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PART II CONTINUITY AND EVOLUTION OF ANIMAL LIFE 5 Genetics: A Review 6 Organic Evolution 7 The Reproductive Process 8 Principles of Development CHAPTER 5 GENETICS: A REVIEW CHAPTER OUTLINE 5.1. A Code for All Life A. History of Central Tenets of Genetics 1. Mendel described particulate inheritance. 2. Watson and Crick described nature of the coded instructions. 3. Evolutionary theory is based on common ancestral groups; genetics establishes this lineage. 4. Genes guide the organization and orderly sequence of differentiation. 5. Genetics accounts for resemblance, fidelity of reproduction, and variation. 6. Genetics is a major unifying concept of biology. 5.2. Mendel’s Investigations (Figure 5.1) A. Gregor Mendel conducted his plant breeding experiments from 1856–1864. B. His discoveries were published in 1866, but not appreciated until 1900, 16 years after his death. C. Genes and chromosomes were as yet unknown; his experiments were based on crossbreeding. 1. Mendel carefully controlled pollination of pea plant stigmas by stamens. 2. Mendel carefully documented offspring of different parents (hybrids) and then crossed the hybrids. 5.3. Chromosomal Basis of Inheritance a. Germ cells (gametes) were recognized as providing genetic information to offspring. b. Nuclei of germ cells, especially chromosomes, were suspected of being the hereditary material. A. Meiosis: Reduction Division of Gametes (Figure 5.2) 1. In all animals, each body cell has two homologous chromosomes; each homolog came from a separate parent. However, animal species differ greatly in the number of chromosomes they have. 2. Following DNA replication, meiosis occurs. Meiosis involves two rounds of cell division that results in gametes that each contain one chromatid from each homologous pair. 3. Body cells are diploid (containing two sets of chromosomes). Gametes are haploid (containing a single set). Fertilization (fusion of two gametes) results in a diploid zygote. 4. The diploid (2n) number in humans is 46 chromosomes; gametes are haploid with 23. 5. In an organism’s diploid cells, there are two genes for each trait. Each gene is l;ocated on a separate homologous chromosome. 6. Alternative forms of a gene are called alleles; one or both may have an effect on a trait and either may be passed on to offspring. 7. “Multiple alleles” is a condition whereby numerous allelic forms of a gene exist among individuals of a population. 8. Most unique features of meiosis occur in prophase of first meiotic division. a. Homologous chromosomes align side-by-side to form a bivalent. The 4 strands of the bivalent are held together by neiosis-specific cohesion proteins collectively called the synaptonemal complex. b. Each chromosome has already replicated to form two chromatids, joined at the centromere. c. The complex of four future chromosomes is a tetrad. d. The location of any one gene on a chromosome is the gene locus. e. In side-by-side contact (synapsis), the gene loci on a chromosome align. f. In preparation for division, the centromeres holding chromatids together do not divide; the dyads are pulled to each pole. g. At end of first meiotic division, daughter cells contain one of each homologous chromosome (each consisting as a dyad of sister chromatids joined by a centromere). h. At end of second meiotic division, dyads are split and each daughter cell contains one haploid set and one allele of each gene. B. Sex Determination (Figures 5.3, 5.4) 1. McClung, in 1902, studied insects within the order Hemiptera (true bugs). a. Half the sperm lacked one chromosome found in the other half and in all eggs. b. When the sperm with the full number fertilized an egg, a female resulted; when a sperm lacking one chromosome fertilized an egg, it produced a male. c. Sex chromosomes were those that determined sex; autosomes were the remainder. d. The bug’s sex determination system is called XX-XO indicating the missing chromosome as “O.” e. Humans and many others use an XX-XY system; the male has the different sex chromosomes. f. Birds, moths, butterflies, and some fish use an XX (or ZZ) –XY (or ZW) system, in which the female is the heterogametic (ZW) sex. g. Some animals across many taxa use environmental and behavioral conditions rather than sex chromosomes. 5.4. Mendelian Laws of Inheritance A. Mendel’s First Law 1. In the law of segregation, during formation of gametes, paired factors segregate independently. a. The phenotype is the visible characteristic. b. Tall and dwarf plants produce tall F1 progeny; hence there is no blending. c. Self-pollinating the F1 progeny produce tall and short plants within the F2 generation in a 3:1 ratio; again there was no blending and this ratio held for crosses of six other traits. 2. Dominance a. Mendel called the tall factor (or allele) dominant. When a tall allele is present, the recessive factor (or allele) is not expressed. b. Recessive traits appear only in the absence of the dominant factor. c. The alleles that represent these factors can be represented by alphabetic symbols. The same letter is often used to represent a locus. Capitalized letters represent dominant alleles. Lower-case letters represent recessive alleles. d. T/t represents the complete genetic constitution of the plant’s traits for height; T and t are the possible gametes. e. T/t and other unlike combinations form a heterozygote. f. T/T and t/t are homozygotes. g. T/T, T/t and t/t are the possible genotypes. h. A cross that considers only one locus is referred to as a monohybrid cross. 3. Punnett Square a. A Punnettt Square is a tool that represents the various combinations of alleles that can result from gametes containing known alleles. b. For example, a Punnett Square demonstrates how a T/t x T/t cross can result in a 3:1 phenotypic ratio of offspring. c. Additional crosses of the progeny demonstrated that one-third of the tall was TT and two-thirds were T/t. d. The short plants, or t/t, always gave rise to short plants when self-fertilized. 4. Testcross a. Products of a monohybrid cross of “pure”-condition tall and short parents produce tall offspring that have both T/t and T/T genotypes. b. To determine whether tall plants are either T/t or T/T, a testcross mates individuals of a dominant phenotype with a “pure”-recessive.. If homozygous (T/T), the testcross yields all tall offspring. If heterozygous (T/t), the testcross yields half tall and half short offspring. 5. Intermediate Inheritance (Figure 5.5) a. Sometimes, neither allele is completely dominant, resulting in intermediate inheritance or incomplete dominance. b. Red and white homozygous four-o-clock flowers cross to form heterozygous pink flowers. c. Chickens with black feathers crossed with splashed white feathered chickens yield blue Andalusian chickens. d. This appears to produce a blending of traits, but additional crosses will reveal the traits are present and still able to be expressed with the appropriate testcross. B. Mendel’s Second Law (Figure 5.6) 1. The law of independent assortment states that genes located on different pairs of homologous chromosomes assort independently during meiosis. a. This law pertains to studies of two pairs of hereditary factors at the same time. b. When tall plants with yellow seeds (both dominant traits) were crossed with dwarf plants with green seeds, the F1 plants were all tall and yellow as expected. c. When the F1 hybrids were self-fertilized, a 9:3:3:1 ratio of tall-yellow, tall-green, dwarf-yellow, and dwarf-green offspring resulted, which is a combination of the two 3:1 ratios for each set or a dihybrid cross. d. Segregation of alleles for plant height was independent of segregation of alleles for seed color. 2. Probability a. All genotypes of gametes of one sex have an equal chance of uniting with all genotypes of gametes of the other sex. b. The probability of two independent events occurring together is the product of their individual probabilities; this is the product rule. (Table 5.1) c. Probability has no “memory.” That is, previous outcomes do not influence future outcomes. C. Multiple Alleles 1. While only two alleles can exist at one locus, more than two types of alleles may exist in a population. 2. For instance, a rabbit may possess two alleles from among four for coat color: C (normal), cch (chinchilla), ch (Himalayan) and c (albino). 3. Multiple alleles arise through mutations at the same locus over time. D. Gene Interaction 1. Polygenic inheritance is a condition in which many different genes (and hence their genotypes) may affect a single phenotype. (Figure 5.7) 2. Pleiotropy is a condition in which a single gene can have multiple phenotypic effects (i.e., eye color and other features). 3. An allele at one location that masks expression of an allele at another locus acting on the same trait is called epistasis. 4. Polygenic characters show continuous variation between extremes (quantitative inheritance); skin pigmentation in humans probably involves 3 or 4 genes. E. Sex-Linked Inheritance (Figures 5.8, 5.9, 5.10) 1. Some traits depend on the sex of the parent carrying the gene. a. Hemophilia is a recessive trait on the X chromosome. b. Red-green color blindness is also a recessive trait and on the X chromosome. c. Carriers are heterozygous for these genes and are phenotypically normal. 2. The inheritance pattern of sex-linked alleles is unique. a. The X-linked trait is expressed when both X chromosomes possess the recessive allele in a female but when only one X-linked recessive allele is present in a male. b. When the mother is a carrier (heterozygous for a X-linked trait) and the father possesses a normal, dominant X-linked allele, half of the sons are affected. c. X-linked recessive phenotypes are more prevalent in males because a single sex-linked recessive gene in the male has a visible effect. 3. In fruit flies, the gene for eye color is carried on the X chromosome. a. When white-eyed males are crossed with red-eyed females, the F1 have red eyes. b. When the F1 is crossed, all F2 females have red eyes, half the males have red eyes and half have white eyes. c. Males are hemizygous for traits carried on the X chromosome. F. Autosomal Linkage and Crossing Over 1. Linkage a. Not all factors segregate as stated in Mendel’s second law. b. Genes on the same chromosome are linked, and the traits are inherited together. 2. Traits on the same chromosome are coded as letters without a slash mark (i.e., AB/ab). 3. Crossing Over (Figure 5.11) a. Linkage is not absolute; some separation of alleles on the same chromosome occurs due to crossing over. b. During protracted prophase of meiosis I, some paired homologous chromosomes break and exchange equivalent portions. c. Crossing over exchanges genes between homologous pairs with great frequency; crossing over occurs nearly of 100% each meiotic cycle for longer chromosomes. d. Because more distant loci are likely to be separated by crossing-over, one can consider. the frequency in crossing over can facilitate mapping the location of genes on chromosomes. G. Chromosomal Aberrations 1. Structural and numerical deviations from the norm that affect many genes are chromosomal aberrations. 2. It is estimated that five of every 1,000 humans are born with a serious genetic defect from chromosomal anomalies. 3. Euploidy is the addition or deletion of whole sets of chromosomes; polyploidy, the possession of three or more complete sets (homologs) of chromosomes, is most common in plants but animals cannot tolerate this type of chromosomal aberration. 4. Aneuploidy is the addition or deletion of a single chromosome. a. It is usually caused by failure of chromosomes to separate during meiosis (nondisjunction). b. This results in one gamete or polar body having an extra chromosome and one lacking a chromosome. c. The monosomic animal (n-1) rarely survives due to uneven balance of genetic instructions. d. Trisomy (n+1) is more common; Down syndrome often occurs within individuals that are trisomy-21, i.e., these individuals have an extra 21st chromosome. 5. Structural aberrations involve whole sequences of genes within a chromosome. a. Inversions reverse the order of a segment of genes. b. Translocation is the movement of a section of genes. c. Deletion is loss of a single, or block of genes. d. Duplication adds an extra section of chromosome; they may add additional genetic information and allow new functions. 6. Genetic Nondisjunction and Syndromes: Klinefelter syndrome and Turner syndrome are the result of genetic nondisjunction. 5.5. Gene Theory A. Gene Concept 1. W. Johannsen coined the term “gene” in 1909 to name the hereditary factors described by Mendel. a. Originally, genes were thought to be indivisible units. b. Alleles are now known to be divisible by recombination; portions are separable. c. Parts of eukaryote genes are separated by introns, which are sections of DNA that do not specify a product. B. One Gene–One Polypeptide Hypothesis 1. Phenotypic expression of genes appears to follow: gene gene product phenotypic expression. 2. Gene products are usually proteins; proteins can act as enzymes, antibodies, hormones and structures. 3. Research with the bread mold Neurospora associated genes with enzymes. a. Neurospora are haploid and unaffected by dominance, and irradiation easily induced mutations. b. Each mutant strain resulted in one defective enzyme; this discovery earned Beadle and Tatum the Nobel Prize in 1958. c. This describes the cause of hundreds of inherited disorders based on missing enzymes. d. However not all proteins specified by genes are enzymes, etc. and some genes direct synthesis of transfer RNA. e. A gene is now defined more inclusively as a nucleic acid sequence that encodes a functional polypeptide or RNA sequence. 5.6. Storage and Transfer of Genetic Information (Figures 5.12; Table 5.2) A. Nucleic Acids: Molecular Basis of Inheritance 1. Nucleotides a. Both DNA and RNA are polymers built of nucleotides; a nucleotide contains a sugar, a nitrogenous base and a phosphate group. b. DNA contains a 5-carbon sugar called deoxyribose. RNA contains a 5-carbon sugar called ribose. c. Nitrogenous bases are either pyrimidines (a single, 6-membered ring) or purines (two fused rings). (Figure 5.13) d. Purines in both DNA and RNA are adenine and guanine. e. Pyrimidines in DNA are thymine and cytosine; in RNA they are uracil and cytosine. f. The DNA backbone is built of phosphoric acid and deoxyribose. g. The 5' end of the backbone has a free phosphate group on the 5' carbon of the ribose and the 3' end has a free hydroxyl group on the 3' carbon. (Figure 5.14) h. DNA is two complementary chains precisely cross-linked by specific hydrogen bonding between purine and pyrimidine bases. (Figure 5.15) i. The number of adenines in a molecule of DNA is equal to the number of thymines, and the number of guanines is equal to the number of cytosine’s. This suggests that these bases are paired. (Figure 5.16) j. The DNA ladder is twisted into a double helix; ten base pairs occur per turn. (Figure 5.17) k. The two DNA strands are antiparallel; the 5' end of one is bonded to the 3' end of the other. l. Strands are complementary; sequence of bases of one strand specifies sequence of the other. m. RNA is similar to DNA except it has a single polynucleotide chain, has ribose instead of deoxyribose, and has uracil instead of thymine. n. DNA is replicated precisely before placed into daughter cells; each strand of a parent cell’s DNA is a template for the new complementary strand. (Figure 5.18) o. Ribosomal, transfer, and messenger RNAs are the most abundant and well-known types of RNA, but many structural and regulatory RNAs, such as micro RNAs, have been reported. 2. DNA Coding by Base Sequence a. The DNA coding sequence is collinear with the sequence of amino acids in a protein. b. The four kinds of DNA nucleotides cannot individually code for each of the identified 20 amino acids. c. Sequences of 3 bases provides 64 (43) combinations, enough to code for the 20 amino acids. d. Later work confirmed the triplet coding sequence with redundancy. (Table 5.3) e. DNA is stable but subject to chemical and radiation damage. f. Excision repair uses enzymes to separate pyrimidines covalently bonded by UV radiation. g. DNA polymerase synthesizes the missing strand according to base-pairing rules. h. DNA ligase joins the end of the new strand to the old one. i. DNA polymerase only synthesizes new strands in the direction of 5' to 3'. The parent DNA strands are antiparallel, so synthesis along one of the strands is continuous, and the other is performed in a series of fragments running 5' to 3'. 3. Transcription and the Role of Messenger RNA (Figures 5.19, 5.20) a. DNA codes for proteins but does not participate directly in protein synthesis. b. An intermediary, messenger RNA (mRNA) is used. c. DNA is transcribed into mRNA with uracil substituting for thymine. (Table 5.3) d. RNA polymerase makes a mRNA that is complementary to one strand of DNA. e. A different RNA polymerase is used to produce ribosomal, transfer and messenger RNA. f. Only one of the two DNA strands, the “sense” strand, is used as a template for RNA synthesis. The strand not used as a template is called the “antisense” strand. g. Genes were thought to be continuous stretches of DNA until introns, sections that do not code for a product, were discovered. h. Genes coding for many proteins may be discontinuous; genes coding for histones and interferon are continuous. i. Some genes are rearranged during development to code for different proteins. j. Some RNA can self-catalyze the excision of introns; since it changes in the reaction, this is not technically an enzyme. 4. Translation: Final Stage in Information Transfer (Figures 5.21, 5.22, 5.23) a. Translation takes place on ribosomes composed of protein and ribosomal RNA (rRNA). b. Ribosomes consist of large and small subunits; together they form a functional unit. c. Many ribosomes may attach to a single mRNA to form a complex called a polyribosome or polysome; thus, several molecules of the same protein can then be synthesized on a mRNA at once, one per ribosome. d. Assembly of proteins requires large transfer RNA molecules. e. The tRNA collects free amino acids and delivers them to the polysome. f. There is a unique tRNA for each amino acid. g. Each tRNA has a specific tRNA synthetase to sort and attach amino acid to the end of each tRNA, called charging. h. On the tRNA, a sequence of three bases (anticodon) forms base pairs with complementary bases (codon) in mRNA. 5. Regulation of Gene Expression a. Though they contain the same genetic information, tissues differentiate because they use only certain sections of genetic material during certain periods of their lives. b. Transcriptional Control (Figure 5.24) 1) Transcription factors are molecules that have a positive or negative effect on transcription of RNA from DNA. 2) Promoters are sequences of DNA upon which RNA polymerase and transcription factors bind to begin transcription. 3) Promoters coding for mRNA and tRNA lie outside the transcribed region of DNA; promoters coding for tRNA lie within the transcribed region of DNA. 4) Expression of genes encoding transcription factors (trans-regulatory genes) can influence transcription of other genes. 5) Steroid hormones enter the cell and bind with a receptor protein in the nucleus; this complex binds with DNA near the target gene; for example, progesterone binds with a nuclear receptor in oviduct cells; this activates transcription of genes encoding egg albumin. c Translational Control 1) Genes can be transcribed but mRNA can be sequestered; consequently, translation can be delayed. For example, egg development is often held back; large amounts of messenger RNA accumulate until fertilization activates metabolism and translation of maternal mRNA. 2) MicroRNAs (miRNAs) or small interfering RNAs (siRNAs), under the regulation of the enzyme Dicer, can be packaged into ribonucleoprotein complexes called RNA-induced silencing complexes that in turn regulate translation of mRNA. d. Gene Rearrangement 1) Rearrangement of DNA sequences coding for antibodies, which allows for vast diversity. B. Molecular Genetics 1. Recombinant DNA (Figure 5.25) a. Restriction endonucleases are enzymes derived from bacteria. b. They cleave double-stranded DNA at particular sites, leaving “sticky ends.” c. Combined with others, they join by rules of complementary base pairing. d. They are sealed together by DNA ligase. e. If the joined DNA is from different sources, this constitutes recombinant DNA. f. Plasmids are extrachromosomal pieces of DNA that exist in multiple copies within a bacterium. g. Both plasmids and bacteriophages that carry recombinant DNA are referred to as vectors. 2. Polymerase Chain Reaction (Figure 5.26) a. If a gene sequence is known, it can be cloned using polymerase chain reaction. b. Short chains of nucleotides called primers, complementary to the sequence, are synthesized. c. Added to the DNA, the mixture is heated to separate the DNA, and cooled. d. DNA polymerase and the four deoxyribonucleotide triphosphates are added; DNA synthesis proceeds from the 3' end of each primer. e. Entire strands are synthesized as the heat-cool cycle is repeated. f. At five minutes per cycle, less than 2 hours is needed to yield a million copies of one strand. 3. Genomics and Proteomics a. Mapping, sequencing and analyzing genomes is genomics. b. Mapping the human genome, originally expected to take until the year 2700, is now complete. c. Mapping is completed or nearly completed on many organisms such as bacteria, yeast, fruit flies and nematodes. d. The human genome is much smaller than previously thought, now estimated at about 40,000 protein-encoding genes, and is responsible for hundreds of thousands of different proteins.. e. There are about 740 gene codes for RNAs; about 90% of sequences in euchromatin (gene-rich portions of chromosomes, contrasted with heterochromatin, areas where there are few genes). f. Only about 5% of the 28% actually transcribed into RNA encoded protein. g. More than half the DNA present is repeated; sequences of several types, including 45% in parasitic DNA elements (“junk” or “selfish” DNA)—DNA that seems to serve no function save its own propagation. h. Nearly 1000 human diseases, such as cystic fibrosis and Huntington’s chorea, result from defects in single genes. i. Almost 300 disease-associated genes have already been identified. j. A single gene can, by some means, give rise to many differing proteins. k. Scientists in the field of proteomics are trying to determine how proteins interact to accomplish their functions, and to outline the folding structure of proteins. 5.7. Genetic Sources of Phenotypic Variation A. There are several sources of phenotypic variation. a. Natural selection preserves favorable phenotypes thus increasing populations of alleles, leading to adaptive evolution. b. Independent assortment of chromosomes, crossing over and random fusion of gametes reshuffle and amplify the genetic material present. c. Gene mutations and chromosomal aberrations provide new genetic variation. B. Gene Mutations a. Chemical or physical changes in genes result in alteration of the sequence of bases in DNA. b. A codon substitution results in incorrect amino acids causing sickle cell anemia. c. Once a gene is mutated, it faithfully reproduces itself. d. The environment imposes a screening process (natural selection) that continues the beneficial and eliminates the harmful. e. A population carries a reservoir of mutations unexpressed in heterozygotes. C. Frequency of Mutations a. A long gene is more likely to have a mutation than a short gene. b. Every person carries approximately one new mutation; most are recessive and not expressed. 5.8. Molecular Genetics of Cancer A. Oncogenes and Tumor Suppressor Genes a. Cancer results from specific genetic changes that take place in a particular clone of cells. b. These changes may include alterations of oncogenes and tumor suppressor genes. c. Normally, oncogenes are in the form of proto-oncogenes. d. One proto-oncogene code for the protein Ras (a guanosine triphosphatase—GTP-ase— is located just beneath the cell membrane). e. When a receptor on the cell surface binds a growth factor, Ras is activated and initiates a cascade of reactions, ultimately leading to cell division. f. Cellular DNA can sustain damage largely by ionizing radiation, ultraviolet radiation, and chemical mutagens, all of which may result in free radicals with unpaired electrons. g. Some damaged DNA can be repaired. h. Gene products such as p53 (for “53-kilodalton protein”) are tumor suppressors that act on cell proliferation. Lecture Enrichment 1. The pea plant traits selected by Mendel matched a clear mathematical model. 2. If you use tongue-rolling, eye color, etc. be sure to qualify that these are oversimplifications used for teaching purposes. 3. Describe how the scientific perspective had changed by 1900 so that three botanists rediscovered Mendel’s ignored work. Consider how some findings can be “ahead of their time” and unappreciated. Mendel worked in the physics lab of Christian Doppler, the physicist for whom the Doppler effect is named and who was adept in applying mathematics and measurements to all experiments. 4. Speculate how an awareness of Mendel’s findings might have impacted on Darwin’s presentation of his theory of evolution. 5. Ask students how Mendel’s pea plant experiments would have responded if the traits had involved epistasis, polygenic inheritance, etc. 6. Consider polygenic inheritance and how it appears to affect height, skin color, and perhaps intelligence. 7. In history, powerful individuals (King Henry VIII) and cultures erroneously believed a female was at fault if there was no male child born. We now know that it is the male’s sperm that determines sex of a child. Why do we not now “blame” the father? This topic allows you to lead discussion to reveal how this knowledge should give us freedom from unjust actions. It is also possible to bring in the history of biology, including those who believed either the ova or the sperm contained fully preformed individuals and only received a “growth factor” from the other parent. 8. Discuss how interaction between the environment and the genotype together produce the phenotype. 9. Elaborate on the advantages of sexual reproduction in evolution and ask whether evolution can occur in asexually reproducing organisms. 10. Explain why organisms that usually reproduce asexually often go through sexual reproduction occasionally to provide genetic recombination. 11. Neospora was a haploid organism. Are there always advantages to being a diploid life cycle (e.g., most animals) and why would any organism select for a mainly haploid life cycle (e.g., fungi and some algae)? 12. Discuss the importance of the human genome project and the new area of proteomics as it affects not only science, but society. Commentary/Lesson Plan Background: Students are usually more interested in human genetic traits, but many human traits are polygenic or complicated by complex genetic factors. Students’ math level relative to both probability and algebra will be a critical factor in understanding probability. Students pick up the social meaning to the term “sex” with all of its baggage; part of being a biology major is re-learning the biological concept of sexual reproduction from a technical perspective. Few of the cellular events are part of our direct experience; visuals are critical in portraying chromosomes and the processes of transcription, translation, etc. Laboratory slide preparations are important if students are to meaningfully understand autosomes and sex chromosomes. The complexity of sex linkage also requires visuals. Misconceptions: The gene concept is so ingrained that many students think that each distinct trait requires a different gene; the idea that one DNA sequence may participate in the production of different products will be contrary to their intuition. Many students have been taught that the human genome includes several hundred thousand genes; this is far too high a number for the same reason. Students often don’t realize that phenotype can change over time (e.g., hair changes from blonde in childhood to dark in an adult, to white in an older person) even though genes remain the same. Students assume the genotype never changes; there are changes in the genotype of cell lineages (e.g., producing cancer) as a person ages. Schedule: Pace will vary substantially depending on prior genetics and math background. HOUR 1 5.1. A Code for All Life A. History of Central Tenets of Genetics B. Mendel’s Investigations C. Chromosomal Basis of Inheritance HOUR 2 5.2. Mendelian Laws of Inheritance A. Mendel’s First Law B. Mendel’s Second Law C. Multiple Alleles D. Gene Interaction E. Sex-Linked Inheritance F. Autosomal Linkage and Crossing Over G. Chromosomal Aberrations HOUR 3 5.3. Gene Theory A. Gene Concept B. One Gene–One Enzyme Hypothesis 5.4. Storage and Transfer of Genetic Information A. Nucleic Acids: Molecular Basis of Inheritance B. Molecular Genetics C. Sources of Phenotypic Variation D. Molecular Genetics of Cancer ADVANCED CLASS QUESTIONS: 1. Consider the proposal that handedness is inherited with right-handedness dominant (RR, Rr) and left-handedness recessive (rr). Of all the possible combinations of parents and offspring by phenotype, what combination of parents and offspring would cast doubt on this simple hypothesis? Answer: In the proposed scenario, where right-handedness (R) is dominant and left-handedness (r) is recessive, the following combinations of parents and offspring would cast doubt on this simple hypothesis: 1. Left-handed offspring from two right-handed parents (RR x RR) : If two right-handed parents (both genotype RR) produce a left-handed offspring (genotype rr), it would contradict the hypothesis that left-handedness is a recessive trait. 2. Left-handed offspring from a right-handed parent and a left-handed parent (RR x rr or Rr x rr) : If a right-handed parent (genotype RR or Rr) and a left-handed parent (genotype rr) produce a left-handed offspring (genotype rr), it would also contradict the hypothesis that left-handedness is a recessive trait. In summary, the occurrence of left-handed offspring from parents with only right-handed phenotypes would cast doubt on the proposed simple inheritance pattern. 2. How could we prove that genes are on the chromosomes or that the genes are linearly arranged? Answer: We can prove that genes are located on chromosomes and are linearly arranged through several experimental approaches: 1. Cytological Studies : • Microscopy : Staining techniques combined with microscopy allow us to observe chromosomes and their behavior during cell division. • Karyotyping : By staining and visualizing chromosomes, scientists can create karyotypes, which are images of an individual's chromosomes arranged in homologous pairs. This helps identify the number, size, and structure of chromosomes. 2. Genetic Studies : • Mendelian Genetics : Observing patterns of inheritance of traits as described by Mendel's laws provides evidence that genes are located on chromosomes. • Linkage Studies : Studying the inheritance patterns of genes located on the same chromosome allows us to determine their relative positions. Genes that are closer together on the same chromosome are less likely to be separated during crossing over. • Crossing Over : The frequency of crossing over between genes on the same chromosome is related to the distance between them. This information helps to create genetic maps that show the linear arrangement of genes on chromosomes. 3. Molecular Biology Techniques : • Chromosome Mapping : Techniques such as fluorescent in situ hybridization (FISH) and chromosome walking allow scientists to physically map genes on chromosomes. • DNA Sequencing : The complete sequencing of genomes has confirmed the linear arrangement of genes on chromosomes. In summary, cytological studies, genetic studies, and molecular biology techniques provide evidence that genes are located on chromosomes and are linearly arranged along the length of the chromosome. These combined approaches offer compelling evidence supporting the chromosome theory of inheritance. 3. In what way do both asexual and sexual reproduction support the cell theory (i.e., all organisms are composed of cells)? Answer: Both asexual and sexual reproduction support the cell theory, which states that all organisms are composed of cells, in the following ways: 1. Asexual Reproduction : • In asexual reproduction, a single parent cell divides to produce offspring that are genetically identical to the parent cell. • The parent cell contains all the necessary organelles, including the nucleus, mitochondria, and other cellular structures. • Each offspring cell produced through asexual reproduction is also a complete cell, containing all the necessary organelles and structures. • Asexual reproduction demonstrates that new organisms can arise from single cells, supporting the idea that all living organisms are composed of cells. 2. Sexual Reproduction : • In sexual reproduction, two parent cells, each containing a nucleus and other organelles, contribute genetic material to produce offspring. • The fusion of two gametes (sperm and egg cells) forms a zygote, which then undergoes cell division and differentiation to develop into a new organism. • Both the sperm and egg cells involved in sexual reproduction are complete cells with all the necessary organelles and cellular structures. • Sexual reproduction demonstrates that new organisms can arise from the fusion of two cells, further supporting the idea that all living organisms are composed of cells. In summary, both asexual and sexual reproduction support the cell theory by demonstrating that new organisms arise from pre-existing cells. Whether through the division of a single parent cell in asexual reproduction or the fusion of two parent cells in sexual reproduction, the formation of new organisms involves the activity of cells. 4. If incomplete dominance results in offspring that are halfway between the pure strains, as the red and white flowers that produce pink offspring, how is this in any way different from the earlier theory of blending? Answer: Incomplete dominance is different from the earlier theory of blending because it preserves the genetic variation of the parent strains, whereas blending theory would predict a permanent loss of genetic diversity. In incomplete dominance, such as the example of red and white flowers producing pink offspring, the heterozygous offspring exhibit an intermediate phenotype (pink) that is distinct from either parent. Importantly, the genetic information for both the red and white flower traits remains in the population, even though the phenotype of the offspring appears to be a blend of the parental traits. In contrast, according to the blending theory, traits from the parental generations would permanently blend together in the offspring, resulting in a gradual loss of genetic diversity over successive generations. However, in incomplete dominance, the genetic variation of the parent strains is preserved, as both the red and white flower traits reappear in subsequent generations. Therefore, incomplete dominance maintains genetic variation within a population, whereas blending theory would predict a loss of genetic diversity over time. 5. Do the same laws of heredity apply for both plants and animals? Answer: Yes, the same laws of heredity apply for both plants and animals. Gregor Mendel's laws of heredity, which include the law of segregation, the law of independent assortment, and the law of dominance, describe how traits are passed from parents to offspring in all sexually reproducing organisms. These laws apply to both plants and animals because they are based on fundamental principles of genetics. 1. Law of Segregation : Mendel's first law states that the two alleles for a trait segregate (separate) during gamete formation, so each gamete carries only one allele for each trait. This law applies to both plants and animals, governing how traits are passed from parents to offspring. 2. Law of Independent Assortment : Mendel's second law states that alleles for different traits are distributed to sex cells (gametes) independently of one another. This law also applies to both plants and animals, explaining how different traits are inherited independently of each other. 3. Law of Dominance : Mendel's third law states that in a heterozygote, one allele will be dominant over the other, which is recessive. This law is observed in both plants and animals, determining the expression of traits. Therefore, the same fundamental laws of heredity discovered by Mendel apply to both plants and animals, providing a basis for understanding how traits are inherited across different species. 6. Compared to the seven pairs of chromosomes in pea plants, corn has 10 pairs or 20 total chromosomes. If Mendel had chosen corn instead of pea plants, what is the maximum number of traits he could have worked with in order to establish his law of segregation (each trait is determined by two factors) and independent assortment (the factors assort independent of other factors)? Answer: Mendel's law of segregation states that each trait is determined by two factors (alleles) that segregate (separate) during gamete formation. Mendel's law of independent assortment states that alleles for different traits are distributed to sex cells (gametes) independently of one another. If Mendel had chosen corn instead of pea plants, with 10 pairs of chromosomes or 20 total chromosomes, he could have worked with a maximum of 10 traits to establish his laws. • Law of Segregation : Each trait would be determined by two factors (alleles), which segregate during gamete formation. With 10 pairs of chromosomes, he could study 10 different traits, each controlled by two alleles. • Law of Independent Assortment : Mendel could have studied the inheritance patterns of these 10 traits independently of each other, as the alleles for different traits are distributed to sex cells (gametes) independently of one another. Therefore, if Mendel had chosen corn instead of pea plants, he could have worked with a maximum of 10 traits to establish his law of segregation and law of independent assortment. 7. Why are you similar in appearance to your parents and brothers and/or sisters, but do not resemble either one exactly unless you are an identical twin? Answer:You are similar in appearance to your parents and siblings because you inherit genetic material from both of your parents. However, you do not resemble either one exactly unless you are an identical twin because of genetic variation and the process of genetic recombination. 1. Genetic Variation : Each parent contributes half of your genetic material, including alleles for various traits. Since each parent has a unique set of alleles, you inherit a combination of alleles from both parents, resulting in genetic variation. 2. Genetic Recombination : During the formation of egg and sperm cells (gametes) through the process of meiosis, genetic recombination occurs. This process shuffles the genetic material, leading to new combinations of alleles in the offspring. As a result, even siblings who have the same parents will have different combinations of alleles and, therefore, different traits. 3. Random Assortment of Chromosomes : During meiosis, homologous chromosomes separate randomly into daughter cells. This random assortment further increases genetic diversity among siblings. 4. Environmental Influences : Environmental factors, such as nutrition, exposure to sunlight, and lifestyle, can also influence your physical appearance, contributing to differences between siblings. Therefore, while you share many physical traits with your parents and siblings due to the inheritance of genetic material, genetic variation, genetic recombination, random assortment of chromosomes, and environmental factors all contribute to the differences in appearance between family members who are not identical twins. 8. Both polygenic traits and codominance produce intermediate phenotypes, yet are due to different mechanisms. How can we distinguish between them? Answer: Polygenic traits and codominance both result in intermediate phenotypes, but they are due to different genetic mechanisms. Polygenic traits are controlled by multiple genes, with each gene contributing additively to the phenotype. The phenotypic expression is a continuous range, rather than discrete categories. Examples include human height and skin color. Codominance, on the other hand, occurs when two different alleles of a gene are both expressed fully in the heterozygous individual. This results in a phenotype that shows the characteristics of both alleles equally. A classic example is the ABO blood group system, where the AB blood type is codominant, and individuals with this blood type express both A and B antigens. The key difference between the two is in the genetic mechanism: polygenic traits involve multiple genes contributing additively to the phenotype, while codominance involves multiple alleles of a single gene, each having its own distinct effect on the phenotype. 9. Contrary to newly-developing Western views of genetics; under Stalin, Lysenko enforced a view stating that if a couple worked hard and developed muscles, their babies would be born more muscular. Why do we not now believe in such inheritance of acquired characteristics? Answer: We no longer believe in the inheritance of acquired characteristics because of our modern understanding of genetics, particularly through the discoveries made by Gregor Mendel and subsequent advancements in genetics. Mendel's experiments with pea plants showed that traits are passed down through discrete units called genes, and these genes are not influenced by the organism's environment or activities during its lifetime. Later discoveries in molecular biology, such as the structure of DNA and the mechanisms of gene expression, further confirmed that genetic information is passed down through the DNA sequence and is not affected by an organism's experiences or acquired traits. The idea that acquired traits could be inherited, as proposed by Lysenko and supported by Lamarckian theory, is not supported by scientific evidence. Inheritance of acquired characteristics, also known as Lamarckism, suggests that changes acquired during an organism's lifetime can be passed down to its offspring. However, this concept has been disproven by modern genetics. Instead, we now understand that genetic information is transmitted through DNA, and changes to an organism's DNA, called mutations, are the primary source of genetic variation. These mutations can lead to changes in traits over generations, but they are not influenced by an organism's environment or behavior during its lifetime. 10. How can an individual who is deformed by an accident have children who lack such deformities? Answer: An individual who is deformed by an accident can have children who lack such deformities because most acquired traits are not heritable. Injuries or deformities caused by accidents typically affect the individual's phenotype but do not alter their genetic makeup. Therefore, these acquired traits are not passed down to their offspring. Heritable traits are those determined by an individual's genetic makeup, which is passed down from parent to offspring through their DNA. Traits caused by genetic mutations or variations may be passed down to offspring, but those caused by environmental factors or injuries are not. As a result, even if an individual has suffered deformities due to an accident, their children will inherit their genetic information but will not inherit the acquired deformities. The children's traits will be determined by their own genetic makeup, not by the experiences or injuries of their parents. 11. How can we demonstrate that the phenotype is controlled by the entire genome? Answer: We can demonstrate that the phenotype is controlled by the entire genome through various genetic experiments and observations: 1. Polygenic Traits : Many traits, such as height, skin color, and intelligence, are controlled by multiple genes. Each gene may contribute a small amount to the overall phenotype. The combined effect of multiple genes across the entire genome determines the phenotype. This is evident from the continuous range of phenotypes observed in populations. 2. Quantitative Trait Loci (QTL) Mapping : By identifying regions of the genome associated with specific traits using techniques like QTL mapping, scientists can show that multiple genes scattered across the genome contribute to the expression of a particular phenotype. 3. Gene Interactions : Genes interact with each other in complex ways. This interaction can be additive, where the effect of each gene adds up to produce the phenotype, or it can be epistatic, where the effect of one gene depends on the presence of another gene. Such interactions demonstrate the influence of multiple genes on the phenotype. 4. Genome-wide Association Studies (GWAS) : GWAS analyze the genomes of large populations to identify genetic variations associated with particular traits or diseases. These studies often reveal that multiple genes across the genome contribute to complex traits. 5. Gene Knockout and Transgenic Studies : By manipulating specific genes in model organisms, researchers can observe the effects on the phenotype. Knocking out or overexpressing individual genes can demonstrate their contribution to the overall phenotype. By considering these lines of evidence, it becomes clear that the phenotype is not controlled by a single gene, but rather by the combined action of multiple genes distributed throughout the entire genome. 12. Duplication-division-division (meiosis) is not the only way to halve chromosome numbers. Why not simply divide the original diploid number of chromosomes to produce two haploid cells? (A primitive organism does this.) What drawbacks would occur? Answer: While duplicating the chromosomes and then undergoing two successive divisions (meiosis) is the common method for halving chromosome numbers, primitive organisms, such as certain types of protists, fungi, and algae, use a simpler method known as "direct division" or "mitosis followed by cytokinesis" to produce haploid cells. In direct division, the original diploid nucleus undergoes mitosis followed by cytokinesis to produce two haploid nuclei directly. However, this method has several drawbacks: 1. Lack of Genetic Variation : Meiosis, which includes recombination (crossing over) and random segregation of chromosomes, generates genetic diversity in the offspring. Direct division does not involve recombination, so there is no genetic variation among the resulting haploid cells. 2. Limited Adaptability : Without genetic variation, organisms produced through direct division may be less adaptable to changing environmental conditions. Meiotic recombination allows for the shuffling of genetic material, providing a mechanism for the generation of new combinations of traits. 3. Accumulation of Mutations : Direct division does not provide an opportunity to repair DNA damage or remove harmful mutations. Meiosis includes mechanisms for repairing DNA damage and eliminating harmful mutations, which helps maintain the integrity of the genome. 4. Inefficient Removal of Non-disjunction : Meiosis includes a process called non-disjunction, where chromosomes fail to separate properly. This can lead to aneuploidy, a condition in which cells have an abnormal number of chromosomes. Meiotic checkpoints usually detect and eliminate cells with non-disjunction, reducing the risk of producing aneuploid offspring. Direct division lacks these checkpoints, so the risk of producing aneuploid offspring is higher. Overall, while direct division may be a simpler method for halving chromosome numbers, it lacks the genetic diversity and genome stability provided by meiosis, making it less advantageous for more complex organisms. 13. Can an organism with asexual reproduction have any variation among offspring? If so, how does sexual reproduction have an advantage in introducing variation? If asexual reproduction does not produce the variation of sexual, and sexual is always an advantage, why are any asexual animals alive today? Why would some organisms such as desert lizards abandon sexual reproduction to be parthenogenetic (females produce females without fertilization of eggs)? Answer: Organisms with asexual reproduction can have variation among offspring, but it is limited compared to sexual reproduction. Here's how both processes introduce variation and why some organisms still rely on asexual reproduction: Asexual Reproduction: 1. Mutation : While asexual reproduction doesn't involve genetic recombination, mutations can still occur, leading to genetic variation among offspring. 2. Clonal Variation : Though offspring are genetically identical to the parent, variations can arise due to environmental factors or random genetic mutations. Sexual Reproduction: 1. Genetic Recombination : Sexual reproduction involves the recombination of genetic material from two parents, leading to a unique combination of traits in each offspring. 2. Increased Variation : Genetic recombination during sexual reproduction leads to increased genetic diversity among offspring, allowing for greater adaptability to changing environments. Advantages of Sexual Reproduction: 1. Adaptability : Sexual reproduction introduces genetic diversity, allowing for greater adaptability to changing environmental conditions. This diversity reduces the risk of extinction due to environmental changes. 2. Elimination of Harmful Mutations : Sexual reproduction allows for the removal of harmful mutations through recombination and genetic shuffling. Why Are Some Organisms Asexual? 1. Efficiency and Rapid Reproduction : Asexual reproduction can be more efficient in rapidly colonizing environments where individuals do not need to spend time and energy finding mates. 2. Stability of Environment : In stable environments with little change, asexual reproduction can be advantageous. The lack of genetic recombination is less of a disadvantage in such environments. 3. Specialized Adaptations : Some asexual organisms have evolved specialized mechanisms to increase genetic variation. For example, some plants can undergo self-pollination, which introduces limited genetic variation. Parthenogenesis in Desert Lizards: 1. Environmental Pressures : In environments where mates are scarce or conditions are harsh, parthenogenesis allows females to reproduce without needing to find a mate, ensuring the survival of their genes. 2. Reproductive Assurance : Parthenogenesis provides reproductive assurance when mates are rare or absent, ensuring that females can produce offspring even in the absence of males. In summary, while sexual reproduction generally offers advantages in terms of genetic diversity and adaptability, asexual reproduction persists in some organisms due to its efficiency, reproductive assurance, and suitability for stable environments. Additionally, parthenogenesis can be advantageous in environments where mates are scarce or conditions are harsh. 14. Bees and ants (order Hymenoptera) have a haploid-diploid system. The queen withholds sperm in her seminal receptacle and an unfertilized egg develops into a female. One species of ant has two chromosomes in a diploid male and one in the haploid female. What effect would having just one chromosome have on the “advantages” of sexual reproduction? Answer: Having just one chromosome in a haploid female, as seen in some species of ants, would significantly impact the advantages of sexual reproduction. Loss of Genetic Variation : • One of the primary advantages of sexual reproduction is the introduction of genetic variation through the recombination of genetic material from two parents. • With just one chromosome in the haploid female, there would be no genetic recombination, leading to offspring that are genetically identical to the mother. • This lack of genetic variation reduces the adaptability of the offspring to changing environmental conditions. Increased Susceptibility to Genetic Diseases : • Genetic diseases or deleterious mutations present in the mother would be passed on to all of her offspring, increasing the risk of genetic disorders within the population. Limited Genetic Diversity : • A population of organisms produced solely through asexual reproduction would lack the genetic diversity necessary for long-term survival. • The population would be more susceptible to diseases, environmental changes, and other selective pressures. Decreased Adaptability : • The lack of genetic diversity resulting from a single chromosome in the haploid female would limit the population's ability to adapt to changing environmental conditions. • This would increase the risk of extinction in the face of environmental challenges. In summary, having just one chromosome in a haploid female would greatly reduce the advantages of sexual reproduction by eliminating genetic recombination and reducing genetic diversity within the population. 15. Reproduction is when one becomes two. How can sexual reproduction, where two cells fuse to become one, be called reproduction? Answer: Sexual reproduction is still considered a form of reproduction because it involves the creation of new individuals, even though it begins with the fusion of two cells. Here's why sexual reproduction is considered a form of reproduction: 1. Creation of New Individuals : Although sexual reproduction involves the fusion of two cells (sperm and egg) to form a single cell (zygote), this single cell then undergoes cell division to produce a new individual. In other words, the fusion of two cells initiates the process of creating a new organism. 2. Combination of Genetic Material : Sexual reproduction combines genetic material from two parent organisms, resulting in genetic variation in the offspring. This genetic variation contributes to the diversity and adaptability of the species. 3. Continuation of the Species : Sexual reproduction allows for the continuation of the species by producing offspring with genetic diversity. This diversity helps populations adapt to changing environments and survive over time. So, while sexual reproduction involves the fusion of two cells to form one, it is still considered a form of reproduction because it leads to the creation of new individuals with genetic variation. 16. Evolution of meiosis, and sexuality in general, is not really a question of how two cells came to fuse to one. This probably involved attempted cannibalism of early cells. The actual question is how the resultant cell with twice the chromosomes evolved mechanisms to reduce the resultant doubled number of chromosomes. This provides a line of questioning that can challenge advanced students. Answer: You're absolutely right, and that's an excellent point. The evolution of meiosis and sexual reproduction involves much more than just the fusion of two cells. It's a complex process that likely evolved as a response to various selective pressures, including the need to deal with the doubling of chromosomes resulting from the fusion of gametes. Here's a more detailed exploration of how the resultant cell with twice the chromosomes evolved mechanisms to reduce the doubled number of chromosomes: 1. Evolution of Meiosis : • Reduction Division : Meiosis is a specialized form of cell division that reduces the chromosome number by half, resulting in the formation of haploid gametes (sperm and egg cells) from diploid cells (somatic cells). • Two Successive Divisions : Meiosis involves two successive divisions, known as meiosis I and meiosis II, which result in the production of four haploid daughter cells from one diploid parent cell. • Crossing Over : Meiosis I includes a process called crossing over, where homologous chromosomes exchange genetic material. This increases genetic variation among the resulting gametes. 2. Advantages of Meiosis : • Genetic Variation : Meiosis generates genetic diversity among offspring, increasing the likelihood of beneficial adaptations in changing environments. • Halving of Chromosome Number : By reducing the chromosome number by half, meiosis ensures that the offspring receive the correct number of chromosomes. 3. Evolution of Sexuality : • Benefit of Genetic Variation : Sexual reproduction, which involves the fusion of gametes from two parents, further increases genetic diversity among offspring. • Selective Advantage : Organisms capable of sexual reproduction have a selective advantage in changing environments due to the increased genetic diversity among offspring. 4. Selective Pressures : • Environmental Changes : Meiosis and sexual reproduction likely evolved as a response to environmental changes and selective pressures. • Competitive Advantage : Organisms capable of meiosis and sexual reproduction had a competitive advantage over those that reproduced asexually, as they could adapt more rapidly to changing environmental conditions. In summary, the evolution of meiosis and sexual reproduction involved the development of mechanisms to reduce the doubled number of chromosomes resulting from the fusion of gametes. These mechanisms, including reduction division, crossing over, and the production of haploid gametes, provided organisms with a selective advantage by increasing genetic diversity and adaptability. 17.Why do oogenesis and spermatogenesis have such different cell products? Why does the female produce only one that is functional while the male produces four? Answer: Oogenesis and spermatogenesis produce different cell products because they have different functions and evolved to meet the specific reproductive needs of each sex. The main reasons for the differences in cell products between oogenesis and spermatogenesis are: Oogenesis: 1. Production of Fewer Functional Gametes: • Oogenesis produces only one functional gamete (the egg or ovum) from each primary oocyte. • This is because the division during oogenesis is unequal, resulting in one large cell (the secondary oocyte) and one small cell (the polar body) with minimal cytoplasm. • The polar bodies, though they receive a set of chromosomes, typically degenerate and do not participate in fertilization. 2. Investment in Nutrients and Cellular Machinery: • The egg cell is larger and contains abundant cytoplasm, organelles, and nutrients to support the developing embryo after fertilization. • This requires more energy and resources, so the female invests more in the development of individual gametes. 3. Conservation of Resources: • Oogenesis aims to produce large, well-equipped gametes that can support the developing embryo. • By producing fewer, but larger, gametes, the female conserves resources and ensures the viability of the offspring. Spermatogenesis: 1. Production of Multiple Functional Gametes: • Spermatogenesis produces four functional sperm cells (spermatozoa) from each primary spermatocyte. • This is achieved through two successive cell divisions, resulting in four equal-sized sperm cells. 2. Efficiency in Fertilization: • Producing multiple sperm cells increases the likelihood of successful fertilization by providing more gametes to compete for fertilization. 3. Genetic Diversity: • Producing multiple sperm cells increases genetic diversity among offspring through recombination during meiosis. 4. Conservation of Resources: • Spermatogenesis is optimized to produce many small, motile gametes using fewer resources. • The smaller size of sperm cells allows them to be more mobile, facilitating their journey to the egg for fertilization. In summary, oogenesis and spermatogenesis produce different cell products because they are tailored to meet the specific reproductive needs of females and males, respectively. Oogenesis produces fewer, larger gametes to support embryonic development, while spermatogenesis produces many smaller gametes to increase the likelihood of successful fertilization and maximize genetic diversity among offspring Instructor Manual for Integrated Principles of Zoology Cleveland Hickman, Jr., Susan Keen, Allan Larson, David Eisenhour, Helen I'Anson, Larry Roberts 9780073524214
