re: Concept discussion
Post by: Yacoubb on January 24, 2013, 04:30:21 pm
So really to explore the structure of mitochondria:
- Cristae:
the compartments in the intermembrane structure of the mitochondrion that is actually formed by the folding of the inner mitochondrial membrane.

- Matrix:
the space within the inner mitochondrial membrane filled with fluid.

I'd just like to clarify what I said above ^ and also what I wrote in that large paragraph regarding the endo-symbiotic theory of evolution + its function?!
Title: Re: Concept discussion
Post by: Scooby on January 25, 2013, 12:13:15 am
Yeah, those definitions are better  :)

Also... might want to clear up one of your points about evidence for endosymbiosis

"...had a plasma membrane, supporting double-membrane in which it is held in within cytosol of eukaryotic cells" doesn't really make sense

Essentially, there was once an independent prokaryotic cell, which, while it was just floatin' around, was engulfed by a eukaryotic cell and encased within a vesicle. But it wasn't digested. The cell membrane of this prokaryote became the inner mitochondrial membrane; the membrane of the vesicle became the outer mitochondrial membrane

Or at least that's the theory of endosymbiosis. Biologists think that the reason the mitochondria has a double membrane is because a prokaryotic cell (which had a single cell membrane) was endocytosed by a eukaryotic cell
Title: Re: Concept discussion
Post by: Yacoubb on January 25, 2013, 12:50:30 am
Essentially, there was once an independent prokaryotic cell, which, while it was just floatin' around, was engulfed by a eukaryotic cell and encased within a vesicle. But it wasn't digested. The cell membrane of this prokaryote became the inner mitochondrial membrane; the membrane of the vesicle became the outer mitochondrial membrane

That is so interesting; so basically the inner-membrane of a mitochondrion is beleived to be the plasma membrane of the prokaryote + the vesicle that the mitochondrion was held in when engulfed, but not digested, by eukaryotic cells, is believed to have formed the outer-membrane of the mitochondria. That is quite interesting.

It's like chloroplasts. I guess you can say that chloroplasts are made up of the grana (small discs containing the green-pigment chlorophyll) and stroma (containing enzymes for photosynthesis and other dissolved substances in solution form). Can we say the inner membrane is believed to be the plasma membrane, whilst the outer membrane is believed to be that of the vesicle it was held in when engulfed, but not digested?

Just making sure that the double-membrane theory can be applied to both chloroplasts AND mitochondria :)
Title: Re: Concept discussion
Post by: Scooby on January 25, 2013, 01:10:21 am
That is so interesting; so basically the inner-membrane of a mitochondrion is beleived to be the plasma membrane of the prokaryote + the vesicle that the mitochondrion was held in when engulfed, but not digested, by eukaryotic cells, is believed to have formed the outer-membrane of the mitochondria. That is quite interesting.

It's like chloroplasts. I guess you can say that chloroplasts are made up of the grana (small discs containing the green-pigment chlorophyll) and stroma (containing enzymes for photosynthesis and other dissolved substances in solution form). Can we say the inner membrane is believed to be the plasma membrane, whilst the outer membrane is believed to be that of the vesicle it was held in when engulfed, but not digested?

Just making sure that the double-membrane theory can be applied to both chloroplasts AND mitochondria :)

Yup, endosymbiosis applies to mitochondria and chloroplasts
Title: Re: Concept discussion
Post by: Yacoubb on January 25, 2013, 01:11:59 pm
Thank you.

So when we come to justify the endosymbiotic theory of evolution, would valid points be:
* mitochondria/chloroplasts have their own DNA.
* the presence of ribosomes within mitochondria/chloroplasts.
* the presence of a double (inner- and outer-) membrane on the structure of mitochondria/chloroplasts

I don't think a potential question that asks that ^ on an exam would require any more points to justify this theory?
Title: Re: Concept discussion
Post by: alondouek on January 25, 2013, 02:01:51 pm
Actually, it's quite likely there would be a question (or possibly only a Multiple Choice) on the Endosymbiotic Theory; I've certainly seen it before.

All those points are valid :) mitochondrial DNA = mtDNA, chloroplast DNA = ctDNA or cpDNA. Both mtDNA and ctDNA molecules are circular.

Here's a ctDNA molecule:
(http://upload.wikimedia.org/wikipedia/commons/2/29/CtDNA.svg)

And an mtDNA molecule:
(http://upload.wikimedia.org/wikipedia/commons/3/3e/Mitochondrial_DNA_en.svg)

Not really necessary to know either of the structures of these in detail, but it's still fascinating to see which sequences code for what.
Title: Re: Concept discussion
Post by: Yacoubb on January 25, 2013, 02:12:20 pm
It certainly is fascinating - perhaps even learning the importance of DNA, ribsomoes and inner- and outer-membranes would be handy.

DNA -
The genetic information that codes for the proteins produced by mitochondria/chloroplasts codes for proteins produced by mitochondria or chloroplasts.

Ribosomes -
The synthesis of proteins (e.g enzymes required in photosynthesis [chloroplasts] or aerobic respiration [aerobic respiration].

Membranes:
Would that just be a structural assistance to these organelles, like a protective layer?!
Title: Re: Concept discussion
Post by: alondouek on January 25, 2013, 03:07:04 pm
It certainly is fascinating - perhaps even learning the importance of DNA, ribsomoes and inner- and outer-membranes would be handy.

DNA -
The genetic information that codes for the proteins produced by mitochondria/chloroplasts codes for proteins produced by mitochondria or chloroplasts.

Ribosomes -
The synthesis of proteins (e.g enzymes required in photosynthesis [chloroplasts] or aerobic respiration [aerobic respiration].

Membranes:
Would that just be a structural assistance to these organelles, like a protective layer?!

Well, let's take a sequential look at it - we'll use mtDNA as the basis for the example.

As we can see, the mtDNA molecule has various regions for coding rRNA (a component of the ribosome) and tRNA (required for translation. Therefore, we can see that the rRNA- and tRNA-encoding genes (orange and yellow respectively in the diagram), when translated, work in conjunction with the translation of the regions required for the synthesis of proteins (green areas).

The areas in the diagram labelled "NADH dehydrogenase subunits" are needed in the construction of the enzyme of NADH dehydrogenase - which fulfils the following reaction:

NADH + H+ + acceptor <---> NAD+ + reduced acceptor

You might recognise this reaction as a side-reaction in aerobic respiration.

There is a region that codes for the cytochrome oxidase enzyme. This also fulfils an important reaction in mitochondrial aerobic respiration:

4 Fe2+-cytochrome c + 8 H+in + O2 ---> 4 Fe3+-cytochrome c + 2 H2O + 4 H+out

Wikipedia summarises this reaction well:

"Two electrons are passed from two cytochrome c's, through the CuA and cytochrome a sites to the cytochrome a3- CuB binuclear center, reducing the metals to the Fe+2 form and Cu+1. The hydroxide ligand is protonated and lost as water, creating a void between the metals that is filled by O2. The oxygen is rapidly reduced, with two electrons coming from the Fe+2cytochrome a3, which is converted to the ferryl oxo form (Fe+4=O). The oxygen atom close to CuB picks up one electron from Cu+1, and a second electron and a proton from the hydroxyl of Tyr(244), which becomes a tyrosyl radical: The second oxygen is converted to a hydroxide ion by picking up two electrons and a proton. A third electron arising from another cytochrome c is passed through the first two electron carriers to the cytochrome a3- CuB binuclear center, and this electron and two protons convert the tyrosyl radical back to Tyr, and the hydroxide bound to CuB+2 to a water molecule. The fourth electron from another cytochrome c flows through CuA and cytochrome a to the cytochrome a3- CuB binuclear center, reducing the Fe+4=O to Fe+3, with the oxygen atom picking up a proton simultaneously, regenerating this oxygen as a hydroxide ion coordinated in the middle of the cytochrome a3- CuB center as it was at the start of this cycle. The net process is that four reduced cytochrome c's are used, along with 4 protons, to reduce O2 to two water molecules."

As you can see, this is quite complicated and nowhere even near VCE level. More briefly, you can see that it is the other side reaction in aerobic respiration.

Finally, we come to the ATP synthase region of the mtDNA molecule (the lightest green regions).

ATP synthase is involved in the 'main', energy-producing reaction of aerobic respiration:
ADP + Pi ---> ATP, where ADP and Pi are joined together by ATP synthase

The membranes serve the same purpose as in other cells/unicellular organisms - partly structural, needed for diffusion of various materials, the site of certain chemical reactions (Electron Transport Chain in this case - thanks Scooby!) etc.

Title: Re: Concept discussion
Post by: Scooby on January 25, 2013, 03:12:35 pm
It certainly is fascinating - perhaps even learning the importance of DNA, ribsomoes and inner- and outer-membranes would be handy.

DNA -
The genetic information that codes for the proteins produced by mitochondria/chloroplasts codes for proteins produced by mitochondria or chloroplasts.

Ribosomes -
The synthesis of proteins (e.g enzymes required in photosynthesis [chloroplasts] or aerobic respiration [aerobic respiration].

Membranes:
Would that just be a structural assistance to these organelles, like a protective layer?!

Inner mitochondrial membrane is also the site of the electron transport chain
Title: Re: Concept discussion
Post by: pi on January 25, 2013, 03:13:46 pm
Well, membranes have a broader role than *just* structural support :)
Title: Re: Concept discussion
Post by: Yacoubb on January 25, 2013, 05:13:19 pm
Inner mitochondrial membrane is also the site of the electron transport chain

That of course comes when investigating aerobic respiration - that is, Kreb's Cycle takes place in the matrix of mitochondria and the Electron Transport Cahin takes place in the Cristae of the Mitochondria. :)

So the cristae are practically the inner folds that form when the inner mitochondrial folds and forms these compartments that are filled with fluid. The matrix of mitochondria are the spaces in between the cristae that are filled with fluids. Probably knowing the significance of each compartment in Cellular respiration is essential :)
Title: Re: Concept discussion
Post by: Yacoubb on January 25, 2013, 05:33:44 pm

Finally, we come to the ATP synthase region of the mtDNA molecule (the lightest green regions).



Glad you said that; I just face-palmed LOL! But no I think what I've mentioned below about knowing the compartments of mitochondria in relation to aerobic respiration, and also a little bit on how to justify the endosymbiotic theory of evolution.

Okay lets start discussing the Nucleus. Now the nucleus is found exclusively in eukaryotic organisms and contains the genetic code and hereditary information DNA of an organism that determines how it functions, behaves, the appearance of the organism, proteins produced for controlling cellular functions, etc. The nucleus is surrounded by a double membrane; it is relatively large compared to other organelles. It contains chrosomes and the nucleolus

Four structures/complexes that are discussed when describing the nucleus:
* nucleus
* nuclear membrane
* nucleolus
* centriole

Nuclear membrane: a double membrane holds the nucleus structure, and it contains many pores on the surface. It seperates the nucleoplasm (the contents including genetic material within the nucleus), seperating it from other organelles/structures that are immersed in the cell's cytosol. It also regulates movement of material between the cytoplasm and the nucleus.

Nucleolus: a granular structure in the nucleus; a nucleoprotein (nucleic acid + protein). The ribosomal RNA that forms part of the structure of ribosomes found in the cytoplasm is synthesised in the nucleolus.

Centriole: a pair of cylindrical structures made up of smaller tubes that form the spindle during cell division along the equator of the cell.

Important key terms:

Protoplasm = cytosol + all organelles including the nucleus.

Cytoplasm = cytosol + all organelles except the nucleus.

That is handy because if you were asked to distinguish between the two, all your answer would have to be is that protoplasm includes all the organelles including the nucleus + cytosol whereas cytoplasm refers to cytosol + all organelles with the exception of the nucleus.

Feel free to add :D Ooh, and also, the nucleus is basically the control centre of the cell, due to the fact that it contains the genetic code and information that manufactures/synthesises proteins used to control cellular functions and activity.

Constructive criticism would be appreciated :D



Title: Re: Concept discussion
Post by: Scooby on January 25, 2013, 06:14:57 pm
Okay lets start discussing the Nucleus. Now the nucleus is found exclusively in eukaryotic organisms and contains the genetic code and hereditary information DNA of an organism that determines how it functions, behaves, the appearance of the organism, proteins produced for controlling cellular functions, etc. The nucleus is surrounded by a double membrane; it is relatively large compared to other organelles. It contains chrosomes and the nucleolus

Be very careful there. The appearance of an organism and its behaviour, etc, are determined both by its genetic material and environmental factors
Title: Re: Concept discussion
Post by: Yacoubb on January 25, 2013, 06:22:57 pm
So I just wanted to mention if the following definition of DNA is acceptable:

DNA, Deoxyribose Nucleic Acid, is the genetic code and hereditary information of an organism that determines the proteome of an organism that control cellular functions and the overall function of an organism.

I've excluded the bit on appearance, because good point, phenotypes are practically determined by the genotype of an organism + the environmental factors/conditions they are around.

Is all the other information valid? Or accurate rather?!
Title: Re: Concept discussion
Post by: Bad Student on January 25, 2013, 10:19:06 pm
I think it would be better if you said:

DNA, Deoxyribonucleic Acid, is a molecule which contains the genetic code and hereditary information of an organism that determines the proteome of an organism that control cellular functions and the overall function of an organism.
Title: Re: Concept discussion
Post by: Yacoubb on January 25, 2013, 10:41:24 pm
Yeah valid point; it is a molecule + not just anything; specific is better. Thanks for the handy tip :D
Title: Re: Concept discussion
Post by: Yacoubb on January 26, 2013, 05:02:08 pm
Ribosomes: organelles that are present in both prokaryotes and eukaryotes that synthesises and manufactures proteins.

* Ribosomes are not held in a membrane.
* Condensation reaction where amino acids are chemically bonded by peptide bonds, and a polypeptide is synthesised within the ribosome.
* Amino acids that make up the primary sequence of a polypeptide are determined by the genetic code found in DNA.
* Ribosomes are actually made up partly of rRNA (i.e. ribosomal RNA)

Feel free to add on.
Title: Re: Concept discussion
Post by: Yacoubb on January 26, 2013, 09:58:26 pm
Oh and constructive criticism please!!