1. Welcome to Genetics: Unit 8 Seminar! Please feel free to chat with your classmates! 1

2. Agenda Brief Review of Unit Material Self Assessment Questions Question 2

3. 12 Molecular Mechanisms of Mutation and DNA Repair

4. 4 Mutations A mutation is any heritable change in the genetic material Mutations are classified in a variety of ways Most mutations are spontaneous: they are random, unpredictable events Each gene has a characteristic rate of spontaneous mutation, measured as the probability of a change in DNA sequence in the time span of a single generation

5. 5 Table 12.1

6. 6 Mutations Rates of mutation can be increased by treatment with a chemical mutagen or radiation, in which case the mutations are said to be induced Mutations in cells that form gametes are germ-line mutations; all others are somatic mutations Germ-line mutations are inherited; somatic mutations are not A somatic mutation yields an organism that is genotypically a mixture (mosaic) of normal and mutant tissue

7. 7 Mutations Among the mutations that are most useful for genetic analysis are those whose effects can be turned on or off by the researcher These are conditional mutations: they produce phenotypic changes under specific (permissive conditions) conditions but not others (restrictive conditions) Temperature-sensitive mutations: conditional mutation whose expression depends on temperature

8. 8 Mutations Mutations can also be classified according to their effects on gene function:  A loss-of-function mutation (a knockout or null) results in complete gene inactivation or in a completely nonfunctional gene product  A hypomorphic mutation reduces the level of expression of a gene or activity of a product  A hypermorphic mutation produces a greater-than-normal level of gene expression because it changes the regulation of the gene so that the gene product is overproduced  A gain-of-function mutation qualitatively alters the action of a gene. For example, a gain-of-function mutation may cause a gene to become active in a type of cell or tissue in which the gene is not normally active.

9. 9 Mutations Mutations result from changes in DNA A base substitution replaces one nucleotide pair with another Transition mutations replace one pyrimidine base with the other or one purine base with the other. There are four possible transition mutations

10. Discussion Question 1 10 Please give an example of a transition mutation?

11. Discussion Question 1 11 Please give an example of a transition mutation? G -> A; purine -> purine C -> T; pyrimidine -> pyrimidine

12. 12 Mutations Transversion mutations replace a pyrimidine with a purine or the other way around. There are eight possible transversion mutations Spontaneous base substitutions are biased in favor of transitions: Among spontaneous base substitutions, the ratio of transitions to transversions is approximately 2:1

13. Discussion Question 2 Please give an example of a transversion mutation? 13

14. Discussion Question 2 Please give an example of a transversion mutation? G -> T; purine -> pyrimidine C -> A; pyrimidine -> purine 14

15. 15 Mutations Mutations in protein-coding regions can change an amino acid, truncate the protein, or shift the reading frame: Missense or nonsynonymous substitutions result in one amino acid being replaced with another Synonymous or silent substitutions in DNA do not change the amino acid sequence Silent mutations are possible because the genetic code is redundant

16. 16 Mutations A nonsense mutation creates a new stop codon Frameshift mutations shift the reading frame of the codons in the mRNA Any addition or deletion that is not a multiple of three nucleotides will produce a frameshift

17. 17 Sickle-cell anemia The molecular basis of sickle-cell anemia is a mutant gene for  -globin The sickle-cell mutation changes the sixth codon in the coding sequence from the normal GAG, which codes for glutamic acid, into the codon GUG, which codes for valine Sickle-cell anemia is a severe genetic disease that often results in premature death The disease is very common in regions where malaria is widespread because it confers resistance to malaria

18. What is sickle cell anemia? (cont’d) 18

19. 19 Transposable Elements In a 1940s study of the genetics of kernel mottling in maize, Barbara McClintock discovered a genetic element that could move (transpose) within the genome and also caused modification in the expression of genes at or near its insertion site Since then, many transposable elements (TEs) have been discovered in prokaryotes and eukaryotes n-equals-one.com

20. 20 Transposable Elements The genomes of most organisms contain multiple copies of each of several distinct families of TEs Once situated in the genome, TEs can persist for long periods and undergo multiple mutational changes Approximately 50 % of the human genome consists of TEs; most of them are evolutionary remnants no longer able to transpose staff.jccc.net

21. 21 Transposable Elements TEs can cause mutations by insertion or by recombination In Drosophila, about half of all spontaneous mutations that have visible phenotypic effects result from insertions of TEs Genetic aberrations can also be caused by recombination between different (nonallelic) copies of a TE

22. 22 Spontaneous Mutations Mutations are statistically random events — there is no way of predicting when, or in which cell, a mutation will take place The mutational process is also random in the sense that whether a particular mutation happens is unrelated to any adaptive advantage it may confer on the organism in its environment A potentially favorable mutation does not arise because the organism has a need for it

23. 23 Mutation Hot Spots Mutations are nonrandom with respect to position in a gene or genome Certain DNA sequences are called mutational hotspots because they are more likely to undergo mutation than others For instance, sites of cytosine methylation are usually highly mutable

24. 24 Mutagenes Almost any kind of mutation that can be induced by a mutagen can also occur spontaneously, but mutagens bias the types of mutations that occur according to the type of damage to the DNA that they produce

25. 25 DNA Repair Mechanisms Many types of DNA damage can be repaired Mismatch repair fixes incorrectly matched base pairs The AP endonuclease system repairs nucleotide sites at which the base has been lost Special enzymes repair damage caused to DNA by ultraviolet light Excision repair works on a wide variety of damaged DNA Postreplication repair skips over damaged bases

26. 26 Mismatch Repair Mismatch repair fixes incorrectly matched base pairs: a segment of DNA that contains a base mismatch excised and repair synthesis followed The mismatch-repair system recognizes the degree of methylation of a strand and preferentially excises nucleotides from the undermethylated strand This helps ensure that incorrect nucleotides incorporated into the daughter strand in replication will be removed and repaired.

27. 27 Mismatch Repair The daughter strand is always the undermethylated strand because its methylation lags somewhat behind the moving replication fork Fig. 12.27

28. 28 Mismatch Repair The most important role of mismatch repair is as a “last chance” error- correcting mechanism in replication Fig. 12.26

29. 29 AP Repair Deamination of cytosine creates uracil which is removed by DNA uracil glycosylase from deoxyribose sugar. The result is a site in the DNA that lacks a pyrimidine base (an apyrimidinic site) Purines in DNA are somewhat prone to hydrolysis, which leave a site that is lacking a purine base (an apurinic site) Both apyrimidinic and apurinic sites are repaired by a system that depends on an enzyme called AP endonuclease

30. 30 Fig. 12.28

31. 31 Excision Repair Excision repair is a ubiquitous, multistep enzymatic process by which a stretch of a damaged DNA strand is removed from a duplex molecule and replaced by resynthesis using the undamaged strand as a template Fig. 12.29

32. 32 Postreplication repair Sometimes DNA damage persists rather than being reversed or removed, but its harmful effects may be minimized. This often requires replication across damaged areas, so the process is called postreplication repair Fig. 12.30

33. 33 Ames test In view of the increased number of chemicals used and present as environmental contaminants, tests for the mutagenicity of these substances has become important Furthermore, most agents that cause cancer (carcinogens) are also mutagens, and so mutagenicity provides an initial screening for potential hazardous agents A genetic test for mutations in bacteria that is widely used for the detection of chemical mutagens is the Ames test

34. 34 Ames test In the Ames test for mutation, histidine-requiring (His - ) mutants of the bacterium Salmonella typhimurium, containing either a base substitution or a frameshift mutation, are tested for backmutation reversion to His + In addition, the bacterial strains have been made more sensitive to mutagenesis by the incorporation of several mutant alleles that inactivate the excision- repair system and that make the cells more permeable to foreign molecules

35. 35 13 Molecular Genetics of Cell Cycle and Cancer

36. 36 There are two major parts in the cell cycle: Interphase: G 1 = gap1S = DNA synthesis G 2 = gap2 Mitosis: M There are two essential functions of the cell cycle:  To ensure that each chromosomal DNA molecule is replicated only once per cycle  To ensure that the identical replicas of each chromosome are distributed equally to the two daughter cells The Cell Cycle

37. 37 The Cell Cycle The cell cycle is under genetic control A fundamental feature of the cell cycle is that it is a true cycle: it is not reversible Many genes are transcribed during the cell cycle just before their products are needed Mutations affecting the cell cycle have helped to identified the key regulatory pathways

38. 38 Key Mutational Targets Many cancers are the result of alterations in cell cycle control, particularly in control of the G1-to-S transition These alterations also affect apoptosis through their interactions with p53 The major mutational targets for the multistep cancer progression are of two types: Proto-oncogenes Tumor-suppressor genes

39. 39 Key Mutational Targets The normal function of proto-oncogenes is to promote cell division or to prevent apoptosis The normal function of tumor-suppressor genes is to prevent cell division or to promote apoptosis

40. 40 Oncogenes Oncogenes are derived from normal cellular genes called proto-oncogenes Oncogenes are gain-of-function mutations associated with cancer progression Oncogenes are gain-of-function mutations because they improperly enhance the expression of genes that promote cell proliferation or inhibit apoptosis

41. 41 Tumor-Suppressor Genes Tumor-suppressor genes normally negatively control cell proliferation or activate the apoptotic pathway Loss-of-function mutations in tumor-suppressor genes contribute to cancer progression.

42. Questions? 42