Proteins: Background and Revision

This should mainly be revision (hence the title), but here goes...

1.  Structural organisation of proteins

See my earlier post on Proteins- Levels of Structure.

2.  Recognise primary sequences and naming conventions

I think that by "naming conventions" they mean whether you use the full name of the amino acid or a 3- or 1-letter code. So, for example, instead of writing Methionine-Aspartate-Glycine, you could just write Met-Asp-Gly, or M-D-G (yup, D is the 1-letter code for aspartic acid as alanine got to A first). As you can imagine, this saves a lot of time. A special code you might see is Xaa or X, which is basically like a "wildcard" that can refer to any amino acid. It's used when an amino acid is unknown, or it could be any amino acid.

3.  Describe the primary structure of a protein

See my earlier post on Proteins- Levels of Structure.

4.  Describe an example of how changes in primary structure can affect protein function

One example of how a change in primary structure can affect protein function is in sickle cell anaemia. In sickle cell anaemia, the red blood cells are shaped weirdly because all of their haemoglobin molecules have formed long chains. Naturally, haemoglobin can't bind to oxygen as well when it's too busy having fun making long chains. Also, the weird "sickle-shaped" cells can clog up blood vessels. Not good.

Amazingly, such a deleterious outcome is a result of only one change in the primary amino acid sequence of haemoglobin: a glutamate residue is changed into a valine residue. This may be because glutamate is negatively charged whereas valine is hydrophobic.

Bear in mind, however, that not all changes to primary structure have such adverse effects. Many different species have proteins that work in pretty much the same way, though some amino acid residues may differ between species.

5.  Describe the key differences with respect to translation for prokaryotes and eukaryotes

1. The ribosomes are of different size. Prokaryotic ribosomes are smaller (70S) and eukaryotic ribosomes are larger (80S). (The "S" refers to "Svedberg coefficient," which is to do with how quickly stuff centrifuges. Bigger particles tend to sediment faster, but shape can affect sedimentation rate as well.)
2. In prokaryotes, transcription and translation occur simultaneously in the cytoplasm. In eukaryotes, transcription occurs in the nucleus and translation occurs in the cytoplasm.
3. Prokaryotic mRNA tends to be polycistronic, which means that it can produce multiple different protein products, which are usually related (for example mRNA derived from the lactose operon codes for genes all involved in breaking down lactose). Eukaryotic mRNA is monocistronic, however, which means that one mRNA = one protein.
4. The initial tRNA is slightly different. In prokaryotes, the first tRNA carries a formylated methionine residue; however in eukaryotes the first tRNA carries a normal methionine residue.

6.  Describe key structural components of prokaryote ribosomes

Prokaryotic ribosomes are 70S and are made up of a large and small subunit, which are 50S and 30S, respectively. (The numbers don't add up because, as I mentioned before, shape can affect sedimentation rate and therefore Svedberg coefficient.) Roughly 2/3 of a prokaryotic ribosome is made up of rRNA (ribosomal RNA) and 1/3 of protein. The rRNAs themselves have secondary structures, and can fold back on themselves and make hairpin loops and so on, but I don't think that's particularly important. Eukaryotic ribosomes are pretty similar too.

7.  Know the direction by which translation occurs for mRNA and protein

The mRNA is read 5' to 3', and the protein is synthesised from N-terminal to C-terminal.