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Lecture 18

Biology 1002B lecture 18

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Biology 1002B
Tom Haffie

Lecture 18 four most common types of cancer in Canada 1. breast cancer 2. prostate cancer 3. lung cancer 4. colon cancer likely factors contributing to cancer incidence in Canada role of cyclin/CDK complexes in cell cycle regulation - G1/S checkpoint: prevents cells form replicating their dna if its damaged. Damaged cells cant get through this checkpoint this checkpoint is regulated by CDK(inase). It is an enzyme that phosporylates targets, but CDKs are only active when they are bound to other proteins called cyclins - cyclins production cycles with the cell cycle (hint: the name). - cyclin is produed early in the cell cycle, binds on and activates CDK, CDK cyclin complex then phosphorylates a whole bunch of targets downstream and that relases the G1 checkpoint. - cyclins and CDKs are examples of post translational regulation of protein function. - EGF (epidermal growth factor receptor)- when there is EGF, it binds on to this receptor and there are transmembrane domains and internal signaling domains in the protein. EGF is ESSENTIAL for normal embryonic growth and development (because EGF is an embryo gene). - but in cancer, embryo genes (EGF) is on all the time and signaling all the time (mutation), which causes a lot of replication and division into a tumor. role of proto-oncogenes, tumor suppressor genes and oncomirs in caner - before gnes are activated (functionaling normally): called proto-oncogenes genes. When there are deregulated, called oncogenes genes. - oncogenes contribute to tumor growth - and any sort of protein in the EGF pathway can be an oncogene - tumor suppressor genes: genes that have evolved to shut down that repid cell growth during embryogenesis. Cells grow very large and need to stop rapid celll division. These genes evolve to be like embroyo suppressors, but mistakenly researchers think they evolved to be tumor suppressors. role of p53 gene - p53 is a TUMOR suppressor. - P53 prevents cell division - It can be activated by dna damage - its activity can evoke dna repair, it can block cyclin/ CDK’s at the first check point (p53 is in charge of that first G1/2S checkpoint). explanation for why increased cancer risk can be inherited - might inherit perfect tumor suppressor genes from both parents, but you might ver the course of ur life suffer mutations in both of those alleles and not you have LOST the tumor suppressor activity and cells then begin to divide out of control. VERY rare though. - If you inherit from ur dad and already defecive tumor suppressor allele then all u have in one u got form ur mom… much higher risk of getting cancer (becoming homozygous) because ull need only one mutation instead of two to develop a tumor. explanation for why cancer incidence tends to increase with age - more time or mutations/ changes - more time exposed to harmful things in environment role of stem cells in tumor growth - pleuri potent stem cells are able to differentiate into a wide range of tissue types. - when stem cells divede to make two daughter cells, one of the daughter cells remain a stem cell and the other one becomes a prpgenetor cell, and these go on to differeintiate into something. The cycle keeps going and keeps throwing off progenetor cells. - BUT all stem cells, progenetor cells, and differentiated cells can suffer a mutation turn into cancer stem cells. - tumors are driven by cancer stem cells evidence that epigenetic regulation may be relevant in cancer - maternal eggs, can reprogram a tumor cell. - when the nucleus f a tumor cell is put in an egg cell (i.e, of a mouse), is looses its tumor making ability and starts to make a mouse. - the egg cell is EPIGENETICALLY programming the nucleus. - maybe tumors start with epigenetic changes (not mutations). Lecture 19 strategies for determining if features are homologous - Homology means share common ancestry (does NOT mean similar). sequences detected by annotation programs to detect open reading frames (ORF) - not as many starts and stops. characteristics that are, and are not, common between homologous genes usefulness of BLAST analysis of sequences in Genbank at NCBI - NCBI is a database, has a lot of information, huge amouts total genome information/ individual genome sequences. - There are tow ways to show regions of similarity in sequences 1. BLAST- look for more local similarities - just looks for regions with very high similarity. Doesn’t try to force two seuences to align perfectly. - just looks for smaller areas (much faster to look for regions than try to force two whole sequences to align) 2. CLUSTAL- look for more global similarities - it tries to align all those similar bases, if they don’t alllign perfectly maybe introduce a gap reasons why amino acid sequence comparisons are more informative than nucleotide sequence comparisons 1. more information in an amino acid sequence of the same length - there are two bits of information in each letter of the nucleotide sequence. - nucleotides have a four letter alphebet. - there are ________ bits of information in a single amino acid. - amino acids have a 20 letter alphabet. 2. Genetic code is redundant (more than one codon can code for the same amino acid). - more noise, nucleotide sequence has more stuff that doesn’t matter - amino acid sequence more highly conserved. Why? What is selection acting upon? 3. DNA databases are much larger: BAD. Dna bases have lots of repretitive junk dna which makes it hard to search. Nucleotide sequences are almost positive that codes for a protein, much more specific and refined because its been through trancription. mathematical relationship among total information, # of symbols, # letters in the alphabet relative number of bits of information in a single nucleotide vs. single amino acid - nucleotide: two bita per letter - amino acid: relationship between E-value and likelihood of homology - chance = e- value - lower e value, less likely that chance happened, the two sequences converged to be just like each other (less likely that they didn’t share a common ansestor or greater likelihood of REAL homology). - small e-value, more homologous (i.e, clammy). Lecture 20 synonymous vs nonsynonymous mutations - synonymous: change in nucleotide sequence but doesn’t change the amino acid. characteristics of the neutral theory of molecular evolution - neutral mutation don’t have any real effect - most mutations are deleterious - few are advantageous. - neutral mutations have no selective advantage or disadvantage, their just there. ** number of differences b/w protein sequences of different species are proportional to the time since those species diverged.** - if species diverged a long time ago than you would expect more differences that species that were recently diverged. (i.e, chimp vs human). AMINO ACID GRAPH - there are more differences in plant and animal cyctochroms c than there are in organisms which diverged more recently,(all of these like mammels, chimp vs human. - Fewer amino acid differences if the two organisms diverged more recently (the further out u get the more differences). - like in the graph, mutations occur at a constant rate (straight line, change as a function of time)–Neutral theory - this is proving that mutations occur at a constant rate because mutations are neutral - molecular clock: if you take bunches of proteins u can get a molecular clock. NUCLEOTIDE GRAPH - rate of change of synonymous (don’t affect the amino acid sequence) occur faster. - synonymous = silent substitution - nonsynonymous = replacement substitution relationship between frequency of amino acid substitutions in given proteins vs. time since common ancestor - α-globin is a protein required for hemoglobin, hemoglobin binds to this and carries oxygen. - histone H4 is a neucleosome complex, structure of chromosome - rate of mutations of histone H4 is really slow and the rate of α-globin is really fast (lots of mutation over evolutionary time). - Why difference in rates? Histone H4 is contrained, not many changes you can make to this sequence sithout affecting its structure and function. - synonymous: weak constraint, nonsynonymous: high constraint relative rates of accumulation of synonymous vs. non-synonymous mutations variables that affect the rate of evolution of a particular protein deduce time of divergence given number of amino acid changes in particular protein characteristics of the "molecular" clock regions of two unrelated proteins that would be expected to be similar if they were the products of convergent evolution - for proteins, you would expect localized regions of high similarity but you wouldn’t excect the entire protein/nucleotide sequence to be similar. (i.e, location of cysteins (diulfide (S-S) bonding), amino acids necessary for catalysts, DNA binding domains, receptor binding sites) - these represent very localized areas of the sequence. - in summary, proteins converge in different areas of the nucleotide sequence but not over the entire sequence. function of lysozyme - lsozyme: is a small enzyme that is antibacterial. It protects the body from infection by attacking the peptiodoglycan wall. - in tears, egg whites, etc. characteristics of ruminant organisms that enable them to extract energy from cellulose - mutations occurred and not lylosome has a different function in recruiting stomach enzymes in ruminants (i.e, cows). - ruminants- these animals can eat cellulose like grass. Then when in the stomach the bacteria in the grass can break down the cellulose into simple sugars. - now it uses lysosoome in the stomach to break down the bacteria because theres lots of nutrients in bacteria. - since evolved into the stomach, the enzyme had to aquire new properties ( lower ph, and lysine has to protect itself from being chewed up from the pepsin that’s in the stomach-proteases). role of lysozyme in digestive physiology of ruminants, langur monkeys and hoisan birds - monkey and cow are not related at all but both can break down cellulose from the grass. - this is because, they have acquired the quality independently. - Lysosoyme in different species - even though langur and baboons are both monkeys, they have a lot of differences!! This is because their lysosoyme amino acid sequence is more divergent then you would predict. - below the line is how many amino acids do they uniquely share. The cow and the monkey share 5 amino acids in common even though they are not phylogenically related, they didn’t diverge from each other. Hoisan bird has the enzyme too through convergent evolution. characteristics that distinguish "digestive" lysozyme from "conventional" lysozyme - through covergent evolution the substitution in amino acid have resulted in the sequences being much more similar than u would otherwise predict. - for amino acids, All three animals at position 75 both have aspartic acid and they have at 87 Asparagine. - there are two different concentrations of pepsin, digestive and non-digestive, when you isolate the protein, and see how long it takes for the protein to get distroyed by the pepsin and forr the lysosome to disappear. - The digestive enzyme is much more resistant to pepsin treament than non digestive one. - the nondigestive enzyme at lower concentrations of urea it starts to fall apart and unfolds. - the diesgestive enzyme takes longer, higher concentrations of urea before it starts to unfold. - The digestive enzymes structure is much more stable, stronger and rigid. – digestive doesn’t flex when it interacts with the active sight of pepsin, pepsin has much harder time accessing the bond that it wants to break. - The digestive enzyme (in cows, langur monkeys , and hoisan birds) doesn’t have the aspartic acid – Proline bond because this bond is very susceptible to cleavage at very low pH. - the 3 dimentional structure of protein is surrounded by a negative charge that repels pepsin, thus resists proteolytic breakdown. Lecture 21 characteristics of model systems that can be used for experimental evolution - subject organisms in the labto various treatments and watch theme volve over time. - model systems include viruses, bacteria, chlammy, drosophila, yeast - characteritics b/w them: they have a very short generation time (so u can look at evolution in real time, and u can look at selection and changes in the genome). origins of genetic novelty (variation) 1. spontaneous mutation: can give rise to genetic novelty, and theres a selective advantage for the organism that has the mutation 2. gene duplication/ amplification 3. Gene rearrangment: distance b/w two genes. Promoters move to a different gene so now its under different distinctive control. possible fates of duplicated genes - usually ur not duplicating a specific gene, ur duplicating a region around the gene. The region that is copied is both the promoter and the structural gene. - after, one of the genes gets destroyed and deleted form the genome and ur back to having a single copy. - so theres basically no effect of duplication bc it leads to disingegration of one of the two copies. - BUT it could be that the second copy is retained , so now you have two genes doing the exact same thing but u only need one copy. When u have two copies the seclective pressure on that second copy is reduced. - There is a little more freedom for the second copy to mutate and change because it wouldn’t be lethal since theres an original copy. Original has a stronger selective pressure. relative impact of selection on duplicated genes - the second gene (duplicated gene) can lead to new function and the structural gene will become different from the original. - Neo- functionalization: the second gene can do different things and more complex things because it can evolve faster. Sub-functionalization: Doesn’t affect the structural gene, just effects the promoter. Just changed the regulatory element (i.e, works under high pressure instead of low pressure, or in a different area, tissue specificity, etc). design of Lenski's long term evolutionary experiment (LEE) with E. coli - Can evolution produce adaption if it depends on random mutations (most of which are harmful or neutral and rare)? - They used E coli (which grows really fast) - don’t want any recombination (meosis crossing over) – too complex. E coli is completely asexual so no recombination. - So any change u see over time is mainly because of spontaneous mutation as well as rearragments and duplications. - population size is huge which is good because new alleles can come about and sustain themselves in the population. Procedure: - he got a peatree plate and ecoli, he streaked that Ecoli and takes ONE colony (one cell that simply divided) and enoculates that flask, grows that flask. Leaves it for a day, comes back and sees 12 replicate populations from that one cell. - the replicates are genetically identical and lets them evolve and over time he sees the evolution of these 12 independent populations. - take part of a culture and put it in a new flask (enoculate it) pour media into the flask so it could grow and keep doing this every day for all 12 populations. value of cryopreservation to LEE - You can freeze a sample at any time and later take that frozen sample and start a culture agiain. - you can COMPARE a culture in different generations by sequencing their genomes, looking at their response to various factors, you can see how they evolved! where citrate enters metabolism - After more than 30 000 generations from the 12 colonies, one of those flasks had a larger concentration of cells. - These cells have aquired the ability to metabolize citrate, it can use citrate as a carbon source. This is VERY rare. - The media contains citrate to keep iron in the solution so u can an Fe-citrate complex and this enables iron to be effieciently taken up and cells NEED a lot of iron. - citrate is not able to be taken up into the celll, only iron is. They also have no ability to use the citrate as a carbon source if theres a lot of oxygen around. ** for final exam compare the cycle of citrate compared to glucose. role of glucose limitation in LEE experiment - cells can’t grow without glucose - so each flask contais a little amount of glucose so the cells only grow a certain amount and stop dividing once they use up all the glucose. - then after, u sub culture it into more glucose the next day, and the cycle continues. - this is a great example of selective advantage because you can use citrate to grow in the presence of oxygen so it can divide for a longer about of time how to determine if Cit+ phenotype arose from one single mutation or was dependent on previous mutations? - How was this citrate positive phenotype acquired? you can go back 2500 generations, 15 000 and even 0, thaw out a sample and grow flasks of its ancestors to see when did this Cit+ phenotype arise. - look at the cells before the mutation and see if there was any citrate+ time. genetic changes giving rise to potentiation, actualization and refinement of Cit+ phenotype - Thaw out cells from just before 33 000 (where the mutation occurred) and find any sense where they can grow on citrate. - plant them on citrate agar. For 32 000 and 33 000, it was found that they have a slight citrate positive phenotype. - the actualization and refinement of the phenoytype was dependent on the potentiation of the mutation. - this mutation allowed for the potential to devlop the citrate+ phenotype. - actualization that around 31 000 you can see the cells astarting to have a slight Cit+ - actualization of Cit+ has to do with the C
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