Protein Synthesis - Transcription Notes

There are three stages in transcription:
1. Initiation
2. Elongation
3. Termination
Transcription in prokaryotes and eukaryotes is similar.
In eukaryotes, mRNA undergoes modifications before leaving the nucleus.

The correct transcription start site is selected, and the transcription machinery is assembled.
This machinery is composed of a large protein-DNA complex.
For each gene, only one strand of DNA is transcribed; it is called the antisense strand or template strand.
RNA Polymerase binds to the DNA at a specific point called a promoter region, which is upstream of the gene.
The promoter region is a sequence of nucleotides (A-T base pairs) in DNA that indicates where the RNA polymerase complex should bind to initiate transcription.
Once bound, the RNA polymerase complex unwinds and opens a section of the double helix.

The RNA polymerase complex moves in the 5’ to 3’ direction to synthesize an mRNA molecule one nucleotide at a time.
The mRNA molecule is complementary to the antisense strand.
In the mRNA strand, thymine (T) is replaced by uracil (U).
Hundreds of mRNA molecules can be synthesized simultaneously if the RNA polymerase complex has moved from the promoter region, allowing other RNA polymerase complexes to bind.
RNA polymerase does not proofread.

Specific nucleotide sequences in the DNA template, downstream of the gene, serve as a signal to stop transcription.
When the RNA polymerase complex reaches this signal, it detaches from the DNA strand.
The new mRNA strand is released from the transcription assembly.
The DNA double helix reforms.

In prokaryotes, transcription and translation can occur simultaneously because prokaryotes do not have a nucleus.
In eukaryotes, precursor mRNA must undergo three modifications (processing) before it becomes mature mRNA.
Mature mRNA may then leave the nucleus.

Cells have nucleases in the cytoplasm that break down any RNA or DNA present.
Nucleases cannot pass through the nuclear membrane, so DNA is safe inside the nucleus.
mRNA sent into the cytoplasm must be protected.
- A methyl cap (7-methyl guanosine) is added to the 5’ end to protect it from digestion and play a role in the initiation of translation.
- A poly-A tail (200 – 300 adenine ribonucleotides) is added to the 3’ end by poly-A polymerase to protect it from degradation by nucleases.
mRNA is still broken down into nucleotides and recycled, but the poly-A tail provides additional time before degradation.

Eukaryotic DNA is composed mostly of non-coding DNA, likely inserted by viruses over time.
Introns are the sections of DNA not expressed, while exons are the sections that are expressed (ex-ons are ex-pressed).
Spliceosomes cut out the introns and join the remaining exons together.

snRNA forms base-pairs with 5' end of intron, and at branch site.
snRNPs associate with other factors to form spliceosome.
5' end of intron is removed and forms bond at branch site, forming a lariat. The 3' end of the intron is then cut.
Exons are joined; spliceosome disassembles.