BIOTECHNOLOGY Module Quarter 3 PDF

Republic of the Philippines Department of Education REGION VI – WESTERN VISAYAS SCHOOLS DIVISION OF ILOILO LEGANES NATIONAL HIGH SCHOOL (JUNIOR HIGH SCHOOL) SELF LEARNING MODULE (SLM) BIOTECHNOLOG...

Republic of the Philippines Department of Education REGION VI – WESTERN VISAYAS SCHOOLS DIVISION OF ILOILO LEGANES NATIONAL HIGH SCHOOL (JUNIOR HIGH SCHOOL) SELF LEARNING MODULE (SLM) BIOTECHNOLOGY QUARTER 3 Prepared by: KRISTINE T. CATIPUNAN  WEEK 1 I. COMPETENCY Analyze the vital role of DNA, RNA, and proteins in the transmission of hereditary traits. CODE: SSP_S8BIOTECH-IIIa-i-8 II. CONTENT GOALS At the end of this module, students should be able to: a. Compare the structure of the DNA and the RNA. b. Identify the parts of the DNA and the RNA. c. Identify the nitrogenous base pairs of the DNA. d. Explain the vital roles of DNA, RNA, and proteins in the transmission of hereditary traits from one generation to the next generation. e. Explain the importance of DNA in the existence of life. III. PRE-TEST Direction: Choose the letter of the correct answer. 1. The DNA molecule is made up of ________ bases. a. 2 b. 4 c. 6 d. 8 2. The DNA is located in what organelle of the cell? a. Mitochondrion c. Nucleus b. Chloroplast d. Ribosome 3. The sugar in RNA is called: a. Ribose c. Deoxyribose b. Pentose d. None of these 4. Which of the following is not a nitrogenous base in the DNA? a. Adenine b. Cytosine c. Uracil d. Thymine 5. In the RNA, Uracil is paired to: a. Adenine b. Cytosine c. Guanine d. Thymine IV. KEY CONCEPTS THE DNA DNA was known to be a chemical in cells by the late 1800s, but Mendel and other early geneticist did all their work without any knowledge of DNAs role in heredity. By the late 1930s, experimental studies had convinced most biologists that one specific kind of molecule, rather than a complex chemical mixture, is the basis of inheritance. Attention focused on chromosomes, which were already known to carry genes. By the 1940s, scientists knew that chromosomes consist of two types of chemicals: DNA and protein. And by the early 1950s, a series of discoveries had convinced 1 the scientific world that DNA was the molecule that act as the hereditary material. DNA and RNA Structure Both DNA and RNA are nucleic acids, which consist of long chains (polymers) of chemical units (monomers) called nucleotides. Nucleotides are joined together by covalent bonds between the sugar of one nucleotide and the phosphate of the next. This results in a sugar-phosphate backbone, a repeating pattern of sugar-phosphate-sugar-phosphate. The nitrogenous bases are arranged like ribs that project from this backbone Each nucleotide consists of three components: a nitrogenous base, a sugar, and a phosphate group. The sugar is called deoxyribose because, compared with the sugar ribose, it is missing an oxygen atom. The full name of DNA is deoxyribonucleic acid, with nucleic referring to DNA’s location in the nuclei (nucleus) of eukaryotic cells. The nitrogenous base has a ring of nitrogen and carbon atoms with various chemical groups attached. The four nucleotides found in DNA differ only in their nitrogenous bases. The bases can be divided into two types. Thymine (T) and Cytosine (C) are single-ring structures. Adenine (A) and Guanine (G) are 2 larger, double-ring structures. Instead of Thymine, RNA has a similar base called Uracil (U). And RNA contains a slightly different sugar than DNA (ribose instead of deoxyribose). Other than that, RNA and DNA polynucleotides have the same chemical structures. In the DNA, Adenine (A) pairs with Thymine (T). Cytosine (C) pairs with Guanine (G). The pairing of the bases is specific and complementary. Thus, one strand of a DNA is said to be complementary to its partner strand in the double helix and both strands will actually bear the same genetic information. The double helix structure of the DNA which was discovered by James Watson and Francis Crick in 1953 explains why in the process of DNA replication, the resulting daughter DNA molecules are identical to the parental DNA helix. The letters A, T, G and C form the code of life. In the human genome, there are about 2.9 billion base pairs which are wound in 24 bundles called chromosomes. About 22,000 genes are written in the human DNA which code for the proteins that help build and maintain our bodies. V. ACTIVITY A. Label and color the DNA and the RNA structures given below. Make sure to color the nitrogenous bases in pairs all throughout. 3 B. Predict the bases that will pair with the following bases on a single strand of DNA during DNA replication. An example is given on the first column. _C__ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ G A T C G C T A A T G C T C. Fill-in the blanks with the correct answer. 1. DNA stands for _____________. 2. DNA is located in the ____________ of the cell. 3. A DNA molecule is made up of long chains of nucleotides. A DNA nucleotide consists of a ___________, ___________, and ___________. 4. The sides of the DNA “ladder” are made up of ___________, and ___________. 5. The rungs of the DNA “ladder” are made up of the ___________. 6. Why is DNA called the blueprint of life? ____________________________________________________________ ____________________________________________________________ 7. RNA stands for ___________. 8. RNA moves genetic information from the ____________ in the nucleus, to the cytoplasm of the cell and is involved in many cellular activities like the building of ___________. 9. In the DNA, Adenine pairs with ___________, and Guanine pairs with ___________. 10. DNA is double stranded, while the RNA is ___________. VI. APPLICATION Answer each question below. 1. Explain the vital roles of DNA, RNA, and proteins in the transmission of hereditary traits from one generation to the next generation. ____________________________________________________________ ____________________________________________________________ 2. Explain the importance of DNA in the existence of life. ____________________________________________________________ ____________________________________________________________ 4 VII. POST- TEST A. MULTIPLE CHOICE. Choose the letter of the correct answer. 1. In the DNA, which of the following bases pairs with Guanine? a. Adenine c. Thymine b. Uracil d. Cytosine 2. Which of the following statements about double-stranded DNA is false? a. The backbone contains alternating ribose sugar and phosphate groups. b. The strands are double helix. c. The bases are on the outside of the helix. d. Adenine pairs with Thymine, and Guanine pairs with Cytosine. 3. A nucleotide in DNA is composed of __________. a. a deoxyribose sugar, a phosphate and a nitrogenous base b. only a deoxyribose sugar and a nitrogenous base c. only a deoxyribose sugar and a phosphate d. none of the above. 4. In RNA, Uracil pairs with: a. Guanine c. Cytosine b. Thymine d. Adenine 5. The shape of the DNA as described by Watsons and Crick in 1953 is called: a. Single helix c. Double helix b. Spiral d. Twisted B. TRUE or FALSE Write the word TRUE if the statement is correct and FALSE if otherwise. 1. Both the DNA and the RNA are nucleic acids. 2. RNA is double stranded, while DNA is single stranded. 3. The sugar in DNA is deoxyribose sugar. 4. One strand of a DNA is said to be complementary to its partner strand in the double helix and both strands will actually bear the same genetic information. 5. Both the DNA and the RNA are located in the nucleus of the cell. 5  WEEK 2-3 I. COMPETENCY Explain how mutation in DNA affects an individual. CODE: SSP_S8BIOTECH-IIIa-i-9 II. CONTENT GOALS At the end of this module, students should be able to: a. Explain how the genetic information is processed inside the cell to make proteins. b. Explain how mutation in DNA affects an individual. III. PRE-TEST Direction: Write the word TRUE if the statement is correct, and FALSE if otherwise. 1. Proteins make up the structures of the cell, run the biochemical reactions in the cell, and are sometimes manufactured for export. 2. Protein synthesis takes place is the nucleus of the cell. 3. The process of Transcription is the copying of the code of the DNA by the mRNA. 4. The process of translation is the production of the amino acids in the ribosomes. 5. Mutation may take place when there is an error in the code copied by the mRNA from the DNA. IV. KEY CONCEPTS THE FLOW OF THE GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN The genetic information stored in DNA is a living archive of instructions that cells use to accomplish the functions of life. Inside each cell, catalysts seek out the appropriate information from this archive and use it to build new proteins- proteins that make up the structures of the cell, run the biochemical reactions in the cell, and are sometimes manufactured for export. Although all of the cells that make up a multicellular organism contain identical genetic information, functionally different cells within the organism use different sets of catalysts to express only specific portions of these instructions to accomplish the functions of life. HOW IS GENETIC INFORMATION PASSED ON IN DIVIDING CELLS? DNA replication is the process by which DNA makes a copy of itself during cell division. When a cell divides, it creates one copy of its genetic 6 information- in the form of DNA molecules- for each of the two resulting daughter cells. The accuracy of these copies determines the health and inherited features of the nascent cells, so it is essential that the process of DNA replication be as accurate as possible. DNA REPLICATION OF THE LEADING AND LAGGING STRAND The Helicase unzips the double-stranded DNA for replication, making a forked structure. The Primase generates short strands of DNA that bind to the single-stranded DNA to initiate DNA Synthesis by the DNA Polymerase. One factor that help ensure precise replication is the double-helical structure of DNA itself. In particular, the two strands of the DNA double helix are made up of combinations of molecules called nucleotides. DNA is constructed from just four different nucleotides- Adenine (A), Thymine (T), Cytosine (C), and Guanine (G)- each of which is named for the nitrogenous base it contains. Moreover, the nucleotides that form one strand of the DNA double helix always bond with the nucleotides in the other strand according to a pattern known as complementary base-pairing- specifically A always pairs with T, and C always pairs with G. Thus, during cell division, the paired strands unravel and each strand serves as the template for synthesis of a new complementary strand. Three general classes of RNA molecules are involved in expressing the genes encoded within a cell’s DNA. Messenger RNA (mRNA) molecules carry the coding sequences for protein synthesis and are called transcripts; ribosomal RNA (rRNA) molecules form the core a cell’s 7 ribosome (the structures in which protein synthesis takes place); and transfer RNA (tRNA) molecules carry amino acids to the ribosomes during protein synthesis. Ribosomes are the sites in a cell in which protein synthesis takes place. Cells have many ribosomes, and the exact number depends on how active a particular cell is in synthesizing proteins. Within the ribosome, the rRNA molecules direct the catalytic steps of protein synthesis- the stitching together of amino acids to make a protein molecule. In fact, rRNA is sometimes called a ribozyme or catalytic RNA to reflect this function. WHAT ARE THE INITIAL STEPS IN ACCESSING GENETIC INFORMATION? TRANSCRIPTION is the first step in decoding a cell’s genetic information. During transcription, enzymes called RNA Polymerases build RNA molecules that are complementary to a portion of one strand of the DNA double helix. Transcription includes three steps: Initiation, Elongation and Termination. Initiation is the attachment of RNA Polymerase to the promoter and the start of RNA synthesis. For any gene, the promoter dictates which of the two DNA strands is to be transcribed (the particular strand varies from gene to gene). Initiation is then followed by Elongation. In Elongation, RNA grows longer. This is called RNA synthesis. As RNA synthesis continues, the RNA strand peels away from its DNA template, allowing the two separated DNA strands to come back together in the region already transcribed. Lastly, Termination takes place. In this case, the RNA polymerase reaches a special sequence of bases in the DNA template called a terminator. This sequence signals the end of the gene. At this point, the polymerase molecule detaches from the DNA molecule and the gene, and the DNA strands rejoin. HOW DOES THE WHOLE PROCESS RESULT IN NEW PROTEINS? After the transcription of DNA to mRNA is complete, TRANSLATION- or the reading of these mRNAs to make proteins begins. Translation occurs at the ribosome, which consists of rRNA and proteins. In translation, the instructions in mRNA are read, and tRNA brings the correct sequence of 8 amino acids to the ribosome. Then, rRNA helps bonds form between the amino acids, producing a polypeptide chain. After a polypeptide chain is synthesized, it may undergo additional processing to form the finished protein. The entire process is shown here. The relationship between genes and proteins was first proposed in 1909, when English physician Archibald Garrold suggested that genes dictate phenotypes through enzymes, the proteins that speeds up chemical reaction. He hypothesized that inherited diseases reflect a person’s inability to make a particular enzyme. 9 HOW DOES A MUTATION IN DNA AFFECTS AN INDIVIDUAL? A mutation is a change in DNA sequence brought about either by a mistake made when the DNA is copied or through chemical damage. Regions of the genome, typically called genes, provide instructions for creation of protein molecules, which perform most of the important jobs in cells. If ever there’s an error during TRANSCRIPTION, this error would be carried up to the end of TRANSLATION and causes a change in the type of protein produced. Thus, creating a change or mutation in a particular organism. V. ACTIVITY A. As shown in the picture below, explain the step-by-step process of the flow of the genetic information from DNA, to RNA to Protein. The numbers are given as guide for you to identify the site and the specific process that take place. 1. _______________________________________________________ _______________________________________________________ _______________________________________________________ 2. _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ 3. _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ 4. _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ 10 B. Fill-in the blanks to complete the sentences given. 1. During DNA replication, the __________ generates short strands of DNA that bind to the single-stranded DNA to initiate DNA synthesis by the DNA polymerase. 2. During transcription, enzymes called __________ build RNA molecules that are complementary to a portion of one strand of the DNA double helix. 3-5. Transcription includes three steps: __________, _________ and __________. 6. _________ is a type if RNA molecule that carry the coding sequences for protein synthesis and are also called the transcripts. 7. _________ are the sites in a cell in which protein synthesis takes place. 8. In _________, the instructions in mRNA are read, and tRNA brings the correct sequence of amino acids to the ribosome. 9. There are three types of RNA molecules, these are ___rRNA___, ___tRNA____, and __________. 10. A _________ is a change in DNA sequence brought about either by a mistake made when the DNA is copied or through chemical damage. VI. APPLICATION Answer each question below. 1. What is/ are the significance of the entire process of protein synthesis? 2. Explain the important roles of DNA and RNA in the protein formation, and how do they affect life on earth. 3. Explain how mutation in DNA affects an individual. VII. POST- TEST A. Choose the letter of the correct answer. 1. DNA does all except for: a. Serves as the genetic material passed from parent to offspring. b. Remains constant despite changes in the environmental conditions. c. Provides instructions for the synthesis of the messenger RNA. d. Is read by ribosomes during the process of translation. 2. According to the central dogma, which of the following represents the flow of genetic information in cells? a. Protein to DNA to RNA b. DNA to RNA to Protein 11  c. RNA to DNA to Protein d. DNA to Protein to RNA 3. Which of the following is the enzyme that unzips the double-stranded DNA for replication, making a forked structure? a. Ligase c. RNA Polymerase b. Helicase d. DNA Polymerase 4. _________ is the adaptor that is key to converting the triplet codons of mRNA into the protein polymers. a. tRNA b. rRNA c. mRNA d. All of these 5. Which of the following will not generally cause mutations? a. Radiation c. Chemicals b. DNA Replication d. Viruses B. TRUE or FALSE Write the word TRUE if the statement is correct and FALSE if otherwise. 1. mRNA are the structures inside the cell in which protein synthesis takes place. 2. Transcription is the process by which DNA makes a copy of itself during cell division. 3. DNA replication takes place inside the nucleus of the cell. 4. DNA can transfer or move from the nucleus to the cytoplasm of the cell. 5. Proteins are produced after the Transcription and Translation of the genetic information inside the cell. 12  WEEK 4 I. COMPETENCY a. Describe the different tools in Genetic Engineering. CODE: SSP_S8BIOTECH-IIIa-i-10 II. CONTENT GOALS At the end of this module, students should be able to: a. Identify the different tools used in genetic engineering and discuss the functions of these tools. b. Explain how the Gel Electrophoresis and Polymerase Chain Reaction is done. c. Discuss the importance of these tools in undergoing some laboratory techniques and in making new products. III. PRE-TEST Direction: Write the word TRUE if the statement is correct, and FALSE if otherwise. 1. DNA ligase is an enzyme that cut the DNA at or near specific nucleotide sequences. 2. Restriction endonuclease is also called the restriction enzyme. 3. The Polymerase Chain Reaction (PCR) allows the amplification of DNA by in vitro replication. 4. The DNA polymerase catalyzes the synthesis of RNA. 5. Charged molecules in DNA move on a medium to the opposite pole when current is applied. IV. KEY CONCEPTS The science of using the living systems to benefit humankind is called Biotechnology. Technically speaking, the domestication of plants and animals through farming and breeding practices is a type of biotechnology. However, in a contemporary sense, we associate biotechnology with the direct alteration with the organism’s genetics to achieve desirable traits through the process of Genetic Engineering. Genetic Engineering involves the use of Recombinant DNA Technology, the process by which the DNA sequence is manipulated in vitro, thus creating Recombinant DNA Molecules, that have new combinations of genetic material. The recombinant DNA is then introduced into a host organism. If the DNA that is introduced comes from a different species, the host organism is now considered to be transgenic. 13 TOOLS OF RECOMBINANT DNA TECHNOLOGY 1. Restriction Enzymes or Restriction Endonucleases cut DNA at or near specific nucleotide sequences. 2. DNA Ligase joins fragments of DNA together. 3. DNA Polymerase catalyzes the synthesis of DNA; RNA Polymerase catalyzes the synthesis of RNA. 4. Gel Electrophoresis separates charged molecules based on charge (neutral, positive, and negative) and size. Charged molecules move on a medium to the opposite pole when current is applied. 5. Polymerase Chain Reaction (PCR) is a technology which allows the amplification of parts of DNA by in vitro replication that involved repeated denaturation, primer attachment and synthesis of DNA. GEL ELECTROPHORESIS The lengths of DNA fragments can be compared using gel electrophoresis, a method for sorting macromolecules- usually proteins or nucleic acids- primarily by their electrical charge and size. Here are the steps: 1. The DNA sample from each source is placed in a separate well (hole) at one end of a flat, rectangular gel, a thin slab of jellylike material that acts as a molecular sieve. 14 2. A negatively charged electrode is then attached to the DNA- containing end of the gel and a positive electrode to the other end. Because the phosphate groups of nucleotides give DNA fragments a negative charge, the fragments move through the gel toward the positive pole. However, longer DNA fragments move more slowly through the thicket of polymer fibers in the gel than do shorter DNA fragments. 3. Over time, shorter molecules move farther through the gel than longer molecules. Gel electrophoresis thus separates DNA fragments by length. 4. When the current is turned off, a series of bands is left in each “lane” of the gel. Each band is a collection of DNA fragments of the same length. The bands can be made visible by staining, by exposure onto photographic film, or by measuring fluorescence. GEL ELECTROPHORESIS sample result. 15  Through gel electrophoresis, forensic scientists can provide evidence that the crime scene DNA comes from the suspect or not. Because gel electrophoresis reveals similarities and differences between DNA samples, this could provide evidence of either guilt or innocence. POLYMERASE CHAIN REACTION (PCR) The Polymerase Chain Reaction (PCR) is a technique by which a specific segment of DNA can be targeted and copied quickly and precisely. Through PCR, a scientist can obtain enough DNA from even a minute amounts of blood or other tissue to allow a DNA profile to be constructed. The PCR Machine In principle, PCR is simple. Here are a few steps: 1. A DNA sample is mixed with nucleotides, the DNA replication enzyme DNA polymerase, and a few other ingredients. 2. The solution is then exposed to cycles of heating (to separate DNA strands) and cooling (to allow double-stranded DNA to re-form). During these cycles, specific regions of each molecule of DNA are replicated, doubling the amount of that DNA. The above photo shows how the DNA doubles in each cycle. 16  In PCR, the number of copies of your template doubles every cycle. After one cycle, one DNA molecule becomes 2. After another cycle, the two DNA molecules becomes 4. After the third cycle, the four DNA molecules becomes 8, so on and so forth. The key to automated PCR is an unusually heat- stable DNA polymerase, first isolated from prokaryotes living in hot springs. Unlike most proteins, this enzyme can withstand the heat at the start of each cycle. Beginning with a single DNA molecule, automated PCR can generate hundreds of billions of copies in a few hours. V. ACTIVITY A. Answer the following questions based on what you know about Gel Electrophoresis. Sample 1: Is the sample of the victim’s DNA. Sample 2: Is the crime scene evidence. It is the mixed blood sample of the victim’s DNA and the killer’s DNA. Sample 3: Is the sample of the suspect’s DNA. Sample 4: Is the control. Questions: 1. Is the suspect guilty of the crime? _______________________________________________________ _______________________________________________________ 2. How do you know? _______________________________________________________ _______________________________________________________ _______________________________________________________ 17 B. Illustrate and explain the step-by-step process of doing the Gel Electrophoresis. Color your work. C. In PCR, the number of copies of your template doubles every cycle. Use the table below to explore what that means. The first five boxes have been started for you. Theoretically, after 30 PCR cycles, how many copies of your template DNA would you expect to have? _______________ Why? _________________ D. Illustrate and explain the step-by-step process of doing the Polymerase Chain Reaction (PCR). Color your work. VI. APPLICATION Answer each question below. 1. Explain the importance of Gel Electrophoresis and Polymerase Chain Reaction (PCR) in the entire fields of Science and in our lives in general. _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ 2. Discuss the uses of Restriction enzymes, DNA Ligase, DNA Polymerase and RNA polymerase in Genetic Engineering. _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ 18  3. Would you agree that plants, animals, and human genes can be easily manipulated? Why? Why not? _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ VII. POST- TEST A. Choose the letter of the correct answer. 1. A technique for making millions of copies of a specific region of DNA. a. DNA ligase c. Restriction enzyme b. Gel electrophoresis d. Polymerase Chain Reaction 2. What is the effect of heating the solution in the PCR? a. To allow the double-stranded DNA to re-form. b. To separate the DNA strands. c. To make the DNA strands double in number every cycle. d. To make the nitrogenous bases be rightly paired together. 3. A technique that can be used to compare the DNA of two or more plants is: a. Cloning c. Chromatography b. Staining d. Gel electrophoresis 4. Which of the following enzymes has the ability to cut specific nucleotide sequences of the DNA? a. DNA Polymerase c. Restriction Endonuclease b. DNA Ligase d. RNA Polymerase 5. Which of the following enzymes catalyzes the synthesis of RNA? a. DNA Polymerase c. Restriction Enzyme b. DNA Ligase d. RNA Polymerase B. TRUE or FALSE Write the word TRUE if the statement is correct and FALSE if otherwise. 1. Transgenic organisms contain some genes from other species. 2. Through PCR, forensic scientists can provide evidence that the crime scene DNA comes from the suspect or not. 3. The PCR uses electric current to make the nucleotides travel through the gel. 4. DNA ligase is very essential in genetic engineering for it is used to paste or attach fragments of DNA together. 5. In the gel electrophoresis, shorter molecules of the DNA move faster than larger/ longer molecules through the gel. 19 REFERENCES: Simon, Eric J., Dickey Jean L., Reece, Jane B. Campbell Essential Biology. Pearson Education South Asia Pte Ltd. Fifth Edition. Pp. 173-229. https://www.nature.com/scitable/topicpage/ribosomes-transcription-and- translation-14120660/ https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/B ook%3A_Introductory_Biology_(CK- 12)/04%3A_Molecular_Biology/4.07%3A_Translation_of_RNA_to_Protein https://sciencing.com/can-mutation-dna-affect-protein-synthesis-2028.html https://www.expii.com/t/dna-and-rna-structure-function-10079 https://courses.lumenlearning.com/microbiology/chapter/microbes-and-the- tools-of-genetic-engineering/ 20