weber uiuc edu 22 October 2007 MCB150 Lecture 24 Lecture 24 22 October 2007 Announcements More broken hand notes Exam I scores are back Blech o If there are questions about grading see Alejandra Missed some of the announcements due to forgetting to turn on the recorder o Probably nothing important for the next exam Sickle Cell Anemia Predictions from the Codon Table Amino acid changes from base substitutions can be predicted using the codon table o We can interpret what the consequence will be in advance Consider the Leucine UUA What are the consequences of changing a base at any of the three positions of the codon o UUX will stay in the same box Can give Leu or Phe Two possible amino acids o UXA will stay in the same row Can give Leu Ser Stop Stop Two possible amino acids and the stop codon twice o XUA will stay in the same column Can get Leu Ile Val Three possible amino acids Can immediately predict what the base substitution will be if one mutation occurs in one of the positions in the codon Consider the Glutamine o CAX His Gln o CXA Leu Pro Gln Arg o XAA Stop Gln Lys Glu Can tell what the base substitution is immediately EXAM If given a question like which of the following amino acids could not be specified with a mutation in the following codon we should be able to eliminate them by looking in the supplied codon table End of discussion of base substitution mutations Frameshift Mutations Technically speaking a frameshift mutation involves the addition or removal of a number of bases that are not divisible by 3 Easier to think about inserting or deleting one or two bases or four or five as long as it isn t divisible by three o Anything larger will be covered later o Frameshift refers to just a few o EXAM If he gives a question about deleting or adding bases one or two will be a frameshift larger numbers will be something else We are talking about heritable mutations Here they are the addition or removal of a number of bases not divisible by three What we mean by insertions and deletions is the addition or removal of large chunks Frameshifts are the insertion or deletion of just a few bases o He will be very clear which one he will be talking about Page 1 of 8 weber uiuc edu 22 October 2007 MCB150 Lecture 24 o Something like 1 or 2 additions not 201 If we add or remove one or two bases we change the entire reading frame The reading frame is shifted to the right or the left The interpretation of the sequence no longer makes sense from the point of mutation downstream Everything upstream is unaffected Everything else from the point of the mutation no longer makes sense Truncation get a premature stop codon This is usually what happens with frame shifts Frameshift Example See the notes for the long sequence of codons The blue is the coding strand the red the mRNA the gold is the protein the polypeptide sequence In this example o What happens if in the diagram the ACCGAC becomes ACCCGAC o Met Thr Asp Glu Met Thr Arg Arg o We have dramatically changed the first AND EVERY FOLLOWING amino acid Everything after the mutation point is changed o Look at the green NTPs and amino acids in the sequence at the bottom A major shift Also there is now a STOP codon that has popped out o The STOP UAG was in the sequence all along but they were not read as a STOP because we had the correct reading frames o When the shift happened a stop was suddenly in the frame The protein terminates prematurely o The protein is truncated early Truncation is almost always the consequence of a frameshift mutation Divisible by Three Deletions Why is divisible by three important What would be the effect of removing three bases in a row You remove a single codon If you remove three bases you delete one amino acid However everything else would be accounted for The frame is still aligned where it should be it is just missing a single frame amino acid Would this be a frame shift o Yes but By the strictest definition a frameshift means that you have changed the reading frame from that point downstream By deleting a multiple of three we have not actually shifted the frame at all o By the strictest of definitions this isn t a frameshift The problem is we don t have any other location for putting this minor example This type of mutational event will be lumped into the category of frameshifts even though the frame hasn t changed It just isn t big enough to be considered a deletion o Even though this is a deletion it isn t by the strictest of definitions a true frameshift o However it will be considered a frameshift mutation for naming purposes What if you take three bases out but they span two different codons Page 2 of 8 weber uiuc edu 22 October 2007 MCB150 Lecture 24 o Ask what would the effect be o Mostly because of degeneracy you can span two codons but you d still only lose one amino acid You re right back where you start from then o Note that in this discussion the loss of three bases is coming at the edge of the frame The loss could be mid codon but will still be lumped in here Our working definition is that a loss of three bases is still a frameshift Cystic Fibrosis If we have a protein that has hundreds or thousand amino acids does it matter if we lose only one Here is an example CFTR is a transmembrane conductance protein an ion pump that helps move Chloride ions out of the cytoplasm to the outside of the cell to maintain proper osmotic balance in the cell The mutation in CFTR that causes cystic fibrosis is the result of a faulty protein that throws off the osmotic balance of the cell because it was supposed to be exporting chlorine Instead the cell draws in water causing the mucous layer to get thicker and thicker 70 of people who are homozygous for this mutation CF cases are due to the loss of a phenylalanine at AA508 This is a case of missing one protein out of 1400 amino acids o The result is a mis folded protein o The result is accumulation of Cl in the cell o The cell compensates by drawing in water instead of disposing the Cl to the mucus layer The mucus then gets thicker and denser o This interferes with respiration digestion etc Most CF people are sterile and die by 30 because they cannot maintain osmotic balance Why would natural selection not eliminated cystic fibrosis o Carriers heterozygous carriers of the CF mutation the mutation helps make you more resistant to bacterial infections because they tend to produce a greater quantity of mucous This is heritable because the carrier is heterozygous not