Teacher Notes for “Introduction to the Functions of Proteins and DNA” 1

These Teacher Notes present a sequence of discussion and analysis activities that will help students understand that proteins and DNA are not just abstract concepts in biology textbooks, but rather important molecules that have major effects on our bodies’ characteristics. Students learn about the functions of proteins and how different versions of a protein can result in different characteristics. Then, students learn that genes in DNA determine which version of a protein is synthesized by a person’s cells, and this is how genes influence our characteristics. These concepts are conveyed through a sequence of class discussions, videos, questions in the Student Handout, and an optional hands-on learning activity. This sequence can be used in an introductory unit on biological molecules or to introduce a unit on molecular biology.

Table of ContentsLearning Goals – pages 1-2I. Proteins – pages 2-4II. DNA – page 4III. Teacher Information about Five Conditions that Illustrate the Effects of Proteins and DNA –

pages 5-11IV. Additional Teaching Resources – pages 11-12

Learning GoalsKey Concepts Proteins are responsible for many important biological functions. Differences in the structure and function of proteins result in differences in the characteristics

of biological organisms. DNA contains genes which provide the information necessary to make proteins. Different versions of the same gene result in different versions or amounts of a protein which

can result in different characteristics.

In accord with the Next Generation Science Standards2 (NGSS): This activity helps to prepare students for the Performance Expectations:

HS-LS1-1, "Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells."

HS-LS3-1, "Ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring."

Students will gain understanding of two Disciplinary Core Ideas: LS1.A: Structure and Function – "All cells contain genetic information in the form of

DNA molecules. Genes are regions in the DNA that contain the instructions that code for the formation of proteins."

LS3.A: Inheritance of Traits – "Each chromosome consists of a single very long DNA molecule, and each gene on the chromosome is a particular segment of that DNA. The instructions for forming species' characteristics are carried in DNA."

1 Dr. Ingrid Waldron, Biology Department, University of Pennsylvania, 2020. These Teacher Notes are available at https://serendipstudio.org/exchange/bioactivities/proteins.

2 Next Generation Science Standards (http://www.nextgenscience.org/next-generation-science-standards)1

Students will engage in the Scientific Practice, “Constructing Explanations. Construct and revise an explanation based on valid and reliable evidence obtained from a variety of sources…”

The proposed activities provide the opportunity to discuss the Crosscutting Concept, "structure and function".

I. ProteinsKey Concepts: Proteins are responsible for many important biological functions. Differences in the structure and function of proteins result in differences in the

characteristics of biological organisms. Instructional Sequence:A. To introduce the topic, discuss these probe questions:

What are proteins? Why are proteins important?

Students may mention that you need to eat protein if you want to build muscles when you work out. To follow this up, it will be useful to ask them why you need to eat protein and what kinds of food contain protein, which can lead to the realization that muscles are full of proteins which are needed for muscle contraction.

B. To introduce or review the structure and function of proteins, show one or more of these videos. “What is a protein?” (https://www.youtube.com/watch?

v=wvTv8TqWC48&feature=youtu.be) (~7 minutes) This is probably the best overview and is recommended in question 1 in the Student Handout. If the first part of this video is too technical for your students, you can either have them start at 4 minutes and 17 seconds, “Shape & Function”, or you can substitute one of the following.

"Protein Functions in the Body" (http://www.youtube.com/watch?v=T500B5yTy58). (Show approximately the first 3 minutes and omit the hormone section at the end, since it has inaccuracies.) This video offers amusing analogies at the macro level.

“Structure and Function of Proteins” (https://www.youtube.com/watch?v=KH-LQSr7rHs + https://www.youtube.com/watch?v=MG8ziGyattk) (~12+6 minutes) This video provides clear, detailed explanations.

C. Have students complete page 1 of the Student Handout; 3 this will reinforce student understanding of the functions of proteins and their relationships to protein structure. Students may benefit from reviewing one of the above videos as they prepare to answer question 1.

As background for question 2, you may want to: introduce familiar examples such as the differences between hands and feet and different

shapes of different types of teeth and the hard enamel surface of teeth explain that this relationship applies at multiple levels from molecules to organs

Collagen is a triple helix which forms long, cable-like fibers that provide tensile strength to ligaments (which connect two bones) and tendons (which connect muscle to bone). Collagen is

3 A key for the Student Handout is available upon request to Ingrid Waldron (iwaldron@upenn.edu).2

also found in skin and some other tissues. Porin proteins provide channels for small molecules like water and amino acids to cross the cell membrane.

The motor protein, kinesin, walks along a microtubule carrying a vesicle with its contents. The microtubule consists of two types of tubulin polypeptides. Kinesin and the microtubules play an important role in intracellular transport, e.g. from the endoplasmic reticulum to the Golgi apparatus. You may want to show your students an animation of kinesin in action (https://www.youtube.com/watch?v=y-uuk4Pr2i8 or http://upload.wikimedia.org/wikipedia/commons/1/1c/Kinesin_walking.gif).

To complete question 3 in the Student Handout, students need to recognize that collagen has a very different structure from a disaccharide, so collagen will not fit in the active site of the enzyme that breaks down maltose. Indeed, the matching between the active site of an enzyme and the substrate is very precise, so different enzymes are required to break down maltose (a disaccharide derived from the digestion of starch) and lactose (the disaccharide in milk), despite the relatively modest differences between these disaccharides (see figure below). The specificity of the active site depends not only on the shape of the active site, but also on which specific amino acids surround the active site.

D. You may want to have your students complete the hands-on activity, “Enzymes Help Us Digest Food” (https://serendipstudio.org/sci_edu/waldron/#enzymes)

In this hands-on, minds-on activity, students analyze the biological causes of the symptoms experienced by José and Ariella. To analyze the causes of the symptoms, students answer analysis and discussion questions and carry out and interpret the results of two experiments. Students learn about enzyme function and enzyme specificity as they figure out that José has lactose intolerance and Ariella has sucrase deficiency. In the final section, students are challenged to generalize their understanding of enzymes to interpret a video of an experiment with starch, iodine and saliva. (This activity helps students meet the NGSS.)

E. Have your students read the top of page 2 in the Student Handout and answer question 4. This will introduce the idea that different versions of a protein can have observable effects on our characteristics. The table below provides additional examples.

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Protein Function Examples Effect if this Protein is Missing or Defective

Enzyme Enzyme for synthesizing melanin (pigment that gives our skin and hair color)

Albinism (very pale skin and hair)*

Lactase (breaks down lactose)

Lactose intolerance (difficulty digesting milk)*

Acetaldehyde dehydrogenase (breaks down acetaldehyde, a harmful product of alcohol metabolism)

Alcohol sensitivity (skin flushing and unpleasant symptoms after drinking alcohol)*

Transport Hemoglobin (protein in red blood cells which transports oxygen in the blood)

Sickle cell anemia*

Clotting Clotting proteins in blood Hemophilia (excessive bleeding)*

*Teacher information on these conditions is provided, in section III, beginning on page 5.

II. DNAKey Concepts: DNA contains genes which provide the information necessary to make proteins. Different versions of the same gene result in different versions or amounts of a protein

which can result in different characteristics.

Instructional Sequence:A. Discuss probe questions:

Why do some people have sickle cell anemia and others don't? What is DNA? What is a gene?

In discussing the first question, students may mention that you can inherit conditions such as sickle cell anemia or albinism from your parents; if they do, it will be useful to probe what it is that you get from your parents that can result in these conditions. If students mention the use of DNA in forensics, you will probably want to ask students why DNA is useful in forensics; this can lead to a discussion of how each person's DNA is unique.

B. After you have discussed student answers to the probe questions, show: “What are DNA and genes?” http://learn.genetics.utah.edu/content/basics/dna (~1

minute) and “What is DNA and how does it work?” http://statedclearly.com/videos/what-is-dna/ (~5

minutes)These brief animations provide a good basic understanding of DNA and genes. Have students complete question 5 in the Student Handout; they may benefit from reviewing the videos as they think about their answers to this question.

C. Have your students complete question 6 to relate different versions of a gene to different versions of a protein which result in different characteristics. For a culminating discussion, you may want to revisit the probe questions.

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III. Teacher Information about Five Conditions that Illustrate the Effects of Proteins and DNA

Much of the information in this section is more sophisticated than would be appropriate for this introduction to proteins and DNA for high school students, but this information can be useful for your own understanding and for responses to questions from your students.

Sickle cell anemiaSickle cell hemoglobin is less soluble in the watery cytosol of the red blood cells than normal hemoglobin, particularly when oxygen concentrations are low. Consequently, sickle cell hemoglobin tends to form long stacks or rods of hemoglobin molecules, which results in the sickled shape of some red blood cells in a person who is homozygous for the sickle cell allele and consequently has sickle cell anemia. The sickled red blood cells tend to clog the tiny capillaries, blocking the circulation in different parts of the body. Also, the sickled red blood cells do not survive as long as normal red blood cells, which contributes to anemia. Resulting symptoms include pain, physical weakness, impaired mental functioning, and damage to organs such as the heart and kidneys.

Genotype (genes) Protein Phenotype (characteristics)

2 copies of the allelethat codes for

normal hemoglobin (SS)

Normal hemoglobin dissolves in the cytosol of red blood cells.

Disk-shaped red blood cells can squeeze through the smallest blood vessels normal health

2 copies of the allelethat codes for

sickle cell hemoglobin (ss)

Sickle cell hemoglobin can clump in long rods

in red blood cells.

When sickle cell hemoglobin clumps in long rods

sickle-shaped red blood cells clogged small blood vessels + fragile red blood cells pain, damage to body organs + anemia = sickle cell anemia

Brief videos are available at: https://www.biointeractive.org/classroom-resources/sickle-cell-diseasehttps://www.youtube.com/watch?v=hRnrIpUMyZQ

Hemoglobin is made up of four polypeptides, two beta globin and two alpha globin (see the figure below). The mutation that causes sickle-cell anemia results in a change in a single amino acid in the outer part of the beta globin polypeptide. The gene for sickle cell beta globin differs in only a single nucleotide, which results in the substitution of a valine for a glutamic acid. Valine is much less water-soluble than glutamic acid, and this is one reason why sickle-cell hemoglobin is less soluble in the watery cytosol and tends to clump in long rods. The alpha globin polypeptides are the same in normal and sickle cell hemoglobin.

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The severity of sickle cell anemia in different individuals varies from relatively mild sickle cell anemia with few sickling crises and nearly normal health and survival to severe sickle cell anemia with frequent sickling crises, significant organ damage and early death. The majority of people with sickle cell anemia have an intermediate severity. One factor that contributes to variation in the frequency of sickling crises is that some people with sickle cell anemia spontaneously produce relatively high levels of fetal hemoglobin (which contains gamma globin instead of beta globin polypeptides), and fetal hemoglobin inhibits clumping of sickle cell hemoglobin into rods. Hydroxyurea, which increases the production of fetal hemoglobin, is one treatment for sickle cell anemia. A good summary of the medical aspects of sickle cell anemia, including symptoms, diagnosis and treatment is available at http://www.mayoclinic.com/health/sickle-cell-anemia/DS00324. Recent progress in gene therapy for sickle cell anemia is described in https://www.nature.com/articles/d41586-019-03698-8 and https://www.mdedge.com/hematology-oncology/article/214321/anemia/bcl11a-directed-gene-therapy-advances-sickle-cell-disease.

Even in a person who has severe sickle cell anemia, most red blood cells are not sickled most of the time. The degree of clumping of sickle cell hemoglobin into rods varies, depending on factors such as differences in dehydration, oxygen levels in the blood, and multiple genetic factors. For example, dehydration increases the concentration of hemoglobin in red blood cells which increases the tendency of sickle cell hemoglobin to clump into rods. The resulting sickled red blood cells can block some of the small blood vessels, which can cause pain and organ damage (called a sickling crisis). An infection that induces vomiting and diarrhea can result in dehydration which can cause a sickling crisis. However, the causes of most sickling crises are unknown.

An individual who is heterozygous for the sickle cell allele (called sickle cell trait) rarely has symptoms of sickle cell anemia because each red blood cell contains both normal and sickle cell hemoglobin and the normal hemoglobin generally prevents clumping of the sickle cell hemoglobin. Athletic associations recommend testing for sickle cell trait and, for athletes who have sickle cell trait, taking appropriate precautions to prevent extreme exertion and dehydration in order to reduce the small but significant risk of exercise-related sudden death. Harmful health effects of sickle cell trait are rare, and life expectancy is not detectable reduced. Sickle cell trait

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has beneficial health effects in areas where malaria is prevalent; individuals with sickle cell trait have less serious malaria infections because the malaria parasite doesn't grow as well in their red blood cells.

AlbinismIn the most common form of albinism, the defective enzyme for producing melanin not only results in albino skin and hair color, but also affects the appearance and function of the eyes. Further information about albinism is available at https://medlineplus.gov/ency/article/001479.htm and http://omim.org/entry/203100.

In a heterozygous individual, the normal allele is dominant because it codes for the functioning enzyme and even when there is only one copy of the normal allele there is enough of this functioning enzyme to produce enough melanin to prevent albinism. This illustrates the generalization that recessive alleles (such as the allele for albinism) often code for a non-functional protein, while dominant alleles often code for a functional protein.

Students may ask about the distinction between inherited albinism and vitiligo. Albinism is the inability of the body's cells to produce melanin and affects the whole body. Vitiligo is a patterned loss of melanin pigment resulting from the destruction of melanocytes; the hypopigmented areas appear on the skin of a person with normal pigmentation (http://www.mayoclinic.org/diseases-conditions/vitiligo/home/ovc-20319041).

Lactose Intolerance This information on lactose intolerance will be particularly relevant if you decide to use the hands-on activity, “Enzymes help us digest food” recommended in item D on page 3. To discuss lactose intolerance, your students need to understand the distinction between lactose and lactase. Lactose is the main sugar in milk and lactase is the protein enzyme that digests lactose into the simple sugars glucose and galactose. These simple sugars can be absorbed into the blood and utilized to provide energy for cellular processes such as muscle contraction.

Human babies and the babies of all other mammals depend on milk for their nutrition. Almost all babies produce lactase. In contrast, many adults produce very little lactase. The decrease in production of lactase as a person gets older is called lactase nonpersistence.

The alleles of the gene for lactase differ in the nucleotide sequence in the regulatory DNA; this difference influences the rate of transcription of the coding DNA for the protein, lactase, and thus influences the rate of production of lactase.

Lactase persistence alleles result in substantial production of lactase throughout life. The lactase nonpersistence allele results in substantial production of lactase by infants,

but very low production of lactase in adults.Thus, for virtually all infants and for adults with lactase persistence, the cells of the small intestine produce enough lactase, so all or most lactose molecules are broken down to glucose

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and galactose, which are absorbed from the lumen of the small intestine into the blood.

Notice that lactose intolerance is due to production of low amounts of the protein, lactase, whereas albinism and the other conditions described are due to the production of defective proteins (see table below).

Different Alleles have: Examples

Different nucleotide sequence in DNA that codes for a protein

Different nucleotide sequence in mRNA

Different amino acid sequence in a protein

AlbinismAlcohol sensitivityHemophilia Sickle cell anemia

OrDifferent nucleotide sequence in regulatory DNA for a gene

Different amount of mRNA

Different amount of protein

Lactose intolerance

Roughly two-thirds of adults worldwide have lactase nonpersistence. Lactase nonpersistence can result in lactose intolerance as a child grows toward adulthood. Lactose that is not digested in the small intestine reaches the colon of the large intestine, where lactose is fermented by anaerobic bacteria (see flowchart and graphic below).

bacterial fermentation

lactose in the colon short-chain fatty acids + gases (e.g. CO2 & H2)

the mixture of water, lactose, and short-chain fatty acids in the colon is hypertonic flatulence and osmotic influx of water diarrhea discomfort

lactose intolerance

(https://www.yogurtinnutrition.com/wp-content/uploads/2017/04/dii002-capsules_infographie_ang-5.jpg)

Lactase nonpersistence is only loosely correlated with lactose intolerance. Some people who have lactase nonpersistence do not have lactose intolerance, perhaps due to lactase produced by bacteria in their small intestines. Some people who think that they have lactose intolerance

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actually produce normal levels of lactase, so they can digest lactose and their symptoms presumably are due to other causes, such as an allergic reaction to one or more of the proteins in milk. Lactose intolerance is not life-threatening, but milk allergies can be life-threatening, so someone with severe symptoms after consuming milk should seek medical advice and possibly be tested for milk allergies. (A good summary of milk allergy is available at http://www.mayoclinic.org/diseases-conditions/milk-allergy/basics/definition/con-20032147.)

Dairy products are an important source of calcium, protein and some vitamins. People with lactose intolerance can continue to gain the nutritional benefits of dairy products, but minimize symptoms by:

using lactase supplements consuming dairy products with reduced lactose due to treatment with lactase (e.g. lactose-

free milk) or due to fermentation by bacteria (e.g. traditionally made cheese or yogurt) consuming small amounts of dairy products at multiple times during the day gradually increasing regular consumption of modest amounts of dairy products which can

select for lactase-producing bacteria in the small intestine.

The lactase persistence allele provides an example of natural selection in humans: Lactase nonpersistence alleles are nearly universal in mammals and were nearly universal in early humans. When some groups of humans began raising dairy animals, milk became available for consumption by older children, teens and adults. In these groups, natural selection favored lactase persistence alleles which became common in these groups. Different lactase persistence alleles are observed in European and African herding groups. This illustrates how similar characteristics can evolve independently in different populations (convergent evolution). If you want to expand your students’ understanding of natural selection and lactose intolerance, you can show them the video with review questions, “Got Lactase? The Co-Evolution of Genes and Culture” (http://media.hhmi.org/biointeractive/interactivevideo/gotlactasequiz/).

For additional information on lactose intolerance, see: “Lactose Intolerance”

(https://www.niddk.nih.gov/health-information/health-topics/digestive-diseases/lactose-intolerance/Pages/facts.aspx and http://ghr.nlm.nih.gov/condition/lactose-intolerance)

“The Science behind Lactose Intolerance” (https://www.carolina.com/teacher-resources/Interactive/the-science-behind-lactose-intolerance/tr38902.tr?s_cid=em_ctgen1_201609)

“Problems Digesting Dairy Products?” (https://www.fda.gov/consumers/consumer-updates/problems-digesting-dairy-products).

“Lactose Intolerance: Fact or Fiction?” (https://www.biointeractive.org/sites/default/files/Lactase_Fact_or_Fiction_Teacher.pdf)

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HemophiliaHemophilia is a bleeding disorder caused by defective blood clot formation. The video available at https://www.youtube.com/watch?v=BoXBuJSURTI provides a good two-minute introduction. A more comprehensive, highly readable and informative introduction is available at https://learn.genetics.utah.edu/content/genetics/hemophilia/.

In most people, an injury to a blood vessel triggers the activation of a series of clotting proteins which results in the formation of a clot. Mutated versions of the gene for one of these clotting factors can result in a protein which does not function properly. If the mutation results in an early stop codon in the gene, then no clotting protein may be produced. When one of the blood-clotting proteins is defective or absent, it takes an abnormally long time for a blood clot to form(https://courses.lumenlearning.com/ap2/chapter/hemostasis/).

Different alleles of the gene for a clotting factor cause different degrees of loss of function for the clotting protein, and this results in different degrees of severity of hemophilia. In mild cases, a person may bleed longer than normal after serious injury or surgery. In severe cases, a person may experience spontaneous internal bleeding (e.g. in the joints), frequent large bruises, and nosebleeds that are hard to stop. Severe cases of hemophilia are treated with infusions of normal clotting factor, as often as two or three times per week. Researchers are developing gene therapies which could provide more long-term relief of symptoms. The most common causes of hemophilia are alleles of one of two clotting factor genes on the X chromosome. Since a male has only one X chromosome in each cell, if his X chromosome has an allele that codes for defective clotting protein, he will not be able to make blood clots properly and he will have hemophilia. In contrast, a female has two X chromosomes; since the alleles for defective clotting protein are recessive, a woman generally only has hemophilia if both of her X chromosomes have a recessive allele for defective clotting protein.4 Thus, almost all people with hemophilia are male, and females may be heterozygous carriers.

4 In most heterozygous women, approximately half of her liver cells have the X chromosome with the normal allele active (due to random inactivation of one X chromosome in each cell), and these cells are able to make enough blood clotting protein to prevent hemophilia. However, in ~30% of heterozygous females, random inactivation of one X chromosome in each cell has resulted in less than half the cells in her liver having the X chromosome with the allele for the normal clotting protein active and these women may have mild hemophilia (e.g. with heavy prolonged menstrual bleeding and frequent nosebleeds).

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Alcohol SensitivityThe enzyme, acetaldehyde dehydrogenase, plays an important role in alcohol metabolism.

alcohol dehydrogenase acetaldehyde dehydrogenasealcohol acetaldehyde acetic acid

An inactive form of acetaldehyde dehydrogenase results in the accumulation of high levels of acetaldehyde after drinking alcohol. The accumulation of acetaldehyde results in unpleasant symptoms including increased heart rate and stroke volume and associated heart palpitations, increased blood flow to the skin and flushing, and a general "terrible feeling overall". This condition is called alcohol sensitivity or alcohol intolerance. Heterozygous individuals have substantial accumulation of acetaldehyde and substantial symptoms, in large part because the functional enzyme is a tetramer and even one abnormal protein in the tetramer may inactivate the enzyme. Although heterozygous individuals are sensitive to alcohol, alcohol sensitivity is more severe in homozygous individuals who experience very unpleasant symptoms whenever they drink alcohol and consequently almost never develop alcoholism. The drug Antabuse (disulfiram), which is given to treat alcohol abuse, works by blocking the enzyme acetaldehyde dehydrogenase. This results in increased concentrations of acetaldehyde and the resultant highly unpleasant symptoms if a person drinks.

The allele that codes for the relatively inactive version of acetaldehyde dehydrogenase which results in alcohol sensitivity is relatively common in people of East Asian descent, but extremely rare in people of European descent.

Additional information is available at:http://www.mayoclinic.org/diseases-conditions/alcohol-intolerance/basics/definition/con-20034907 http://en.wikipedia.org/wiki/Alcohol_flush_reactionhttp://omim.org/entry/100650.

IV. Additional Teaching Resources These learning activities will help students to meet the NGSS. How do Siamese Cats Get Their Color?

(http://ngss.nsta.org/Resource.aspx?ResourceID=487)This is a 6 or 7-day unit in which students learn about the connections between genes, proteins and traits. This unit includes analysis and discussion activities, a hands-on experiment, and work with a paper model and a computer model. This unit can be used as an introduction to molecular biology, before discussing transcription and translation.

A Scientific Investigation – What types of food contains starch and protein? (https://serendipstudio.org/sci_edu/waldron/#starch)In this activity, students first learn about the structure and functions of starch and protein and the basics of the synthesis of starch, amino acids and proteins. Then, students learn about scientific investigation by carrying out key components of the scientific method, including developing experimental methods, generating hypotheses, designing and carrying out experiments to test these hypotheses and, if appropriate, using experimental results to revise the hypotheses. Students carry out two experiments which test whether starch and protein are found in some or all foods derived from animals or plants or both.

Molecular Biology: Major Concepts and Learning Activities (https://serendipstudio.org/exchange/bioactivities/MolBio)

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This overview reviews key concepts and learning activities to help students understand how genes influence our traits by molecular processes.  Topics covered include basic understanding of the important roles of proteins and DNA; DNA structure, function and replication; the molecular biology of how genes influence traits, including transcription and translation; the molecular biology of mutations; and genetic engineering.  To help students understand the relevance of these molecular processes, the suggested learning activities link alleles of specific genes to human characteristics such as albinism, sickle cell anemia and muscular dystrophy. Suggested activities include hands-on laboratory and simulation activities, web-based simulations, discussion activities and a vocabulary review game.

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