Biology Final Exam: Nov 30- Transcription in prokaryotes- main enzyme involved is RNA polymerase (no helicase or primase). o In a bacterial cell, the RNA polymerase sees the promoter (TATA box) and it burrows into the DNA molecule at the promoter. Then is starts transcribing. 3 steps: Initiation- when RNA polymerase burrows into the promoter and starts transcribing Elongation- travels down the gene, unzipping the DNA as it does so. When it does this, it forms the RNA transcript, which isthe series of ribonucleotides. Uses ATP, GTP, CTP, UTP to synthesize RNA transcript.  Termination- at some point in this transcript, there is going to be a stop codon, which is the signal to stop translation. Downstream of the stop codon the terminator occurs. It is an inverted repeat. The RNA polymerase will continue past the stop codon and keep transcribing the DNA. As the RNA polymerase continues past the terminator, the transcribed terminator forms a loop. This loop is the inverted repeat. It has a series of complementary bases. This 3-dimensional structure causes the RNA polymerase to detach and stop transcription. Final product is mRNA, which will eventually be translated.- Transcription in eukaryotes- one of the major differences is that in eukaryotes, you get a transcription initiation complex. The RNA polymerase cannot find the promoter all by itself. It needs help, which comes in the form of proteins called transcription factors (proteins that bond to the promoter. When they do this, the RNA polymerase can see the promoter and start transcribing). o Elongation-same as in prokaryotes. Use NTPo Termination- the terminator is not an inverted repeat. It is a sequence(AAU AAA). Terminator is downstream past the stop codon, just as theinverted repeat was. o Product of transcription is pre-messenger RNA.- If typical protein is 400 amino acids long, the mRNA should be 1200 because each codon in the mRNA codes for an amino acid and the mRNA are 3 codons long. Typical mRNA should be about 1200 nucleotides in length.o They did an experiment and took cytoplasm from a eukaryotic cell and purified the mRNA, then they took DNA from nucleus and boiled it, which breaks the hydrogen bonds so that the DNA becomes separated into 2 separate strands. Then they hybrodized the DNA with the mRNA. Put 2 single strands of DNA and RNA and let them bond together.  There were regions where the bases of the DNA bonded with regions of the RNA following usual base pairing rules There are also regions that aren’t complementary to the RNA- These form introns (jutting out) and exons (closer to mRNA molecule). DNA gene composed of introns and exons- Exons- expressed sequence, are transcribed into mRNA, which is transcribed into a protein.- Introns- intervening sequence, between the exons, are initially transcribed but are later spliced out of mRNA. in the nucleus, the entire gene is transcribed into pre-messenger RNA, which contains all of the introns and exons. Then the pmRNA is processed in RNA processing and the introns are spliced out. Initially in transcription, the entire gene is transcribed into pre messenger RNA, including the introns. Then during RNA processing the introns are spliced out. This makes the RNA shorter than the original.o Pre messenger RNA processing (steps not in any particular order): Introns are cut out and the exons are spliced together. Exactly like making a movie. - Introns cut out using a spliceosome- composed of “snurps” (snRNP)o Small nuclear ribonucleoproteino It is small RNA molecule bonded to proteinso “snurps” all combine together to form the spliceosome CAP is added to the pre-messenger RNA.- Is a special guanine nucleotide that is added to the 5’ end of the pmRNA. Add a poly A tail- means that the pmRNA is going to have a long tail of adenine nucleotides bonded to it.- Enzyme that makes it is poly A polymerase- Knows to do that because the terminator is a poly A signal. Triggers poly A polymerase to add the poly A tail Final mRNA has a cap and a poly A tail added, and the introns spliced out and the exons spliced together. Final mRNA is a lot shorter than the pmRNA. Cap and the poly A tail are important in protecting the mRNA from exonucleases (some can attack a poly nucleotide at the 3’ end and digest 1 nucleotide at a time, others can attack at the 5’end). - They slow down the attack from the exonucleases and the longer the mRNA is in the cytoplasm, the more timesit can be translated into proteins. Some mRNA’s have a long tail, and they are around for a good bit and are translated a lot, while others have a shorter tail and are eaten up by exonucleases faster.  Cap and poly A tail also help transport the mRNA form the nucleus, where it was made out into the cytoplasm.  The Cap is important in bonding the mRNA to the ribosome. It has to attach to the mRNA so that the start codon is in exactly the right place. If the start codon isn’t in the right place you get a frame shift.o Why are introns there? The best reason is probably alternative splicing. - Don’t always have to splice the exons together in the same way. - Could splice e1 to e3 and leave 2 out, etc.- It allows one gene to produce/code for many proteinso Ex: your immune system protects you by making antibodies. It can produce a phenomenal # of antibodies (are proteins). It can produce more than a million antibodies, all of which are different.o Human has roughly 22,000 genes and alternativesplicing is how they form into different antibodies Another reason is the way the gene evolved.- Some prokaryotic ancestor with a gene for protein X and another gene for protein Y. The eukaryotes could have produced a protein with more functions by combining two genes together from the ancestor. Perhaps the original ancestral genes correspond with the prokaryotic genes today. o Instead of producing 2 small proteins that work independently, we produce 1 large protein with 2 main parts that often correspond to the domains of a protein A domain of a protein is part of a protein that has a specific function (ex: hemoglobin has a domain that bonds to O and another domain that bonds to CO2. It has a third domain that can bond to protons). Third reason is for variation- Genes are on chromosomes, so have a chromosome with introns and exons. (see diagram in notes)o The introns make the genes longer, and by making the genes longer, it increases the chancesof making a