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Chapter 6 DNA: The Molecule of Life Lecture Presentation by Wendy Kuntz © 2015 Pearson Education, Inc. Chapter 6 DNA: The Molecule of Life: Unit Hyperlinks • • • • • • • • • • 6.1 DNA intro 6.2 DNA replication 6.3 DNA directs the production of proteins 6.4 Flow from DNA to RNA to protein 6.5 Transcription 6.6 Translation part one 6.7 Translation part two 6.8 Gene expression regulation 6.9 Signal transduction 6.10 Mutations effects © 2015 Pearson Education, Inc. Chapter 6 DNA: The Molecule of Life: Unit Hyperlinks • • • • • • • • • 6.11 Cancer part one 6.12 Cancer part two 6.13 Genetic engineering 6.14 DNA manipulation 6.15 Genetically modification 6.16 PCR 6.17 DNA profiles 6.18 Genome mapping 6.19 Gene therapy © 2015 Pearson Education, Inc. 6.1 Opening Questions: What molecule holds the instructions for living things? Do these organisms all share the same genetic code? Explain. Mushroom Aquatic Algae Caterpillar Elephant Protist © 2015 Pearson Education, Inc. Flower Human 6.1 DNA is the molecule that holds the instructions for all living things • DNA is shorthand for Deoxyribose Nucleic Acid • A DNA molecule is a double helix with two strands made up of a long string of nucleotides. © 2015 Pearson Education, Inc. 6.1 Each nucleotide consists of a sugar, a phosphate, and a base Bases © 2015 Pearson Education, Inc. 6.1 In a DNA molecule there are four bases with specific pairing rules • Adenine (A) can only bond with thymine (T). • Guanine (G) can only bond with cytosine (C). Each strand of DNA in a double helix is complementary. © 2015 Pearson Education, Inc. A-T C-G 6.2 Opening Questions: Can you build a DNA molecule? • In a DNA double helix, adenine (A) can only bond with thymine (T) and guanine (G) can only bond with cytosine (C). • Given a half strand of DNA, build the other strand. © 2015 Pearson Education, Inc. A • ?T T • ?A C•? G A • ?T C•? G G•C ? C•? G 6.2 What makes DNA a great molecule for hereditary information? • DNA strands are complementary! – If you know ½ of the molecule, you can build the other. • To replicate, the DNA molecule unzips. • Each strand serves as a template to build a new strand following the base-pairing rules. Genetic instructions are passed down via DNA replication. © 2015 Pearson Education, Inc. 6.2 During DNA replication a cell duplicates its chromosomes • New DNA molecules are made up of one of the original parental strands plus a new half. • As a result, DNA replication is called semi-conservative. © 2015 Pearson Education, Inc. 6.3 Opening Questions: True or false? • True or false. DNA codes for all the information needed to make up an organism uses only four building blocks (A,T,C,G). • True or false. All the DNA molecules in your body put end to end would reach from the Earth to the Sun and back over 600 times. • True or false. Typing 60 words per minute, eight hours a day, it would take about 50 years to type the human genome. • True or false. Humans and bananas share about 50% common DNA. All true! © 2015 Pearson Education, Inc. 6.3 DNA directs the production of proteins via an intermediate molecule of RNA • RNA is also a nucleic acid (like DNA): Ribonucleic Acid • RNA has three major differences: 1. Single-stranded (not a helix) 2. Sugar in RNA is ribose 3. Thymine (T) is replaced by uracil (U) © 2015 Pearson Education, Inc. 6.3 DNA holds information on how to produce proteins • DNA is able to act as the molecule of heredity because it can direct the production of proteins. • DNA first directs the production of RNA, which in turn controls the manufacture of proteins. • Proteins then perform the majority of cellular functions and control physical traits. © 2015 Pearson Education, Inc. DNA RNA Proteins 6.3 The flow of genetic information © 2015 Pearson Education, Inc. 6.4 Opening Questions: How does DNA make brown eyes? • What color are your eyes? • What color are your neighbor’s eyes? • How might your DNA instructions for eye color vary from your neighbor’s? • How are the instructions in DNA turned into the physical pigment in your eye? © 2015 Pearson Education, Inc. 6.4 Genetic information flows from DNA to RNA to protein in two steps © 2015 Pearson Education, Inc. 6.4 Transcription rewrites the DNA code into RNA, which then leaves the nucleus • Transcription follows the DNA base-pairing rules with one exception: – Uracil (U) is used instead of thymine (T). • The molecule that results from transcription is called messenger RNA (mRNA). © 2015 Pearson Education, Inc. 6.4 In translation, the RNA molecule serves as instructions for making a protein • At the ribosomes in the cytoplasm, each mRNA codon is translated into an amino acid to build a protein. © 2015 Pearson Education, Inc. 6.5 Opening Questions: What is a gene? • How would you define a gene? • Write your answer down and then share it with your neighbor. • Are your answers the same? © 2015 Pearson Education, Inc. 6.5 Transcription creates a molecule of RNA from a molecule of DNA • During transcription, the DNA double helix separates. • One strand of DNA is used to generate a molecule of RNA. • The RNA is processed to become messenger RNA, which then exits the nucleus via a nuclear pore. © 2015 Pearson Education, Inc. 6.5 Review Question: What is a gene? • There is no simple, agreed-upon definition that accurately describes all known genes. – Is it a stretch of DNA? – Does it produce a protein? – What if a protein is made from two different genes? • As we study the genome, it actually becomes harder to find one definition. • For now, we can define a gene as a discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA. © 2015 Pearson Education, Inc. 6.6 Opening Questions: DNA and you • Would you get a personal DNA test if you could? Why or why not? • Would you get a personal DNA test before you had a baby? Why or why not? • Should we run personal DNA tests on newborn babies? Why or why not? © 2015 Pearson Education, Inc. 6.6 Translation involves the coordination of three kinds of RNA • Translation is done in the cytoplasm by ribosomes. • Ribosomes are made from rRNA and protein. • Ribosomes read mRNA and use tRNA to produce a string of amino acids. © 2015 Pearson Education, Inc. 6.6 The genetic code uses triplets • “Language” of nucleotides is in three-letter codons. • Each mRNA codon matches one of 20 amino acids. • One end of a transfer RNA (tRNA) holds an amino acid. • At the other end is an anticodon that matches up with the mRNA. © 2015 Pearson Education, Inc. 6.6 The genetic code: © 2015 Pearson Education, Inc. 6.7 Opening Questions: Can you translate the genetic code? • What amino acid would be produced from an mRNA with the sequence: AUG-ACU-AAA-GAG-UCA-UAA Hint: Use your genetic code table! Met-Thr-Asn-Glu-Ser © 2015 Pearson Education, Inc. 6.7 Translation creates a molecule of protein via the genetic code • Translation is divided into three phases: – Initiation – Elongation • Translation begins when two subunits of a ribosome assemble on an mRNA. • A transfer RNA (tRNA) then brings in amino acids that match the codon in the mRNA. © 2015 Pearson Education, Inc. 6.7 Translation results in a polypeptide • Elongation continues until the ribosome reaches a stop codon on the mRNA. • The ribosome machinery then disassembles. • The completed polypeptide is now available to be used or modified by the cell into a functioning protein. © 2015 Pearson Education, Inc. Polypeptide Amino acid 6.8 Opening Questions: Are you your genes? • We are a product of both our genes and our environment. • What are ways your physical or behavioral traits might be influenced by your genes, your environment, or both? © 2015 Pearson Education, Inc. 6.8 Gene expression, the production of proteins, is regulated in several ways • Gene regulation is the process of turning genes on and off. • Different cell types express different genes. – For example, not all cells need lactase (enzyme that digests milk). In what cell types would you expect lactase gene expression? © 2015 Pearson Education, Inc. 6.8 X-chromosome inactivation is an extreme case of gene regulation • In female mammals one X chromosome in each body cell is highly compacted and almost entirely inactive. © 2015 Pearson Education, Inc. 6.8 There are several points along the path from DNA to protein that can be regulated 1. Special transcription factors must bind to DNA to “turn on” transcription. © 2015 Pearson Education, Inc. 6.8 After transcription, the RNA may be altered in several ways 2. Before leaving the nucleus, the RNA is modified: – A cap and tail are added. – Non-coding introns may be removed. – Protein-coding exons may be rearranged. © 2015 Pearson Education, Inc. 6.8 Translation offers more opportunities for gene regulation 3. The cell can control the following: – Whether translation proceeds – How proteins are modified after translation – When proteins are broken down © 2015 Pearson Education, Inc. 6.9 Opening Questions: Are all your cells the same? • All the cells in your body contain the same DNA. But do all the cells make the same proteins? • How might the following cell types differ in the functions of proteins produced? How might they be similar? – Liver cell – Brain cell – Stomach cell © 2015 Pearson Education, Inc. 6.9 Cell-to-cell communication can control gene expression • Multicellular life depends on cell-to-cell signaling. • Molecules exit one cell and bind to a receptor protein on the outside of another cell. • This binding triggers a signal transduction pathway. © 2015 Pearson Education, Inc. 6.9 A signal from another cell can regulate genes (turn on or off) in the receiving cell • signal transduction pathways • Cells can regulate other cells by turning genes on or off in the target cell • Cells communicate with each other either directly or by sending molecules through the blood © 2015 Pearson Education, Inc. 6.9 A signal from another cell can regulate genes (turn on or off) in the receiving cell © 2015 Pearson Education, Inc. 6.9 Cell-to-cell communication is particularly important in a developing embryo • Development involves frequent cell division (to increase body size) that must be carefully coordinated. © 2015 Pearson Education, Inc. 6.9 Cell-to-cell communication is particularly important in a developing embryo • Inductive signals can cause cells to change shape, migrate, or even destroy other cells. © 2015 Pearson Education, Inc. 6.9 Cell-to-cell communication is particularly important in a developing embryo • Homeotic genes are master control genes; they direct the location of the head and body parts. © 2015 Pearson Education, Inc. 6.10 Opening Questions: What difference does a letter make? • We only will make sentences with three-letter words (triplet). Start with the sentence: THE CAT ATE THE RAT • Change one letter (R to H): THE CAT ATE THE HAT • Delete letter C and move everything over: THE ATA TET HER AT • Add a letter B in the sixth letter place: THE CAB TAT ETH ERA T What happens to the meaning of each sentence? © 2015 Pearson Education, Inc. 6.10 A mutation is any change in the nucleotide sequence of DNA • Replacing, deleting, or adding a nucleotide base can have a wide range of effects. • Mutations are the raw material of evolution by natural selection. • However, most mutations are harmful. What might happen to the protein product if there is a change in the nucleotide sequence? © 2015 Pearson Education, Inc. 6.10 Mutations in DNA can change the protein produced • Mutations can be: – Point mutations – Frame shift mutations – Spontaneous – Induced by mutagens • High-energy radiation • Chemicals © 2015 Pearson Education, Inc. 6.10 Point mutations occur at a single nucleotide No mutation: DNA ACA RNA UGU Amino Acid CYSTEINE Silent mutation: ACG UGC CYSTEINE Missense: TCA AGU SERINE Nonsense: ACT UGA STOP Point mutations can have varying effects. © 2015 Pearson Education, Inc. 6.10 Frameshift mutations are due to the addition or deletion of a nucleotide Added A Frameshift mutations often result in different or defective proteins. © 2015 Pearson Education, Inc. 6.11 Opening Questions: What do you know about cancer? • List three things you know about cancer. • List something you want to know about cancer. © 2015 Pearson Education, Inc. 6.11 Loss of gene expression control can result in cancer • Mutations can lead to a mass of body cells growing out of control, a tumor. • If a tumor spreads to other tissues, the person is said to have cancer. © 2015 Pearson Education, Inc. 6.11 Genes regulate the cell cycle • A cell cycle control system regulates the timing of cell duplication. • A proto-oncogene codes for proteins that tell the cell when to duplicate. GO © 2015 Pearson Education, Inc. STOP 6.11 Mutations in regulator genes can lead to an overgrowth of cells • A mutated proto-oncogene fails to regulate cell division and is called an oncogene. ? ? Cancer is caused by out-of-control cell growth due to a breakdown of the cell cycle control system. © 2015 Pearson Education, Inc. 6.11 Cancer can occur when protooncogenes are mutated to oncogenes • A mutation in a growth factor gene can produce a hyperactive protein that promotes unnecessary cell division. • A mutation that deactivates a tumor suppressor gene may result in uncontrolled growth. GO! X STOP Mutations may result in proteins that either don’t stop the cell cycle or stimulate growth. © 2015 Pearson Education, Inc. 6.12 Opening Questions: What is cancer? • Imagine your cousin texted you that your aunt has just been diagnosed with cancer. Your cousin knows you are taking a biology course, so she asks, “What is cancer?” • Send a text explaining how we define cancer. © 2015 Pearson Education, Inc. 6.12 Cancer is caused by out-of-control cell growth • Cancer begins within a single cell when proto-oncogenes mutate into oncogenes. © 2015 Pearson Education, Inc. 6.12 A tumor is an abnormally growing mass of body cells • The spread of cancer cells in the body is called metastasis. A benign tumor A malignant tumor - No spreading - Spreading © 2015 Pearson Education, Inc. 6.12 There are several ways to treat cancer Surgery can remove a tumor. Radiation can disrupt cell division locally. What might happen to your normally dividing cells? © 2015 Pearson Education, Inc. Chemotherapy drugs can disrupt cell division throughout the body. 6.12 There are ways to reduce cancer risk Healthy diet Exercise Regular screenings Not smoking Sun protection © 2015 Pearson Education, Inc. 6.13 Opening Questions: True or false? • True or false. You can pay to save a sample of your dog’s or cat’s DNA for future cloning. • True or false. Condo associations can use DNA to identify the proper owner of a poop sample. • True or false. Some of us are carrying Neanderthal DNA. • True or false. The U.S. Supreme Court has ruled police can take DNA upon arrest. • True or false. DNA-based computers may one day hold more data than our fastest server today. All true! © 2015 Pearson Education, Inc. 6.13 Genetic engineering involves manipulating DNA for practical purposes Biotechnology is the manipulation of organisms or their components to make useful products. © 2015 Pearson Education, Inc. DNA technology is a set of methods for studying and manipulating genetic material. Genetic engineering is the direct manipulation of genes for practical purposes. Making Humulin – In 1982, the world’s first genetically engineered pharmaceutical product was produced. • Humulin, human insulin, was produced by genetically modified bacteria. • is used today by more than 4 million people with diabetes. – Today, Humulin is continuously produced in gigantic fermentation vats filled with a liquid culture of bacteria © 2015 Pearson Education, Inc. 6.13 Gene cloning is an example of genetic engineering • How can we produce large quantities of a protein (such as human insulin)? • We can insert DNA into bacteria and have them do the work. © 2015 Pearson Education, Inc. PLASMID A small circular DNA molecule that replicates separately from the much larger bacterial chromosome. (The plasmid is not drawn to scale here.) 6.13 Cutting and pasting DNA is an important step in genetic engineering • Restriction enzymes are proteins that cut DNA at specific nucleotide sequences. • The resulting fragments are called restriction fragments. © 2015 Pearson Education, Inc. 6.14 Opening Questions: Who owns genes? Part 1 Real-World Case Study: In the 1990s a private company discovered a set of genes that increase the risk of getting breast and ovarian cancers (BRCA1 and BRCA2). They applied for and received a patent for the genes, which means they are the only company that can offer a genetic test for the BRCA1 and BRCA2 genes, earning the company over $400 million in 2012. In June 2013 the U.S. Supreme Court took up the issue. © 2015 Pearson Education, Inc. 6.14 Opening Questions: Who owns genes? Part 2 • The company president says they have invested more than $500 million to study and isolate the BRCA genes. • Opponents say genes are made by nature and can’t be patented. • Doctors and patients say they should be able to access tests at a reasonable cost in order to prescribe relevant treatments. What do you think? Should a private company be able to patent a gene? Present your arguments. © 2015 Pearson Education, Inc. 6.14 DNA may be manipulated many ways within the laboratory • Scientists can now answer questions and solve problems by manipulating DNA. • Let’s explore some of the tools in the genetic engineering toolbox. © 2015 Pearson Education, Inc. 6.14 DNA can be isolated from a cell and put into a genomic library • A genomic library is a collection of cloned DNA fragments that includes an organism’s entire genome. • Once created, a genomic library can be used to hunt for and manipulate any gene from the starting organism. © 2015 Pearson Education, Inc. This collection of bacteria constitutes a genomic library that can be used for later experiments. 6.14 DNA can be visualized using nucleic acid probes • In order to find a gene of interest a researcher can use a nucleic acid probe. • A complementary molecule made using radioactive or fluorescent building blocks will bind with DNA. © 2015 Pearson Education, Inc. 6.14 DNA can be synthesized from scratch • An automated DNA synthesizer machine can quickly and accurately produce customized DNA molecules up to lengths of a few hundred nucleotides. © 2015 Pearson Education, Inc. 6.14 DNA produced from a cell’s mRNA • Reverse transcriptase can synthesize DNA from the mRNAs within the cell. • The result is complementary DNA (cDNA) representing the genes that were being transcribed in the cell at the time. © 2015 Pearson Education, Inc. 6.14 Case Study Update: Who owns genes? • In June 2013, The U.S. Supreme Court case Association for Molecular Pathology et al. v. Myriad Genetics, Inc., et al. was presented. • The Court’s opinion was that “a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated.” Do you agree with the Supreme Court’s decision? © 2015 Pearson Education, Inc. 6.15 Opening Questions: What is a GMO? • Have you ever eaten a genetically modified organism (GMO)? If yes, describe what you’ve eaten. • Write down a question that you have about GMOs. • Share your question with your neighbor. © 2015 Pearson Education, Inc. 6.15 Plants and animals can be genetically modified • Genetically modified organisms (GMOs) are ones that have acquired one or more genes by artificial means. © 2015 Pearson Education, Inc. 6.15 GM plant crops currently make up a significant part of our food supply Bt corn has been genetically modified to express a protein that acts as an insecticide, © 2015 Pearson Education, Inc. Golden rice is a transgenic variety, created with genes that produce betacarotene. Hawaii papaya is genetically engineered to be resistant to the ring-spot virus. Genetically Modified (GM) Foods – In the United States today, roughly half of the corn crop and more than three-quarters of the soybean and cotton crops are genetically modified. – Corn has been genetically modified to resist insect infestation, attack by an insect called the European corn borer. © 2013 Pearson Education, © 2015 Pearson Education, Inc. Inc. Genetically Modified (GM) Foods – “Golden rice 2” • is a transgenic variety of rice that carries genes from daffodils and corn • could help prevent vitamin A deficiency and resulting blindness. © 2013 Pearson Education, © 2015 Pearson Education, Inc. Inc. 6.15 GM animals are not part of our food supply (yet), but do have other uses • Pharmaceutical companies have produced various GM animals that produce drugs. • The FDA (Food and Drug Administration) is considering approval for the first GM food, a fast-growing transgenic salmon. © 2015 Pearson Education, Inc. 6.15 Pros and cons of GMOs Complete the comparison table: PROS © 2015 Pearson Education, Inc. CONS 6.16 Opening Questions: What role should DNA play in the criminal process? Real-World Case Study: In 2013, a Texas man convicted in a 1981 stabbing death was freed by DNA evidence after serving 29 years in prison. In the original crime, the victim’s abandoned car was found with several pieces of evidence, including a black hairnet. In 2011, hair samples preserved for three decades underwent DNA testing and linked the samples to someone else. Randolph Arledge’s conviction was overturned. • Should DNA testing of evidence be mandatory? • Who should pay for DNA testing in trials? • What do you think is the responsibility of the state for old cases? Explain. © 2015 Pearson Education, Inc. 6.16 Polymerase chain reaction (PCR) copies target DNA quickly and precisely • Heating splits apart DNA helix into two complementary strands. • A heat-stable DNA polymerase (enzyme that synthesizes DNA) is used to build new strands. • Billions of gene copies are generated in just a few hours. Using PCR, one drop of blood can provide enough DNA for analysis. © 2015 Pearson Education, Inc. 6.16 PCR involves cycles of heating and cooling © 2015 Pearson Education, Inc. 6.16 PCR is generally used to amplify one region of DNA • Primers (short single strands of DNA) bind to the start and end points of the segment of DNA being amplified. © 2015 Pearson Education, Inc. 6.17 Opening Questions: Is your DNA showing? If you knowingly (or unknowingly) provide a DNA sample, who should have access? – – – – – – You? Doctor? Insurance company? Police department? Spouse? Girlfriend/boyfriend? Rank the above by their level of access. Who else would you include or deny? © 2015 Pearson Education, Inc. 6.17 DNA profiling can prove a match between two samples • Imagine that you have a sample of DNA from a crime scene and a second sample from a suspect. • How can you prove they match? • Entire genome matching is impractical, but we can compare regions of DNA. © 2015 Pearson Education, Inc. What can be learned with just a drop of blood? 6.17 DNA profilers focus on specific sites that are known to vary considerably • Scattered throughout the genome are short tandem repeats (STRs) sites. • At each STR site, a four-nucleotide sequence is repeated many times in a row. For example: AGATAGATAGATAGATAGAT • The number of repeats varies widely within the human population. © 2015 Pearson Education, Inc. 6.17 STR analysis compares 13 sites within the human genome • These sites vary so widely that no two humans have ever had the same number of repeats at all 13 sites (except identical twins). © 2015 Pearson Education, Inc. 6.17 Follow a crime scene blood drop • STR analysis can determine if the sample matches the suspect. © 2015 Pearson Education, Inc. 6.17 Gel electrophoresis provides comparison of DNA samples © 2015 Pearson Education, Inc. 6.18 Opening Questions: What can we learn from the entire genome? • In the 1990s, scientists set out on a quest to map the entire set of human genes. • This quest was a huge undertaking. What are at least three things we might be able to learn with knowledge of all the genes in the human genome? © 2015 Pearson Education, Inc. 6.18 Whole genomes can be sequenced and mapped • In 1995, a team of biologists announced they had determined the DNA sequence of the entire genome of Haemophilus influenzae, a disease-causing bacterium. • This marked the first successful experiment in genomics, the science of studying the complete sets of genes (genomes) and their interactions. © 2015 Pearson Education, Inc. 6.18 The Human Genome Project was completed in 2003 • The human genome contains 21,000 genes that encode for 100,000 different proteins. • The data are providing insight into development, evolution, and many diseases. © 2015 Pearson Education, Inc. Human Genome Facts 6.18 Genome mapping involved several separate techniques • The set of techniques used to sequence an entire genome from an organism is called the whole-genome shotgun method. © 2015 Pearson Education, Inc. 6.18 The field of proteomics examines the proteins encoded by a genome • The number of proteins in humans vastly exceeds the number of genes. • Understanding proteins and their tasks is at the forefront of biological research. © 2015 Pearson Education, Inc. 6.19 Opening Questions: Can we fix genes? • From what you’ve learned about DNA and genetic information, do you think it is possible to “fix” someone’s genes? • Several diseases are the result of a single gene mutation. • How can we fix genes? • What might be some benefits? • What might be some risks? © 2015 Pearson Education, Inc. 6.19 Gene therapy aims to cure genetic diseases • Gene therapy is the alteration of a person’s genes in order to treat or cure a disease by inserting the “correct” DNA into the cell. • As you can imagine, the easiest disorders to “fix” are those with a single defective gene. © 2015 Pearson Education, Inc. 6.19 Gene therapy aims to cure genetic diseases 1. Gene therapy begins with isolation of the normal gene from a healthy person. 2. Enzymes are used to produce an RNA version of the target DNA gene. © 2015 Pearson Education, Inc. 6.19 Gene therapy aims to cure genetic diseases 3. The RNA gene is combined with an infectious, but harmless, retrovirus The virus is the vector. 3. The virus is used to infect a patient’s bone marrow cells, transferring the proper gene to a diseased individual. © 2015 Pearson Education, Inc. A genetically engineered bone marrow cell carrying the correct version of the gene 6.19 Gene therapy in practice • Gene therapy has been used to treat a disease caused by a defect in the genes of the immune system. • Some children were cured, but others died or developed cancers. • Although gene therapy remains promising, there are still problems with its application. • Better vectors are needed to insert the corrected gene into the cells of a person with a genetic disease © 2015 Pearson Education, Inc.