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3/22 Study Guide pages 109, 110 3/19 (104) Study Guide pages 3/18 (103) Nitrogen Cycle Terms and Diagram with arrows. Write and fill in the 11 nitrogen cycle facts. Write the abiotic and boitic factors of the nitrogen cycle as shown. Then use the reading and pictures in the textbook to show how nitrogen flows through the cycle. 3/15 (102) Ecosystem Recycling Diagrams Draw the Water cycle, Carbon Cycle, and Nitrogen Cycle. (From textbook) (101) Bio Study Guide 97, 98 (100) Bio Study Guide 95, 96 (99) Ecology Drawings (98) Ecology Terms (97) Hold 3/3 (96) Gene Regulation 1. A .......... is all the genes of an organism. 2. ............ occurs when genes are transcribed into pieces of mRNA. Bell Work – see (94) 3/2 (95)(104bio) Inheritance Patterns – Draw three pedigrees and three Punnett squares for. 1. A Sex -Linked trait, 2. An Autosomal Dominant trait, 3. A Lethal Autosomal Recessive trait

3/1 (94)(103) Bell Work: Blood type paragraph, table, and pedigree Finish Questions Chromosome Mutations and Gene Mutation drawings. 2/26 3/1 (93)(102) Review Questions: 1,2,5-8,9-16, 19, 21, 22 on page 250 Cooperative Learning: Review questions 1,2,5-8,9-16, 19, 21, 22 on page 250 were assigned. Students were having trouble on this review, so it was turned into a cooperative assignment. Each student was given the answer to one question. The students were to figure out which question it was the answer to. The students then shared the answers with each other. Two copies of every answer were printed and handed out to the students.

2/25 Pedigree Activity Copy this Pedigree on the top half of your paper. Answer questions in complete sentences with no pronouns.

1. (write) Pedigrees can be used to determine a parents genotype.

2. Label the first row in the pedigree “I. Grandparents.” Label the second row “II. Parents.” Label the third row “III. Children.”

3. Label each individual in the pedigree with their phenotype.

4. Does deafness skip a generation or is someone deaf in every generation?

5. What is the genotype of an individual with deafness?

6. What are the two possible genotypes for hearing people in this pedigree?

7. Is any of the Grandparent generation deaf? Is all of the Child generation deaf or not?

8. As evidenced by the answers above, Is the allele for deafness dominant or recessive and how do you know?

9. The three genotypes are homozygous dominant, homozygous recessive, and heterozygous. Write the genotypes of individual numbered 6, 10, and 14 under their circle or square.

10. Look at the offspring on number 6 and 7. The fact that number 7 had deaf offspring means she has a deaf allele. Write the genotype of number 7 under her circle.

11. Children numbered 8, 9, 11, 12, & 13 must get their hearing allele from their mother and their father has only non hearing alleles to provide. Write the genotypes for the rest of the III generation under their circles or squares.

12. Look at the grandparents numbered 1 and 2. Use the fact that they have deaf off­spring to write their genotypes under their circle or Square.

13. Use a Punnett square to figure out the probability of individual number 5 being homozygous dominant verses heterozygous.

14. What are the possible genotypes for the grandparents numbered 3 and 4. 15. For all heterozygous individuals in the pedigree, color in half of their circle or square. 2/24 100 Study Guide pages 63 and 64

2/23 99 Study Guide pages 61 and 62

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2/22 Fruit Fly Experiments (89) 1. Morgan studied the four pairs of fruit fly chromosomes. 2. Only in male flies, one pair was differed in size. 3. Sex chromosomes – contain gender determining genes 4. Autosomes – contain genes not involving gender 5. The “Sex Determining-region Y, (SDY) on the “Y” in mammals codes for a protein that causes testes to form instead of ovaries. 6. Sex Chromosomes have genes for many traits, not just gender. 7. Morgan crossed a white eyed male with red eyed females and in the F2 generation only males had white eyes. 8. In flies, eye color gene is on the X chromosome and Y lacks this gene. 9. Make a Punnet for F1: XR, XR and Xr, Y 10. Make a Punnet for F2: XR, Xr and XR, Y 11. Sex-linked trait – genes on sex chromosome. 12. X-linked – gene on X chromosome 13. Y-linked – gene on Y chromosome 14. X is bigger than Y chromosome, so there are more X-linked Traits 15. SDY is a Y-linked trait 16. If genes are inherited more often together, then they are on the same chromosome. 17. Linked genes – pairs of genes that tend to be inherited together. 18. Linked genes exhibit less independent assortment. 19. Crossing-over swaps genes on the pairs of chromosomes and produces independent assortment 20. Chromosome map – Shows what genes are on the same chromosome and how far apart. 21. Map unit- frequency of crossing over is 1 percent. 22. The closer two genes are together on a chromosome the less likely they will be separated by crossing over.

2/18 Test (88) 10th Chapter Test (87) Protein Synthesis Model

2/19 Genes & Cancer (86) Genes, Cell Division, and Cancer: A variety of genes are involved in the control of cell division. The cell cycle is how the cell replicates itself in a step-by-step fashion. Tight regulation of this process ensures that a dividing cell’s DNA is copied properly, any errors in the DNA are repaired, and each daughter cell receives a full set of chromosomes. The cycle has checkpoints, which allow certain genes to check for mistakes and halt the cycle for repairs if something goes wrong. If a cell has an error in its DNA that cannot be repaired, it may undergo programmed cell death (apoptosis). Apoptosis is a common process throughout life that helps the body get rid of cells it doesn’t need. Programmed cell death protects the body by removing genetically damaged cells that could lead to cancer, and it plays an important role in the development of the embryo and the maintenance of adult tissues. Cancer results from a disruption of the normal regulation of the cell cycle. When the cycle proceeds without control, cells can divide without order and accumulate genetic defects that can lead to a cancerous tumor. The division of cells is regulated by many genes, including genes called proto-oncogenes, which regulate cell division. These genes code for regulatory proteins that ensure that the events of cell division occur in the proper sequence and at the correct rate. A mutation in a proto-oncogene can change the gene into an oncogene, a gene that can cause uncontrolled cell proliferation. The mutation may lead to the over expression of proteins that initiate cell division or to the expression of such proteins at inappropriate times during the cell cycle. These conditions can lead to uncontrolled cell division. A tumor is an abnormal proliferation of cells that results from uncontrolled, abnormal cell division. The cells that make up a Benign tumor remain within a mass. Benign tumors generally pose no threat to life unless they are allowed to grow until they compress vital organs. Examples of benign tumors are the fibroid cysts that can occur in a woman's breasts or uterus. Most benign Tumors can be removed by surgery if necessary. In a malignant tumor, the uncontrolled dividing cells may invade and destroy healthy tissues elsewhere in the body. This uncontrolled growth of cells that can invade other parts of the body is called cancer. The spread of cancer cell beyond their original site is called metastasis. When metastasis occurs, cancer cells can invade healthy tissue and begin forming new tumors. Some genes act as "brakes" to suppress tumor formation. tumor-suppressor genes code for proteins that prevent cell division from occurring too often. In cancer, these tumor-suppressor genes are damaged, and a decrease in the activity of tumor-suppressing proteins can increase the rate of cell division. Cells have three types of tumor-suppressing genes, all of which must be damaged before cancer can occur. Mutations in proto-oncogenes and tumor-suppressor genes may lead to cancer. The mutations that alter the expression of genes coding for cell-regulating proteins are most likely to occur as a result of the organism's exposure to a carcinogen. A carcinogen is any substance that can induce or promote cancer. Most carcinogens are mutagens, agents that cause mutations to occur within a cell. The risk of cancer increase with the number of exposures to carcinogens. Well-known carcinogens include the chemicals in tobacco smoke, asbestos, and ionizing radiation, such as X rays or ultraviolet light from the sun. Tobacco smoke has been found to be the cause of more than 85 percent of all lung cancers. Certain viruses can also cause cancer. Viruses can stimulate uncontrolled growth in host cells by causing mutations in proto-oncogenes or tumor-suppressor genes, thus accelerating the rate of cell division in the host cell. Viruses have been found to cause some cancers in blood-forming tissues, and the human papilloma virus has been shown to cause cervical cancer. Kinds of cancer: Cancers are categorized by the kinds of tissue they affect. Carcinomas grow in the skin in the tissues that line the organs of the body. Lung cancer and breast cancer are examples of carcinomas. Sarcomas grow in bone and muscle tissue. Lymphomas are solid tumors to grow in the tissues of the lymphatic. Tumors in the blood forming tissues may cause leukemia, the uncontrolled production of white blood cells. 1. The cell cycle has ...... that allow genes to check for errors. 2. If a cell has error that can be repaired it undergoes programmed ... 3. Genetically damaged cells can lead to ... 4. ...... results from a disruption of the cell cycle. 5. ...... are genes that regulate cell division. 6. ...... can cause uncontrolled cell division. 7. A ...... results from abnormal cell division. 8. ...... tumors remain within an abnormal cell mass. 9. ...... may invade and destroy healthy tissue else where in the body. 10. ...... occurs when cancer cells spread beyond their original site. 11. ...... genes code for proteins that prevent cell division. 12. Mutations in ...... and ...... may lead to cancer. 13. Exposure to ...... can cause mutations in genes coding for cell regulating proteins. 14. ...... are substances that can promote cancer. 15. ...... are agents that cause mutations in cells. 16. The risk of cancer increases with the ...... of exposures to carcinogens. 17. Tobacco smoke, asbestos, and radiation that affects the electrons of atoms are ... 18. Tobacco smoke causes ..... of all lung cancers. 19. ...... can affect proto-oncogenes and tumor suppressing genes and cause cancer. 20. Cancers are named by the kind of ...... they affect. 21. ...... affect tissues that line the body. 22. ...... grow in bone and muscle. 23. ...... grow in the lymphatic system. 24. ...... is the uncontrolled production of white blood cells.

2/18 __ Test __ using the two make up assignments

2/17 Mutation (85/99) Answer the questions using the reading after it. 1. What is a mutation? A gene mutation is a permanent change in the DNA sequence that makes up a gene. Mutations range in size from a single DNA building block (DNA base) to a large segment of a chromosome.

2. How can gene mutations affect health and development? To function correctly, each cell depends on thousands of proteins to do their jobs in the right places at the right times. Sometimes, gene mutations prevent one or more of these proteins from working properly. By changing a gene’s instructions for making a protein, a mutation can cause the protein to malfunction or to be missing entirely. When a mutation alters a protein that plays a critical role in the body, it can disrupt normal development or cause a medical condition. A condition caused by mutations in one or more genes is called a genetic disorder.

3. How do mutations occur? Gene mutations occur in two ways: they can be inherited from a parent or acquired during a person’s lifetime. Mutations that are passed from parent to child are called hereditary mutations (because they are present in the egg and sperm cells).

4. Compare and contrast inherited and acquired mutations. Hereditary mutations that occur only in an egg or sperm cell, or those that occur just after fertilization, are called new mutations. This type of mutation is present throughout a person’s life in virtually every cell in the body. New mutations may explain genetic disorders in which an affected child has a mutation in every cell, but has no family history of the disorder.

Acquired (or somatic) mutations occur in the DNA of individual cells at some time during a person’s life. These changes can be caused by environmental factors such as ultraviolet radiation from the sun, or can occur if a mistake is made as DNA copies itself during cell division. Acquired mutations in somatic cells (cells other than sperm and egg cells) cannot be passed on to the next generation.

Mutations may also occur in a single cell within an early embryo. As all the cells divide during growth and development, the individual will have some cells with the mutation and some cells without the genetic change.

Some genetic changes are very rare; others are common in the population. Genetic changes that occur in more than 1 percent of the population are called polymorphisms. They are common enough to be considered a normal variation in the DNA. Polymorphisms are responsible for many of the normal differences between people such as eye color, hair color, and blood type. Although many polymorphisms have no negative effects on a person’s health, some of these variations may influence the risk of developing certain disorders.

5. Describe the different kinds of mutations that are possible. The DNA sequence of a gene can be altered in a number of ways. These alterations affect codons on mRNA, thus they affect the sequence of amino acids making up a protein. Gene mutations have varying effects on health, depending on where they occur and whether they alter the function of essential proteins. The types of mutations include:

Base pair mutation: This type of mutation is a change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene. Nonsense mutation: A nonsense mutation is also a change in one DNA base pair. Instead of substituting one amino acid for another, however, the altered DNA sequence prematurely signals the cell to stop building a protein. This type of mutation results in a shortened protein that may function improperly or not at all. Insertion: An insertion changes the number of DNA bases in a gene by adding a piece of DNA. As a result, the protein made by the gene may not function properly. Deletion: A deletion changes the number of DNA bases by removing a piece of DNA. Small deletions may remove one or a few base pairs within a gene, while larger deletions can remove an entire gene or several neighboring genes. The deleted DNA may alter the function of the resulting protein(s). Duplication: A duplication consists of a piece of DNA that is abnormally copied one or more times. This type of mutation may alter the function of the resulting protein. Frameshift mutation: This type of mutation occurs when the addition or loss of DNA bases changes a gene’s reading frame. A reading frame consists of groups of 3 bases that each code for one amino acid. A frameshift mutation shifts the grouping of these bases and changes the code for amino acids. The resulting protein is usually nonfunctional. Insertions, deletions, and duplications can all be frameshift mutations. Repeat expansion: Nucleotide repeats are short DNA sequences that are repeated a number of times in a row. For example, a trinucleotide repeat is made up of 3-base-pair sequences, and a tetranucleotide repeat is made up of 4-base-pair sequences. A repeat expansion is a mutation that increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly.

(85/99) Mutation Facts – Copy (Make up assignment because the majority of students didn't answer questions four and five. ) A mutation is a change in the sequence of bases in a gene. Mutations are due to replication errors or the damaging of DNA. Mutations may alter proteins, so they don't function or are not made. Improperly functioning or missing proteins can cause genetic disorders. Mutations that occur in eggs and sperm, or just after fertilization can be inherited. Hereditary mutations are present from the start and are in every cell of the person. Acquired mutations occur in the DNA of individual cells at some time during the person's life. Acquired mutations are caused by exposure to chemicals and radiation, or errors during replication. Mutations alter codons on mRNA, and thus change the amino acid sequences of proteins. Base pair mutations- result in the substitution of one amino acid for another. Nonsense mutation- results in a premature stop signal Insertion – a number of bases are added Deletion- a number of bases are removed Frameshift – shift in how groups of three bases are read. Repeat expansion – short sequences repeated a number of times.

2/16 (84) 10th Chapter Test Review 2 Copy the questions and look up the answers. 1. Genes direct the making of proteins through and intermediate called? mRNA 2. What acts as a template for the synthesis of RNA? DNA 3. What directs the assembly of proteins at the ribosome? mRNA 4. Using three words and two arrows, descibe protein synthesis. DNA → mRNA 5. What are the three differences between DNA and RNA? 6. What does mRNA do? Brings instructions to the ribosome 7. What does rRNA do? Make up the ribosome 8. What does tRNA do? Brings amino acids to the ribosome 9. What do ribosomes do? Holds mRNA, tRNA and connects amino acids Transcription: 10. What does RNA polymerase do in step 1? Unzips the DNA strands 11. What does RNA polymerase do in step 2? Adds bases into make mRNA 12. What does RNA polymerase do in step 3? Releases new mRNA 13. A specific nucleotides sequence where transcription initiates is? Promoter 14. A specific nucleotides sequence that marks the end of a gene is? Termination signal Translation: 15. How the three bases of a codon specify a particular amino acid and how order of codons in a gene produce a specific sequence of amino acids is called what? Genetic code 16. Each three-nucleotide sequence in mRNA is called what? Codon 17. The decoding of genetic instructions to produce a protein is called? Translation 18. What is an anticodon and where is it found? three bases on tRNA 19. Where on the mRNA does translation begin? At the start codon 20. What four components join together to initiate translation? Ribosome subunits, mRNA, and tRNA 21. What happens when an amino acid is detached from the tRNA in the first position? a bond forms between the amino acids. 22. What does the ribosome do after two amino acids are bonded? shift over one codon 23. What happens to the amino acid chain when the ribosome reaches the stop? the amino acid chain is released 24. Where do the components of translation disassemble? At the stop codon 25. How can one mRNA instruct the synthesis of many proteins at the same time? more than one ribosome translates it simultaneously 26. The total set of genes for an organism is called? Genome

2/11 (83) 10th Chapter Test Review 1. Copy the questions and look up the answers. 1. Process by which DNA is copied? 2. Process by which proteins are produced? 3. Process by which mRNA is produced? 4. Process by which chains of amino acids are produced? 5. Molecule consisting of a phosphate, sugar, and nitrogen base? 6. Molecule that makes up DNA and RNA? 7. Consists of a double nucleotide strand? 8. Consists of a single nucleotide strand? 9. Nucleotide that contains the sugar, deoxyribose? 10. Nucleotide that contains the sugar, ribose? 11. Nucleotide that contains the base thymine? 12. Nucleotide that contains the base uracil? 13. Molecules that make up the side strands of DNA? 14. Molecules that make up complementary pairs in DNA? 15. Adenine and guanine are called? 16. Double ring bases are called? 17. Thymine and cytosine are called? 18. Single ring bases are called? 19. A pairing with T and C paring with G is called? 20. The order of nitrogen bases on DNA is called? 21. The order of nitrogen bases on DNA that codes for a protein? 22. The molecule that separated DNA strands in replication? 23. Places where replication starts? 24. Location where helicase is separating DNA strands? 25. Enzyme that adds complementary nucleotides? 26. Enzyme that makes the new strand of DNA? 27. New strand that is made in one piece? 28. New strand that is made in fragments? 29. Enzyme that joins DNA fragments? 30. The fact that DNA copies are each made of a new and old strand? 31. Produced by an error in replication? 32. Replication errors that can cause cancer? 10th Test Review 1: 1. Replication 2. Protein Synthesis 3. Transcription 4. Translation 5. Nucleotide 6. Nucleotides 7. DNA 8. RNA 9. DNA 10. RNA 11. DNA 12. RNA 13. Sugar and phosphate 14. Nitrogenous bases 15. Purines 16. Purines 17. Pyrimidines 18. Pyrimidines 19. Complementary pairing 20. Base sequence 21. Gene 22. Helicase 23. Origins 24. Replication fork 25. DNA polymerase 26. DNA polymerase 27. Leading strand 28. Lagging strand 29. DNA ligase 30. Semi-conservative replication 31. Mutation 32. Mutation

2/9-10 Gene Expression (82) Four pictures and 22 notes Control of Gene Expression: Read and copy the numbered items. Gene Expression is the “turning on” of a gene that results in transcription or the making of mRNA. Most of the mRNA produced in a cell is translated into a protein. 1. A gene is expressed when it is transcribed and used to make a protein. 2. Each cell contains all the genes for making every protein. 3. Genome – all the genetic material of an organism. 4. Cells only make the proteins they need when they need them. 5. Gene expression is controlled so that each protein is produced only when it is needed. __ Prokaryotic gene regulation __ : Controlling gene expression is simple in prokaryotes. Gene regulation was discovered in E. coli a bacteria that lives in our intestines. In E. coli, three enzymes breakdown the sugar lactose. The production the structural genes for these enzymes are controlled by a regulator gene, a promoter, and an operator. Regulator genes produce repressor proteins bind to operator codes on a structural gene. Repressor proteins keep RNA polymerase from binding to the promoter for structural genes, so transcription can't start. Molecules called inducers inactivate repressor proteins. Lactose is the inducer for the structural genes that produce enzymes to break lactose down. 6. Structural genes – code for a specific amino acid chain/polypeptide 7. Regulatory gene – code for a repressor protein 8. Promoter – sequence where RNA polymerase binds to start transcription. 9. Operator – sequence where a repressor protein can bind and block access to the promoter. 10. Operon include structural genes, promoter, and operator collectively. 11. Repressor proteins act like switches and inhibit genes from being expressed. 12. Inducers are molecules that inactivate repressor proteins, so gene expression begins. __ Eukaryotic gene regulation __ : Control of gene expression in eukaryotes is complex. First sections of chromosomes containing the genes must uncoil. Parts of chromosomes that contain genes that are not used don't uncoil. For example blood cell genes are not used by nerve cells. Gene expression is also controlled by sections of mRNA called introns. Introns are pieces of mRNA that are removed from the total piece of mRNA made during transcription. Once these introns are removed the mRNA can leave the nucleus and be translated for the making of the protein. In addition, transcription factors and enhancers help regulate genes in eukaryotes. Transcription factors help or hinder the placement of RNA polymerase on the promoter of a structural gene. Enhancers may be located far way from a structural gene. Enhancers bring loops of DNA that code for transcription factors closer to the structural genes where they are used. 13. Gene expression is partly due to the coiling and uncoiling of chromosome sections 14. Only the genes on a section that is uncoiled can be transcribed. 15. Genes in eukaryotes contain introns and exons. 16. Introns are sections of a structural gene that are transcribed but are not translated. 17. Exons are the sections of a structural gene that are both transcribed and translated. 18. Introns appear to have a regulatory function 19. Some medications work by affecting introns. 20. In eukaryotes, gene regulation involves the modification of transcribed RNA before it leaves the nucleus. 21. Regulatory proteins in eukaryotes are known as transcription factors. 22. Enhancers may produces loops in the DNA to bring codes together to start transcription.

2/8 Bell Work 2/8 (81)

Copy facts off the board to reinforce concepts used in the activity.

Finish Protein Synthesis Activity.

2/5 Protein Synthesis Activity and test prep.

2/4 Bell Work – Copy figures off the board. Translation Notes (80/94) *Protein synthesis occurs by two processes. __ Steps of Translation __ : 1. Initiation The ribosomal subunits, mRNA, and the tRNa with the start codon bind together. (AUG) 2. Elongation A. Pairing and bonding: The tRNA carrying the amino acid specified by the next codon pairs with the codon. A bond forms forms between the amino acids. B. Tranlocation and departing: The ribosome moves the tRNA and mRNA over. The first tRNA departs and leaves behind its amino acid. C. Growing: A and B repeat. The chain of amino acids continues to grow. 3. Termination and Disassembly Elongation ends when a stop codon is reached on the mRNA.(UAG) A stop codon is one for which there is no tRNA that has a complementary anticodon. The three kinds of RNA come apart and the amino acid chain is released to fold into a protein. (Make four sketches showing the steps of translation.) 2/3 Bell Work – Copy figures off the board Transcription Notes (79/93) 1. Transcription is the process of making an RNA copy of a gene. 2. A gene is a section of DNA that codes for a characteristic. 3. Thousands of genes are the instructions for making proteins. 4. The bases on DNA are a complementary template for making RNA. 5. The enzyme RNA polymerase “reads” one side of the DNA, template strand. 6. Initiation, elongation, and termination are the three steps of transcription. 7. Initiation: RNA polymerase binds to the gene's promoter and the two DNA strands separate. 8. A promoter is a specific sequence of nucleotide where RNA polymerase binds. 9. Elongation: Complementary RNA nucleotides are added and then joined. 10. Termination: RNA polymerase reaches a termination signal on the DNA, so it releases the DNA and new RNA. 11. A termination signal is a specific sequence of nucleotides that mark the end of a gene. 12. Translation – amino acids are assembled based on the sequence of nucleotides in mRNA 13. The sequence of nitrogen bases on mRNA nucleotides that determines to the sequence of amino acids making up a protein is the genetic code. 14. Codons are every three nucleotides in sequence on a piece of mRNA. 15. A codon specifies an amino acid to be used in the chain of amino acids making up a protein. 16. There is also a start codon and a stop codon for making a chain of amino acids. 17. Codons are represented by three letters of the base names on mRNA nucleotides. 18. Proteins are made of chains of amino acids. 19. Chains of amino acids are called polypeptides. 20. Proteins are made of hundreds to thousands of amino acids. 21. The sequence of amino acids determines how a polypeptide will fold into the 3D shape of the protein.
 * The first process is transcription, where mRNA is made off of the DNA by complementary base pairing. The second process is translation, where the three kinds of RNA work together to make proteins.
 * Translation occurs when tRNAs bring amino acids to the ribosome and tRNA's bases form complementary pairs with the mRNA. At the ribosome, the tRNA's amino acids are bonded together in the order determined by the mRNA. This chain of bonded amino acids formed at the ribosome will be folded into a protein.

2/2 Bell Work – Copy figures off the board

Finish Protein Synthesis Intro Notes/lecture Discuss presentation of pictures relating to replication, transcription, and translation.

2/1 Bell Work – copy figures off the board Protein Synthesis Intro Notes/lecture (78/92) 1. The process of making proteins starts in the nucleus and ends in the cytoplasm. 2. Transcription and translation are the two steps in protein synthesis. 3. Transcription occurs in the nucleus and produces mRNA 4. Translation is done outside the nucleus by ribosomes and produces a chain of amino acids. 5. Proteins start as chains of amino acids that fold into special shapes. Protein Synthesis Introduction 6. Ribosomes make proteins outside the nucleus. 7. The instructions for making proteins are on genes inside the nucleus. 8. Messenger RNA brings the instructions for making a protein from the DNA to the ribosome. 9. The bases of DNA act as a template when RNA polymerase makes mRNA. 10. Ribosomes use the order of the bases on mRNA to make proteins. 11. The order of the bases on mRNA determines the order of amino acids that make up a protein. 12. Genes on DNA in the nucleus are the code for making proteins. 13. Messenger RNA (mRNA) is a copy of a gene that moves from inside the nucleus to a ribosome outside the nucleus. 14. Transcription is the process of making mRNA from a gene on the DNA 15. Protein Synthesis = gene expression Path of genetic information: DNA → RNA → protein 16. During transcription: a. mRNA is made/transcribed b. DNA is used as a template/pattern c. DNA is unzipped d. RNA nucleotides form complementary pairs with the exposed DNA bases e. Pairing occurs with one difference from DNA. f. Uracil pairs with adenine instead of thymine. g. RNA polymerase connects the RNA nucleotides into a single strand 17. RNA- Made of nucleotides like DNA 18. Four differences of RNA from DNA i. Single strand ii. Shorter compared to DNA iii. Contains ribose, not deoxyribose iv. Has base uracil, not thymine 19. Some regions fold together to form double strand sections 20. Bases pair complementary in folded double strand sections Transcription Introduction 19. Some regions fold together to form double strand sections 20. Bases pair complementary in folded double strand sections 21. Three types of RNA that each have a different role/function. Transcription Introduction 22. Messenger RNA (mRNA) Carries instructions from genes for making proteins in the nucleus to ribosomes in the cytosol. 23. Transfer RNA (tRNA) Brings amino acids to the ribosome 24. Ribosomal RNA (rRNA) Gives structure and binding sites to ribosomes Transcription Introduction 25. Ribosomes are complex structures made of rRNA and proteins that have two parts that join to use mRNA

1/28  #75 Explanation of Replication ( Part 2 - Use what you learned.) Yesterday you read and reread the handout describing the process of replication. You also manipulated your nucleotide models to simulate replication in an effort to gain an in depth understanding of the process. Today you will benefit from the amount of effort you used to learn about replication.

Take your nucleotide models and run them through the process of replication. As you do this, describe each step of the process in your own words. Use the 18 underlined words in your explanation. Underline these words as you explain them for credit. Also cut out the pictures you were given and place them appropriately in your explanation. Also label the different items in the pictures. Grades will be based on effort, accuracy, and completeness.

1/27 Use the nucleotide models you cut out to simulate replication. Follow the instructions below and use the picture as a guide. Learn the underlined terms in each numbered items. The numbered items actually explain the terms and what happens during replication. The lettered items are instructions for manipulating your model pieces. Manipulating the model pieces will help you visualize and understand the replication process described by the numbered items. . __**DNA Replication Activity**__.
 * 1) 75 DNA Replication Activity (Part 1- learn and manipulate)

DNA, the molecule that holds genetic information, makes an exact copy of itself whenever a cell divides. This copying process is called __replication__. Replication occurs during interphase of the cell cycle and two identical copies of every chromosome must be produced before mitosis, meiosis, or binary fission can take place. Replication occurs inside the nuclear membrane of a cells nucleus. In this activity, it's up to you to use the process of replication and make the copy.

Materials: Cut out paper nucleotide models. 24 nucleotide models separated into two sets. Each set must have three nucleotide models for each of the four bases. Each set must have: three nucleotide models with a__denine__ as the base, three nucleotide models with __thymine__ as the base, three nucleotide models with __cytosine__ as the base, and three nucleotide models with __guanine__ as the base.

Procedure: 1. __Nucleotides__ are the subunit molecules that make up DNA. The __sugars__ and __phosphates__ on the models will make up the sides of the model DNA molecule. The bases between the sides must consist of __complementary pairs__. In other words, adenine is paired with thymine and cytosine is paired with guanine. This model strand of DNA will represent an original strand of DNA before replication. __**A.**__ Take one set of models and arrange the nucleotides into a double nucleotide strand of DNA.

2. Replication starts at thousands of places called __origins__ along a chromosome. The two strands that make up DNA are separated at an origin. The molecule that separates or unzips the two strands is called __helicase__. Helicase is an enzyme that breaks the hydrogen bonds between complementary bases. Two helicase molecules move in opposite directions at each origin. The two strands make a “Y” shaped region called a __replication fork__ where they are separated. Separate one end of the model strand of DNA into a replication fork. __**B.**__ Make the fork by sliding first nucleotides apart about 4.5 inches and slide the second nucleotides apart about half as much.

3. As the replication fork, made by the helicase enzyme, moves down the strand of DNA, the bases on its nucleotides are exposed. Free nucleotides in the cell's nucleus are paired in a complementary manner to these exposed bases. Molecule called DNA polymerase moves down each original side strand of DNA connecting these bases into a new side-strand of DNA. DNA polymerase is an enzyme that helps form the covalent bonds between the sugars and phosphates of adjacent nucleotides on the new growing side-strand of DNA. __**C.**__ Look for the side of the fork that has a phosphate molecule at the end. Place a nucleotide with a complementary base next to the nucleotide you just found.

4. The original DNA side-strand to which you just added a nucleotide is called the __leading strand__. A new DNA side-strand starts with the nucleotide you just placed. This new DNA strand “grows” one nucleotide at a time following the helicase and opening replication fork. DNA polymerase also follows the helicase bonding the sugars and phosphates of each nucleotide on the growing strand. Because the growth of the leading stand follows the opening replication fork, it is added as __one continuous piece__. __**D.**__ Open the replication fork on your model pieces one more nucleotide. Add a nucleotide with a complementary base. Repeat this two more times.

5. The original DNA side-strand to which there are no nucleotides added is called the __lagging strand__. DNA polymerase can only move down DNA in one direction, so nucleotides on the lagging strand are added opposite to the direction of nucleotides being added to the leading strand. In other words, nucleotides are added to the lagging strand in the direction away from the replication fork and movement of the helicase enzyme. Because DNA polymerase can only move down the lagging strand away form the replication fork, the new growing side-strand is __added in fragments__/pieces. __**E.**__ Add complementary nucleotides to the bases exposed on the lagging strand starting at the replication fork and moving away from it.

6. At this point, both new side-strands of DNA are growing on the leading and lagging strands of the original double strand of DNA. When finished, the leading and lagging strands will be two identical, separate, double strands of DNA. Each of these double strands will have one new and one old strand of DNA. Because of this replication is called __semi-conservative__. __**F.**__ Open the replication fork the rest of the way one base at a time. Place complementary nucleotides on the exposed bases of the leading strand as you open the fork. __**G.**__ Place a complementary nucleotide on the exposed base of the lagging strand farthest away from the bases already already on the lagging strand. Starting next to this nucleotide, add complementary nucleotides to the lagging strand until it is complete. A DNA polymerase will move down the lagging strand bonding the sugars and phosphates of nucleotides being added. DNA polymerase can't bond the fragments of the new strand that has been added to the lagging strand. Another enzyme called __DNA ligase__ connects the new pieces that will make up the new strand that complements the lagging strand. Replication is now complete resulting in two identical double strands of DNA.



1/26 Prepare to explain replication shown in this picture. Answer the following questions using pages 200 and 201 1. What is replication? 2. When does replication occur? 3. Why does replication occur? 4. What does the original piece of DNA become?. 5. What are origins of replication? 6. What is the job of helicases? 7. How do helicases function? 8. What is a replication fork? 9. What is the job of DNA polymerases? 10. What are nucleotides? 11. How do DNA polymerases function? 12. Where do the covalent bonds and hydrogen bonds form? 13. What is DNA synthesis? 14. How is each original strand used as a template? 15. Why is DNA synthesis different for the leading and lagging strands? 16. How is DNA synthesis different for the leading and lagging strands? 17. Which new strand is made in fragments and what joins these fragments? 18. What do DNA polymerases do when they run out of DNA consisting of a single strand? 19. What is the result of replication? 20. Why is replication considered semi-conservative? 21. Why does replication occur at multiple origins along a chromosome? Reading: Replication is the process by which DNA is copied in a cell before a cell divides by mitosis, meiosis, or binary fission. During DNA replication, the two nucleotide strands of the original double helix separate at complementary bases. Because the two strands are complementary, each strand serves as a template to make a strand. After replication, the two identical double-stranded DNA molecules separate and move to the new cells formed during cell division. __Steps of DNA Replication__ Step 1: Enzymes called helicases separate the DNA strands. Helicases move along the DNA molecule, breaking the hydrogen bonds between the complementary nitrogenous bases. This action allows the two DNA strands of the double helix to separate from each other. The Y-shaped region that results when the two strands separate is called a replication fork. Step 2: Enzymes called DNA polymerases add complementary nucleotides, found floating freely inside the nucleus, to each of the original strands. As the nucleotides on the newly forming strand are added, covalent bonds form between the adjacent nucleotides. Covalent bonds form between the deoxyribose sugar of one nucleotide and the phosphate group of the next nucleotide on the growing strand. Hydrogen bonds form between the complementary nitrogenous bases on the original and new strands. DNA polymerase can only add nucleotides in one direction, so there is a leading and lagging strand. Step 3: DNA polymerases finish replicating the DNA and fall off. The result is two separate and identical DNA molecules that are ready to move to new cells in cell division. In each new DNA double helix, one strand is from the original molecule, and one strand is new. This type of replication is called semi-conservative replication because each of the new DNA molecules has kept (or conserved) one of the two (or semi) original DNA strands. __Action at the Replication Fork__: DNA synthesis occurs in different directions on each strand, as shown by the arrows by the DNA polymerases. As the replication fork moves along the original DNA, synthesis of one strand follows the movement of the replication fork. Synthesis on the other strand, however, moves in the opposite direction, away from the replication fork, which leaves gaps in the newly synthesized strand. The gaps are later joined together by an enzyme called DNA ligase. __Many Forks Along a Chromosome__: At the rate that one DNA polymerase adds nucleotides (about 50 nucleotides per second in eukaryotic cells), it would take 53 days to replicate the largest human chromosome. Instead, replication begins at many points or origins along the DNA. Replication starts at each origin with two replication forks moving in opposite directions. For example, in a fruit fly chromosome, replication begins simultaneously at about 3,500 sites in a DNA molecule. Only simultaneous replication along chromosomes could allow rapid enough copying of the organism's entire DNA.
 * 1) 74 Replication Questions

1/25 Use the material at the link above to answer these questions. Also use your knowledge of cell parts or your textbook. Lab Questions: 1. After step 6, what did you see in the alcohol and describe what it looked like? 2. What is another word or phrase for DNA? 3. What 4 nitrogenous bases are found in DNA? 4. What part of the cell did the DNA come from? 5. What usually keeps the DNA in its usual place in the cell? 6. What are cell membranes and nuclear membranes made of? 7. What does soap do to the stuff that membranes are made of? 8. Why do you think the soap helped to free the DNA? 9. DNA is less dense than water & alcohol. Why does the DNA move up into the alcohol? 10. We want the DNA to clump together, but like charges repel and DNA has a negative charge. Salt can provide a positive charge, so what is its purpose?
 * 1) 73 DNA Extraction Activity

1/20 and 1/21 See textbook pages 197, 198, and 199 for better pictures and an explanation. Copy the notes of this presentation: [|DNA Structure Terms] Look at the links below to see how to use your model pieces. Replication 1 and Replication 2 and More information.
 * 1) 72 DNA Sturcture - Students coppied the notes in the picture, cut out model pieces and assembled them.

Model Sheet - Label each phosphate group, deoxyribose sugar, and nitrogenous base with a single letter. Assemble these pieces into a double strand of DNA composed of repeating nucleotide subunit like the picture above.





1/19 [|Discovery of DNA]
 * 1) 71 Discovering DNA - Copy the notes in the presentation - read the experiments on pages 193-195 in the Biology text.

Extra Credit: Make a cartoon of the animation at this link: DNA Replication []