With the above diagram, I'm wondering what the minus sign (-) next to the O in Phosphate means. Also, what does the dash (') next to the C in Deoxyribose mean?

Could you explain this diagram for me? All the arrow chains and stuff are confusing.

Is this diagram just random? Do I just need to know only that the protein structure has peptide bonds?

There are no labels apart from this?

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2 Answers

I'm not a biology student, and I think Eukaryote (did I spell that right? proof I'm not a biology student), but because I've studied some biochemistry in university and VCE Chemistry, here are my attempts with the 1st and 3rd diagram (no idea what the 2nd diagram is even about).

The minus sign on the Phosphate molecule indicates a charge on the molecule. There is a negative charge located at that O (oxygen atom).

The dash sign near the C (carbon atoms) of Deoxyribose are actually part of the numbers: 1', 2', 3', 4', 5'. I'm not sure why they didn't just go 1, 2, 3, 4, 5 (there may be a story behind it), but it's just the way it's done. You pronounce it like this: "1 prime, "2 prime", etc. (i.e.: the dash is called a "prime").

With the 3rd diagram:

Yes, the blocks are completely random, just to show you the idea that a protein is a chain of amino acid subunits. You should basically be aware a protein is made up of lots of amino acids that are linked up together by peptide links.

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Yea you did Collin, it's Eukaryote :P

Diagram 1: The (-) sign indicates a negative charge, and without trying to complicate things, it’s due to the bonding patterns and charge distribution (uni level, don’t worry about it). And if you’re thinking ‘hmm that double bond could be on any of the 4 oxygen’s, that’s true!

For (‘) next to the 1,2,3,4 and 5 just means ‘prime’. Like already said it’s just nomenclature, with dna made of deoxyribose bound from 5’ to 3’ because that’s the only direction DNA polymerase can synthesise DNA. This gives rise to the ‘interesting’ phenomenon of okazaki fragments due to DNA polymerase's one direction of synthesising nature.

Diagram of cell.  I’m giving a lot of detail for your level but it’ll help if you’re asked to elaborate on it.

Going left to right, in this case we are talking about amino acids. They are used by ribosomes to synthesises peptides, oligopeptides or in this picture proteins from a mRNA strand via Ribosomes. Since we know only eukaryotes have a ‘true’ membrane bound nucleus (prokaryotes have a ‘nucleoid’ which is not a nucleus but just a region of genetic material) we know the Ribosomes are of the 80S variety.  S is a unit of sedimentation, with bigger number = sediments faster in a centrifuge, it’s a unit of size.

What we need to draw a clear distinction to is that there are two ‘types’ of ribosomes in the eukaryotic cell: free and bound. Free are ones that float around and synthesise polypeptides in the cytosol, while bound ones synthesise polypeptides into the endoplasmic reticulum. While the freely synthesised ribosomes produce proteins for the cell, the ones produced in the RER tend to be exported from the cell to other cells or are integral membrane proteins via the golgi.

Smooth endoplasmic reticulum on the other hands mainly deals with lipid synthesis and carbohydrate metabolism.  

So we have vesicles from the RER going to our golgi (proper name is golgi apparatus) where the proteins made in the ER are packaged, modified such as by glycosylation and then the protein via exocytosis is sent out of the cell (secretion).

All you need to know about lysosomes are they degrade ‘stuff’ that comes into the cell from endocytosis most of the time.

You might have now wondered ‘but if vesicles are moving all over the spot, then won’t a membrane bound organelle such as the ER be gone? Well true, but there is a system where a patch of membrane in the form of a vesicle from the receiving membrane is sent back to the original location. This happenes to the smooth and rough ER.

Protein diagram is random, but it’s just to show that proteins are made up of amino acids that are linked by peptide bonds.

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