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Diabetes and the Central Dogma

Students will learn about the central dogma of biology (DNA→RNA→Protein) by examining the production and use of insulin and other regulatory hormones in the body and the ramifications of those processes for society with respect to diabetes.

Author: Kenneth A. Gill Port St. Lucie High School Indian River State College

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Contents Introduction………………………………………………………….…………………………………………………3 Tips about the Curriculum……………………………………………………………………………………….4 Lesson Summaries…………………………………………………………………………………………………..5 Lesson Sequencing Summary………………………………………………………………………………….6 Master Vocabulary List…………………………………………………..………………………………………7–9 Next Generation Sunshine State Standards…………………………………..…………………….10–11 Lesson #1 – Pre-Test…………………………………………………………….................................12 – 13 Lesson #2 – Tour of the Basics Teacher Pages……………………………………………………...…………………………………14–17

Student Pages………………………………………………………………………………………….18–19 Tour of the Basics Answer Key……………………….…………………………………………20–21

Lesson #3 - Diagnosing Diabetes Teacher Pages ……………………………………………………………………………..………….22–27 Lesson #4 - Diabetes and the Central Dogma Powerpoint Teacher Pages………………………………………………………………………………………….28–32 PowerPoint screenshots……………………………………………..……………………………34–39 Lesson #5 – From DNA to Protein Structure and Function Teacher Pages ………………………………………...………………………………………………..40–44 Lesson #6 – Post-Test………………………………………………………………………………………………45–46 Pre/Post-Test Answer Key……………………..……………………………………………………………..…47–48 Acknowledgements……………………………………………………………………………………………………49

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Introduction The central dogma of molecular biology states in simple terms that genetic information for all living organisms is contained in the nucleotide sequences of DNA, is transcribed by RNA and is then translated into sequences of amino acids that become functional proteins. At least a rudimentary understanding of this concept is a prerequisite to making sense of the nearly endless array of processes that go on in living organisms. I have been trying, with varying degrees of success, to teach this to high school biology students for nearly a decade but have not been satisfied with the outcomes. Many concepts in biology can be visualized on a macro-scale, but the central dogma is not one of those concepts and so must be visualized indirectly. Abstract concepts are often the hardest ones for adolescents (or even adults) to grasp and trying to teach them completely abstractly is, I believe, the root of my lack of success at teaching them. Nearly everyone has a fear of, and/or a fascination with, disease. If a link can be demonstrated between the symptoms of a disease and the production, or lack of production, of proteins it might be possible to pique the interest of students in an otherwise dry and pedantic topic such as the central dogma. Diabetes touches the lives of nearly everyone. With the near epidemic proportions of Type 2 diabetes in the United States and other developed nations most people either have it, are related to someone that has it or at least know someone that has it. Depending on gender and ethnicity, the average adult in the U.S. has a 30 to 40% probability of developing diabetes in their lifetime. Diabetes comes in more than one form, is incompletely understood and is the focus of an enormous amount of research. One thing that is understood, however, is that all forms of it involve the production, or lack of production of certain proteins which leads us back to the central dogma. If the pedagogical approach to the central dogma involves hanging it on a framework of a nearly ubiquitous disease such as diabetes perhaps students will be more motivated to apply that part of their brain that processes the abstract.

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Tips about this Curriculum

Lesson Plan Format: All lessons in this curriculum unit are formatted in the same manner. In each lesson you will find the following components: KEY QUESTION(S): Identifies key questions the lesson will explore. OVERALL TIME ESTIMATE: Indicates total amount of time needed for the lesson, including advanced preparation. LEARNING STYLES: Visual, auditory, and/or kinesthetic. VOCABULARY: Lists key vocabulary terms used in the lesson. Also collected and defined in master vocabulary list. LESSON SUMMARY: Provides a 1-2 sentence summary of what the lesson will cover and how this content will be covered. Collected in a master list. STUDENT LEARNING OBJECTIVES: Focuses on what students will know, feel, or be able to do at the conclusion of the lesson. STANDARDS: Specific state benchmarks addressed in the lesson. Collected in a master list. MATERIALS: Items needed to complete the lesson. BACKGROUND INFORMATION: Provides accurate, up-to-date information from reliable sources about the lesson topic. ADVANCE PREPARATION: This section explains what needs to be done to get ready for the lesson. PROCEDURE WITH TIME ESTIMATES: The procedure details the steps of implementation with suggested time estimates. The times will likely vary depending on the class. ASSESSMENT SUGGESTIONS: Formative assessment suggestions have been given. Additionally, there is a brief summative assessment (pre/post test) that can be given. Teachers should feel free to create additional formative and summative assessment pieces. RESOURCES/REFERENCES: This curriculum is based heavily on primary sources. As resources and references have been used in a lesson, their complete citation is included as well as a web link if available. All references and resources are also collected in one list. STUDENT PAGES: Worksheets and handouts to be copied and distributed to the students. TEACHER PAGES: Versions of the student pages with answers or the activity materials for preparation. SCIENCE SUBJECT: Biology GRADE AND ABILITY LEVEL: Grades 9-12, Standard, Honors, International Baccalaureate SCIENCE CONCEPTS: genetics, replication, transcription, translation, complementary base pairing, mutation, nucleotide, nitrogenous base, DNA, hydrogen bonding, double helix, RNA, genes, chromosomes, hormones, homeostasis, regulation, enzymatic function

OVERALL TIME ESTIMATE: Five 90 minute block periods LEARNING STYLES: Visual, auditory, and kinesthetic

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Lesson Summaries LESSON ONE: Pre-test/Post-test This serves as both an elicitation of prior knowledge and a summative assessment of acquired knowledge on the twin topics of diabetes and the central dogma. By presenting the same questions on a two column sheet, students can demonstrate both to themselves and the teacher the outcomes of their exposure to the other lessons. LESSON TWO: Tour of the Basics This lesson summarizes for the students the basic terms and concepts of the central dogma of biology utilizing an animated, narrated website on the topic and accompanying student handout/worksheet. LESSON THREE: Diagnosing Diabetes Students sequence graphically presented information about the maintenance of blood sugar homeostasis in both the healthy and diabetic person. Students analyze simulated blood plasma samples collected during a glucose tolerance test for diabetes. They test glucose and insulin levels to determine if the patient has Type 1 or Type 2 diabetes. LESSON FOUR: Diabetes and the Central Dogma Powerpoint This lesson is a straightforward exercise in transmitting content via powerpoint while students take notes and are encouraged to ask questions based on the text and images they are seeing. LESSON FIVE: From DNA to Protein Structure and Function Students model how information in the DNA base sequence is transcribed and translated to produce a protein molecule. They model how interaction between amino acids causes a protein to fold into a three-dimensional shape that enables the protein to perform a specific function.

LESSON SIX (AND ONE): Pre-test/Post-test This serves as both an elicitation of prior knowledge and a summative assessment of acquired knowledge on the twin topics of diabetes and the central dogma. By presenting the same questions on a two column sheet, students can demonstrate both to themselves and the teacher the outcomes of their exposure to the other lessons.

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Lesson Sequencing Guide

Block 1 Block 2 Block 3 Block 4 Block 5

Pre-test Tour of the Basics internet activity

Diagnosing Diabetes – Introductory discussion Overview Part 1 Part 2

Diagnosing Diabetes – Part 3 Diabetes & The Central Dogma PowerPoint

DNA to Protein Structure and Function Introductory discussion Part A Part B Part C

Wrap up discussion Post-test

Note: This sequencing summary is based on 90 minute block periods. As currently administered in our district these occur every other day.

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Master Vocabulary List Allele – one of two or more alternate forms of a gene Ambiguity –the idea in reference to the genetic code that a particular codon might code for more than one amino acid. This is not true of the genetic code, i.e., there is no ambiguity. Amino acid – one of twenty monomers of proteins. Each of them have a central carbon atom surrounded by an amine group, a carboxyl group, a hydrogen atom and a side group (referred to as the “R-group” that is unique to each one. Anti-codon – a group of three nitrogen bases found at one end of a transfer RNA that would be complementary to a codon found on a messenger RNA Blood plasma – the liquid component of blood. In humans approximately 1% of it consists of a variety of solutes such as glucose, hormones, salts and the like Central Dogma – more properly called a hypothesis, rather than a dogma, but it refers to the flow of genetic information from DNA to RNA to proteins Chromosome – a DNA molecule of varying length containing hundreds to thousands of genes and usually found coiled around some histone proteins Codon – a group of three nitrogen bases found in sequences of messenger RNA that code for a specific amino acid Complementary Base Pairing – an attraction between pairs of nitrogen bases found in nucleic acids based on easily broken hydrogen bonds. Two of the five bases found in nucleic acids, adenine and guanine are purines and they respectively bond with thymine and cytosine which are pyrimidines. In RNA thymine is replaced by uracil, another pyrimidine DNA – deoxyribonucleic acid, a molecule which is the main repository of genetic information in most living organisms. It is a double-stranded polymer which assumes a helical shape and consists of monomers of nucleotides which in turn consist of one deoxyribose sugar, one phosphate and one of four nitrogen bases, adenine, guanine, cytosine and thymine Degeneracy – the phenomenon that the genetic code is redundant, i.e., a given amino acid can be coded for by more than one codon Deletion – a form of genetic mutation wherein a nitrogen base is removed or left out thus leading to a frame shift, i.e, the manner in which a sequence is read Diabetes - group of similar disease states that in one way or another disrupt the body’s ability to maintain homeostasis with respect to blood sugar levels. The two main forms would be: Type 1 diabetes, wherein the pancreas fails to produce insulin, and Type 2 diabetes, wherein there is a failure of the receptor proteins on multiple cell surfaces that prevent insulin from promoting the uptake of glucose.

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Double Helix – the shape of a DNA molecule as postulated by Watson and Crick. It is like a twisted ladder wherein the sides are constructed of alternating sugars and phosphates and the rungs of nitrogen bases held weakly together by nitrogen bonds.

Enzyme – a protein that serves as an organic catalyst, i.e., it promotes biochemical reactions without being consumed in them by lowering the activation energy required to make them go forward. Their shape is critical to their function as there is an active site on them that conforms to the shape of the substrate (reactants) Exon – that part of a primary mRNA transcript that will actually serve as a source of coding to construct the protein Feedback Control Mechanisms - process in which the level of one substance influences the level of another substance Frame shift Mutation – a change in a gene sequence consisting of either an insertion or a deletion of a nucleotide that from that point forward changes the manner in which the sequence will be transcribed or translated Gene – a sequence of nucleotides along one side of a DNA molecule that contains coded information for a specific polypeptide Genetics - the study of heredity and the variation of inherited characteristics Glucose - A monosaccharide sugar, C6H12O6, occurring widely in most plant and animal tissue. It is the principal circulating sugar in the blood and the major energy source of the body. Hemoglobin - the oxygen-carrying pigment of red blood cells that gives them their red color and serves to convey oxygen to the tissues Heredity - the transmission of genetic characters from parents to offspring Heterozygous – the condition in a diploid organism of having two different alleles for a particular trait Homeostasis - the tendency of a system, especially the physiological system of higher animals, to maintain internal stability, owing to the coordinated response of its parts to any situation or stimulus that would tend to disturb its normal condition or function Homozygous – the condition in a diploid organism of having two of the same allele for a particular trait Hormone - any of various internally secreted compounds, as insulin or thyroxine, formed in endocrine glands that affect the functions of specifically receptive organs or tissues when transported to them by the body fluids Hydrophilic – having an affinity for water Hydrophobic – having a repulsion to water

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Insertion – a form of genetic mutation wherein a nucleotide is added to an existing sequence thus leading to a frame shift, i.e., a change in the manner the sequence is transcribed or translated Insulin - a polypeptide hormone, produced by the beta cells of the islets of Langerhans of the pancreas,

which regulates the metabolism of glucose and other nutrients.

Intron – a non-coding sequence within a primary mRNA transcript Mutation – a change in a gene sequence Nitrogen Base – nitrogen containing organic molecules found within the nucleic acids DNA and RNA that have a weak affinity for one another and thus allow for complementary base pairing Nucleotide – a monomer of the polymers DNA or RNA consisting of one sugar, one phosphate and one of the nitrogen bases adenine, thymine, guanine, cytosine or uracil Point Mutation – a change in a gene sequence of a single nucleotide Polymer – a molecule consisting of a series of repeating similar units, or monomers. Examples would be complex carbohydrates, proteins and nucleic acids Polypeptide – a long, continuous and unbranched chain of amino acids held together by peptide bonds Protein - large biological molecules consisting of one or more chains of amino acids that perform a vast array of functions within living organisms Protein Structure - the biomolecular structure of a protein molecule. Each protein is a polymer – specifically a polypeptide – that is a sequence formed from various L-α-amino acids Receptors – a molecule usually found on the surface of a cell that receives chemical signals from outside the cell Regulation – the process of turning genes on and off Replication – the process of producing two identical DNA copies from one original DNA molecule Trait - a distinct variant of a phenotypic character of an organism that may be inherited, be environmentally determined or be a combination of the two Transcription - the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme, RNA polymerase Translation - is the process in which cellular ribosomes create proteins. It is part of the process of gene expression Zygote – the initial cell resulting from the fertilization of an egg by a sperm

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Next Generation Sunshine State Standards (NGSSS)

S.C.912.N.1.1 Define a problem based on a specific body of knowledge, for example: biology, chemistry, physics, and earth/space science, and do the following: 1. pose questions about the natural world, 2. conduct systematic observations, 3. examine books and other sources of information to see what is already known, 4. review what is known in light of empirical evidence, 5. plan investigations, 6. use tools to gather, analyze, and interpret data (this includes the use of measurement in metric and other systems, and also the generation and interpretation of graphical representations of data, including data tables and graphs), 7. pose answers, explanations, or descriptions of events, 8. generate explanations that explicate or describe natural phenomena (inferences), 9. use appropriate evidence and reasoning to justify these explanations to others, 10. communicate results of scientific investigations, and 11. evaluate the merits of the explanations produced by others S.C.912N1.3 Recognize that the strength or usefulness of a scientific claim is evaluated through scientific argumentation , which depends on critical and logical thinking, and the active consideration of alternative scientific explanations to explain the data presented. S.C.912N1.4 Identify sources of information and assess their reliability according to the strict standards of scientific investigation S.C.912.N.3.1 Explain that a scientific theory is the culmination of many scientific investigations drawing together current evidence concerning a substantial range of phenomena; thus, a scientific theory represents the most powerful explanation scientists have to offer. S.C.912.N.4.1 Explain how scientific knowledge and reasoning provide an empirically-based perspective to inform society’s decision making. SC.912.L.14.6 Explain the significance of genetic factors, environmental factors, and pathogenic agents to health from the perspectives of both individual and public health. S.C.912.L.14.30 Compare endocrine and neural controls of physiology S.C.912.L.14.31 Describe the physiology of hormones including the different types and the mechanisms of their actions. S.C.912.L.14.46 Describe the physiology of the digestive system, including mechanical digestion, chemical digestion, absorption and the neural and hormonal mechanisms of control. SC.912.L.16.3 Describe the basic process of DNA replication and how it relates to the transmission and conservation of the genetic information

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SC.912.L.16.4 Explain how mutations in the DNA sequence may or may not result in phenotypic change. Explain how mutations in gametes may result in phenotypic changes in offspring. S.C.912.L.16.5 Explain the basic processes of transcription and translation, and how the result in the expression of genes. S.C.912.L.16.6 Discuss the mechanisms for regulation of gene expression in prokaryotes and eukaryotes at transcription and translation level S.C.912.L16.8 Describe the relationship between mutation, cell cycle and uncontrolled cell growth potentially resulting in cancer. S.C.912.L.16.9 Explain how and why the genetic code is universal and is common to all organisms SC.912.L.16.10 Evaluate the impact of biotechnology on the individual, society and the environment, including medical and ethical issues. SC.912.L.18.1 Describe the basic molecular structures and primary functions of the four major categories of biological macromolecules. SC.912.L.18.4 Describe the structures of proteins and amino acids. Explain the functions of proteins in living organisms. Identify some reactions that amino acids undergo. Relate the structure and function of enzymes.

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LESSON #1 – Pre-test TIME ESTIMATE: 30 minutes

Pre-test

1. List at least five symptoms of diabetes.

2a. What is the principal organ involved in the development of diabetes? 2b. List 3 organs involved in long-term complications of diabetes.

3. As a member of the U.S. population what are the chances you will develop diabetes in your life time? A. 0-10% B. 20-25% C. 30-40% D. 60-70%

4. Are you more likely to get Type 1 Diabetes or Type 2 Diabetes?

5. Compare and contrast Type 1 Diabetes and Type 2 Diabetes

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6. What, if any, is the relationship between DNA and Diabetes?

7. What, if any, is the relationship between DNA and proteins?

8. List at least 3 functions for proteins.

9. State, in as few words as possible, the central dogma of molecular biology.

10. What is a gene?

11. What is a mutation?

12. Name at least two possible outcomes of a genetic mutation.

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LESSON #2 – Tour of the Basics KEY QUESTIONS: What structures and molecules in cells are involved in heredity and how do they work? SCIENCE CONCEPTS: genetics, heredity, replication, transcription, translation OVERALL TIME ESTIMATE: 60 minutes LEARNING STYLES: Visual and auditory. VOCABULARY: Allele – one of two or more alternate forms of a gene Chromosome – a DNA molecule of varying length containing hundreds to thousands of genes and usually found coiled around some histone proteins DNA – deoxyribonucleic acid, a molecule which is the main repository of genetic information in most living organisms. It is a double-stranded polymer which assumes a helical shape and consists of monomers of nucleotides which in turn consist of one deoxyribose sugar, one phosphate and one of four nitrogen bases, adenine, guanine, cytosine and thymine Gene – a sequence of nucleotides along one side of a DNA molecule that contains coded information for a specific polypeptide Hemoglobin - the oxygen-carrying pigment of red blood cells that gives them their red color and serves to convey oxygen to the tissues Heredity - the transmission of genetic characters from parents to offspring Heterozygous – the condition in a diploid organism of having two different alleles for a particular trait Homozygous – the condition in a diploid organism of having two of the same allele for a particular trait Nucleotide – a monomer of the polymers DNA or RNA consisting of one sugar, one phosphate and one of the nitrogen bases adenine, thymine, guanine, cytosine or uracil Protein - large biological molecules consisting of one or more chains of amino acids that perform a vast array of functions within living organisms Replication – the process of producing two identical DNA copies from one original DNA molecule Trait - a distinct variant of a phenotypic character of an organism that may be inherited, be environmentally determined or be a combination of the two Transcription - the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme, RNA polymerase Translation - is the process in which cellular ribosomes create proteins. It is part of the process of gene expression Zygote – the initial cell resulting from the fertilization of an egg by a sperm LESSON SUMMARY: This lesson summarizes for the students the basic terms and concepts of the central dogma of biology utilizing an animated, narrated website on the topic and accompanying student handout/worksheet. STUDENT LEARNING OBJECTIVE: Students should be able to:

1. Define the basic terminology of heredity at the organismic, cellular and molecular levels 2. Sequence the steps of the central dogma of biology

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STANDARDS: SC.912.L.16.3 Describe the basic process of DNA replication and how it relates to the transmission and conservation of the genetic information SC.912.L.16.4 Explain how mutations in the DNA sequence may or may not result in phenotypic change. Explain how mutations in gametes may result in phenotypic changes in offspring. S.C.912.L.16.5 Explain the basic processes of transcription and translation, and how they result in the expression of genes. S.C.912.L.16.6 Discuss the mechanisms for regulation of gene expression in prokaryotes and eukaryotes at transcription and translation level MATERIALS:

1. Internet source for each student or pair of students (laptop carts, computer lab, I-phones, etc.) 2. Comprehension worksheet for each student

BACKGROUND INFORMATION: The central dogma of biology is an explanation of the flow of genetic information in living organisms. The term central dogma is attributed to Francis Crick, one of the co-discoverers of the double helix shape of DNA, who later acknowledged that his use of the term “dogma” was perhaps unfortunate in that it implied a rigidity of thinking that would stand in opposition to the scientific method. More than a half century of myriad lines of research have unequivocally confirmed, however, that information contained in the nitrogen base sequences of DNA is transcribed on to RNA and then translated into proteins. Genetic information is conserved from parent to progeny by the process of DNA replication and, in some special cases involving reverse transcription, RNA can be used as a template to produce DNA, but an understanding of the central hypothesis that genetic information flows from DNA to RNA to protein is critical to an understanding of biological function. Prior to Watson and Crick’s discovery there were some in the scientific community that thought proteins might be the repository of genetic information but no credible evidence has turned up to support this idea. Some recent research has shown that a high percentage of DNA is transcribed, but not necessarily for proteins. If these genes are coding for something other than proteins, and what they are coding for, is still open to debate, but this is an area of research that is probably beyond the scope of a high school biology class. For students to understand the central dogma they need to have an understanding of the structure of DNA at the levels of nucleotides, genes and chromosomes and an understanding of the structures of the different forms of RNA. The “Tour of the Basics” website will give them a visual and auditory introduction to the basic terminology of molecular genetics and an overview of the processes of replication, transcription and translation.

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ADVANCE PREPARATION: Though Biology curricular sequencing may vary from district to district, from school to school and from teacher to teacher, it is assumed for the purposes of this lesson that students will have already been introduced to the four basic macromolecules, cellular structure and function, cell reproduction and Mendelian genetics. The material in this lesson will review and extend those concepts. A brief lecture on the idea of the central dogma preceding the lesson might be beneficial but the intent of this lesson is to introduce the students to the terminology they need to better understand the broader concepts.

1. Arrange for sufficient internet access 2. (Optional) make arrangements for screen projection of powerpoints and/or animations. 3. Make copies of “Tour of the Basics” comprehension worksheet.

PROCEDURE:

1. Initiate a class discussion about how it is that students seem to be a blend of the traits in their two parents and how their siblings are a different blend of these traits to introduce the idea of heredity.

(5 minutes) 2. Give a brief lecture/overview of the idea of the central dogma of biology. At this point limit the

content to DNA to RNA to protein and where this happens. This could be done with whiteboard or chalkboard, or if screen projection from computer is available, with powerpoints or animations. Suggestions for animations can be found in references/resources below. (5 minutes).

3. Distribute “Tour of the Basics” comprehension worksheet and instruct students to access the internet and navigate to the URL address given at the top of the worksheet. Explain the use of the navigation tools at the top and bottom of that website to answer the comprehension questions. (35 - 50 minutes).

ASSESSMENT SUGGESTIONS: Check worksheet for completion and comprehension. REFERENCES AND RESOURCES:

1. ^ Crick, F.H.C. (1958): On Protein Synthesis. Symp. Soc. Exp. Biol. XII, 139-163. (pdf, early draft of original article)

2. ^ a b Crick, F (August 1970). "Central dogma of molecular biology.". Nature 227 (5258): 561–3. Bibcode:1970Natur.227..561C. doi:10.1038/227561a0. PMID 4913914.

3. ^ Leavitt, Sarah A.; Marshall Nirenberg (June 2010). "Deciphering the Genetic Code: Marshall Nirenberg". Office of NIH History.

4. ^ Ahlquist P (May 2002). "RNA-dependent RNA polymerases, viruses, and RNA silencing". Science 296 (5571): 1270–3. Bibcode:2002Sci...296.1270A. doi:10.1126/science.1069132. PMID 12016304.

5. ^ B. J. McCarthy and J. J. Holland (September 15, 1965). "Denatured DNA as a Direct Template for in vitro Protein Synthesis". Proceedings of the National Academy of Sciences of the United States 54 (3): 880–886. Bibcode:1965PNAS...54..880M. doi:10.1073/pnas.54.3.880. PMC 219759. PMID 4955657.

6. ^ .T. Uzawa, A. Yamagishi, T. Oshima (2002-04-09). "Polypeptide Synthesis Directed by DNA as a Messenger in Cell-Free Polypeptide Synthesis by Extreme Thermophiles, Thermus thermophilus HB27 and Sulfolobus tokodaii Strain 7". The Journal of Biochemistry 131 (6): 849–853. PMID 12038981.^ Wilkins, Adam S. (January 2012). "(Review) Evolution: A View from the 21st Century". Genome Biology and Evolution. doi:10.1093/gbe/evs008.

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7. ^ Moran, Laurence A (May–June 2011). "(Review) Evolution: A View from the 21st Century". Reports of the National Center for Science Education 32.3 (9): 1–4.

8. ^ Horace Freeland Judson (1996). "Chapter 6: My mind was, that a dogma was an idea for which there was no reasonable evidence. You see?!". The Eighth Day of Creation: Makers of the Revolution in Biology (25th anniversary edition). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. ISBN 0-87969-477-7.

9. ^ a b http://www.nature.com/nature/journal/v496/n7446/full/496419a.html?WT.ec_id=NATURE-20130425

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Name ____________________ Period ________

Tour of the Basics Comprehension Worksheet

Instructions: Type in the following URL address and use the navigation tools at the top and bottom of the screen to answer the following comprehension questions with the appropriate word(s), phrase or sentence:

http://learn.genetics.utah.edu/content/begin/tour/

DNA What is the shape of DNA? What does “DNA” stand for? What four letters symbolize the genetic code that is found in the interior of a DNA molecule? What do these four letters stand for?

Gene What is a gene? Approximately how many genes do we find in a human? Hemoglobin is a protein that is coded for by a few genes. What does it do? What do we call it when there is a change in a gene?

Chromosome What is a chromosome? How many chromosomes do we find in most human cells? Which pair of chromosomes determines our sex?

Protein What is a protein? What relationship do genes have to proteins? Where in a cell does transcription occur?

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What organelle is the site of translation?

Heredity What is heredity? How many chromosomes do we receive from each parent? What is the name of the cell that results from a sperm cell fertilizing an egg? Explain how each human born is genetically unique?

Trait What is a trait? Name three types of traits. What, besides our genes, determines our traits? What is an allele? In a heterozygous condition which allele will be expressed? What percentage of our DNA do all humans share?

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Name _____________________ Period ________

Tour of the Basics Comprehension Worksheet Answer Key

Instructions: Type in the following URL address and use the navigation tools at the top and bottom of the screen to answer the following comprehension questions with the appropriate word(s), phrase or sentence:

http://learn.genetics.utah.edu/content/begin/tour/

DNA What is the shape of DNA? Double helix What does “DNA” stand for? Deoxyribonucleic Acid What four letters symbolize the genetic code that is found in the interior of a DNA molecule? A, T, C, G What do these four letters stand for? Adenine, Thymine, Cytosine, Guanine

Gene What is a gene? Genes are instruction manuals for our bodies. They are directions for all the proteins that make our bodies function Approximately how many genes do we find in a human? 25,000 Hemoglobin is a protein that is coded for by a few genes. What does it do? It’s a part of our blood that captures and carries oxygen. What do we call it when there is a change in a gene? A mutation.

Chromosome What is a chromosome? They are efficient storage units for DNA wrapped tightly around some proteins. How many chromosomes do we find in most human cells? 46 Which pair of chromosomes determine our sex? The X and Y chromosomes

Protein What is a protein? Proteins are the tiny machines that make all living things function, much like the different parts of a car make it function. What relationship do genes have to proteins? Each gene in the DNA encodes information about how to make an individual protein. Where in a cell does transcription occur? In the nucleus.

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What organelle is the site of translation? A ribosome

Heredity What is heredity? The passing of traits from parent to child. How many chromosomes do we receive from each parent? 23 What is the name of the cell that results from a sperm cell fertilizing an egg? A zygote Explain how each human born is genetically unique? Since the parents contribute chromosomes randomly to each new child, every child inherits a unique set of chromosomes.

Trait What is a trait? A trait is a notable feature or quality in a person. Each of us has a different combination of traits that makes us unique. Name three types of traits.

1. Physical traits 2. Behavioral traits 3. Predisposition to medical conditions.

What, besides our genes, determines our traits? The non-genetic, or “environmental”, influences in our lives are just as important in shaping our traits as the instructions encoded in our genes. What is an allele? An allele is a set of instructions for each form of a particular trait. In a heterozygous condition which allele will be expressed? The dominant allele will be expressed. What percentage of our DNA do all humans share? 99.9%

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Lesson #3 – Diagnosing Diabetes KEY QUESTIONS: How does the human body maintain homeostasis with respect to blood sugar levels? What is the role of hormones and other proteins in both the healthy and diseased state? SCIENCE CONCEPTS: diabetes, genetics, mutation, hormones, homeostasis, regulation, enzymatic function OVERALL TIME ESTIMATE: Two 40 minute class periods plus homework. Part one may be done as pre-lab homework. LEARNING STYLES: Visual, Auditory and Kinesthetic VOCABULARY: Blood plasma – the liquid component of blood. In humans approximately 1% of it consists of a variety of solutes such as glucose, hormones, salts and the like Diabetes - group of similar disease states that in one way or another disrupt the body’s ability to maintain homeostasis with respect to blood sugar levels. The two main forms would be: Type 1 diabetes, wherein the pancreas fails to produce insulin, and Type 2 diabetes, wherein there is a failure of the receptor proteins on multiple cell surfaces that prevent insulin from promoting the uptake of glucose. Enzyme – a protein that serves as an organic catalyst, i.e., it promotes biochemical reactions without being consumed in them by lowering the activation energy required to make them go forward. Their shape is critical to their function as there is an active site on them that conforms to the shape of the substrate (reactants) Feedback Control Mechanisms - process in which the level of one substance influences the level of another substance Genetics - the study of heredity and the variation of inherited characteristics Glucose - A monosaccharide sugar, C6H12O6, occurring widely in most plant and animal tissue. It is the principal circulating sugar in the blood and the major energy source of the body. Homeostasis - the tendency of a system, especially the physiological system of higher animals, to maintain internal stability, owing to the coordinated response of its parts to any situation or stimulus that would tend to disturb its normal condition or function Hormone - any of various internally secreted compounds, as insulin or thyroxine, formed in endocrine glands that affect the functions of specifically receptive organs or tissues when transported to them by the body fluids Insulin - a polypeptide hormone, produced by the beta cells of the islets of Langerhans of the pancreas, which regulates the metabolism of glucose and other nutrients. Receptors – a molecule usually found on the surface of a cell that receives chemical signals from outside the cell Regulation – the process of turning genes on and off LESSON SUMMARY: Students sequence graphically presented information about the maintenance of blood sugar homeostasis in both the healthy and diabetic person. Students analyze simulated blood plasma samples collected during a glucose tolerance test for diabetes. They test glucose and insulin levels to determine if the patient has Type 1 or Type 2 diabetes.

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STUDENT LEARNING OBJECTIVES: Students should be able to:

1) Sequence graphic information about the causes, symptoms and treatments of maintenance of blood sugar homeostasis in the healthy and diabetic condition

2) Test and graph the glucose levels in simulated blood plasma samples collected during the fictional patient’s glucose tolerance test.

3) Test and graph the insulin levels in simulated blood plasma samples collected during the fictional patient’s glucose tolerance test.

4) Analyze the test results to determine if the patient has Type 1 or Type 2 diabetes. STANDARDS: SC.912.N.1.1 Define a problem based on a specific body of knowledge, for example: biology, chemistry, physics, and earth/space science, and do the following: 1. pose questions about the natural world, 2. conduct systematic observations, 3. examine books and other sources of information to see what is already known, 4. review what is known in light of empirical evidence, 5. plan investigations, 6. use tools to gather, analyze, and interpret data (this includes the use of measurement in metric and other systems, and also the generation and interpretation of graphical representations of data, including data tables and graphs), 7. pose answers, explanations, or descriptions of events, 8. generate explanations that explicate or describe natural phenomena (inferences), 9. use appropriate evidence and reasoning to justify these explanations to others, SC.912.L.14.6 Explain the significance of genetic factors, environmental factors, and pathogenic agents to health from the perspectives of both individual and public health. S.C.912.L.14.29 Define the terms endocrine and exocrine S.C.912.L.14.30 Compare endocrine and neural controls of physiology S.C.912.L.14.31 Describe the physiology of hormones including the different types and the mechanisms of their actions. S.C.912.L.14.46 Describe the physiology of the the digestive system, including mechanical digestion, chemical digestion, absorption and the neural and hormonal mechanisms of control.

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MATERIALS: Science Take-Out Kit STO-117 “Diagnosing Diabetes” (see Advance Preparation section) which includes: • 5 tubes of simulated “Blood Plasma” (0, 30, 60, 90 and 120 minutes)* • 1 tube of simulated “Insulin Indicator” ** • 6 labeled droppers • Simulated “Glucose Test Paper”*** • Glucose/Insulin Test Color Charts • Glucose Tolerance Testing Sheet • Colored sheet of graphics for What You Should Know About Diabetes and the Glucose Tolerance Test Teacher provided supplies: Safety goggles Paper towels for clean up Scissors Tape or glue *simulated Blood Plasma is actually: Product Ingredients - % Weight/Volume (balance is water) pH 3 buffer Sulphamic acid (0.10%), Potassium biphthalate (0.35%) pH 7 buffer Potassium phosphate monobasic (0.15%), Sodium phosphate dibasic (0.30%) pH 9 buffer Sodium carbonate (0.10%), Sodium bicarbonate (0.35%) ** Simulated Insulin Indicator is actually: Methyl Red (0.05%), Bromothymol Blue Sodium Salt (0.05%), Water (99.9% ***Glucose Test Paper is actually: Hydrion pH paper strips scale 1 to 12 BACKGROUND INFORMATION: Diabetes is not a single disease, but rather a group of similar disease states that in one way or another disrupt the body’s ability to maintain homeostasis with respect to blood sugar levels. In a healthy (i.e, non-diabetic) person a high level of glucose in the blood stream due to intake and digestion of carbohydrates would stimulate beta cells in structures called the islets of Langerhans located in the pancreas to release the hormone insulin into the blood stream. Insulin is a protein that travels throughout the body via the blood stream and encounters other receptor proteins on the surface of liver and muscle cells. Those receptor proteins in turn stimulate the intake of glucose into those cells so it can be stored as the complex carbohydrate glycogen in the liver (anabolic reactions) or directly utilized by muscle cells to drive cellular activities. In the opposite scenario, that is, when glucose levels in the blood stream fall below a set level, the pancreas responds by producing another hormone called glucagon which stimulates the liver to initiate catabolic breakdown of glycogen back into glucose and re-release into the blood stream. If these processes are disrupted by diabetes the initial symptoms may include frequent urination, increased thirst, increased hunger, blurred vision and a number of skin rashes. More acute symptoms might include diabetic ketoacidosis (which makes the breath smell of acetone), hyperventilation, nausea, vomiting, abdominal pain and altered states of consciousness (up to and including coma). Long term complications are mostly related to damage to blood vessels in various

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tissues and organs throughout the body and might include increased risk of cardiovascular disease, blindness, nerve damage and chronic kidney disease.

There are many forms of diabetes, but most cases fall into two categories, Type 1 diabetes mellitus and Type 2 diabetes mellitus. In Type 1, which accounts for about 10% of U.S. cases, pancreatic production of insulin declines to essentially zero so there is no check on blood sugar levels. Despite a great deal of research the reasons for this are incompletely understood. Much of the research points toward it being an autoimmune response, i.e, so-called autoantibodies develop in response to some environmental trigger and they in turn induce the development of activated T cells capable of destroying the insulin producing beta cells. Over time secretion of insulin declines to a point where 80 to 90% of the beta cells are destroyed and the symptoms start to become apparent. Recent research has shown that another protein with the rather ironic acronym IHoP (Islet Homeostasis Protein), which is not expressed in the post-diabetic state, may play a role in maintaining the ability of the pancreatic islet cells to produce insulin. In Type 2, which accounts for about 90% of U.S. cases, the ability of the pancreas to produce insulin is not compromised, but the aforementioned receptor proteins on the surface of liver and other cells do not respond to insulin and thus the blood glucose levels can remain dangerously high. At present neither Type 1 nor Type 2 is curable, but both are treatable. Type 1 treatment includes regulation of diet and exercise, strict life-long monitoring of blood sugar levels and administration of exogenous insulin. Type 2 treatment also involves regulation of diet and exercise, monitoring of blood sugar, oral medications to increase insulin uptake and sometimes administration of exogenous insulin. Insulin is a fairly small protein consisting of only 51 amino acids in two chains linked together with disulfide bonds. Its biochemical nature is fairly consistent in mammals and it was first extracted from dog pancreatic tissue in the 1920’s by Frederick Banting and J.R.R. Macleod at the University of Toronto. Shortly thereafter they found that it could be more easily extracted from fetal bovine pancreas. They injected it in children in diabetic comas who prior to that treatment would have been considered terminal and for the next half century that became the standard source of exogenous insulin for diabetic patients. Bovine insulin certainly saved many lives but it is not an exact match to human insulin and so presented immunological problems for some patients. The amino acid structure of insulin was characterized by Frederick Sanger in the early 1950’s and synthetic insulin was first produced in the early 1960’s. When the field of recombinant DNA technology began to heat up in the 1970’s scientists at Genentech collaborated to produce the first genetically engineered human insulin which became commercially available in 1982. Today nearly all human insulin is mass-produced by introducing the human gene for insulin into either E.coli bacteria or yeast (Saccharomyces cerevisiae) cultures. The fact that this can be done and is such an important part of the lives of so many people makes it a good linkage to showing students the universality of DNA and the validity of inquiry in to molecular genetics.

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ADVANCE PREPARATION:

As noted above some of the materials for Diagnosing Diabetes should be readily available in any reasonably equipped high school science department. The kit itself and the accompanying supplies, background information, question sheets, directions and graphics are available from the Life Sciences Learning Center at the University of Rochester. The contact information for them is:

Science Take-Out P.O. Box 205 Pittsford, NY 14534

(585)764-5400 phone (585)381-9495 fax contact@sciencetakeout.com A pdf version of Diagnosing Diabetes can be found at the following URL: http://www.shop.sciencetakeout.com/products.php?id=32 Depending on curricular sequence, molecular genetics should fall far enough into the academic year that some sample kits could be obtained well in advance of the actual need for them. By doing this at the beginning of the school year decisions could be made about how many kits need to be obtained for the actual lab and how much of the material can be formulated from supplies on hand. At minimum the pdf version should be accessed, downloaded, read and fully considered well in advance of attempting the lab. If cost is not a consideration and the intent is just to obtain, use and discard the materials from Science Takeout then the following advice can be ignored, but if the intent is to reuse the graphics it would be wise to follow one particular optional direction in the kit under the heading “Teacher preparation”. That would be to laminate the “Graphics for what you should know about Diabetes and the Glucose Tolerance Test” sheets. PROCEDURES:

1. Using the pre-test questions on diabetes as a starting point, initiate a class discussion on prior knowledge of diabetes. (5 – 10 minutes).

2. Using the background information above and references and resources below give a brief overview of the molecular basis of blood glucose homeostasis and its relationship to diabetes. (5 – 10 minutes)

3. Carry out Part 1 of the Diagnosing Diabetes protocol involving the sequencing of diabetes related knowledge. While the Science Takeout instructions suggest that this could be done as a pre-procedure homework assignment it would probably save on paper to just do this in class. (20 – 30 minutes)

4. Carry out Part 2 of Diagnosing Diabetes - Analyzing Blood Glucose Levels (40 minutes) 5. Carry out Part 3 of Diagnosing Diabetes – Analyzing Blood Insulin Levels (40 minutes)

The length of your class periods will, of course, determine how you divide up the procedures.

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ASSESSMENT SUGGESTIONS: Students can be assessed on their successful sequencing of graphical information and completion of comprehension questions in Part 1; plotting and interpretation of data in Part 2; and plotting and interpretation of data in Part 3 of the Diagnosing Diabetes laboratory. REFERENCES AND RESOURCES: Diagnosing Diabetes is available from Science Takeout (see contact information in Advance Preparation above). STUDENT PAGES: Accessible in Diagnosing Diabetes pdf: http://prod.cpet.ufl.edu/wp-content/uploads/2013/10/Diabetes-with-student-pages.pdf TEACHER PAGES: Accessible in Diagnosing Diabetes pdf: http://prod.cpet.ufl.edu/wp-content/uploads/2013/10/Diabetes-with-student-pages.pdf

1. ^ "Diabetes Blue Circle Symbol". International Diabetes Federation. 17 March 2006. 2. ^ a b c d Shoback, edited by David G. Gardner, Dolores (2011). Greenspan's basic & clinical

endocrinology (9th ed.). New York: McGraw-Hill Medical. pp. Chapter 17. ISBN 0-07-162243-8. 3. ^ a b Williams textbook of endocrinology (12th ed.). Philadelphia: Elsevier/Saunders. pp. 1371–

1435. ISBN 978-1-4377-0324-5. 4. ^ Lambert, P.; Bingley, P. J. (2002). "What is Type 1 Diabetes?". Medicine 30: 1–5.

doi:10.1383/medc.30.1.1.28264. Diabetes Symptoms edit 5. ^ Rother KI (April 2007). "Diabetes treatment—bridging the divide". The New England Journal of

Medicine 356 (15): 1499–501. doi:10.1056/NEJMp078030. PMID 17429082. 6. ^ a b "Diabetes Mellitus (DM): Diabetes Mellitus and Disorders of Carbohydrate Metabolism:

Merck Manual Professional". Merck Publishing. April 2010. Retrieved 2010-07-30. 7. ^ Dorner M, Pinget M, Brogard JM (May 1977). "Essential labile diabetes". MMW Munch Med

Wochenschr (in German) 119 (19): 671–4. PMID 406527. 8. ^ Lawrence JM, Contreras R, Chen W, Sacks DA (May 2008). "Trends in the prevalence of

preexisting diabetes and gestational diabetes mellitus among a racially/ethnically diverse population of pregnant women, 1999–2005". Diabetes Care 31 (5): 899–904. doi:10.2337/dc07-2345. PMID 18223030.

9. ^ Handelsman Y, MD. "A Doctor's Diagnosis: Prediabetes". Power of Prevention 1 (2). 10. ^ a b "Definition, Diagnosis and Classification of Diabetes Mellitus and its Complications" (PDF).

World Health Organisation. 1999. 11. ^Atkinson, M.A. “The Pathogenesis and Natural History of Type 1 Diabetes”. Cold Spring Harbor

Perspectives in Medicine 2012;2:a007641. 12. Herold, K.C., Vignali, D.A.A., Cooke, A., Bluestone, J.A., (April 2013). “Type 1 diabetes: translating

mechanistic observations into effective clinical outcomes”. Nature Reviews/Immunology. 13: 243-256

13. Oh, Seh-Hoon, Darwiche, H, Cho, J, Shupe, T., Petersen, B.E. “Characterization of a novel functional protein in the pancreatic islet: IhoP regulation of glucagon synthesis in alpha-cells” Pancreas. 2012 January ; 41 (1): 22-30

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LESSON #4 – Diabetes and the Central Dogma (PowerPoint) KEY QUESTIONS: How is genetic information stored, transcribed and translated into functional proteins in humans and other living organisms? What is the relationship between an organism’s ability to make specific proteins and its ability to maintain homeostasis? SCIENCE CONCEPTS: DNA, genetic expression, mutation, regulation, replication, RNA, transcription, translation OVERALL TIME ESTIMATE: 60 - 80 minutes LEARNING STYLES: Visual and auditory. VOCABULARY: Ambiguity –the idea in reference to the genetic code that a particular codon might code for more than one amino acid. This is not true of the genetic code, i.e., there is no ambiguity. Amino acid – one of twenty monomers of proteins. Each of them have a central carbon atom surrounded by an amine group, a carboxyl group, a hydrogen atom and a side group (referred to as the “R-group” that is unique to each one. Anti-codon – a group of three nitrogen bases found at one end of a transfer RNA that would be complementary to a codon found on a messenger RNA Central Dogma – more properly called a hypothesis, rather than a dogma, but it refers to the flow of genetic information from DNA to RNA to proteins Codon – a group of three nitrogen bases found in sequences of messenger RNA that code for a specific amino acid Complementary Base Pairing – an attraction between pairs of nitrogen bases found in nucleic acids based on easily broken hydrogen bonds. Two of the five bases found in nucleic acids, adenine and guanine are purines and they respectively bond with thymine and cytosine which are pyrimidines. In RNA thymine is replaced by uracil, another pyrimidine DNA – deoxyribonucleic acid, a molecule which is the main repository of genetic information in most living organisms. It is a double-stranded polymer which assumes a helical shape and consists of monomers of nucleotides which in turn consist of one deoxyribose sugar, one phosphate and one of four nitrogen bases, adenine, guanine, cytosine and thymine Degeneracy – the phenomenon that the genetic code is redundant, i.e., a given amino acid can be coded for by more than one codon Deletion – a form of genetic mutation wherein a nitrogen base is removed or left out thus leading to a frame shift, i.e., the manner in which a sequence is read Diabetes - group of similar disease states that in one way or another disrupt the body’s ability to maintain homeostasis with respect to blood sugar levels. The two main forms would be: Type 1 diabetes, wherein the pancreas fails to produce insulin, and Type 2 diabetes, wherein there is a failure of the receptor proteins on multiple cell surfaces that prevent insulin from promoting the uptake of glucose. Double Helix – the shape of a DNA molecule as postulated by Watson and Crick. It is like a twisted ladder wherein the sides are constructed of alternating sugars and phosphates and the rungs of nitrogen bases held weakly together by nitrogen bonds. Enzyme – a protein that serves as an organic catalyst, i.e., it promotes biochemical reactions without being consumed in them by lowering the activation energy required to make them go forward. Their

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shape is critical to their function as there is an active site on them that conforms to the shape of the substrate (reactants) Exon – that part of a primary mRNA transcript that will actually serve as a source of coding to construct the protein Frame shift Mutation – a change in a gene sequence consisting of either an insertion or a deletion of a nucleotide that from that point forward changes the manner in which the sequence will be transcribed or translated Gene – a sequence of nucleotides along one side of a DNA molecule that contains coded information for a specific polypeptide Glucose - A monosaccharide sugar, C6H12O6, occurring widely in most plant and animal tissue. It is the principal circulating sugar in the blood and the major energy source of the body. Homeostasis - the tendency of a system, especially the physiological system of higher animals, to maintain internal stability, owing to the coordinated response of its parts to any situation or stimulus that would tend to disturb its normal condition or function Insertion – a form of genetic mutation wherein a nucleotide is added to an existing sequence thus leading to a frame shift, i.e., a change in the manner the sequence is transcribed or translated Intron – a non-coding sequence within a primary mRNA transcript Mutation – a change in a gene sequence Nucleotide – a monomer of the polymers DNA or RNA consisting of one sugar, one phosphate and one of the nitrogen bases adenine, thymine, guanine, cytosine or uracil Point Mutation – a change in a gene sequence of a single nucleotide Polymer – a molecule consisting of a series of repeating similar units, or monomers. Examples would be complex carbohydrates, proteins and nucleic acids Polypeptide – a long, continuous and unbranched chain of amino acids held together by peptide bonds Protein - large biological molecules consisting of one or more chains of amino acids that perform a vast array of functions within living organisms Protein Structure - the biomolecular structure of a protein molecule. Each protein is a polymer – specifically a polypeptide – that is a sequence formed from various L-α-amino acids Replication – the process of producing two identical DNA copies from one original DNA molecule Transcription - the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme, RNA polymerase Translation - is the process in which cellular ribosomes create proteins. It is part of the process of gene expression LESSON SUMMARY: This lesson is a straightforward exercise in transmitting content via powerpoint while students take notes and are encouraged to ask questions based on the text and images they are seeing. STUDENT LEARNING OBJECTIVE: Students should be able to:

1. Define the basic terminology of heredity at the organismic, cellular and molecular levels 2. Sequence the steps of the central dogma of biology 3. Explain the relationship between homeostasis and protein production

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STANDARDS: SC.912.L.14.6 Explain the significance of genetic factors, environmental factors, and pathogenic agents to health from the perspectives of both individual and public health. S.C.912.L.14.29 Define the terms endocrine and exocrine S.C.912.L.14.30 Compare endocrine and neural controls of physiology S.C.912.L.14.31 Describe the physiology of hormones including the different types and the mechanisms of their actions. S.C.912.L.14.46 Describe the physiology of the the digestive system, including mechanical digestion, chemical digestion, absorption and the neural and hormonal mechanisms of control. SC.912.L.14.52 Explain the basic functions of the human immune system, including specific and nonspecific immune response, vaccines, and antibiotics. SC.912.L.16.3 Describe the basic process of DNA replication and how it relates to the transmission and conservation of the genetic information SC.912.L.16.4 Explain how mutations in the DNA sequence may or may not result in phenotypic change. Explain how mutations in gametes may result in phenotypic changes in offspring. S.C.912.L.16.5 Explain the basic processes of transcription and translation, and how they result in the expression of genes. S.C.912.L.16.6 Discuss the mechanisms for regulation of gene expression in prokaryotes and eukaryotes at transcription and translation level SC.912.L.18.1 Describe the basic molecular structures and primary functions of the four major categories of biological macromolecules. SC.912.L.18.4 Describe the structures of proteins and amino acids. Explain the functions of proteins in living organisms. Identify some reactions that amino acids undergo. Relate the structure and function of enzymes. MATERIALS: Computer Projection equipment

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BACKGROUND INFORMATION: The central dogma of biology is an explanation of how genetic information is stored, transcribed and translated into functional proteins in living organisms. A basic understanding of its tenets is critical to making sense of genetics and molecular biology, and, by extension, physiology, medicine, and many other aspects of biology currently at the forefront of the living sciences. Given that most of the processes involved are occurring at a scale below that perceivable by light, and in some cases, electron microscopy, the teaching of it relies heavily on the student’s ability to understand concepts they can only visualize indirectly. DNA (Deoxyribonucleic acid) was shown by James Watson and Francis Crick to be a molecule that assumes a double helix (twisted ladder) shape. The sides of the ladder are composed of alternating deoxyribose sugars and phosphates. The rungs of the ladder are, however, the repository of genetic information that directs the production of proteins in both prokaryotic and eukaryotic cells. That information is contained in the sequence of four nitrogen bases, adenine, thymine, guanine and cytosine which are often symbolized as A, T, G, and C. Adenine is weakly attracted by hydrogen bonds to thymine and similarly guanine is attracted to cytosine in a phenomenon known as complementary base pairing. The genetic information is in the form of triplets of nitrogen bases that ultimately code for amino acids, the building blocks of proteins. Because of complementary base pairing each side of a DNA molecule can serve as a template for reliable replication of this genetic information as an antecedent to cell division so that each new cell will have a complete set of instructions to make all the proteins necessary for that particular organism. This replication is accomplished with the aid of several enzymes that are themselves proteins. Helicase opens up the helix at several locations. Polymerase brings in free nucleotides, consisting of one sugar, one phosphate and the complementary base. Ligase ties the nucleotides together. RNA (Ribonucleic acid) differs from DNA in that it is single stranded, contains the sugar ribose and ′′contains the nitrogen base uracil in place of thymine; uracil being complementary to adenine in the way thymine is in DNA. RNA comes in three forms, messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA),all of which are involved in the transfer of information from nuclear DNA to cytoplasmic organelles for the production of proteins. Recent research has also unearthed some small endogenous classes of RNA, microRNA (miRNA) and small interfering RNA (siRNA) that regulate the production of proteins, but their modus operandi is not completely understood at this time. DNA and mRNA are the molecules directly involved in transcription. This is a process wherein a section of DNA, known as a gene, that codes for a protein opens up and with the help of the enzyme RNA polymerase free RNA nucleotides temporarily bind to the appropriate section of DNA. The process is initiated at sequences of DNA known as promoter regions, continues through the coding region and is terminated by one of three possible stop codons called terminators. The mRNA then peels away from the DNA and makes its way through the nuclear pores to a two-part organelle made of rRNA called a ribosome. Some of these are free in the cytoplasm and some are found on the surface of endoplasmic reticulum. Before they reach the ribosomes, however, some non-coding parts of the mRNA, called introns, are excised from the message with the help of enzymes and the coding parts, called exons, are spliced together. Other enzymes aid in adding a guanine nucleotide cap to the 5′ end and a poly-A (adenine) cap to the 3′ end to distinguish which end should go in to the ribosome first and to prevent hydrolytic enzymes from destroying the mRNA before it gets translated. Once transcription and post-transcriptional processing are completed the mRNA is ready to be translated at a ribosome. A ribosome is made of two sub-units, a small one and a large one. The small sub-unit attaches to the 5′ end of the mRNA and a tRNA with the amino acid methionine attached to it. The small subunit moves along the mRNA until it reaches the start codon AUG whereupon the complementary anti-codon UAC on the tRNA binds temporarily to the mRNA, the large sub-unit attaches and the process of translation commences. The ribosome starts moving along the mRNA three bases at

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a time and tRNAs with anti-codons complementary to the codon being presented at that site and the appropriate amino acid at the other end of the tRNA are added to a growing polypeptide chain. Eventually one of three codons, UAA, UAG, or UGA that all signify “Stop”, is reached and the process of translation is terminated. The mRNA peels away from the ribosome as does the polypeptide. The sequence of amino acids at this point is referred to as the primary structure. Post-translationally the side chains of the various amino acids in the polypeptide begin to interact with their aqueous environment and one another and fold into secondary and tertiary structures and thence into functional proteins. If another polypeptide is required to interact with the first one to achieve functional status the combination of the two (or more) of them is referred to as the quaternary structure. All of this works amazingly efficiently given how frequently it has to occur to maintain the proper functioning of cells in unicellular organisms and cells, tissues and organs in multicellular organisms. There is, however, the occasional mutation. It depends on the nature of the mutation as to whether its effect is negative, positive or moot. If, for instance, a single nitrogen base is replaced with another one in a point mutation known as a substitution, and it happens to be the third base in the triplet or codon there is a good chance it will have no effect due to the redundant nature of the genetic code. If it’s the first or second base in the codon chances are that a different amino acid will be called for and that can change the structure and therefore function of the resulting protein. If a single base is removed or added, known respectively as a deletion or an addition, and collectively as frame-shift mutations, then, as the name implies all of the message after that mutation will be read differently and most likely the structure and function of the resulting protein will be radically altered. Occasionally these altered proteins actually work better than the original protein and/or give the organism some adaptive trait that it didn’t previously possess. This is the basis of evolutionary change. ADVANCE PREPARATION: Read through the PowerPoint for comprehension and make editorial changes as desired. Ensure that embedded links to animations function properly on your system if you choose to use them. PROCEDURES: Depending on your individual teaching style this PowerPoint can serve as just a straight dissemination of content/note-taking exercise or a jumping off point for a dialogue on the concepts depicted. ASSESSMENT SUGGESTIONS: Post test Unit test Performance on From DNA to Protein Structure and Function lab Biology EOC IB, AP, or AICE Biology tests. REFERENCES AND RESOURCES:

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Helpful animations: http://www.dnalc.org/resources/3d/central-dogma.html http://www.wiley.com/college/boyer/0470003790/animations/central_dogma/central_dogma.swf http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter3/animation__mrna_synthesis__transcription___quiz_1_.html http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter3/animation__how_translation_works.html http://naturedocumentaries.org/2149/central-dogma-biology-2008/ http://www.wisc-online.com/objects/ViewObject.aspx?ID=AP1302

1. ^ Crick, F.H.C. (1958): On Protein Synthesis. Symp. Soc. Exp. Biol. XII, 139-163. (pdf, early draft of original article)

2. ^ a b Crick, F (August 1970). "Central dogma of molecular biology.". Nature 227 (5258): 561–3. Bibcode:1970Natur.227..561C. doi:10.1038/227561a0. PMID 4913914.

3. ^ Leavitt, Sarah A.; Marshall Nirenberg (June 2010). "Deciphering the Genetic Code: Marshall Nirenberg". Office of NIH History.

4. ^ Ahlquist P (May 2002). "RNA-dependent RNA polymerases, viruses, and RNA silencing". Science 296 (5571): 1270–3. Bibcode:2002Sci...296.1270A. doi:10.1126/science.1069132. PMID 12016304.

5. ^ B. J. McCarthy and J. J. Holland (September 15, 1965). "Denatured DNA as a Direct Template for in vitro Protein Synthesis". Proceedings of the National Academy of Sciences of the United States 54 (3): 880–886. Bibcode:1965PNAS...54..880M. doi:10.1073/pnas.54.3.880. PMC 219759. PMID 4955657.

6. ^ .T. Uzawa, A. Yamagishi, T. Oshima (2002-04-09). "Polypeptide Synthesis Directed by DNA as a Messenger in Cell-Free Polypeptide Synthesis by Extreme Thermophiles, Thermus thermophilus HB27 and Sulfolobus tokodaii Strain 7". The Journal of Biochemistry 131 (6): 849–853. PMID 12038981.

7. ^ Wilkins, Adam S. (January 2012). "(Review) Evolution: A View from the 21st Century". Genome Biology and Evolution. doi:10.1093/gbe/evs008.

8. ^ Moran, Laurence A (May–June 2011). "(Review) Evolution: A View from the 21st Century". Reports of the National Center for Science Education 32.3 (9): 1–4.

9. ^ Horace Freeland Judson (1996). "Chapter 6: My mind was, that a dogma was an idea for which there was no reasonable evidence. You see?!". The Eighth Day of Creation: Makers of the Revolution in Biology (25th anniversary edition). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. ISBN 0-87969-477-7.

10. ^ a b http://www.nature.com/nature/journal/v496/n7446/full/496419a.html?WT.ec_id=NATURE-20130425

STUDENT PAGES: N/A

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TEACHER PAGES: see attached powerpoint “Diabetes and the Central Dogma” and screen shots below:

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LESSON #5 - From DNA to Protein: Structure and Function KEY QUESTIONS: How is genetic information stored in DNA and how is it used to direct the synthesis of the many different kinds of proteins that each cell requires? How is the shape of a specific protein determined? What relationship does the shape of a protein have to its function? SCIENCE CONCEPTS: central dogma, complementary base pairing, DNA, genetic expression, mutation, protein function, protein synthesis, RNA, transcription, translation OVERALL TIME ESTIMATE: Two 40 minute class periods plus homework LEARNING STYLES: Visual, auditory, and kinesthetic VOCABULARY: Amino acid – one of twenty monomers of proteins. Each of them have a central carbon atom surrounded by an amine group, a carboxyl group, a hydrogen atom and a side group (referred to as the “R-group” that is unique to each one. Complementary Base Pairing – an attraction between pairs of nitrogen bases found in nucleic acids based on easily broken hydrogen bonds. Two of the five bases found in nucleic acids, adenine and guanine are purines and they respectively bond with thymine and cytosine which are pyrimidines. In RNA thymine is replaced by uracil, another pyrimidine DNA – deoxyribonucleic acid, a molecule which is the main repository of genetic information in most living organisms. It is a double-stranded polymer which assumes a helical shape and consists of monomers of nucleotides which in turn consist of one deoxyribose sugar, one phosphate and one of four nitrogen bases, adenine, guanine, cytosine and thymine Gene – a sequence of nucleotides along one side of a DNA molecule that contains coded information for a specific polypeptide Hydrophilic – having an affinity for water Hydrophobic – having a repulsion to water Mutation – a change in a gene sequence Nitrogen Base – nitrogen containing organic molecules found within the nucleic acids DNA and RNA that have a weak affinity for one another and thus allow for complementary base pairing Nucleotide – a monomer of the polymers DNA or RNA consisting of one sugar, one phosphate and one of the nitrogen bases adenine, thymine, guanine, cytosine or uracil Polypeptide – a long, continuous and unbranched chain of amino acids held together by peptide bonds Protein - large biological molecules consisting of one or more chains of amino acids that perform a vast array of functions within living organisms Transcription - the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme, RNA polymerase Translation - is the process in which cellular ribosomes create proteins. It is part of the process of gene expression LESSON SUMMARY: Students model how information in the DNA base sequence is transcribed and translated to produce a protein molecule. They model how interaction between amino acids causes a protein to fold into a three-dimensional shape that enables the protein to perform a specific function. STUDENT LEARNING OBJECTIVE: Students should be able to:

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1. Define the basic terminology of protein expression and function. 2. Sequence the steps of the central dogma of biology. 3. Explain the relationship between structure and function in proteins.

STANDARDS: SC.912.L.16.3 Describe the basic process of DNA replication and how it relates to the transmission and conservation of the genetic information SC.912.L.16.4 Explain how mutations in the DNA sequence may or may not result in phenotypic change. Explain how mutations in gametes may result in phenotypic changes in offspring. S.C.912.L.16.5 Explain the basic processes of transcription and translation, and how the result in the expression of genes. S.C.912.L.16.6 Discuss the mechanisms for regulation of gene expression in prokaryotes and eukaryotes at transcription and translation level S.C.912.L.16.9 Explain how and why the genetic code is universal and is common to all organisms SC.912.L.16.10 Evaluate the impact of biotechnology on the individual, society and the environment, including medical and ethical issues. SC.912.L.18.1 Describe the basic molecular structures and primary functions of the four major categories of biological macromolecules. SC.912.L.18.4 Describe the structures of proteins and amino acids. Explain the functions of proteins in living organisms. Identify some reactions that amino acids undergo. Relate the structure and function of enzymes. MATERIALS: Science Take-Out Kit STO-106 “From DNA to Protein Structure and Function” (see Advance Preparation section) which includes: 19 inch chenille stem Universal genetic code chart Beads – red, blue, yellow, white From DNA to Protein Record Sheet Teacher optionally provides red, blue and yellow colored pencils, markers or crayons.

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BACKGROUND INFORMATION:

The central dogma of biology is an explanation of the flow of genetic information in living organisms. The term central dogma is attributed to Francis Crick, one of the co-discoverers of the double helix shape of DNA, who later acknowledged that his use of the term “dogma” was perhaps unfortunate in that it implied a rigidity of thinking that would stand in opposition to the scientific method. More than a half century of myriad lines of research have unequivocally confirmed, however, that information contained in the nitrogen base sequences of DNA is transcribed on to RNA and then translated into proteins.

This lesson focuses on the transcription and translation of DNA sequences and the post-translational interactions between the parts of a polypeptide chain that transform it into a functioning protein. The so-called genetic information in DNA sequences comes in the form of DNA nitrogen base triplets. These could consist of any one of 64 (43) possible combinations of the four nitrogen bases, i.e., adenine (A) and guanine (G), also known as the purine bases, and thymine (T) and cytosine (C), also known as the pyrimidine bases. Adenine has an affinity to form a hydrogen bond with thymine and similarly, guanine bonds with cytosine. This tendency to form complementary base pairs allows for accurate replication of DNA molecules via the addition of complementary free DNA nucleotides to either side of an opened double helix structure with the aid of appropriate enzymes. It also allows for the accurate transcription of DNA sequences into sequences of messenger RNA (mRNA) by the temporary addition of complementary free RNA nucleotides to one side of one section of the DNA molecule known as a gene. The triplets of mRNA molecules thus transcribed are known as codons because they later code for specific amino acids by peeling off of the transcribed DNA sequence, leaving the cell nucleus to seek out a ribosome and translating their information into a specified chain of amino acids. Each codon only codes for one amino acid but there are 64 codons and only 20 amino acids so there is more than one codon that can code for a particular amino acid.

A chain of amino acids in a specific sequence as described above is referred to as a polypeptide because the amino acids are held together by peptide bonds. Interactions that occur between different parts of the chain post-translationally are what make the chain a functional protein. All amino acids have in common an amine group, a carboxyl group and a hydrogen atom extending from 3 of the possible bonds of a central carbon atom, but the 4th bond, the so-called “R” side chain is different in each one. Some of these side chains are hydrophobic, some are hydrophilic, some are negatively charged and some are positively charged. Since they exist in the polar medium water the interactions of the different side chains with the water and with each other make them contort into the shapes that give them their specific function. This phenomenon explains why a change in a single nitrogen base back at the DNA level of information (known as a point mutation) can potentially change the structure and thus the function of the protein that results. For students to understand the central dogma they need to have an understanding of the structure of DNA at the levels of nucleotides, genes and chromosomes, an understanding of the structures of the different forms of RNA, and an understanding of amino acids, polypeptides and functional proteins This lab will give them a hands-on means of visually and kinesiologically demonstrating to themselves how these molecules interact with one another to construct the thousands of different proteins necessary for complex living processes.

43

ADVANCE PREPARATION:

As noted above some of the materials for From DNA to Protein Structure and Function should be readily available in any reasonably equipped high school science department. The kit itself and the accompanying supplies, background information, question sheets, directions and graphics are available from the Life Sciences Learning Center at the University of Rochester. The contact information for them is:

Science Take-Out P.O. Box 205 Pittsford, NY 14534

(585)764-5400 phone (585)381-9495 fax contact@sciencetakeout.com A pdf version of Diagnosing Diabetes can be found at the following URL: http://www.cpet.ufl.edu/wp-content/uploads/2012/10/Structure-to-Function.pdf Depending on curricular sequence, molecular genetics should fall far enough into the academic year that some sample kits could be obtained well in advance of the actual need for them. By doing this at the beginning of the school year decisions could be made about how many kits need to be obtained for the actual lab and how much of the material can be formulated from supplies on hand. At minimum the pdf version should be accessed, downloaded, read and fully considered well in advance of attempting the lab. If cost is not a consideration and the intent is just to obtain, use and discard the materials from Science Takeout then the following advice can be ignored, but if the intent is to reuse the graphics it would be wise to laminate the “Universal Genetic Code Charts” PROCEDURE:

1. Reference the Diabetes to Central Dogma power point notes, the background information above, and the introductory material from the lab kit itself to conduct a short review of the basic tenets of the central dogma and the relationship of protein folding to their structure and function. (5 - 10 minutes)

2. Divide students into lab groups and distribute instructions, Universal Genetic Code Charts, Record Sheets, chenille stems and beads. I would highly recommend you have shallow containers to corral the beads and have towels or paper towels on the bench top surface or the beads will be rolling everywhere except where you want them. (If this lab is being done with multiple classes these items can be distributed to lab benches before class, otherwise allow about 5 minutes)

3. The instructions are fairly self-explanatory, but depending on the level of the class you may need to read through them aloud as a group to clear up any misunderstandings. (5 -10 minutes)

4. Carry out Part A. Modeling Protein Synthesis and Protein Folding (30 – 40 minutes) 5. Carry out Part B. Protein Shape and Function (15 – 20 minutes) 6. Carry out Part C. Sickle Cell Anemia – An Error in Protein Structure and Function (15 – 20

minutes)

44

ASSESSMENT SUGGESTIONS:

Successful completion and demonstration of comprehension of the questions embedded in the lab

Demonstration of comprehension of those questions in the post-test related to this topic. RESOURCES AND REFERENCES: From DNA to Protein Structure and Function available from Science Takeout (see contact information in Advance Preparation above). Helpful websites: http://publications.nigms.nih.gov/structlife/chapter1.html http://publications.nigms.nih.gov/psi/timeline_text.html REFERENCES

1. ^ Brocchieri L, Karlin S (2005-06-10). "Protein length in eukaryotic and prokaryotic proteomes". Nucleic Acids Research 33 (10): 3390–3400. doi:10.1093/nar/gki615. PMC 1150220. PMID 15951512.

2. ^ Pauling L, Corey RB, Branson HR (1951). "The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain". Proc Natl Acad Sci USA 37 (4): 205–211. doi:10.1073/pnas.37.4.205. PMC 1063337. PMID 14816373.

3. ^ Chiang YS, Gelfand TI, Kister AE, Gelfand IM (2007). "New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage.". Proteins. 68 (4): 915–921. doi:10.1002/prot.21473. PMID 17557333.

4. ^ Govindarajan S, Recabarren R, Goldstein RA. (17 September 1999). "Estimating the total number of protein folds.". Proteins. 35 (4): 408–414. doi:10.1002/(SICI)1097-0134(19990601)35:4<408::AID-PROT4>3.0.CO;2-A. PMID 10382668.

5. ^ . PMID 23056252. Missing or empty |title= (help) 6. ^ Murzin, A. G.; Brenner, S.; Hubbard, T.; Chothia, C. (1995). "SCOP: A structural classification of

proteins database for the investigation of sequences and structures". Journal of Molecular Biology 247 (4): 536–540. doi:10.1016/S0022-2836(05)80134-2. PMID 7723011. edit

7. ^ Orengo, C. A.; Michie, A. D.; Jones, S.; Jones, D. T.; Swindells, M. B.; Thornton, J. M. (1997). "CATH--a hierarchic classification of protein domain structures". Structure (London, England : 1993) 5 (8): 1093–1108. doi:10.1016/S0969-2126(97)00260-8. PMID 9309224. edit

8. ^ Zhang Y (2008). "Progress and challenges in protein structure prediction". Curr Opin Struct Biol 18 (3): 342–348. doi:10.1016/j.sbi.2008.02.004. PMC 2680823. PMID 18436442.

STUDENT PAGES: Accessible in From DNA to Protein Structure and Function pdf: http://www.cpet.ufl.edu/wp-content/uploads/2012/10/Structure-to-Function.pdf TEACHER PAGES: Accessible in From DNA to Protein Structure and Function pdf: http://www.cpet.ufl.edu/wp-content/uploads/2012/10/Structure-to-Function.pdf

45

LESSON #6 – Post-test TIME ESTIMATE: 30 minutes

Post-test

1. List at least five symptoms of diabetes.

2a. What is the principal organ involved in the development of diabetes? 2b. List 3 organs involved in long-term complications of diabetes.

3. As a member of the U.S. population what are the chances you will develop diabetes in your life time? A. 0-10% B. 20-25% C. 30-40% D. 60-70%

4. Are you more likely to get Type 1 Diabetes or Type 2 Diabetes?

5. Compare and contrast Type 1 Diabetes and Type 2 Diabetes

46

6. What, if any, is the relationship between DNA and Diabetes?

7. What, if any, is the relationship between DNA and proteins?

8. List at least 3 functions for proteins.

9. State, in as few words as possible, the central dogma of molecular biology.

10. What is a gene?

11. What is a mutation?

12. Name at least two possible outcomes of a genetic mutation.

47

Pre/Post-test Answer Key

1. List at least 5 symptoms of diabetes. Frequent urination Excessive Thirst Hunger Blurry Vision Weight Loss/Gain Fatigue Diabetic Ketoacidosis Hyperventilation Nausea Vomiting

2a. What is the principal organ involved in the development of diabetes? Pancreas Liver 2b. List 3 organs involved in long-term complications of diabetes. Kidney Heart Blood Vessels Eyes Nerves

3. As a member of the U.S. population what are the chances you will develop diabetes in your life time? C. 30-40%

4. Are you more likely to get Type 1 Diabetes or Type 2 Diabetes? Type 2

5. Compare and contrast Type 1 Diabetes and Type 2 Diabetes. In Type-1, the beta cells in the pancreas (which produce insulin) are destroyed by the individual’s own immune system, meaning those people produce no insulin. In Type-2, individuals can produce insulin but the insulin receptors on their cell membranes do not respond properly to the insulin message (signal)

6. What, if any, is the relationship between DNA and Diabetes? DNA contains the genetic information to create proteins that function all over the body. Changes in DNA (mutations) can lead to less functional or non-functional proteins, which leads to diseases such as Diabetes.

7. What, if any, is the relationship between DNA and proteins? DNA contains the genetic information to create proteins that function all over the body. Changes in DNA (mutations) can lead to less functional or non-functional proteins.

48

8. List at least 3 functions for proteins. Structural Enzymes Hormones Regulators Movement/Transfer

9. State, in as few words as possible, the central dogma of molecular biology. DNA RNA Protein

10. What is a gene? A sequence of nucleotides along one side of a DNA molecule that contains coded information for a specific polypeptide

11. What is a mutation? A change in the gene sequence

12. Name at least two possible outcomes of a genetic mutation. No Change Less functional protein More functional protein Non-functional protein

49

Acknowledgements As the author of this work I would like to express my sincere gratitude to Mary Jo Koroly, Julie Bokor, Drew Joseph, Houda Darwiche and the entire CPET staff for two consecutive great learning experiences, last summer at the Emerging Pathogens/ICORE Summer Institute and this summer at the CPET Research Internship. I believe I have learned more than my head can hold. I would also like to thank Bryon Petersen and all the members of his laboratory for allowing me to be a nosy fly on the wall observing a truly remarkable research team.

Diabetes and the Central Dogma

What do the two types of diabetes

have in common that involves the

Central Dogma?

Proteins that are missing

Why should you care?

Why should you care?

• Odds of getting diabetes depends on race,

gender and level of education

• If you understand the connection

between diet, exercise & lifestyle you

improve the odds of avoiding diabetes

Central Dogma

DNA

• James Watson & Francis

Crick proposed:

• DNA shape a double

helix

• DNA contains genetic

information

• The term “Central

Dogma”

• DNA → RNA → protein

DNA

• Deoxyribonucleic

acid

• Double helix

(twisted ladder)

• Sides =

deoxyribose sugar

& phosphates

• Rungs = nitrogen

bases (A,T,G,C)

DNA nucleotides

• DNA is a polymer of nucleotides

• Poly = many, mer = unit

• DNA nucleotide = one deoxyribose

sugar, one phosphate & one

nitrogen base

Nitrogen bases – complementary

base pairing

• A = Adenine

• T = Thymine

• G = Guanine

• C = Cytosine

• A attracted to T

• G attracted to C

Complementary Base Pairing

• Insures

accurate

replication of

DNA for cell

division

Complementary Base Pairing

• Insures accurate

transcription of

DNA → RNA

Genetic information

Stored in Nitrogen Base

Sequences • Nitrogen base triplet

codes for an amino acid

• Example – TAC codes for methionine

• The four bases can be combined 64 different ways into groups of 3

• 43 = 64

Genetic information

Stored in Nitrogen Base

Sequences

• DNA base triplet sequences = genes

• genes code for sequences of amino acids

• Amino acid sequences become proteins

• Human genome in our 46 chromosomes

holds about 20,000 genes (a complete set

of instructions)

DNA Replication

• DNA replication must

occur before cells

divide so each new

cell will have a

complete set of

genetic instructions

DNA Replication (simplified)

DNA Replication (with enzymes)

DNA Replication (end result)

• Two strands of original chromosomes

were mirror images of each other

• Complementary base pairing allows each

original strand to serve as template

• Replication produces two perfect copies

consisting of one original strand and one

new strand

Back to the Central Dogma

Transcription

• Noun

• (plural transcriptions)

• The act or process of transcribing.

• Something that has been transcribed, including: – (music) An adaptation of a composition.

– These frame tale interludes frequently include transcriptions of Italian folk songs.

– A recorded radio or television programme.

– (linguistics) A representation of speech sounds as phonetic symbols.

• (genetics) The synthesis of RNA under the direction of DNA.

Transcription

• Genetic information for proteins is coded

in DNA.

• DNA does not leave the nucleus.

• Proteins are made in the cytoplasm.

• Therefore, DNA information must be

transcribed and carried from the nucleus

to the cytoplasm.

• Messenger RNA (mRNA) does this.

RNA vs. DNA

• RNA

• Single

stranded

• Ribose sugar

• Uracil

• DNA

• Double

stranded

• Deoxyribose

sugar

• Thymine

Messenger RNA (mRNA)

• Transcribes genes from DNA in nucleus

• Formed from free RNA nucleotides in the

nucleus

• Uses complementary base pairing and

enzymes to transcribe genes

• Is modified after transcription before

leaving the nucleus

DNA to RNA transcription

http://www.google.com/url?sa=i&rct=j&q=transcription%2Banimation&source=images&cd=&cad=rja&docid=Akkk59RcoZVSZM&tbnid=jYGoCrJ0PSWr2M:&ved=0CAUQjRw&url=https%3A%2F%2Fib-biology2010-12.wikispaces.com%2FTranscription%2Band%2BTranslation&ei=4bfJUd3aNoP69QTP_YHwDA&psig=AFQjCNGdgiP4ne25HUBc7XyPCkhm5BW3CQ&ust=1372260504355855

Transcription animation

• http://highered.mcgraw-

hill.com/sites/0072507470/student_view0/

chapter3/animation__mrna_synthesis__tra

nscription___quiz_1_.html

Post – transcription changes

• After the mRNA peels off it is modified before it leaves the nucleus.

• A guanine cap is added to the 5ˊ end and a poly A (Adenine) cap is added to the 3ˊ end

• Non-coding parts of the message called introns are cut out & the coding parts called exons are spliced together by enzymes.

• The mature mRNA then moves through a nuclear pore to find a ribosome and be translated

Post transcription animation

• http://www.execulink.com/~ekimmel/mrna_

flash.htm

Translation

• trans·la·tion (tr ns-l sh n, tr nz-)

• n.

• 1.

• a. The act or process of translating, especially from one language into another.

• b. The state of being translated.

• 2. A translated version of a text.

• 3. Physics Motion of a body in which every point of the body moves parallel to and the same distance as every other point of the body.

• 4. Biology The process by which messenger RNA directs the amino acid sequence of a growing polypeptide during protein synthesis.

Translation

• The information that was transcribed from

DNA to mRNA was in the language of

nucleotide base triplets which are called

codons in mRNA.

• The codons will be translated into the

language of amino acids

Translation

• Translation occurs in the cytoplasm

• It requires two other forms of RNA in addition

to mRNA:

rRNA (ribosomal RNA)

tRNA (transfer RNA)

rRNA & tRNA Ribosomes (rRNA)

Made of small sub-unit

& large sub-unit

Free or on endoplasmic

reticulum

Transfer RNA (tRNA)

Have anti-codon

complementary to

codons at one end

Amino acid on the other

end

Translation Initiation

• mRNA joins small sub-unit of ribosome with “start” tRNA (methionine) on it

• Small sub-unit moves along mRNA until AUG codon on mRNA joins UAC anti-codon on tRNA

• Large sub-unit joins small and ribosome moves along mRNA one codon at a time

• tRNAs bring amino acids based on base pairing and polypeptide chain grows

Translation

Translation animation

• http://highered.mcgraw-

hill.com/sites/0072507470/student_view0/

chapter3/animation__how_translation_wor

ks.html

Post-translation

• The product of translation is a chain of amino

acids called a polypeptide.

• This polypeptide is the primary structure of the

eventual protein.

• The 20 different amino acids have different

chemical properties based on their side chains.

• Some are hydrophobic; some are hydrophilic;

some are negatively charged; some are

positively charged

Post-translation

• Because of their different properties they bend into a secondary structure then fold over on each other into a tertiary structure until they become functional proteins.

• Some proteins require two or more polypeptides to join together to achieve full function. This would be its quaternary structure.

Functional Protein Structure

Functional Structure of

Genetic Code Charts

Genetic Code Charts - Circular

Genetic Code

• There are 64 (43) ways for the 4 nitrogen bases

to be assembled in groups of 3.

• There are only 20 amino acids

• So the code is redundant, that is, there is more

than one codon that codes for a particular amino

acid. This property is referred to as the

degeneracy of the code

• There is no ambiguity, however. Any particular

codon only codes for one amino acid (or stop)

Mutations

• Replication, transcription and translation are remarkably efficient and accurate given how often they must occur.

• The occasional mistake in the placing of a nitrogen base, however, is referred to as a mutation.

• Because the code is redundant some mutations don’t result in a change in the protein

Point Mutations

• A point mutation, or

single base

substitution,

depending on where it

is, might not change

the resulting protein.

• This is particularly

true if the third base

of the triplet or codon

is involved.

Point Mutations

• Some point mutations will change the protein

Frame shift mutations

• Frame shift mutations occur in two ways

• An insertion means a base was added

• A deletion means a base was removed

• Either way it shifts the frame of how the

message is read and almost always

radically changes the protein

Frame shift mutations

Effects of Mutations

• As you have seen mutations might have

no effect.

• They might make the resulting protein less

effective.

• They might make the resulting protein not

work at all.

• They might make the resulting protein

work better. This is the basis of evolution.

Back to Diabetes

• Type 1 diabetes is a result of the pancreas failing to produce the protein insulin.

• Type 2 diabetes is a result of a failure of many body cells to properly produce the surface receptor proteins that allow insulin to allow glucose into those cells.

• Neither of these processes are completely understood as there are numerous regulatory proteins involved. The failure of any of them could result in downstream effects.

• Only further research will clarify the causes and effects of the production or non-production of these proteins