Biochemistry

Task 1: DNA and RNA
Scenario:

You are a biochemistry specialist who has been asked to provide information on the role of DNA and RNA in the transmission of information within the cell. The audience for your report is a group of medical paraprofessionals at a community health center.

Requirements:
A. Create an original diagram, or series of diagrams, with clear labels, that demonstrates the process of DNA replication of the leading and lagging strands.
Note: Including the following components can aid in demonstrating this process: DNA, replication fork, helicase, single-stranded binding proteins, 5’ and 3’ ends of DNA, primase, RNA primer, DNA polymerase, and Okazaki fragments. Additionally, providing a brief description of the functions of the enzymes can clarify their role in your diagram.

B. Create an original diagram, or series of diagrams, with clear labels, that demonstrates the role of the ligase enzyme in the replication of the lagging strand.
Note: Including the following components can aid in demonstrating this process: DNA, Okazaki fragments, and DNA ligase. Additionally, providing a brief description of the functions of the enzymes can clarify their role in your diagram.

C. Create an original diagram, or series of diagrams, with clear labels, that demonstrates each of the following:

● the process of transcription
● the process of translation
● how mRNA connects the processes of transcription and translation

Note: Including the following components can aid in demonstrating these processes: DNA, mRNA, RNA polymerase, nucleus, ribosome, tRNA, amino acids, and growing protein/polypeptide. Additionally, providing a brief description of the functions of the enzymes can clarify their role in your diagram.

D. Explain the role of RNA polymerase inhibition in causing the poisonous effect of the death cap mushroom.

E. When you use sources, include all in-text citations and references in APA format.
Task 2: Protein Structure
Introduction:

Bovine spongiform encephalopathy (BSE), also known as mad cow disease, is a worldwide problem. While the United States and many countries in the European Union have regulatory legislation in place to combat the spread of BSE, many other countries do not yet have the ability to enact such regulations, making the import and use of possibly tainted beef a health risk.

You should compile your work for this task in a single document (e.g., Microsoft Word, Google Document) that will include diagrams, models, text explanations, and references. If a requirement asks for an explanation, you should provide a written response in a narrative style (i.e., complete sentences rather than bullet points).

Scenario:

As a specialist in biochemistry, you have been asked to be part of a team that will assist a country that currently does not have regulatory legislation. You will help the other workers in understanding BSE at a chemical level. Because these workers are unfamiliar with the basic biochemistry concepts necessary to understand how BSE occurs, you will need to include an overview of proteins.

Requirements:
A. Create an original model of an essential amino acid (e.g., lysine, threonine) that shows the atoms and bonds in both the backbone and the side chain.

B. Create an original diagram, or series of simple diagrams, with clear labels, of the different levels of protein structure (i.e., primary, secondary, tertiary, and quaternary).

C. Create an original diagram, or series of simple diagrams, that demonstrates how a peptide bond is made through dehydration, using a complete chemical equation.

Note: A complete chemical equation includes the chemical structures of all reactants, an arrow indicating the direction of the reaction, and the chemical structures of all products.

D. Create an original diagram, or series of simple diagrams, that demonstrates how a peptide bond is broken through hydrolysis, using a complete chemical equation.

Note: A complete chemical equation includes the chemical structures of all reactants, an arrow indicating the direction of the reaction, and the chemical structures of all products.

E. Explain the four forces (i.e., bonds or interactions) that stabilize a protein’s structure at the tertiary level.

F. Explain how bovine spongiform encephalopathy (BSE) occurs at a molecular level by doing the following:
1. Explain the role of prions in BSE, including each of the following:
● how prions are formed
● the connection between misfolding and aggregation
● how prions lead to the disease
2. Explain one possible role of a chaperone protein in BSE, including each of the following:
● how chaperones normally act in the cell
● how a chaperone protein can contribute to BSE
3. Recommend two ways that a country without regulations in place can decrease the risk of transmitting the prion involved in BSE (e.g., feeding practices, animal disposal).

G. When you use sources, include all in-text citations and references in APA format.
Task 3: Protein Function
Introduction:

Hemoglobin is an essential protein necessary for the transport of oxygen in the body. Biochemists study the molecular activities necessary for the exchange and transport of oxygen between the body cells and lungs.

You should compile your work for this task in a single document (e.g., Microsoft Word, Google Document) that includes diagrams, models, text explanations, and references. If a requirement asks for an explanation, you should provide a written response in a narrative style (i.e., complete sentences rather than bullet points).
.

Requirements:
A. Create an original model of hemoglobin, with clear labels, that shows how oxygen is carried by the molecule.

Note: The inclusion of the following components aids in showing how oxygen is carried: subunits, heme groups, iron atoms, and oxygen molecules.

1. Explain two differences between the oxygenated and deoxygenated states of hemoglobin.
2. Explain how pH impacts the binding and release of oxygen by hemoglobin.
a. Create an original graph that demonstrates the relationship between hemoglobin’s oxygen binding and oxygen concentration at different pH levels.
3. Create an original diagram, or series of diagrams, with clear labels, that compares the biochemical (protein) structure of hemoglobin to myoglobin.

Note: The inclusion of the following components aids in showing the comparison: subunits, heme groups, and iron atoms.

B. Demonstrate your understanding of sickle cell anemia by doing the following:
1. Create an original diagram that demonstrates the amino acid difference between normal and sickle forms of hemoglobin.

2. Create an original diagram that demonstrates the difference between normal and sickle red blood cells at the cellular level.

3. Explain how diseased cells differ from normal red blood cells in their capacity to transport oxygen.
4. Explain the molecular inheritance of sickle cell anemia by doing the following:
a. Identify the type of inheritance seen in sickle cell anemia.
b. Create an original diagram (e.g., pedigree charts, Punnett squares), or series of simple diagrams, that demonstrates how sickle cell genes are inherited.

Task 4: Metabolism

Introduction:

More and more researchers are discovering that many diseases are caused by biochemical deficiencies or defects. That is, instead of indicating that a disease is caused by a nutritional deficiency, researchers recognize that an underlying cause may be a single molecular structure within a cell that fails to turn a cellular process on or off. This is particularly true regarding metabolism. For this task, you will consider the biochemical implications in a metabolic disorder involving a normal component of food—fructose.

You should compile your work for this task in a single document (e.g., Microsoft Word, Google Document) that includes diagrams, text explanations, and references. If a requirement asks for an explanation, you should provide a written response in a narrative style (i.e., complete sentences rather than bullet points).

Requirements:
A. Demonstrate your understanding of the biochemical basis of hereditary fructose intolerance (HFI) by doing the following:
1. Describe two important features that make all enzymes catalysts.
2. Create an original diagram, or series of diagrams, with clear labels, that demonstrates the entire enzymatic cycle described by the lock and key model OR the induced fit model.
3. Create an original diagram, or series of diagrams, with clear labels, that illustrates the activation energy of a reaction in the presence and absence of an enzyme.
4. Explain the reactions catalyzed by enzymes in the first two steps of fructose metabolism in the liver, including each of the following:
● the substrates acted on
● the enzyme catalysts
● the products generated
5. Discuss how a deficiency in aldolase B is responsible for HFI by doing the following:
a. Explain how the amount of the substrate of aldolase B is impacted by the deficiency.
b. Explain the role of the substrate in producing one condition of HFI (e.g., hypoglycemia, liver failure).

B. Explore how mitochondrial disease can occur at multiple levels in different mitochondrial processes by doing the following:
1. Explain what would hypothetically happen to the amount of ATP available to a cell if the entire Cori cycle were to occur and remain within a single cell (e.g., a muscle cell).
a. Identify specific numbers of ATP generated and used in the different parts of the cycle, in conjunction with your response from part B1.
2. Create an original dynamic diagram that shows how the citric acid cycle (CAC) is central to aerobic metabolism.

Note: A dynamic diagram is a clearly labeled diagram that uses arrows to indicate movement and interactions.

3. Explain where in the CAC a hypothetical defect of an enzyme could occur that would decrease the overall ATP production of the mitochondria, including each of the following:
● whether the entire cycle will continue to function
● what will happen to the cycle products
● why ATP production decreases

Note: This is a hypothetical defect, so the explanation should not include descriptions of any known disease.

4. Explain how a proton gradient is formed and used to make ATP during aerobic metabolism.

Note: The inclusion of a discussion of the electron transport chain and oxidative phosphorylation, including the role of oxygen, aids in the explanation of this process.

C. When you use sources, include all in-text citations and references in APA format.

Task 5: Lipids

Introduction:

Despite the negative attention they often receive, fats (and other lipid molecules) play an extremely important role in the biochemical processes in our bodies. For this task, you will consider some of the biochemical roles of lipids (especially fatty acids) and demonstrate how a complete lack of fat in the diet would affect these biochemical roles and human health in general.

You should compile your work for this task in a single document (e.g., Microsoft Word, Google Document) that includes diagrams, text explanations, and references. If a requirement asks for an explanation, you should provide a written response in a narrative style (i.e., complete sentences rather than bullet points).

Scenario:

You have been asked to help dietitians in a local community health center to better understand the importance of fat in the diet and particularly how no-fat diets affect the biochemical processes of the body.

Requirements:
A. Explain how lipids, in the form of triglycerides, are broken down to produce ATP, including each of the following:
● the pathways involved in the breakdown
● the substrate(s) and end product(s) of the pathways

B. Explain two differences between saturated and unsaturated fatty acids (not fats).
1. Create one original 3-D model to demonstrate the chemical structure of a saturated fatty acid.
2. Create one original 3-D model to demonstrate the chemical structure of an unsaturated fatty acid.

Note: For definitions of terms commonly used in the rubric, see the Rubric Terms web link included in the Evaluation Procedures section.

Note: When using sources to support ideas and elements in an assessment, the submission MUST include APA formatted in-text citations with a corresponding reference list for any direct quotes or paraphrasing. It is not necessary to list sources that were consulted if they have not been quoted or paraphrased in the text of the assessment.

Note: No more than a combined total of 30% of a submission can be directly quoted or closely paraphrased from sources, even if cited correctly. For tips on using APA style, please refer to the APA Handout web link included in the General Instructions section.

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