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4.1.1 Read: Cell Reproduction AP Biology Sem 1 (S3043799) Reading Guide Name: ____________________ Date: ____________ Reading Assignment: Principles of Life (2nd edition) Please read the following sections of your textbook. As you read, use this reading guide to check your understanding of the material. Part Reading Assignment I Chapter 7 The Cell Cycle and Cell Division (7.1, 7.2, 7.3, 7.4, 7.5) II Chapter 3 Nucleic Acids, Proteins, and Enzymes (3.1) Chapter 8 Inheritance, Genes, and Chromosomes (8.3, 8.4) Chapter 9 DNA and Its Role in Heredity (9.1, 9.2) Part I Describe the products of asexual reproduction. The new organisms are identical copies of the parent. Genetic variation in organisms produced by asexual reproduction can only be due to mutations. Compare haploid and diploid cells. Haploid cells are cells that contain half as much (n) genetic information as a diploid cell (2n). In humans, haploid cells are gametic cells (sperm and eggs), and diploid cells are somatic cells (body cells). Identify and describe the three steps of the cell cycle. Interphase: This is the growth phase and includes DNA replication. The cell nucleus is visible. Mitosis: This is when nuclear segregation of DNA takes place. Cytokinesis: This consists of cell division and formation of a cleavage furrow in animals and a cell plate in plants. In the space below, draw a chromosome with sister chromatids, a centromere, and kinetochores. Students should draw an image of a chromosome as on page 129. Describe the function of the spindle. The spindle serves as the structure to separate the sister chromatids during mitosis. In the space below, identify the phases of mitosis and draw a typical cell in each of the phases. Then describe the events that occur during each of the phases. Phase (Students' drawings should resemble those on pp. 130 - 131.) Events Prophase During prophase, the condensed chromosomes, the centrosome, and the spindle are present. Prometaphase The nuclear envelope disintegrates and the chromosomes (which are very condensed at this point) attach to the kinetochore microtubules. Metaphase The chromosomes are lined up on the equator (metaphase plate) to prepare for segregation. Telophase Separation of the chromatids occurs as each sister chromatid moves toward each end (pole) of the cell. Explain the structural differences between cytokinesis in animal cells and in plant cells. A cleavage furrow (pinching of the cell membrane) occurs during cytokinesis in animals. The membrane is able to pinch in because it is composed of contractile proteins. The microfilaments that are composed of these proteins form a ring on the surface of the membrane. In plant cells, vesicles from the Golgi apparatus fuse together, form a new plasma membrane, and distribute their contents to form a new cell plate. How do cells know when to enter the cell cycle to divide? Eukaryotes do not divide whenever environmental conditions are appropriate the way prokaryotes do. They require growth factors to stimulate cell division and differentiation. Eukaryotic cells divide to repair damaged cells, replace dead cells, or for growth purposes. In the space below, draw a picture of the eukaryotic cell cycle and label the subphases and checkpoint. Students should draw an image as on page 133. Describe the function of a cyclin-dependent kinase. Cdks become active by binding to a cyclin protein. This interaction causes the Cdk to change shape so that its active site is open. Each Cdk has a particular shape and therefore a particular cyclin protein that can activate it. If a growth factor is released, cyclin proteins will be synthesized. These will interact and activate the corresponding Cdk, which will cause the cell cycle to proceed. Describe how the function of meiosis differs from that of mitosis. Meiosis functions as a reductive division process (from diploid to haploid). The purpose is to create daughter cells that contain half as much genetic information (as compared to a full complement in mitosis) yet contain a complete set of chromosomes for reproductive purposes. During the process, variation is generated (whereas no variation is generated in mitosis). In the space below, draw mitosis as compared to meiosis. Use different colors for different chromosomes and label each cell as haploid or diploid. Students should draw images as seen on page 135. Explain the mechanism of crossing over during prophase of meiosis I, and describe how it generates genetic variation. During crossing over, homologous chromosomes pair up in synapsis (in what is called a tetrad). In synapsis, genetic material is exchanged between nonsister chromatids of the homologous chromosomes at locations called chiasmata. This ensures that the chromosomes are reshuffled and contain varying alleles of the same genes (genetic variation). In the space below, draw a recombinant chromosome. Students should draw an image similar to that on page 139. What happens when something goes wrong in meiosis? In the space below, list the possible errors during meiosis, describe the events, and explain their consequences for offspring. Meiotic error Nondisjunction Description Explanation of consequences The failure of a homologous chromosome to separate at anaphase I or the failure of sister chromatids to separate at anaphase II Anaphase I consequence: Two of the four daughter cells will have both copies of the homologous chromosome, and two daughter cells will have none. Anaphase II consequence: Two daughter cells will be normal. One daughter cell will have one extra chromosome, and one daughter cell will be missing one chromosome. Polyploidy Extra sets of chromosomes are Speciation (often in plants) present (3n, 4n, ..., xn). This can be caused by extra DNA replication, no spindle formation in meiosis II, and all chromosomes going to one cell, with none separating to the other. Translocation Chromatids break and rejoin during prophase (crossing over) of prophase I. Can be deleterious to offspring Explain the purpose of apoptosis. Removal of cells that are no longer needed (development) Removal of cells that are damaged due to old age In the space below, draw a flow chart describing the events of apoptosis. Students should draw an image as on page 141 with the labels 1a, 1b, 2, and 3. Part II Describe the structure and function of a bacteriophage. Bacteriophages are viruses that infect bacteria. They have DNA and perhaps a few different types of proteins. However, upon infection of a bacterial cell, the virus uses the bacterial cell's machinery to replicate its viral genetic information. Describe Chargaff’s rule. The total number of purines (adenine and guanine molecules) will equal the number of pyrimidines (thymine and cytosine molecules) if the DNA molecule is a double helix. Therefore, if we know the abundance of one or two bases in a DNA molecule, we can deduce the complete composition of the DNA molecule. As an example, if we know that 20% of a given DNA molecule is composed of adenine, what are the other percentages? The entire molecule is equal to 100%. Use the formula below to calculate the rest of the percentages. A+G=T+C A = 20, therefore T = 20. A + G = T + C, and A + T + C + G = 100. Therefore C + G = 60. C = 30, G = 30. An important discovery in the study of DNA was that DNA is replicated semiconservatively. In the space below, draw a semiconservative round of replication using two different colors for the parental strands and the new strands. Students should draw an image similar to the image on page 172. To which end are nucleotides added to the growing new strand during DNA replication? Why? The nucleotides are always added to the 3' end (forming a new 5' → 3' strand). This is due to the necessary orientation for the formation of the bond. How does the quantity of origins of replications differ in number in prokaryotes and eukaryotes? What would be the consequences to eukaryotes if they used the same number of origins? The number of origins is higher in eukaryotes, as their DNA is linear and larger (up to a billion bp). Without multiple origins, the time necessary for replication in eukaryotes would be very long. For each of the following structures or enzymes necessary for DNA replication to occur, describe the function. Structure/Enzyme Function Primer Starter strand made up of RNA; degraded after DNA replication occurs; necessary for DNA replication to begin Primase Enzyme that synthesizes the RNA primer DNA polymerase Enzyme that catalyzes the polymerization of the DNA nucleotides on the leading and lagging strands Leading strand Continuous replication at the 3' end Lagging strand Discontinuous replication away from the replication fork Okazaki fragment Section of DNA nucleotides assembled in a discontinuous pattern on the lagging strand DNA ligase Enzyme that catalyzes the formation of a phosphodiester linkage between adjacent Okazaki fragments on the lagging strand Telomere Repetitive sequences at the end of a chromosome (for instance, TTAGGG x 2500). They function to protect the chromosome. Telomerase Enzyme that catalyzes the formation of any lost telomeres In the space below, draw a typical DNA replication fork and label the structures and enzymes listed above. Students should draw an image similar to that on page 175. Explain antiparallelism as it relates to DNA formation. DNA must be synthesized in the 5' to 3' direction. Since only the 3' ends can support continuous replication, one strand gets built in one direction, and the other strand gets build in the opposite direction. The analogy of a cross highway where cars are traveling in different directions next to one another applies to how the DNA molecule is replicated. Key Terms As you come across these terms during your reading, write your own definition in the space provided. Asexual reproduction The production of offspring that are genetically identical to the single parent (and other offspring produced by that parent). It may be accomplished by binary fission of prokaryotes, by mitotic cell division of unicellular eukaryotes, by fragmentation or various forms of budding, or by development of an unfertilized egg (parthenogenesis). Clone A genetically identical cell or organism. Mitosis The process of nuclear division in which two identical daughter nuclei are produced by an original parental nucleus. Mitosis is typically, but not necessarily, accompanied by cell division. Meiosis The double division of a nucleus to produce four haploid nuclei from an original diploid parental nucleus that has undergone chromosome replication. Meiosis is accompanied by cell division. Chromosome A structure that contains a single DNA molecule and associated proteins and that is found in the nucleus of eukaryotes and in the cells of bacteria and archaea. In eukaryotes there are typically several or many linear chromosomes. In bacteria and archaea there is one circular chromosome. Chromatin The material from which eukaryotic chromosomes are composed. It contains DNA and proteins. Somatic cells Cells of the body of a multicellular organism, excluding the gametes and the cells that give rise to them. Homologous pairs A pair of chromosomes containing genes that code for the same proteins. Haploid Describes a cell or organism with one copy of each chromosome. Diploid Describes a cell or organism with two copies of each chromosome. Zygote The cell that results from fertilization. Fertilization The union of gametes. Binary fission Separation into two similar and genetically identical individuals, especially by division of the cell in prokaryotes, but also by division of the multicellular body in some eukaryotes. Segregation The separation of sister chromatids during mitosis or meiosis; results in one copy of each chromosome being passed on to offspring during fertilization. Cell cycle The sequence of events that occur between one nuclear division and cell division and the next in a eukaryotic cell. Interphase The phase of the cell cycle between cell divisions. Prophase The first phase of a nuclear division in mitosis and meiosis, during which the chromatin becomes condensed and the spindle begins to form. Sister chromatids copies of a single chromosome that are produced during DNA replication Centromere A chromosome region at which sister chromatids attach and to which spindle fibers attach. Kinetochores Structures that form on the centromeres of eukaryotic chromosomes. Spindle fibers attach to them during mitosis or meiosis. Karyotype The shape, size, and number of the chromosomes of a eukaryotic organism. Centrosome A structure in animal cells that contains the centrioles and that acts as a microtubule-organizing center for the spindle during mitosis or meiosis. Centriole A self-replicating organelle of eukaryotic cells (excluding plants, most fungi, and some protists) that organizes the microtubules that form the spindle during mitosis and meiosis. Spindle apparatus The structure of microtubules that forms in cells undergoing mitosis and meiosis and that functions to move chromosomes to opposite poles of the cell. Daughter cell A cell produced by cell division. Growth factors proteins capable of stimulating growth, proliferation and differentiation of cells. Cyclin dependent kinases (Cdks) An enzyme that acts to stimulate some aspect of the cell cycle when it is bound by a cyclin. Checkpoint A point during the cell cycle when the status of the cell is assessed and the cell cycle either proceeds to the next stage or remains at the present stage. Condensation A change in state from a more diffuse form to a more dense form, such as occurs to chromatin during mitosis or meiosis, when it changes from a diffuse form to compact chromosomes. Crossing over The process by which segments of genes of homologous chromosomes are exchanged during meiosis Tetrad equatorial (metaphase) plate The location where crossing over takes place during meiosis Recombinant Describes a molecule of DNA composed of segments originating from two sources, such as two homologous chromosomes or two species. Independent assortment The independent segregation (with a gamete's two alleles for two genes coming from the same chromosome or coming from different chromosomes by random chance) of the alleles of two or more genes into different gametes. Nondisjunction Nondisjunction occurs when homologous chromosomes or sister chromatids fail to separate properly in meiosis, and both chromosomes or chromatids segregate to one daughter nucleus. This produces one daughter nucleus with two copies and one daughter nucleus with no copies of the chromosome. Polyploidy A condition in which an organism or cell has more than two complete sets of chromosomes. Aneuploid An organism or cell that has an abnormal number of chromosomes as a result of extra or missing individual chromosomes (rather than whole sets). Translocation A type of mutation in which a portion of a chromosome is detached and joined to another chromosome. Apoptosis A programmed cell death. Caspases A group of proteins that are involved in initiating and carrying out apoptosis. Oncogene A gene that when mutated causes cancer. Tumor suppressor gene A gene for a protein that is involved in a signal pathway that prevents mitosis. Bacteriophage Viruses that infect bacteria. Transformation The alteration of a genotype and phenotype through the uptake of environmental DNA. Purine A double-ring nitrogenous base. Pyrimidine A single-ring nitrogenous base. Semiconservative replication The model of DNA replication, in which each daughter DNA double strand consists of one complete parent strand paired with a complete daughter strand. This is different from the models of conservative replication and dispersive replication, which do not occur in cells. Template strand The single strand of DNA from which a new DNA strand is being synthesized. Deoxyribonucleoside triphosphate (dNTPs) The form of a nucleoside that is incorporated into a new DNA strand using the energy of the phosphate bonds to form phosphodiester bonds between nucleotides. DNA polymerase In DNA replication, an enzyme that adds single nucleotides to the growing DNA strand. Origin of replication The point at which DNA replication begins on a chromosome. Replication fork The structure formed during DNA replication when the double helix is unwound, forming two single-strand regions. Primer A short sequence of RNA nucleotides that is added to the exposed 3' end of a single DNA strand at the beginning of replication. DNA polymerase is then able to add new nucleoside triphosphate molecules to the primer. Primase The enzyme that adds a primer to initiate DNA replication. Topoisomerase An enzyme that affects the shape (topology) of the DNA molecule; it unwinds the DNA molecule by causing single-strand nicks in the backbone. Leading strand The strand of DNA on which a new DNA strand is synthesized continuously, toward the replication fork. Lagging strand The strand of DNA on which a new DNA strand is synthesized discontinuously, away from the replication fork. Okazaki fragment Okazaki fragments are synthesized in a discontinuous fashion on the "lagging strand" because the replication fork is moving in the 5' to 3' direction, while the lagging strand is being synthesized in the opposite direction. DNA ligase The enzyme that links the backbone of the strand of replicated DNA together. Telomere A region at the ends of eukaryotic chromosomes composed of many repeated short sequences that prevents the shortening of the chromosome during replication. Telomerase An enzyme that replenishes lost telomere segments after DNA replication. 4.1.3 Study: Modeling DNA Replication AP Biology Sem 1 (S3043799) Study Sheet Name: ____________________ Date: ____________ 1. Several enzymes participate in DNA replication. In the column on the left, write the correct enzyme type next to each description. Enzyme types: DNA polymerase, helicase, ligase, topoisomerase Replication Enzymes Type of enzyme Description Helicase Opens DNA double helix Topoisomerase Clips and unwinds DNA DNA polymerase Adds nucleotides and corrects errors Ligase Seals DNA strands together along its length 2. In what way is inference related to direct observation? Inference is the process of formulating a conclusion based on indirect evidence rather than on direct observation. 3. In what way does the coiling of DNA as a helix affect the position of its 3' and 5' ends? The 3' and 5' ends remain in the same locations on the DNA molecule. The 3' end of one strand is linked to the 5' end of the other strand, and vice versa. 4. What is semiconservative replication in DNA? Semiconservative replication means that each replicated DNA molecule consists of one strand of original DNA and one strand of newly synthesized DNA. 5. In the area below, draw a simple representation of a DNA replication fork with Okazaki fragments. Label the Okazaki fragments, the leading and lagging strands, and the 5' and 3' ends. Use arrows to show the direction of replication. 4.1.5 Study: Cell Cycle Checkpoints and Cancer AP Biology Sem 1 (S3043799) Study Sheet Name: ____________________ Date: ____________ As you read through the study, use this study sheet to help you organize your thoughts and collect data. Record the events that occur during each phase or checkpoint of the cell cycle. Phase or checkpoint Events/Requirements G1 phase Cell growth Duplication of cell structures G1 checkpoint Cell-size check Growth factors present DNA error check S phase Chromosome replication Duplication of cell structures G2 phase Cell growth G2 checkpoint Cell-size check Chromosome replication check DNA error check DNA error correction First portion of M phase Spindle fibers attach to chromosomes M-spindle checkpoint Spindle-fiber attachment check Second portion of M phase through cytokinesis Chromosome separation Cytoplasm division Daughter-cell formation In the area below, identify the error for each of the following cells. Cell β Insufficient organelles are present. Cell θ Mutations are present. Cell Ψ The cell is not large enough to proceed. Cell A chromosome did not attach to the spindle apparatus. For each of the following processes, explain how nondisjunction can cause varying consequences to the individual and offspring. Process Consequence Mitosis When nondisjunction occurs during mitosis, the effects are only on the immediate daughter cells, not on the gametes and therefore not on the offspring. Meiosis When nondisjunction occurs during meiosis, the gametes are affected, and therefore the offspring are affected 4.1.7 Practice: Cell Reproduction AP Biology Sem 1 (S3043799) Points possible: 25 Practice Assignment Name: ____________________ Date: ____________ 1. During human embryonic development, many neurons arise and form connections with one another. However, much later these same neurons are found to be absent. Describe the process that accounts for this loss of early neurons, and explain how this process achieves the changes described. (5 points) Answer: Some neurons that arise early in development later die during apoptosis, which is a normal, programmed process of cell death. Cells may arise during an early stage in development because they are necessary to create an environment for later stages of development. These early cells may not retain their usefulness once the organism has reached a certain stage of development. Apoptosis ensures that these cells are removed at the right time, so they do not take up valuable energy reserves or interfere with the continuing maturation of the organism. 2. The transmission of genetic information from parent to daughter cells is highly accurate. Describe the features of DNA replication responsible for this fidelity of information transfer. Explain why this mechanism allows the high level of accuracy of information transfer that is observed. (5 points) Answer: Genetic information is encoded in a sequence of bases along a strand of DNA. This strand of DNA is copied during cell division to form two daughter cells from a parent cell. The high accuracy of copying the parent DNA comes about because the parent strand can be used as a template for building a daughter strand. DNA synthesis involves specific pairing of new bases in the daughter strand to existing bases in the parent strand. This base pairing ensures that the same sequence of bases is transmitted at each replication phase, which ensures that the genetic information transfer remains highly accurate no matter how many generations go by. 3. DNA is the primary source of heritable information in cells. Explain how the chemical structure of DNA makes this possible. (5 points) Answer: DNA is a polymeric molecule composed of a sugar phosphate backbone bonded to four different nitrogenous bases. Although the sugar phosphate backbone is chemically the same throughout the polymer, the sequence of the four bases bonded to this backbone varies. Genetic information is encoded in the linear sequence of bases in the DNA molecule. 4. Compare and contrast the processes of sexual reproduction in eukaryotes and conjugation in bacteria in terms of how they contribute to genetic variation in a population. (5 points) Answer: In bacterial conjugation, genetic material moves directly from one organism to another. This is a one-way type of sharing of genes that allows the recipient to obtain new alleles. Thus, each generation of bacteria can itself undergo genetic transformation as alleles become mixed through conjugation. In sexual reproduction, genetic material does not move between individuals, but rather two individuals donate genetic material that is then combined in the formation of new offspring. Thus, genetic variation occurs as mating produces new mixes of alleles in the new generation. However, sexual reproduction does not allow genetic changes to the parental generation, as it does in bacterial conjugation. 5. A population of the species Polymita picta is shown in the image below. Explain two mechanisms that could have contributed to the variations apparent in this population.(5 points) Answer: Variation in a population is due to differences in alleles present in the gene pool for that population. These variations arise as the result of random assortment during meiosis and also during mutation events, some of which occur at low frequency as errors during DNA replication or RNA transcription 4.1.9 Discuss: Meiosis and Mitosis AP Biology Sem 1 (S3043799) Points possible: 15 Discussion Name: ____________________ Date: ____________ This worksheet will help you organize your thoughts for the discussion. Answer the questions and prompts below to help you prepare for the discussion. 1. Predict the consequences to sexual reproduction if meiosis did not occur and all cells divided mitotically. Discuss chromosome number, variation, and the implications of these changes on the success of sexual reproduction. (5 points) Answer: Answers will vary. Students should recognize that if meiosis did not occur, the chromosome number would double with each generation (1 point) and that life could not reproduce due to a fusion of haploid gametes (1 point). They should also recognize that there would be less genetic variation (1 point), since crossing over and independent assortment (1 point) are both a part of meiosis. Students may mention that sexual reproduction drives evolutionary change. Without sexual reproduction and subsequent genetic variation for natural selection to act upon, evolution has less variation to work on (1 point). 2. Chemotherapy drugs target specific cells in our body. However, there are also side effects to other body cells during chemotherapy. Explain why these drugs are effective against cancerous cells. What do you think are the dangers of chemotherapy drugs? Identify other types of cells that are likely to be quick to divide and therefore to be impacted by chemotherapy drugs. (5 points) Answer: Answers will vary. Students should note that cancer cells are targeted by chemotherapy drugs because cancer cells divide extremely quickly (1 point) due to the fact that they interrupt the cell cycle's natural shut-off mechanisms (1 point). However, cancer cells are not the only quickly dividing cells in the body, so chemotherapy is dangerous because it can kill healthy body cells. Chemotherapy also affects hair and nail cells (1 point), stomach lining (1 point), and immune system cells (lymphocytes) (1 point). 3. Summarize what you learned about the environmental effects on mitosis in your investigations. Which factors had the largest impact? What data support that conclusion? Were those data statistically significant? (5 points) Answer: Answers will vary. Certain chemicals, such as caffeine, can affect the mitotic division rate. Students should indicate which variable had the largest impact on division time (1 point), and what that impact would be (1 point). For example, if they noticed that caffeine increases the cell division rate, then they should talk about caffeine being a dangerous chemical for cancer patients, since it could increase the division rate of the cancer cells. Students should also discuss their data for that conclusion (1 point). They should then give the chi-squared calculations for their data (1 point) to describe whether they are statistically significant, and whether they are able to accept or reject the null hypothesis (1 point). 4.2.1 Read: Genetics and Gene Expression AP Biology Sem 1 (S3043799) Reading Guide Name: ____________________ Date: ____________ Reading Assignment: Principles of Life (2nd edition) Please read the following sections of your textbook. As you read, use this reading guide to check your understanding of the material. Part Reading Assignment Inheritance, Genes, and Chromosomes (8.1 – 8.4) I Chapter 8 II Chapter 11 Regulation of Gene Expression (11.1 – 11.4) III Chapter 12 Genomes (12.3) IV Chapter 14 Genes, Development, and Evolution (14.1, 14.3, 14.4) Part I Compare the following terms: Gene/Allele: An allele is a form of a gene. For example: Gene = Hair color, Alleles = Brown, blonde, red Homozygous/Heterozygous: Homozygous individuals possess two dominant or two recessive alleles. Heterozygous individuals possess one dominant and one recessive allele. Phenotype/Genotype: A genotype is the combination of alleles an individual has (for example, GG, Gg, or gg), whereas a phenotype is the expression of the genotype (for example, tall, short, round, or wrinkled). Complete dominance/Codominance/Incomplete dominance: In complete dominance, one allele is dominant over the other allele. In codominance, alleles are expressed independently of each other. In incomplete dominance, the resulting phenotype is a blend of the traits corresponding to the alleles. Plasmid/Bacterial chromosome: A plasmid is a small, circular piece of DNA that contains a few dozen genes. The bacterial chromosome contains the rest of the genome. How does a monohybrid cross illustrate Mendel’s law of segregation? In a monohybrid cross, offspring can only receive one allele from each parent. Parents cannot pass on both alleles for one gene without deleterious effects. How does a dihybrid cross illustrate Mendel’s law of independent assortment? In a dihybrid cross, the gametes possess all possible allele combinations. Again, parents can only pass on one allele for each gene, but the inheritance of one allele is not dependent upon the inheritance of another allele. What is the purpose of a testcross? Individuals who are homozygous dominant or heterozygous possess the same phenotype. By crossing an individual with a dominant phenotype with an individual with a recessive phenotype (who must be homozygous recessive), we can predict the genotype of the parent based upon the likelihood of the offspring produced. If homozygous recessive individuals are produced, the parent must be heterozygous. How could you determine that genes are linked? Phenotypic ratios would be different than expected. Some genes would be inherited together and most of the offspring would show phenotypes matching those of the parents. This is due to the fact that some genes don't assort independently. Recombinant phenotypes are due to the fact that two homologous chromosomes physically exchange genetic information during meiosis (crossing over) so that each chromatid ends up with genes from both of the organism's parents. What is the significance of a recombination frequency in terms of gene mapping? The farther apart the loci are, the greater the chance of recombination. Describe the mechanism of recombination in prokaryotes. In bacteria, a sex pilus can cause two bacteria to come close together. Once this happens, a conjugation tube forms and DNA can be transferred from one bacterium to another. The DNA that is exchanged can be incorporated into the linear DNA of the bacteria. Note the image on page 161. Part II Describe how gene expression can be positively regulated or negatively regulated. Protein synthesis can either be inhibited (prevented) or stimulated. The binding of a repressor near the promoter region of a gene will stop transcription and therefore negatively impact gene expression. If an activator is bound to the gene, then positive gene expression will occur. These regulatory proteins (repressors and activators) are called transcription factors and they determine which genes are transcribed and which are not. In the space below, draw the lac operon, labeling the promoters, operator, repressor, and structural genes. Students should draw an image similar to figure 11.7 on page 213. Explain the difference between an inducible operon and a repressible operon. In an inducible operon, like the lac operon, transcription can be turned on when there is a need for the product. In a repressible operon, like the trp operon, transcription can be blocked when there is ample product. Describe the TATA box. The TATA box, composed primarily of A-T pairs, is the most common eukaryotic promoter sequence. Compare DNA methylation and histone protein modification. DNA methylation and histone protein modification both alter the rate of transcription. During DNA methylation, the DNA is chemically modified by the addition of a methyl group. This heritable change causes the silencing of methylated genes. During histone protein modification, positively charged histone proteins wrap around the DNA, and these nucleosomes make DNA physically inaccessible to RNA polymerases. Therefore transcription ceases. Gene expression can also be modified after transcription. Describe the process of alternative splicing. Pre-mRNA segments can be spliced differently in different cells of the body. Therefore, different proteins (and combinations of proteins) can be made in different cells of the body. Groups of proteins with different functions can be created from a single gene. Identify the three main ways that translation of eukaryotic mRNA can occur: miRNA Formation of a 5' cap Translational repressors Explain the main differences between eukaryotic and prokaryotic genomes. Size: Eukaryotic genomes are much larger. Regulation: Eukaryotes contain more regulatory sequences. Coding: Eukaryotic DNA contains a lot of noncoding regions and repeated sequences. In the space below, define each type of stem cell and describe its location in the body. Type of stem cell Function Multipotent Multipotent describes cells that can form a limited number of types of differentiated cells. Pluripotent Pluripotent describes cells that can individually give rise to an organism. They are found in the earliest embryos or are induced. Explain pattern formation. In pattern formation, tissues need to know where they're located in relation to one another and need to ensure that the correct genes are expressed. Describe the function of organ identity genes. Some genes encode proteins that work together to cause specific gene expression. Describe loss of function and gain of function mutations. Mutations in one combinatorial gene cause no gene expression in a loss of function mutation. If a promoter for one combinatorial gene can be linked to another combinatorial gene, there can be an increase, decrease, or different pattern of gene expression. Explain the function of hox genes. Hox genes determine patterns of organ and tissue location. Cells in different regions of the body differentiate in unique patterns. Describe the function of genetic switches. Genetic switches include promoters, enhancers, associated proteins, and transcription factors. They determine when a gene is turned on and when it is turned off. There are many switches — switches for each gene, at each time, and in each place. In the space below, draw an image that shows how hox regulatory genes have similar expression patterns. Students should draw an image in which a specific gene sequence is matched to specific body segments on an organism — for instance, mouse, drosophila, and so on, as on page 279. Explain how specific body structures, including wings, may have evolved by changes in how genes were expressed. Gain of function or loss of function mutations in homeotic genes could have caused the changes seen in the evolution of wings, as shown in figure 14.20. Key Terms As you come across these terms during your reading, write your own definition in the space provided. Key Terms As you come across these terms in your reading, write your own definitions in the spaces provided. Parental generation The individuals that contribute gametes in the first cross in a series of genetic crosses. First filial generation The first generation of offspring in a series of genetic crosses; offspring of the parental generation. Second filial generation The second generation of offspring in a series of genetic crosses; offspring of crosses among the first filial generation. Dominant Describes an allele that is expressed in the phenotype of a heterozygote. Recessive Describes an allele that is not expressed in the phenotype of a heterozygote. Allele A version of a gene. Homozygous Having two identical alleles for a given trait. Heterozygous Having two different alleles for a given trait. Phenotype The observable appearance of an organism, resulting from the combination of genetic characteristics and the environment. Genotype The combination of versions of a gene (called alleles) in an organism. Testcross A cross between an individual with a dominant phenotype and an individual with a recessive phenotype, used to identify the genotype of the individual with the dominant phenotype. Monohybrid cross A cross between individuals differing in one genetic character. Dihybrid cross A cross between individuals differing in two genetic characters. Independent assortment The independent segregation (with a gamete's two alleles for two genes coming from the same chromosome or coming from different chromosomes by random chance) of the alleles of two or more genes into different gametes. Pedigree A diagram of familial relationships with indications of phenotypes that is used to identify the mode of inheritance of a genetic character. Wild type Describes the most common allele or phenotype in nature for a character. Mutation A change in genetic material. Mutations range from change in a single nucleotide to rearrangements of chromosomes to gain or loss of chromosomes or chromosome sets. Codominance Describes alleles that are both expressed in the phenotype of a heterozygote. Incomplete dominance Describes alleles that interact to express an intermediate phenotype in a heterozygote. Hybrid vigor The phenomenon of increased growth, survivorship, or fertility of individuals produced from a cross between parents from two different inbred lines. Genetic linkage The tendency of the alleles of two genes to be inherited together because the genes reside near each other on the same chromosome. Recombination frequency The number of recombinant offspring divided by the total number of offspring from a testcross of the F1progeny produced from a dihybrid cross. Hemizygous Describes the genotype of any trait located on a sex chromosome, which therefore exists in only one copy in the cells of the individual. Sex-linked inheritance The inheritance pattern of genes located on one of the sex chromosomes. Recessive traits tend to appear more often in the phenotypes of the heterogametic sex (e.g., males, XY, in mammals), because traits on the sex chromosome are hemizygous. Transcription factor A protein that binds to a specific sequence of DNA and regulates transcription either by stimulating it or blocking it. Operon A set of enzyme-coding genes that are normally transcribed together and that are associated with a single operator sequence, which is capable of binding a repressor protein, and with a promoter sequence, which binds RNA polymerase when the repressor is not present. Operons are important in prokaryotic gene expression. Operons have also been found in eukaryotic genomes. Structural gene A gene that codes for the amino acid sequence of a protein. Epigenetic Describes inheritance mechanisms that do not alter DNA sequences, such as chromatin modification. Histone A protein that is used in packaging DNA molecules. Alternative splicing Producing different proteins from one pre-mRNA transcript by forming different combinations of exons. microRNA Small RNA molecules that have a role in regulating gene expression at translation by binding with and degrading mRNA or preventing translation. Bacterial conjugation The transfer of DNA between two cells joined by a pilus. Transposon A sequence of DNA that moves from one location in a genome to another, or copies itself and inserts the copy in a new location in a genome. The transposon typically contains genes for enzymes that allow for its own movement. Gene families Sets of genes that have similar sequences but different, though usually related, functions. Gene families arise through duplication and subsequent evolution of new functions. Single nucleotide polymorphisms (SNPs) Differences between alleles in a population caused by differences in individual nucleotides. Short tandem repeats (STRs) DNA sequences consisting of fewer than 10 nucleotides repeated many times immediately adjacent to each other. Their high mutation rates make short tandem repeat sequences excellent identifiers of individuals, and they are used in forensic identification and genealogy. Organ identity genes Hox genes in floral development; genes that define the different parts of the flower. Hox genes A group of homeobox genes that code for regulatory proteins that are expressed in different parts of the developing embryo and signal to developing tissues their location within the embryo. Homeobox A highly conserved DNA sequence (present in plants, animals, and fungi) that codes for protein regions that bind DNA and that is thus involved in regulating transcription and that usually controls genes affecting anatomical development. Genetic switches A recognition sequence and associated regulatory protein that control the transcription of a gene. Totipotent Describes a single cell that has the ability to give rise to cells that can differentiate into any cell type in a multicellular organism. Plasmid A circular DNA molecule common in prokaryotes that is often used as a vector for recombinant DNA. 4.2.3 Study: Probability Demonstrations and Punnett Squares AP Biology Sem 1 (S3043799) Study Sheet Name: ____________________ Date: ____________ As you read through the study, use this study sheet to help you organize your thoughts. Distinguish between phenotype and genotype, and give an example of each. A genotype is the unique combination of alleles found at one or more gene loci. A phenotype is the expression of that genotype or the observable features in an organism, such as pea shape. In pea plants, smooth seeds are dominant to wrinkled seeds. If two pea plants that are heterozygous for the smoothness gene are crossed, what proportion of their offspring will have smooth seeds? Ss x Ss = 3 (smooth):1 (wrinkled); ¾ of the offspring will have smooth seeds. Why do human X-linked recessive traits appear in the phenotypes of males more often than in the phenotypes of females? Many more males than females express X-linked recessive traits, as males have only one X chromosome, and females have two Xs. Thus, males need only a single allele to show the recessive condition; they don't have another X to offset the condition. Inheritance patterns may follow simple Mendelian principles or may be more complex than predicted by simple Mendelian genetics. In the chart below, distinguish the inheritance patterns by writing Mendelian trait or Non-Mendelian trait in the column on the right. Draw lines matching the main ideas of this study with the four Big Ideas of AP Biology. For each main idea, explain how it is related to the Big Idea. 4.2.5 Study: Pedigree Analysis of Human Genetic Disorders AP Biology Sem 1 (S3043799) Study Sheet Name: ____________________ Date: ____________ 1. What is the initial question you are trying to answer? Question What is the mode of inheritance for each disease? 2. Is there an initial prediction you can make about the question you've been asked? What information leads you to make that prediction? Write your prediction in the table below and explain the justifications for your prediction. Initial prediction Justification "I can make this prediction because..." My prediction is that each disease will follow Mendel's rules and be either dominant or recessive. Dominant and recessive are two common types of inheritance. 3. What questions do you have right now? What are you hoping the next section explains to you? I'm unsure of how to analyze pedigrees. I'm hoping the next section will explain how to use them. I'm also not sure what all the symbols and lines refer to and what it means to see a circle or square filled in. 4. As you read through the study, record the evidence that you are given that could help you answer the question. Evidence Significance of the evidence "This evidence is important because..." In the De Luca family, both males and females can be afflicted with the disease. The gene for the disease is probably not carried on a sex chromosome. Frederica does not have the disease, but both of her parents did. This shows that the disease could not be recessive. If it were, Frederica's parents would beaa, and so would she. Therefore, she would have the disease. Dina's father must be heterozygous (Aa), while her mother is homozygous (aa). This reveals that Dina's odds of inheriting the disease are 50%. In the Torres family, the disease only appears in males. This reveals that it is probably on a sex chromosome. In the Torres family, the trait is passed from unafflicted mothers to their sons. This reveals that the trait is X-linked recessive. In the Williams family, inherited blindness is passed from mothers to both their sons and daughters. This reveals that the disease is mitochondrial. 5. What conclusions did you draw at the end of the study? Pedigrees are really useful tools for studying how human diseases are inherited. 6. Congratulations on solving the mystery!! As you look back on the case study, were there additional clues that you missed? If so, how would they have helped you to make your final prediction more accurate? Yes, I missed the clue in the De Luca family that the disease doesn't skip generations. If I had realized what that meant, I probably would have decided it was a dominant disease sooner. 7. Are there additional clues that could have been provided that would have been helpful to you without giving away the answer to the questions? No, I think the case study did a good job of giving clues without giving away the answer. 4.2.7 Practice: Genetics and Gene Expression AP Biology Sem 1 (S3043799) Practice Assignment Name: ____________________ Points possible: 25 Date: ____________ 1. A woman buys seeds for an annual flowering plant. After planting the seeds in her garden, she is happy to see that all of them produce red flowers. She collects the seeds produced by the flowers at the end of the season and stores them over the winter. When she plants them the next spring, she is surprised to find that 8 plants produced white flowers and 32 plants produced red flowers. Explain this outcome by comparing the observed numbers of white and red flowering plants to those expected if the following conditions are assumed: The plants are self-pollinating (that is, seeds are only produced by crosses between plants in the garden). The flower color trait results from two alleles, one dominant and the other recessive. (3 points) Answer: The seeds that were purchased were heterozygous for the red and white flower alleles. The plants all had red flowers because red flower color is dominant. However, because all of the plants carried both alleles, a cross resulted in the following distribution: 25% AA, 50% Aa, 25% aa A a A AA Aa a Aa aa The red phenotype shows up approximately 75% of the time, corresponding to the sum of 25% AA + 50% Aa. The white phenotype only shows up 25% of the time. These percentages correlate reasonably well with the observed frequencies of these two phenotypes in the population: 32/40, or 80%, red and 8/40, or 20%, white. 2. A human needs at least one functional allele for a particular protein in order to have normal metabolic behavior. A man and a woman marry and produce 8 children. Neither parent has the metabolic disorder related to the protein described above, but 3 of their children do. Explain the most likely pattern of inheritance, based on the data below. (3 points) Family Member Normal metabolism Father ✓ Mother ✓ Daughter 1 ✓ Daughter2 ✓ Metabolic disorder ✓ Son 1 ✓ Son 2 ✓ Son 3 Son 4 ✓ Son 5 ✓ ✓ Son 6 Answer: If this disease is an autosomal recessive, any children with the disorder must have inherited two mutant alleles, assuming that the gene follows normal Mendelian patterns of inheritance. That means that both parents would have to be heterozygous. In that case, only 25% of their children would be likely to inherit a mutant allele from each parent and suffer from the disease. However, half of the children have the disease, and, in addition, the disease appears to be limited to sons. These pieces of information suggest that the gene is located on the X chromosome, and that the mother carries the mutant allele. In this case, each son would have a 50% chance of receiving the mutant allele, which would cause him to suffer from the disease. XA XA XAXA (normal female) Xa XAXa (normal female) Y XAY (normal male) XaY (afflicted male) 3. The following table shows the results of a breeding experiment to study the inheritance of flower color and grain length in plants, two genes that exhibit complete dominance in phenotypes. True-breeding parent plants with purple flowers and long pollen grains were crossed with true-breeding parent plants with red flowers and short pollen grains. A second experiment was also conducted between members of the F1 generation to produce an F2 generation. The phenotypes of the resulting offspring in the F1 and F2 generations are in the figure below. a. Using the data in the table, identify the dominant alleles for flower color and grain length. Explain your response. (3 points) A Punnett-square analysis provides a way to predict the expected outcome of the cross of a true-breeding dominant strain of both alleles (AABB) with a true-breeding recessive strain of both alleles (aabb). The square below shows that 100% of the offspring of the cross described will have a phenotype expressing both dominant traits. Since 100% of the F1 offspring were purple with long grains, purple is dominant to red, and long is dominant to short. AB AB Ab AaBb AaBb Ab AaBb AaBb b. Analyze the distribution of phenotypes in the F2 generation. Explain whether the observed results match those expected based upon the results of the first cross. (3 points) Answer: The observed phenotypic ratios do not match the expected phenotypic ratios derived from the Punnett-square analysis below. The phenotypic ratio observed is close to 6:1:1:3, while the Punnett square predicts a ratio of 9:3:3:1. This is not a Mendelian pattern of inheritance, which means that some Mendelian assumption is not holding in this case. One possibility is that the traits of flower color and pollen size do not sort independently. If the two traits are located on the same chromosome, they would tend to sort together, as is observed here — the highest numbers of offspring have both traits of the parents. AB Ab aB ab AB AABB AABb AaBB AaBb Ab AABb AAbb AaBb Aabb aB AaBB AaBb aaBB aaBb ab AaBb Aabb aaBb aabb Expected phenotypic ratios: Purple, long: AABB + 2AABb + 2AaBB + 4AaBb = 9 Purple, short: AAbb + 2Aabb = 3 Red, long: aaBB + 2aaBb = 3 Red, short: aabb = 1 4. Wild fruit flies have a gray body, red eyes, and long wings. The three genes for these traits are all located on the same chromosome. Each gene has a normal, dominant allele and a mutant allele that gives rise to a different, recessive trait. The mutant traits are a black body (b), cinnabar eyes (cn), and vestigial wings (vg). The normal, dominant alleles are indicated with a plus-sign superscript — gray body (b+), red eyes (cn+), and long wings (vg+). The table below shows the results of two testcrosses involving dihybrids with two of the three mutant traits. Use the data from the two testcrosses to roughly sketch a chromosome and map the locations of the three genes. Then, write a couple of sentences that justify your chromosome map. (3 points) Answer: 1 point: The chromosome map can be sketched as follows: 1 point: The greater the distance between genes on a single chromosome, the greater the chance for crossing over to occur and the greater the number of recombinants that will result among the offspring. 1 point: Therefore, the larger percentage of recombinants in the first testcross indicate that there is a greater distance between the genes for eye color (w) and wing size (m) than between the genes for eye color (w) and body color (y). 5. A study was conducted to examine the influence of vitamin A on gene expression in developing fish larvae. Fish larvae were divided into control and experimental groups. The control group received a complete diet; the experimental group received a complete diet minus vitamin A. Larvae from the experimental group did not demonstrate the same pattern of gene expression at different stages during development that was observed in larvae from the control group. At the end of the study, experimental larvae showed signs of skeletal deformities that were not observed in the control group. a. Explain the relationship between vitamin A and normal development. (2 points) Answer: Vitamin A appears to be a factor in normal gene expression controlling the development of skeletal characteristics. b. Describe how the process of gene expression can affect the development of specialized structures such as bones. (2 points) Answer: Gene expression in cells is coordinated by a series of chemical messages coming from other cells in the organism and from the external environment. As the organism develops, its cells respond to these chemical messages. Cells shift their metabolism over time to take in various nutrients from the environment in response to shifting chemical messages. Development proceeds normally if the pattern of genes turning on and off is not disrupted and if all of the necessary nutrients are present to supply the building blocks for each different stage. 6. Researchers studied the effects of atrazine, a herbicide, on developing frog larvae. They found that administration of atrazine did not affect the frog’s life span or its overall health. Atrazine also had no observable effect on female frog larvae. However, atrazine did convert the male larvae into hermaphrodites — organisms with both male and female sex organs — capable of producing viable eggs. a. Describe how gene expression differs during the normal process of sexual differentiation in animals. (2 points) Answer: During normal development, hormones cause the expression of different patterns of genes in males and females. These hormones signal cells to express specific genes needed for sexual development. This leads to the observed differences in sex organs and mating behaviors of the two sexes. b. Explain a possible mechanism for atrazine's effect on developing male frogs. (2 points) Answer: The pattern of hormone expression is specific to each sex. Therefore, if a new chemical compound is introduced that mimics a hormone, the cells will respond as if the hormone was present. Atrazine must mimic a female hormone, because it induces the expression of genes that lead to the development of female traits in males, but it does not affect the development of females. 7. Explain how regulation of gene expression allows a cell to efficiently use its energy supply to carry out specific metabolic reactions that are necessary at specific times. (2 points) Answer: The cell has the capability of carrying out a vast array of metabolic reactions. However, the energy requirements the cell would need to carry out all of these reactions at once would far exceed its normal energy reserves. Instead, the cell only carries out the reactions needed at each moment in time, which is a small subset of its total capacity. In order to limit this subset, the cell regulates the expression of genes that code for enzymes and other proteins needed for metabolic reactions. By only expressing those genes needed for carrying out processes of immediate importance, the cell efficiently uses the energy available to it. 4.2.8 Explore: Embryonic Stem Cells and Gene Expression AP Biology Sem 1 (S3043799) Points possible: 25 Exploration Name: ____________________ Date: ____________ 1. Explain the similarities and differences of embryonic stem (ES) cells and organ-specific stem cells. (4 points) Ideal Answer: Both cells are classified as stem cells, which means that they are capable of dividing to generate new cells that can then go on to differentiate into specialized cells. The difference is that organspecific stem cells have already undergone partial differentiation and cannot change their path of differentiation. Organ-specific stem cells are restricted to being able to generate new cells with specializations associated with the organ they come from. In contrast, embryonic stem cells have not undergone any differentiation and are able to be used for the formation of any type of differentiated cells. Score: 2 points for explaining the similarities between the two types of stem cells, and 2 points for explaining their differences. 2. Some people object to the use of embryonic stem (ES) cells for scientific study or for medical applications. One of the objections raised concerns the ethics of sacrificing embryonic cells. People with this objection think that cells that could potentially become a human should not be used for any other purpose. a. Based upon this information, explain why organ-specific stem cells do not elicit the same objections. (3 points) Ideal Answer: Organ-specific stem cells are not totipotent and are therefore, not capable of being used for organismal cloning. These stem cells do not require the extraction from a sacrificial human embryo which is potentially, or actually, depending on your point of view, a human being. Score: 1 point for recognizing that these cells are not totipotent. 1 point for identifying that embryonic stem cells require the sacrifice of a human embryo. 1 point for identifying that organ-specific stem cells do not require this sacrifice. b. Would your answer to part a, above, change if recent studies are confirmed claiming that organspecific stem cells can be converted into totipotent cells? Explain your reasoning. (3 points) Ideal Answer: Yes, my answer would change. Theoretically such stem cells could be used to develop into a full human being, and so that potential would be sacrificed if they were used for any other reason. It seems that if a person objected to stem cells on this basis, then they would object to using any cell with such enormous potential for any other purpose. Score: 1 point for stating an answer of yes or no, and 2 points for providing a thoughtful answer to explain reasoning behind the answer. 3. Additional ethical questions surround the use of stem cells. For example, some people feel that using stem cells to cure disease opens the possibility of extending the human life span far beyond the normal biological limit. a. Evaluate whether you think it is possible to indefinitely extend human life using stem cells to replace worn-out cells. (3 points) Ideal Answer: Yes, I think that eventually, given enough research, scientists should be able to determine how to replace worn-out cells with fresh cells derived from stem cells. This process should be able to go on indefinitely as long as there are ways to locate cells that need to be replaced, and there are suitable replacements and methods for effectively replacing the old with the new cells. Score: 1 point for stating an answer of yes or no, and 2 points for providing a thoughtful explanation of the reasoning behind the answer. b. If stem-cell technology can be advanced to the extent of extending human life indefinitely, is it ethical to develop such technology? Explain your reasoning. (3 points) Ideal Answer: No, in my opinion, it is not ethical to extend life indefinitely. Society needs to evolve, which means that new generations must replace older generations. If one generation was to live forever, there would be no change and therefore no forward progress. Each generation must accept its place in history and then relinquish their hold on society to the next generations that come after them. Score: 1 point for stating an answer of yes or no, and 2 points for providing a thoughtful answer to explain reasoning behind the answer. 4. What will be gained and what will be lost if stem cells are developed for curing the diseases listed by the authors in the opening paragraph? Explain your answer. (4 points) Ideal Answer: There will be many more gains than losses. Many people will have extended lives and/or better quality of life if stem cells are able to cure diabetes, Parkinson's disease, neurological degeneration, and congenital heart disease. Society will also gain by avoiding spending a lot of money by keeping these people functional and out of costly nursing homes and care facilities. The only loss will be any taxpayer money needed to develop these technologies; however, this money will repay itself in reduced costs for care. Score: 2 points for identifying gains and 2 points for identifying losses and providing thoughtful explanations for each. 5. The authors spend considerable effort to distinguish between reproductive cloning and therapeutic cloning. a. Evaluate their intention in making this distinction clear. What do you think the authors hope to gain by their clarification of terms? (2 points) Ideal Answer: The authors want the public to understand that therapeutic cloning does not directly lead to the creation of a new whole organism. They probably hope to promote the use of therapeutic cloning for medical purposes and want to be sure that the public sees it as a non-threatening technology. Score: 1 point for differentiating between reproductive and therapeutic cloning and 1 point for recognizing that the public confuses the two and need to realize that therapeutic cloning will not lead to any Frankenstein scenarios. b. Do you think that the authors’ suggestion of clarifying these terms will make a difference to public reaction about this technology? Are there additional discussions involving the public that need to occur at the same time that scientists discuss the scientific principles underlying stem-cell biology? Explain your thinking. (3 points) Ideal Answer: Yes, I think it is helpful for people to understand the scientific distinction between the two types of cloning. They are more likely to support the positive uses of such technologies if they understand their limitations. Ethical discussions should be part of the development of technologies like stem cell research. These discussions should be open to anyone so there can be plenty of dialogue to flesh out any potential problems that scientists may not have considered. Scientists should listen to the rest of society to put a cap on any work that does not fit society's moral and ethical standards. Score: 1 point for answering the two questions posed, and 2 points for providing thoughtful explanations for each.