Enduring Understanding 3.C The processing of genetic information is

1. BIG IDEA IIILiving systems store, retrieve, transmit and respond to information essential to life processes. Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation. Essential Knowledge 3.C.1 Changes in genotype can result in changes in phenotype.

2. Essential Knowledge 3.C.1: Changes in genotype can result in changes in phenotype. • Learning Objectives: • (3.24) The student is able to predict how a change in genotype, when expressed as a phenotype, provides a variation that can be subject to natural selection. • (3.25) The student is able to create a visual representation to illustrate how changes in a DNA nucleotide sequence can result in a change in the polypeptide produced. • (3.26) The student is able to explain the connection between genetic variations in organisms and phenotype variations in populations.

3. Alterations in a DNA sequence can lead to changes in the type of amount of the protein produced and the consequent phenotype. • A mutation is any change in the genetic information of a cell (or virus). Mutations are the primary source of genetic variation. • Mutations may involve large portions of a chromosome or affect just one base pair of nucleotides. • DNA mutations can be positive, negative or neutral based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein. • If the mutation is in a cell that gives rise to a gamete, it may be passed on to offspring.

4. Types of DNA Mutations • Point mutations can are chemical changes in just one base pair of a gene. • The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein.

5. Types of Point Mutations • Point mutations within a gene can be divided into two general categories: • Base-pair substitutions • Base-pair insertions or deletions

6. Fig. 17-23 http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter11/animation_quiz_4.html Wild-type DNA template strand 3 5 3 5 mRNA 5 3 Protein Stop Amino end Carboxyl end A instead of G Extra A 5 3 5 3 5 5 3 3 U instead of C Extra U 5 5 3 3 Stop Stop Silent (no effect on amino acid sequence) Frameshift causing immediate nonsense (1 base-pair insertion) T instead of C missing 3 3 5 5 5 5 3 3 A instead of G missing 5 3 5 3 Stop Missense Frameshift causing extensive missense (1 base-pair deletion) missing A instead of T 5 3 5 3 5 3 5 3 U instead of A missing 5 3 5 3 Stop Stop Nonsense No frameshift, but one amino acid missing (3 base-pair deletion) (a) Base-pair substitution (b) Base-pair insertion or deletion

7. Errors in DNA replication or repair mechanisms and external factors can cause random changes (mutations) in the DNA. • Mutations can occur in a number of ways. • Spontaneous mutations include base-pair substitutions, insertions, deletions and longer mutations that occur during DNA replication, repair, or recombination. • Physical agents, such as X-rays and UV light, and various chemical agents that cause mutations are called mutagens. • Whether or not a mutation is detrimental, beneficial or neutral depends on the environmental context.

8. Errors in mitosis or meiosis can result in changes in phenotype. • Nondisjunction occurs when a pair of homologous chromosomes does not separate properly in meiosis I or sister chromatids do not separate in meiosis II. • As a result, a gamete receives either two or no copies of that chromosome. • A zygote formed with one of these aberrant gametes has a chromosomal alteration known as aneuploidy, a non-typical number of a particular chromosome. This can include trisomy (2n+1) or monosomy (2n-1). • Changes in chromosome number often result in new phenotypes, including sterility caused by triploidy and increased vigor of other polyploids. • Changes in chromosome number often result in human disorders with developmental limitations, including Trisomy 21 (Down syndrome) and XO (Turner syndrome).

9. Fig. 15-13-3 Meiosis I Nondisjunction Meiosis II Nondisjunction Gametes n – 1 n + 1 n – 1 n n n + 1 n + 1 n – 1 Number of chromosomes (b) Nondisjunction of sister chromatids in meiosis II (a) Nondisjunction of homologous chromosomes in meiosis I

10. Alterations of Chromosome Number • Polyploidy is a condition in which an organism has more than two complete sets of chromosomes • Triploidy (3n) is three sets of chromosomes • Tetraploidy (4n) is four sets of chromosomes • Polyploidy is common in plants, but not animals • Polyploids are more normal in appearance than aneuploids

11. New Phenotypes Can Arise from Changes in Chromosome Number • Sterility can be caused by triploidy: • An extra X chromosome in a male (XXY) produces a disorder known as Klinefelter. These individuals have male sex organs, but the testes are abnormally small and the man is sterile. • Increased vigor can be seen in some polyploids: • A common example in plants is the observation of hybrid vigor whereby the polyploid offspring of two diploid individuals is more vigorous and healthy than either of the two diploid parents.

12. Human Disorders Due to Chromosomal Alterations • Alterations of chromosome number and structure are associated with some serious disorders. • Some types of aneuploidy appear to upset the genetic balance less than others, resulting in individuals surviving to birth and beyond. • These surviving individuals have a set of symptoms, or syndrome, characteristic of the type of aneuploidy.

13. Fig. 15-16

14. Aneuploidy of Sex Chromosomes • Nondisjunction of sex chromosomes produces a variety of aneuploid conditions: • Klinefelter syndrome is the result of an extra chromosome in a male, producing XXY individuals. • Monosomy X, called Turner syndrome, produces X0 females, who are sterile; it is the only known viable monosomy in humans.

15. Monosomy X – Turner Syndrome XO individuals are phenotypically female, but their sex organs do not mature at adolescence, and they are sterile. Most have normal intelligence.

16. Alterations of Chromosome Structurehttp://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter15/changes_in_chromosome_structure.html • Breakage of a chromosome can lead to four types of changes in chromosome structure:

17. Disorders Caused by Structurally Altered Chromosomes • The syndrome cri du chat (“cry of the cat”), results from a specific deletion in chromosome 5: • A child born with this syndrome is mentally retarded and has a catlike cry; individuals usually die in infancy or early childhood.

18. Translocation Associated with Chronic Myelogenous Leukemia (CML) Reciprocal translocation Normal chromosome 9 Translocated chromosome 9 Translocated chromosome 22 (Philadelphia chromosome) Normal chromosome 22

19. Changes in genotype may affect phenotypes that are subject to natural selection. • Genetic changes that enhance survival and reproduction can be selected by environmental conditions. • Selection results in evolutionary change. • Illustrative examples include: • Antibiotic Resistance Mutations • Pesticide Resistance Mutations • Sickle Cell Disorder and Heterozygous Advantage • Bozeman #33: http://www.bozemanscience.com/ap-biology/

20. BIG IDEA IIILiving systems store, retrieve, transmit and respond to information essential to life processes. Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation. Essential Knowledge 3.C.2 Biological systems have multiple processes that increase genetic variation.

21. Essential Knowledge 3.C.2: Biological systems have multiple processes that increase genetic variation. • Learning Objectives: • (3.27) The student is able to compare and contrast processes by which genetic variation is produced and maintained in organisms from multiple domains. • (3.28) The student is able to construct an explanation of the multiple processes that increase variation within a population.

22. The imperfect nature of DNA replication and repair increases variation. • Initial pairing errors in nucleotide placement may occur as often as 1 per 100,000 base pairs. • The amazing accuracy of DNA replication (one error in ten billion nucleotides) is achieved as DNA polymerases check each newly added nucleotide against its template and remove incorrect nucleotides. • While the DNA proofreading and repair mechanisms are highly accurate, sometimes errors in DNA replication are not detected. These errors (mutations) can increase variation among individuals of the same species and, in some cases, can be selected for among individuals in a population. • In Darwin’s theory of evolution by natural selection, genetic variations present in a population result in adaptation as the individuals with the variations best suited to an environment produce the most offspring.

23. The methods of horizontal acquisition of genetic information in prokaryotes increase variation. • Transformation (the uptake of foreign DNA from the surrounding environment). • Conjugation (the direct transfer of genes from one prokaryote to another). • Transduction (the transfer of genes from one prokaryote to another via a viral vector). • Transposition (movement of DNA segments within and between DNA molecules).

24. Transformation | Transduction | Conjugation

25. R Plasmids and Antibiotic Resistance • R plasmids carry genes for antibiotic resistance. • Antibiotics select for bacteria with genes that are resistant to the antibiotics. • Antibiotic resistant strains of bacteria are becoming more common. • Exposing a bacterial population to a specific antibiotic, will kill antibiotic-sensitive bacteria but not those that happen to have R plasmids with genes that confer antibiotic resistance.

26. Antibiotic Resistance and the R Plasmid

27. Transposonshttp://www.youtube.com/watch?v=6vWrxt1ZCUY • Stretches of DNA that can move about within a genome through a process called transposition are called transposable genetic elements, or transposable elements. • Transposons move about a genome as a DNA intermediate, either by a “cut-and-paste” or a “copy-and-paste” mechanism. • Read Article: Barbara McClintock & Mobile Genetic Elements

28. Sexual reproduction mechanisms involving gamete formation in eukaryotes serve to increase genetic variation. • Reproduction processes that increase genetic variation are evolutionarily conserved and are shared by various organisms. These processes include: • Crossing over during meiosis • Random assortment of chromosomes during meiosis. • Fertilization

29. BIG IDEA IIILiving systems store, retrieve, transmit and respond to information essential to life processes. Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation. Essential Knowledge 3.C.3 Viral replication results in genetic variation, and viral infection can introduce genetic variation into the hosts.

30. Essential Knowledge 3.C.3: Viral replication results in genetic variation, and viral infection can introduce genetic variation into the hosts. • Learning Objectives: • (3.29) The student is able to construct an explanation of how viruses introduce genetic variation in host organisms. • (3.30) The student is able to use representations and models to describe how viral replication introduces genetic variation in the viral population.

31. The basic structure of viruses includes a protein capsid that surrounds and protects the genetic information (DNA or RNA). • Viruses are not cells. • Viruses are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope. • Viral genomes may consist of either: • Double- or single-stranded DNA, or • Double- or single-stranded RNA • Depending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus.

32. Fig. 19-3 RNA Membranous envelope Head DNA RNA DNA Capsomere Capsid Tail sheath Tail fiber Capsomere of capsid Glycoproteins Glycoprotein 18  250 nm 70–90 nm (diameter) 80  225 nm 80–200 nm (diameter) 20 nm 50 nm 50 nm 50 nm (a) Tobacco mosaic virus (b) Adenoviruses (d) Bacteriophage T4 (c) Influenza viruses

33. Viral replication differs from other reproductive strategies and generates variation via various mechanisms. • Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes: • They replicate via a component assembly model allowing one virus to produce many progeny (lytic cycle). • Viral replication allows for mutations to occur through usual host pathways. • Some viruses lack replication error-checking mechanisms, and thus have higher rates of mutation. • Related viruses can combine/recombine if they infect the same host cell. • Some viruses can integrate into host DNA and establish latent (lysogenic) infection – can result in new properties for host cell.

34. Fig. 19-4 VIRUS Entry and uncoating 1 DNA Capsid Transcription and manufacture of capsid proteins 3 Replication 2 HOST CELL Viral DNA mRNA Capsid proteins Viral DNA Self-assembly of new virus particles and their exit from the cell 4

35. Reproductive Cycles of Phages

36. Fig. 19-5-5 Attachment 1 2 Entry of phage DNA and degradation of host DNA 5 Release Phage assembly 4 Assembly 3 Synthesis of viral genomes and proteins Head Tail Tail fibers

37. Fig. 19-6 Daughter cell with prophage Phage DNA The phage injects its DNA. Cell divisions produce population of bacteria infected with the prophage. Phage DNA circularizes. Phage Bacterial chromosome Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle. Lytic cycle Lysogenic cycle The bacterium reproduces, copying the prophage and transmitting it to daughter cells. The cell lyses, releasing phages. Lytic cycle is induced Lysogenic cycle is entered or Prophage Phage DNA integrates into the bacterial chromosome, becoming a prophage. New phage DNA and proteins are synthesized and assembled into phages.

38. The reproductive cycles of viruses facilitate transfer of genetic information. • During infection, some viruses introduce variation into the host genome in the form of DNA or RNA. • When the host cell is bacterial, it is referred to as lysogenesis; whereas in eukaryotic cells, this is referred to as transformation. • Since viruses use the host metabolic pathways, they experience the same potential as the host for genetic variation that results from DNA metabolism. • Illustrative examples include: • Transduction in Bacteria • Transposons present in incoming DNA

39. Generating Genetic Variation via Lysogenic Infections • Viral replication often allows for mutations to occur through usual host mechanisms. • While many prophage genes are silenced as a viral genome “hides” in the host cell during a latent infection, other prophage genes may be expressed during lysogeny. • Expression of these genes may alter the host’s phenotype.

40. RNA Viruses • Often times, the viruses that infect animals are RNA viruses (retroviruses). • Retroviruses are RNA viruses that are equipped with an enzyme called reverse transcriptase, which transcribes an RNA template into DNA, providing an RNADNA information flow, the opposite of the usual direction. • RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation.

41. Fig. 19-8 https://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter24/animation__hiv_replication.html Viral envelope Glycoprotein Capsid RNA (two identical strands) Reverse transcriptase HIV Membrane of white blood cell HIV HOST CELL Reverse transcriptase Viral RNA RNA-DNA hybrid 0.25 µm DNA HIV entering a cell NUCLEUS Provirus Chromosomal DNA RNA genome for the next viral generation mRNA New virus New HIV leaving a cell

42. Emerging Viruses • Emerging viruses are those that appear suddenly or suddenly come to the attention of scientists • Severe acute respiratory syndrome (SARS) recently appeared in China • Outbreaks of “new” viral diseases in humans are usually caused by existing viruses that expand their host territory

43. Absence of Replication Error-Checking Mechanisms • RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation. • This often leads to emerging viruses and epidemics within populations. • An error in replicating the genome of an RNA virus is not corrected by proofreading. • Some mutations change existing viruses into new genetic varieties that can cause disease.

44. Emerging Viruses

45. Fig. 19-UN1 The phage attaches to a host cell and injects its DNA Phage DNA Bacterial chromosome Prophage Lytic cycle Lysogenic cycle • Virulent or temperate phage • Destruction of host DNA • Production of new phages • Lysis of host cell causes release • of progeny phages • Temperate phage only • Genome integrates into bacterial • chromosome as prophage, which • (1) is replicated and passed on to • daughter cells and • (2) can be induced to leave the • chromosome and initiate a lytic cycle