Know the meanings and
importance of the key words
(Again, these are my own half-assed definitions, not proper textbook definitions, so they might not be 100% accurate.)
Transcription factor: Proteins that bind to the DNA to promote transcription of genes.
Promoter: The area that directs the binding of RNA polymerase II. Promoters are located close to the start site. There are also enhancer regions, which may also help regulate genes, but these are often located far away from the start of the gene.
Regulatory sequences: Binding sites for regulatory proteins. Can be located pretty much anywhere, even within introns.
Half-life: The time that it takes for half of a particular type of molecule to be degraded.
mRNA degradation: The degradation of mRNA... This generally starts with shortening of the poly-A tail by an exonuclease. When the tail is short enough, degradation speeds up.
UTR (untranslated region): Parts of mRNA that are not translated.
Have an understanding of
the mechanisms of control of
gene expression from
transcriptional to translational.
Understand the different facets of transcriptional control.
Realise that transcription factors bind sequentially.
Understand intron-exon splicing.
Transcription
Just like for prokaryotes, the main point of control is at the transcriptional level. This is regulated by cis-acting control elements, which are motifs and sequences along the DNA itself. These include promoter, enhancer and repressor regions- see my definition of "promoter" above.
Around 25 base pairs from the starting site, there is a sequence known as the "TATA box" as it contains the TATA sequence. This binds TATA-binding protein, or TBP. TBP is a part of transcription factor for RNA polymerase II, subunit D, otherwise known as TFIID. TFIID is one of several transcription factors that bind near the TATA box. They all bind in a specific order, though I don't think knowledge of the order is necessary at this stage. Sometimes other proteins might bind to enhancers, which are often located far away from the start site. Proteins at both the TATA box and at the enhancer can be joined together by other proteins known as mediators.
When everything is in place, RNA polymerase can bind to the DNA. RNA polymerase II, which creates mRNA transcripts, has a tail known as the CTD, or C-terminal domain. For transcription to begin, the CTD must first be phosphorylated.
(Oh, and by the way, there are other RNA polymerases. I'll just include them here for completeness. RNA polymerase I is used to synthesise most types of rRNA, including 5.8S, 18S and 28S rRNA. RNA polymerase III is used to synthesise 5S rRNAs as well as most other types of RNA in the cell.)
Pre-mRNA Processing
Once the gene has been transcribed, it is time for pre-mRNA processing. Processing at this stage is also vital to the function of the proteins that are being produced. Processing includes the splicing out of introns (non-coding regions) and the splicing together of exons (the coding regions). Exons can also be spliced in different orders, resulting in many different proteins that can be produced from the same gene depending on how it is spliced. Processing also includes the addition of a 7-methylguanosine cap on the 5' end and a poly-A tail on the 3' end, both of which contribute towards the stability of the mRNA.
The enzymes and other factors required for capping and splicing mRNA are located on the C-terminal domain of RNA polymerase. The addition of the poly-A tail is catalysed by poly-A polymerase.
Splicing is quite complex, and so I won't go into a lot of details now (mainly because I don't know a lot of details at this stage :P). The pre-mRNA has special splicing sequences that indicate where splicing is to occur, and these are recognised by the "spliceosome"- a complex of proteins that catalyse splicing. Many of these proteins are snRNPs, or small nuclear ribonucleoproteins.
mRNA Transport and Localisation
mRNA is often translated in places where its products will eventually be needed, as this is often more efficient. Also, damaged mRNA is prevented from leaving the nucleus at all by being taken to exosomes to be degraded by exonucleases.
There are several ways through which mRNA can be localised to a specific location. Firstly, mRNA can be transported via cytoskeletal proteins. Secondly, mRNA can diffuse through the cytosol to later become trapped in certain locations. Finally, mRNA may diffuse through the cell, progressively degrading everywhere except for in certain locations where protective factors are present.
Translation
Most translational control occurs at the initiation of translation. The 5' cap is required for the binding of the small ribosomal subunit. Additionally, certain eukaryotic initiation factors have to bind to the 5' and 3' ends to allow translation to occur, thereby ensuring that translation only occurs on mRNA that are intact.
Degradation
The half-lives of eukaryotic mRNA can differ from only a few minutes to many hours. They are determined by specific sequences in the mRNA. As I mentioned before, the poly-A tail is shortened before the rest of the mRNA is degraded. Proteins that catalyse these processes compete with translational proteins that bind to the same region. Hence translation and degradation will not occur at the same time.
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