Concept discussion

[slothpomba]

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.

[Yacoubb]

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.

[Russ]

I doubt you need to worry about random coil for VCE

[Yacoubb]

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?!

[Stick]

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.

[Yacoubb]

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?

[Stick]

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.

[Yacoubb]

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

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.

[Russ]

Redefine antibodies

[Yacoubb]

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!

[Stick]

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

[Yacoubb]

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.

[Stick]

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. :|

[Yacoubb]

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. Hope that helped.

[Stick]

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?