BIOL 213 1st Edition Lecture 17 Outline of Last Lecture I. Splicinga. Introns and exonsII. Comparing eukaryotes and prokaryotes processes III. Translationa. Codonsb. It takes place at a ribosomec. Initiation and terminationIV. Protein synthesis and longevity are regulatedOutline of Current Lecture I. All cells of the same organism contain the same DNAa. Cloning II. Gene expression regulationa. Early stage and late stageb. Transcription regulation is most commonIII. Regulatory proteins in transcription regulationa. Activators or repressorsb. DNA-binding motifsIV. Gene regulation in bacteria and virusesa. OperonThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.i. Negative or positive feedback loopii. Ex: CAP and lac repressorV. Gene regulation in eukaryotesa. More complex than prokaryotesb. Activators and enhancersc. Chromatin structure can be transmitted to next generations and can be altered so that transcription can happenVI. Transcriptional network motifsCurrent LectureI. All cells of the same organism contain the same DNAa. Even if their functions are very different, like a neuron and lymphocyteb. This was proven by cloningi. The nucleus of an unfertilized frog egg was destroyed by UV light, therebydestroying all of its DNAii. The nucleus was replaced by the nucleus of a skin cell (could be any cell)iii. The egg was allowed to grow and it grew into a tadpoleiv. All of the different specialized cells required to make up an organism werepresent, it wasn’t just a bunch of skin cellsv. Seen in plants too: the same experiment was done with a carrot and a whole carrot plant was able to grow from a single carrot cellc. Conclusion: cell differentiation must be due to changes in gene expressionII. Gene expression regulationa. Regulation can happen at any step in the process of protein synthesis, from transcription of DNA to mRNA to regulation of protein activityb. Early stage regulationi. This is the most energetically efficient1. It saves the cell a lot of energy by not even going through the laterstepsii. But it takes a lot of time to make a protein if it’s needed1. The cell has to go through the whole process of making the protein instead of just easily activating an inactive proteinc. Late stage regulationi. This is energetically inefficient1. The cell has to spend a lot of energy making a protein2. It’s a lot of energy wasted if the cell doesn’t use the proteinii. But it takes hardly any time to activate a protein1. Since the proteins are already made, or close to already made, they can be quickly finished/activated if the cell needs themd. Transcription regulation is most commonIII. Regulatory proteins in transcription regulationa. Proteins can bind to a regulatory sequence of DNA i. Regulatory DNA sequences range from 10 – 10,000 base pairs (this size seen only in eukaryotes)ii. They are usually upstream of the initiation siteb. These can either be activators or repressorsi. Activators – help to start transcriptionii. Repressors – inhibit transcriptionc. The proteins recognize the regulatory sequence of DNA by features at the major groove and form various bonds with the DNA without disrupting the base pairingi. Regulatory proteins usually form about 20 contacts with the DNA sequence1. This causes them to be very highly specificd. DNA-binding motifs i. These are different folding patterns that help stabilize the protein-DNA interaction1. Different ways a protein can bind to the DNA2. These are most often seen in transcription factors, but not alwaysii. Homeodomain1. 3 alpha helices of the protein2. 2 helices are parallel and are pushing the third into the major groove of the DNA3. The third is able to bond with the nucleotides without compromising the hydrogen bonds between the base pairsiii. Zinc finger1. Loops of the polypeptide chain are made and held together by theinteraction of a zinc atom, 2 cysteines and 2 histidines 2. These loops are attracted to the DNA, causing the alpha helices to bond with the DNAiv. Leucine zipper 1. Formed by two alpha helices, each of a different subunita. The fact that it is made of 2 different subunits makes it a dimer2. They are held together by leucinesa. The parts of the subunits that touch each other have leucines as the side chainb. Leucines are hydrophobic which allows them to group together like this3. It binds to the DNA and it fits into the major grooves4. The part of the protein that binds to the DNA is positivea. Because the DNA is negativeb. The opposing charges make the bond more stableIV. Gene regulation in bacteria and virusesa. There is an operator in the promoter region of the DNA that helps to regulate transcriptionb. It is a protein that binds to the DNA and will either activate or inhibit transcriptionc. Bacteria does this because they always want to save the most energy possiblei. If they don’t have to make a protein, they won’td. Operons help with this – the protein made is usually the signal molecule that activates or inhibits transcriptioni. Therefore operons can be negative or positive feedback regulatione. Example of negative feedbacki. Tryptophan is a protein made by bacteriaii. But the bacteria doesn’t want to make too muchiii. There is a regulatory protein to which tryptophan can bindiv. When tryptophan binds to this protein, it will slightly alter the protein’s shapev. This allows the protein to bind to the DNAvi. When the protein is attached to the DNA, the RNA polymerase can’t get to the DNA to transcribe itvii. Therefore, tryptophan will essentially turn its own synthesis offf. Example: the presence of glucose versus the presence of lactosei. All cells like to use glucose as their energy sourceii. If there’s glucose present, cells will use this before anything elseiii. But if it’s not, the cell will spend extra energy to create proteins that will utilize another energy source1. But only if glucose is not presentiv. The table below tells whether or not the bacterial cell would spend extra energy to create proteins that would utilize lactose as the cells energy source1. + = present - = not presentLactoseGlucose - + - No Yes + No Nov. CAP1. This protein is regulated by the presence or absence of cyclic AMP2. Cyclic AMP is present when there isn’t enough glucosea. So, when there’s not enough glucose, CAP will be present3. CAP binds to the promoter region of the DNA