Section 9 Junaid Malek, M.D.
Mutation Objective: Understand how mutations can arise, and how beneficial ones can alter populations Mutation= a randomly produced, heritable change in the nucleotide sequence of a genome Three types of mutations-neutral, deleterious, and beneficial Case study: bacteria and antibiotic resistance
How Mutations Occur Mutations in cells are usually a result of rare mistakes made during DNA replication or of a failure in DNA repair following DNA damage Eukaryotic cells have many checks in place to prevent mutations from occurring Proof-reading by DNA Polymerase: The eukaryotic genome is replicated by DNA polymerase. After inserting each new base, DNA polymerase goes back and checks whether it has put the right base in. If it hasn t, it removes the errant base out and tries again. Mismatch repair: Incorrect base pairs are occasionally inserted into DNA during replication (remember tautomerization of nucleotides can give rare structural isomers). This produces a bulge in the double-helix that is recognized by proteins of the mismatch repair system. The incorrect base is cut out of the DNA and the resulting gap is replaced with the correct base pair by DNA polymerase.
Mutation and HIV The RNA genome of HIV is replicated by Reverse Transcriptase (RT), which compared to DNA Pol is a fairly sloppy enzyme It has no proof-reading function and mismatch repair does not occur During reverse transcription of the viral RNA into DNA the chance of making a mutation at any given base is roughly 1 in 30,000 In contrast, the rate of mutation for replication of cellular DNA it is somewhere between one in a billion and one in 10 billion It is HIV s high rate of mutation that makes AIDS such a difficult disease to cure
Question A mutation is produced in an HIV virus that compromises the activity of integrase such that the enzyme has 100X less activity Is this mutation beneficial, deleterious or neutral for the virus? Will it take over the population of viruses?
Combination therapy and HIV mutation Combination therapy requires two simultaneous mutations to produce resistance, a very rare event Remember the example of throwing dice
Combination therapy and HIV mutation
Equilibrium vs. Steady State Equilibrium Forward rate = Backward rate Forward reaction = Backward reaction Catalysis changes rate, but not balance Steady State Forward rate = Backward rate Forward reaction Backward reaction Catalysis changes rate AND balance G = 0 G < 0 No energy input needed Continuous energy input needed
Equilibrium vs. Steady State Key concept is to understand why steady states require the continual input of energy, and how altering the kinetics of processes can greatly alter steady states Many biological processes need to be maintained in a narrow range to be compatible with life The balance or steady state that is created is often far from its equilibrium and in order to keep it there energy is necessary Cells must harvest energy from their environment to maintain steady state If a biological reaction is allowed to reach its equilibrium it often equals death
Evolution and the Central Dogma Today: DNA makes RNA makes protein; reverse transcriptase as an anomaly First: RNA as information carrier and catalyst (remnants: self splicing RNA & RNA active site in ribosome) Second: Ribosomal protein synthesis allow proteins to emerge as catalysts, regulators, & structural elements Third: DNA evolved as stable, specialized, information repository Key to the evolution is to reproduce successfully and leave lots of prodigy We don t really exactly know how that was achieved when life was first evolving
Diseases and Darwinian Evolution Key concept is to understand how diseases and DNA and protein sequences provide strong evidence for Darwinian evolution The sequences of DNA and especially proteins demonstrate the existence of deep, common ancestors Evolution is visible on short time scales (DDT and antibiotic resistance) and within individuals (e.g. AIDS and cancer patients)
Question Q: Why is genetic variability beneficial for a species? A: It enhances the species ability to adapt to changing conditions Q: Why then, does a cell go to great lengths to assure the fidelity of DNA replication? A: The answer lies in the need for a cell to maintain a balance between stability and change. If the mutation rate were too high, a species would eventually die out because all of its individuals would accumulate too many mutations in genes essential for survival. For a species to be successful-in evolutionary terms-it is important for individual members to have good genetic memory (fidelity in DNA replication), but also to introduce occasional variations. If the change leads to an improvement, it will persist by selection; if it proves disastrous, the individual organism that was the unfortunate subject of nature s experiment will die- not the entire population.
Cancer Cancer= disease caused by abnormal and uncontrolled cell division Cell growth= an increase in the mass of a cell Cell proliferation= an increase in cell number Tumor= mass of cells that have grown and divided where they shouldn t have Benign cancer= confined to one part of the body Malignant cancer= some of their cells escape from the original site, enabling them to migrate to other sites and establish secondary tumors (=metastases)
Germ Cells vs. Somatic Cells Evolutionary purpose: to pass genetic material to as many progeny as possible Germ line: eggs, sperm, and the cells that give rise to them All cells except egg and sperm are diploid (egg and sperm are haploid) Germ-line mutation rate: 75 mutations per genome per human generation, roughly 4 in non-junk DNA Soma: all other cells Soma supports germ line because germ-line and somatic cells are genetically identical Somatic mutations: most innocuous, a small fraction can give rise to cancer
Question Could a spontaneous mutation in a germ line cell be passed on to an organism s prodigy? Could a spontaneous mutation in a soma cell be passed on to an organism s prodigy?
Cell Growth, Proliferation & Death Key concept is to understand how multicellular organisms enforce strict rules governing cell growth, proliferation, and death Human body: a cooperative of more than 100 cell types Proliferation and death of each cell type must be carefully regulated Proliferation is regulated by matching supply and demand: small imbalances could lead to long term problems Most cells in the human body are neither growing nor proliferating and if they are, they obey strict rules Cancer cells ignore these rules to allow them to grow and proliferate out of control
Question Q: About 10 16 cell divisions take place during a lifetime, yet an adult human body consists of only about 10 13 cells. Why are these two numbers so different? A: Every cell division generates one additional cell; so if the cells were never lost or discarded from the body, the number of cells in the body should equal the number of divisions plus one. The number of divisions is 1000-fold greater than the number of cells because, in the course of a lifetime, 1000 cells are discarded and replaced for every cell that is retained in the body.
Mutation and Cancer Cancer is an evolutionary disease- it arises because a cell accumulates mutations that alter its behavior in a way that allow it to eventually proliferate uncontrollably Best defense against cancer is to allow as few mutations to occur as possible Most deleterious human mutations are recessive to the wild type form of the gene Number of mutations can be estimated from analyzing: 1) dependence of cancer incidence on age and 2) tracking down and counting important mutations in cancer cells Cancer has not been selected against because it occurs too late in human life
Mutation and Cancer Cancer cells differ from normal cells in multiple ways: 1) Grow and proliferate when they should not 2) Ignore instructions to commit suicide (apoptosis) 3) Induce blood vessel growth 4) Metastasize: enter blood vessels, exit, and establish tumors at new sites 5) Genetic instability (increased point mutation, chromosome breakage or loss)
Environment, Genetic Factors and Cancer Cancer rates show wide geographic variation & population migrations cause changes in cancer rates Conclusion: important environmental factors play a major role in setting population cancer rates Consider lung cancer: Heavy smokers or industrial workers exposed for a limited time to a chemical carcinogen that induces mutations in DNA do not usually begin to develop cancers characteristic of their habit or occupation until 10, 20, or even more years after the exposure. Why the delay? During exposure to the carcinogen, mutations are induced, but the number of relevant mutations in any one cell is usually not enough to convert it directly into a cancer cell. Over the years, the cells accumulate progressively more mutations until one eventually turns into a cancer cell.
Environment, Genetic Factors and Cancer Consider sex hormones: High levels of the female sex hormone estrogen can increase the incidence of some forms of cancer. Further, male transsexuals who use estrogen preparations to give themselves a female appearance have an increased risk of breast cancer. High levels of androgens (male sex hormones) also increase the risk of some other forms of cancer, such as cancer of the prostate. Can one infer that estrogens and androgens are mutagenic? By definition, a carcinogen is any substance that promotes the occurrence of one or more types of cancer. The sex hormones can therefore be classified as naturally occurring carcinogens. While most carcinogens act by directly causing mutations, carcinogenic effects are also exerted in other ways. The sex hormones increase both the rate of cell division and the number of cells in hormone sensitive organs such as breast, uterus, and prostate. The first effect increases the mutation rate per cell; the second effect increases the number of cells at risk.
Known Genetic Mutations Associated with Cancer Rare, strong mutations strongly predispose individuals to cancer Examples: HNPCC (mismatch repair defective), adenomatous polyposis coli (APC) HNPCC (increased frequency of point mutations) APC (increased chromosome loss)