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Biochemistry Topics & Concepts Covered

TOPICS	CONCEPTS
Biomolecules	Proteins, Nucleic Acids, Lipids, Carbohydrates
Enzymes	Enzyme Kinetics, Inhibition, Catalysis
Metabolism	Glycolysis, TCA Cycle, Oxidative Phosphorylation
Molecular Genetics	DNA Replication, Transcription, Translation
Cell Signaling	Signal Transduction Pathways, Cellular Communication
Biochemical Pathways	Biosynthesis of Macromolecules, Metabolic Pathways
Protein Structure & Function	Primary, Secondary, Tertiary, Quaternary Structure
Enzyme Mechanisms	Active Sites, Substrate Binding, Catalytic Reactions
Bioenergetics	ATP, Thermodynamics, Energy Conversion
Carbohydrate Metabolism	Glycogenesis, Glycogenolysis, Gluconeogenesis
Lipid Metabolism	Fatty Acid Synthesis, β-Oxidation, Lipid Signaling
Amino Acid Metabolism	Amino Acid Catabolism, Biosynthesis, Urea Cycle
DNA Replication & Repair	DNA Polymerases, Proofreading, Mismatch Repair
RNA Transcription & Processing	Promoters, RNA Splicing, Ribosome Biogenesis
Protein Synthesis	Translation Initiation, Elongation, Termination
Cell Cycle & Division	Cell Cycle Phases, Cell Cycle Regulation
Hormones & Signaling Peptides	Endocrine Signaling, Hormone Classes, Signal Cascade
Membrane Structure & Function	Fluid Mosaic Model, Transport Mechanisms
Enzyme Regulation	Allosteric Regulation, Covalent Modification
Biochemical Techniques	Spectroscopy, Chromatography, Electrophoresis

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Recently Asked Biochemistry Questions

Expert help when you need it

Q1: Explain the role of eicosanoids formed as a result of metabolism of n-3and n-6 fatty acids in human physiological processes. In your answer consider data from relevant observational (epidemiological) studies alongside explanation of mechanism of action of these eicosanoids.2.See Answer
Q2:Calculate the plasma osmolality and comment on its significance. See Answer
Q3:Explain the pathophysiology of the different types of Diabetes Mellitus. See Answer
Q4:Consider the enzyme-catalyzed reaction AB. You determine experimentally that the maximal initial velocity. Vmax for the amount of enzyme you have added is 50 mM of B appearing per minute. You also determine that the Michaelis constant, K. for this enzyme is 20 mM of A. What concentration of A will give an initial velocity of 25 mM of B appearing per minute?See Answer
Q5: Short Answer 1. A study on rat metabolism is being conducted. There are 3 different groups of rats involved. Group 1 Diet rich in fat but normal in carbohydrates and protein Group 2 Diet rich in protein but normal in carbohydrates and fat Group 3 Diet rich in carbohydrates and normal protein and fat a. The three groups are kept in identical environments with opportunities for physical activity. Write a hypothesis, predicting the expected energy levels for each group for the first 4 days of the experiment. Please explain your predictions. (A-4, 2-C) 3 Scanned with CamScanner b. You run the experiment for 20 days and then analyze the results. How do you expect the three groups to compare in terms of body size/mass and general health? (A-4, 2-C) de toutes 2. Track athletes often say that the 400m sprint is much more exhausting and harder on the legs than the 100m sprint. What type of respiration would a 400m sprinter rely mostly on as they reach the end of the race? Explain. (A-4, 2-C) 3. Several anti-nuclear war protesters claim that inhabitants of the earth did not perish from nuclear bombs or the radiation afterwards, that the people would slowly succumb to changes brought on during the "nuclear winter". During a "nuclear winter", a lot of dust would be drifting in the atmosphere causing the blockages of the sun's electromagnetic spectrum. Based on your knowledge of photosynthesis, what impact would this have on humans that are still alive and why? (A-4, 2-C) Scanned with CamScannerSee Answer
Q6:b) MHETase is believed to use a catalytic triad to hydrolyze the ester linkage in MHET, just like the catalytic triad in the serine proteases. Examine the structure of MHETase complexed with the analog and identify the 3 residues in the catalytic triad. For each one, find the most important distance between that residue and its partner in the mechanism and fill out the chart, identifying the 2 atoms used and the distance between them. Also identify the secondary structure in which it is found (e.g., a-helix, ß-strand, tight turn, or loop). Residue (name & #) Ser His Asp Identify the most relevant inter-atomic distance and identify the atom name (click on it in PyMOL) (e.g., "CB" or "C4" or "OG") Atom in Ser: Atom in substrate analog: Atom in His: Atom in Ser: Atom in Asp: Atom in His: distance between atoms (Å) 2° structural context/nWhat other residues in the enzyme are important for binding MHET? Identify at least 4 that seem to play an important role. Residue (chain, name & #) Atom of the residue and the substrate analog? distance Type(s) of interaction (e.g., H-bond, between charge-charge, coordination bond, van der Waals) atoms (Å) 2⁰ structural context Which, if any, of these residues might explain why MHET is a good substrate, but BHET is not? And how would it explain the substrate specificity?See Answer
Q7:c) The enzyme contains 5 disulfide bonds. Given that this is a secreted enzyme, is this expected or surprising? List the 5 disulfide bonds below (e.g., "Cys41 - Cys142") and circle the one that you would expect to be most important for enzyme activity.See Answer
Q8:d) Going back to the first question, briefly discuss the roles of the 2 (sub)domains in the mechanism of MHET hydrolysis. Broadly speaking, what role does each one play?See Answer
Q9:Assigned topic- Alcoholic Liver Disease Assigned Section- Treatments and Conclusion |See Answer
Q10:Bonus: Determine the primary sequence of the following peptide. (10 Pts) A. Trypsin treatment generated the following fragments: (LFVCYMGFR) (HDITNAATYR) (AEK) (CPS) (K) (QIVAAR) (LWVANK) B. Chymotrypsin treatment generated the following fragments: (AEKL) (F) (VCY) (MGF) (RHDITNAATY) (RL) (W) (VANKKQIVAARCPS) C. Thermolysin treatment generated the following fragments: (LF) (VCY) (MGFRHD) (ITNAATYR) (AEK) (LW) (VANKKQ) (1) (V) (AARCPS) Legend: Trypsin = Lys & Arginine (R.) Chymotrypsin = Tyr, Trp, Phe, Leu (R.) Thermolysin = Leu, Val, lle, Met (R₂)See Answer
Q11:1. Why does EDTA (structure shown below) quench DNA polymerization reactions at physiological pH? Show the mechanism involving the atoms in EDTA that may be responsible (3 points) میری HO HO OH OHSee Answer
Q12:4. Reto is an aspiring medicinal chemist whose project involves screening a library of compounds to find molecules that bind with high affinity to the opioid receptor (a membrane protein). Based on our discussion of the thermodynamics of binding, answer the following questions (10 points) A. Reto titrated a candidate compound C (fluorescently tagged) against the purified receptor and obtained the isotherm below. Reto concluded that he found a high affinity specific binder. Is Reto's conclusion correct? Why or Why not? What is missing from the experiment? (2) 1/Fluorescence polarization 450 400 350 300 250 200 150 100 50 0 0 10 20 30 40 [Ligand] (n) 50 60 70/nB. After performing the required controls, Reto obtained the following binding isotherm (left) and the associated Scratchard plot (right). What is the value of K, for the interaction between C and the receptor? What is the total protein concentration used in this experiment? (2) Binding isotherm Scratchard plot 1/Fluorescence anisotropy 300 250 200 150 100 50 0 0 10 20 30 40 [Ligand] (nM) 50 60 [bound ligand]/[free ligand] 0.6 0.5 0.4 0.3 0.2 0.1 0 1 2 3 4 bound ligand [L]bound (nM) in 6/nC. Next, Reto performed the affinity measurements on mammalian cells that express the opioid receptor. He is surprised to find that the K, from these measurements is over 10-fold higher than what he measured with the purified protein. Can you speculate a possible reason that could explain this observation? D. Given the poor affinity of the compound C, Reto modified the library, rescreened and found a candidate molecule R that binds the opioid receptor with a K, of 2nM. A high throughput measurement of binding isotherms of R and other receptors revealed that R also binds to the glucagon receptor with a K₁ of 5 μM. Based on this data, what should be the concentration of R that Reto should recommend for further testing of the compound R in vivo (i.e. in a living human body)? (2)/nE. In an in vitro experiment with R and the opioid receptor, what is the fractional saturation of the receptor, when the concentration of R is 200 nM? (2)See Answer
Q13:Q7. The notion of treating sickle cell disease (SCD) by stabilizing the R (oxy) conformation was introduced by Beutler. He proposed that converting a fraction of sickle hemoglobin (HbS) to the oxidized form or to the carbon monoxide complex of HbS would reduce sickling by maintaining a fraction of HbS molecules in the nonpolymerizing R conformation of oxyhemoglobin, while understanding that such a treatment would compromise oxygen delivery to the tissues. Solution 000 ↑↓ от R Polymer/nA. How will you measure the kinetics of this reaction? Below are only one of the two options available to you (3+3 = 6 points total). i. Oxygen tank and the dark (non fluorescent) dye shown below ii. Ultracentrifuge and uv-vis absorbance Juge R Fluorescent Dark/nCompound 9; compound 23; Len 2 Val 73 Ser 131 Ser 131 Arg 141 The 134 Au 78 Ser 131 al Asp 75 Val 1 al Met 76 Val 73 B. Based on the PDB structures, which compound will have higher affinity for Hb? Explain your answer based on molecular interactions between the compound and the structure of Hb (you may need to look at the relevant paper from hints)See Answer
Q14:Q9. A ribozyme (catalytic RNA molecule, E) catalyzes the cleavage of a 7-nucleotide RNA (S7) to produce a 6 nucleotide RNA (P6). The reaction follows the Michaelis-Menten (MM) kinetics as shown below (8 points, 2 points each): S7+ ES7.E=> P6 + E In an experiment starting concentration of S7 is 150uM, E is 10nM, and Km = 250 nM A. Why is the second reaction considered irreversible? B. 20 uM of S7 is converted to P6 in the first 10s of the reaction. Determine the reaction rate (in M/s) in this experiment/nC. Use the result from B and the MM equation to determine the maximum rate of reaction (in M/s) at the given ribozyme concentration and k2 for the conversion of S7 to P6. D. A DNA (D7) is a competitive inhibitor of this reaction. Binding between D7 and E is quantified by: E + D7 → E.D7 Ki = [E].[D7]/[E.D7] In the presence of 10uM D7 the reaction was 50% of the maximal rate when the substrate S7 is 1500 nM. Determine the value of Ki.See Answer
Q15: Introduction to Chemical and Biological Engineering Laboratory (CBE 101B) Enzymatic Reaction Rates Experiment Last Revision: 09/08/2023 Background Enzymes for production of biofuels from biomass Current biofuel production in the USA relies on the conversion of carbohydrates, mainly from corn kernels, to ethanol via fermentation. This technology was developed to reduce dependence on imported oil for transportation needs and to reduce the climate impacts of combusting non- renewable fuels. However, using only the grain from corn neglects the rest of the plant (as is the case when we use it for feeding ourselves or animals). A possible alternative to using only the corn kernels lies in the use of the rest of the plant, including as the leaves, stalks, and corncobs. In the same way, other plants can be used, including grasses that can grow rapidly with less fertilizer. A significant portion of these plant tissues are made up of lignocellulose, an important structural material in cell walls. Lignocellulose has three primary components: cellulose, which is a polymer of glucose; hemicellulose, a polymer of xylose and other sugars; and lignin, a complex polymer that also helps protect plants from predation. Following pretreatment of cellulosic materials (such as mechanical grinding and exposure to dilute acid), enzymes called cellulases can hydrolyze cellulose to produce glucose. This glucose can then be used to grow bacteria or yeast to produce ethanol (and other fuels and chemicals). This experiment is focused on the reaction of cellulose to glucose. Enzyme kinetics Enzymes are biological catalysts - compounds that accelerate the rate of a reaction. In the terminology of enzymes, a chemical that is reacted in an enzyme-catalyzed reaction is called "substrate". Most enzymes act on substrates that are dissolved in water. Cellulases (there are many types) are unusual in that their substrate (cellulose) is a solid and does not dissolve in water. This results in a different form of equation describing the reaction kinetics. Rather than the first-order reaction rate equation you may have seen in a chemistry course, the rate of cellulase-catalyzed reactions is represented by Equation 1: reaction rate = r = KCSCE Kd+CE Eqn. 1 با 10 OH OH OH cellulose O + 2n H₂O cellulases OH LO PO OH OH glucose C6H12O6 Equation 1 relates the rate of the cellulase-catalyzed reaction to the concentration of cellulase (CE). The equation also involves the parameters k (a rate constant), and Kd (a measure of binding affinity of the cellulase to the cellulose), as well as Cs (the initial concentration of enzyme binding sites on the solid substrate). A standard method of determining the rate parameters, k and Kd, for a cellulase is to measure the rate of glucose production at three different enzyme concentrations using the same type and amount of substrate. The glucose meter used in this lab uses an enzyme in a test strip to generate an electrical current proportional to the concentration of glucose. It is designed to measure glucose in human blood samples. In blood, the monitor can measure glucose in concentrations between 20 and 600 mg/dL (What are the equivalent concentrations in g/L?). Research questions 1. Can a blood glucose monitor be used to accurately and precisely measure glucose that isn't in blood? If it isn't accurate, what is the quantitative correlation between the measurement with a known standard concentration? 2. What experimental conditions are required for the cellulase to generate a glucose concentration within the limits of detection for the blood glucose meter? 3. What are the rates of glucose generation for this enzyme? 4. What other variables impact the reaction rate? For example, how would the rate change if you doubled the enzyme concentration or doubled the mass or surface area of the substrate? 5. If you were tasked with designing an industrial process that used these cellulases to generate glucose for biofuel production, qualitatively describe the important process variables you would need to control in order to optimize the amount of glucose generated. Tasks 1. Determine the accuracy of the glucose meter. This will allow us to better account for error in readings during the experiments you will be conducting. To accomplish this you will take several readings with the glucose meter between the range provided earlier (20- CARACA control positive compare Actual glucose concentration 0.42 9/L negative enzyme + ice 600 mg/dL). To make a measurement, place a test strip in the glucose meter, take a small sample (10 μL) and put it on a clean surface. Touch the tip of the strip to the solution sample, when the meter asks how to mark the sample, select "No mark". Please record your readings below: Native Hay 0.29 0.49 0.69 991L 2.79/L 5g/L Glucose meter-reported concentration 68 mg/dL over 600 mg/dL 257 mg/dL 580mg/dL 2. Design an experimental plan to answer as many of the 'Research Questions' as possible. Please determine what factors you plan to vary, how you expect these factors will affect the reaction rate (proportionally or inversely proportionally) what you plan to hold constant, what your dependent variable is, how many levels you will test, what positive and negative controls you will use, how many replicates you will use, and how many total experiments you will need. ● In this experiment you will have the following information from previous studies involving glucose meter: dependent: rate of change Time: 5 minutes ● Substrate: 1 cm x 1 cm squares of Whatman filter paper substrate or blades of Temperature: Room temperature., approx. 25 °C independent varies of amounts grass hay 1:1000 → 10ml: 1000ml • Enzyme dilution: 1:500 to 1:2000 in 1 mL of 25 mM NaHCO3, pH 6 Use these parameters above to ensure glucose readings can be gathered. In this glucose experiment there will be a major limitation, each team will only have access to 20 test strips, and therefore must limit their total experiments. 10 PL enzyme 1000μl buffer When your team has a rough outline of the kind of experiments you want to perform ask an instructor or TA to review your plan and provide feedback and approval. 3. Create an experimental outline in which you will use hay as the source of cellulose, attempt to change the surface area, the independent variable, of the hay for this experimental plan. 4. Once approval is received, begin your experiments and carefully record all data observations. art 32 51 417 87g|RL \/ BL₁=8.5m BL2=10,5mm BL3=6.5MM Data Analysis 1. 2. Part 1 (plotting and curve fitting): a. Use Matlab to plot the glucose standards measurements and determine the correlation describing the relationship between the actual glucose concentration and the glucose meter reading. What is the accuracy and precision of the meter at the low and at the high glucose concentration? b. What is the precision of the measurements? Precision can be described by the x 100%. Is the precision different range as a percent of the average, or at the two different concentrations? Part 2 (use the actual glucose concentration as determined using your correlation): 3. Part 3: a. Assuming zero glucose at t = 0 min., calculate the rate of the reaction in all of your enzyme experiments. What are the units of the rate you have calculated? What is the relationship between the reaction rate and enzyme concentration? b. The rate parameters for the solid substrate enzyme reaction can be found using the rates measured at three different enzyme concentrations. Assume the starting enzyme concentration was 100 g/L and that the cellulase molecular weight is 50,000 g/mol. Use Matlab to plot 1/CE (in units of liters/mol) on the x-axis against 1/rate on the y-axis. Find the correlation between these transformed variables. 1 r Take the inverse of the rate equation, r = 1 ŕ kd CE + KCSCE KCSCE kd KCSCE (max- 1 + average kCs KCSCE ka+CE to obtain: Eqn. 2 Eqn. 3 Compare the form of Eqn. 3 to y = mx + b to see that 1/(k*Cs) is the y-intercept of the correlation and Ka/(k*Cs) is the slope of the correlation. What are the values and units for k*Cs and Ka? a. Estimate by what factor you increased the surface area of the cellulosic material. How does this compare to the change in the reaction rate? [1] Mathematically, the reaction rate is dCs/dt but in experiments, we approximate it as ACs/At 1See Answer
Q16:2. Draw the structure of the peptide DTLH, showing the backbone and side-chain atoms in the ionization states favored at pH = 7.0. a. Draw a water molecule making a hydrogen bond to a side-chain H- bond donor. b. Draw a water molecule making a hydrogen bond to a main-chain H- bond acceptor. c. Using the values of pKs given in Table 5.1, calculate the pl for DTLH.See Answer
Q17: İstanbul Bilgi Üniversitesi BIOE 222 CELL BIOLOGY LABORATORY Experiment 2 2023-2024 SPRING Dr. Tuğba KÖSE Ar. Gör. Betül BUDAK Page 1 EXPERIMENT 2: OSMOSIS and Diffusion Part 1. Diffusion with Starch solution Background: Diffusion is the passive movement of particles of a solute from an area of high concentration to an area of low concentration. Osmosis is the passive movement of a solvent, such as water, through a semipermeable membrane from a region of high solvent concentration to an area of low solvent concentration. Diffusion Solute molecules move from high to low concentration (VS) Osmosis Solvent molecules move from low to high solute concentration Solute molecules Solvent molecules High solute concentration Diffused evenly (Equilibrium) Semipermeable membrane Low solute concentration High solute concentration Same concentration (Equilibrium) Science Facts.net Solute: a substance that has been dissolved in a given solution. Solvent: a substance, usually a liquid, that is capable of dissolving or dispersing one or more other substances. Exp: To create salt-water, salt is dissolved into water. Solute: salt Solvent: water Semipermeable membrane: A membrane or barrier that allows only certain molecules or substances to pass through it and does not allow others. Ex: Dialysis tubing acts as a semipermeable membrane. Lugol's iodine: a solution of potassium iodide that turns blue in the presence of starch. Page | | 2 Laboratory Exercise: Materials: • 10 cm piece of dialysis tubing • 250 mL beaker • Dental floss • Lugol's iodine . 1% starch solution Procedure: 1. Soak a piece of dialysis tubing in 250 mL of deionized water for at least 5 minutes. 2. Seal off one end of the dialysis tubing by gently twisting the end and tying dental floss tightly around it. 3. Gentle rub your fingers on the other end of the tube to open it. Make sure to open it as far down as you can towards your knot. 4. Pipette a small volume of 1% starch solution into the dialysis tube. Make sure you leave enough room to tie the end closed. 5. Twist the open end of the dialysis tubing closed and tie off with another piece of dental floss. 6. Trim excess dental floss and dialysis tubing from the ends of your sealed dialysis bag. 7. Add a few drops of Lugol's iodine to your beaker of 250 mL of water until it appears a pale yellow. 8. Place your dialysis bag into the beaker and wait 30-40 minutes. Review the background information and fill in the Start of Experiment section of Table 1. 9. After 30 min have elapsed, fill out the remainder of Table 1 and answer questions 1-4. Results: Table 1: Dialysis Tubing Contents Beaker Contents Start of Experiment Color Contents End of Experiment Color Contents Page 3 Questions: 1. What happens when starch interacts with Lugol's iodine? 2. Based on your results, was the starch able to pass through the semipermeable membrane that was the dialysis tubing? Explain how you reached your conclusion. 3. Based on your results, was the Lugol's iodine able to pass through the semipermeable membrane? Explain how you reached your conclusion. 4. What would happen if the contents of the dialysis bag and beaker were reversed? What would the final colors of the dialysis tubing content and beaker content be? (The beaker would be filled with 1% starch solution and the dialysis tubing would contain water and Lugol's iodine.) Part 2. Osmosis in Elodea Leaf Cells ● Take 3 microscope slides, draw a perpendicular line dividing each slide into two parts and label the all parts according to the sample and the solution to be added. • • • • Take an Elodea leaf, cut it into two. Using a micropipette, place 80 μl of water to one side of the slide, and place the half Elodea leaf on the solution. Place the coverslide on the leaf. In the same slide, place 80 µl of 0.5 % NaCl solution to the other side of the slide, and place the half Elodea leaf on the solution. Place the coverslide on the leaf. Observe and compare them under 40X magnification 5 min after the solutions are added. Repeat the procedure and compare water with 5% NaCl. For the third slide, compare the effects of 0.5 % NaCl solution and 5 % NaCl solution on Elodea leaf cells. Note which solution induces shrinking or swelling. You should define the solutions in terms of hyper-, hypo- and isotonicity. Page | 4/n • Cover Page How to write? • Name of Experiment • Aim of Experiment • Introduction Materials and Methods • Results • Discussion 1 Table of Content Introduction......... • Materials & Method......... ● Results.......... 1 .3 ........7 2 TABLE OF FIGURES ? 3 TABLE OF FIGURES Figure 5.1: The name of the figure DO NOT PUT «FIGURES» ON THIS PAGE! 4 St TABLE OF FIGURES Figure 1.1: The name of the figure….... ● Figure 1.2: ……………………. ● Figure 3.1: !Each figure has to have a name!!! Figure 1.1: The name of the figure…………………………………..1 Number of Chapter Number of Figure for that Chapter .1 18 5See Answer
Q18:2:061 82 Assessment 6 for EMS690U Viva and presentation 25% of total module mark (15% Group, 10% Individual) 15 mins group presentation + 8 mins questions / person Group presentation maximum delivery time: 15 minutes There follow some guidelines to help you shape your presentation. Feel free to move around the order to better present your project, which may be organised in a slightly different way. You can prepare and present the project however you like - but it is a presentation of the whole, not the individual parts. A single mark will be given for the presentation, which means that NOT everyone has to present but all parts of the proiect need to be present. the press on clear to the 2nd examiner (who will not be rammar SH Introduction 2. A visual introduction that references your client/problem/brief. Something interesting you learned that will engage the audience/the examiners. This brings them into your presentation and makes it more engaging. You could tell an anecdote about an experience that your group had at the start of the project or relate an interesting fact that you learned. It could be a memorable quote from a meeting. Frame 1. One or two slides to talk about the situation; growth stalled, new business, new markets, etc. Emphasize the good before you touch on the challenges. 2. Frame the issue. Talk about the initial brief and what you are trying to accomplish, you can also introduce secondary issues that you included in your project. 3. A slide that illustrates your process, showing what you have done and how you planned to do this. Research/Hypotheses 1. Present the research that will be supporting the issue and defining your project. This is where you can insert the tools that you have been using: User journey, SWOT, etc. Only present information directly relevant to your case. Concepts 1. Present a range of concepts - these should be developed to the point where they can be quickly understood. Ideally you will create some type of visual for each concept accompanied by some bullet point text to explain what it is. Other Guidelines Show passion and commitment. •Keep your presentation as visual as possible. Do not overload a slide with information, it is better to move through three slides quickly than stare at one slide for a long time. • Build bullet points and text as you present the information, you want to lead people qmplus.qmul.ac.ukSee Answer
Q19: Life on Earth Plant Practical 2 - Seed Protein Analysis Aim: To help you understand how and why plant seeds are used for protein production Why? Because of the importance of amino acid production in plants to the living world and its implications for animal nutrition Introduction The seeds of many species are used by humans in a variety of ways. Over 55% of human nutritional needs are supplied directly by seeds, and this figure is even higher when seed products such as vegetable oils and margarine are also included. Seeds are also extremely important in animal feeds. Furthermore, seed products are used industrially; seed oils are used as lubricants, in chemical syntheses and nowadays even as fuel for advanced combustion engines. During seed development, low molecular weight metabolites formed via photosynthesis and nitrogen metabolism, such as sucrose and amino-acids, are imported into the developing seeds and converted into storage lipids and polymerised into starch and storage proteins. It is because of these storage products that certain seed plants have been domesticated. These plants are very important in human nutrition. Understanding something about seed proteins should deepen your understanding of human nutrition especially the production of essential amino acids. In this practical the protein content of the seeds of a variety of plants will be determined using the Bradford protein assay. Proteins represent the most abundant nitrogen store in seeds and are usually deposited in discrete membrane-bound organelles called protein bodies. The Species These are examples of the crop species whose seeds we have used in the lab. Have a look at them whilst you are centrifuging your extracts. To find out more about these species visit the websites of the research institutes of the Consultative Group on International Agricultural Research (CGIAR http://www.cgiar.org) which are dedicated to the various crops. The CGIAR is a very large research organisation dedicated to improving the food crops of the world, with particular emphasis on providing nutritionally balanced food for all. It has 16 very large research institutes around the world. For general information about human nutrition worldwide some of the pages of the Food and Agriculture Organisation of the UN are useful, try: http://www.fao.org/ Peanut (Arachis hypogea): This is a native of South America and was not known elsewhere until the discovery of the New World. It is often used with maize flour in staple diets in South America. The USA is now the world's biggest producer (about 120 million tonnes each year in US - a lot of peanuts!). ICRISAT is the CGIAR centre with responsibility for peanuts (also called groundnuts). If you explore their pages there's information about peanuts. http://www.icrisat.org/ Peas (Pisum sativum): These are native to the Mediterranean basin and were spread round Europe by the Romans. They are classically accompanied by wheat products in many European staple diets. Chickpeas (Cicer arietinum): These are native to the near east and perhaps northern India. Chickpeas dishes are very often accompanied by wheat products in staple diets of the near east and India. ICRISAT is the CGIAR centre with responsibility for chickpeas. If you explore their pages there's quite a bit of relevant info. http://www.icrisat.org/ Soya Beans (Glycine max): Native to China where they are often used to accompany rice dishes. The USA is now the world's biggest producer. Maize (Zea mays): Native to S. America where the Aztecs were responsible for its domestication. Classically accompanied by peanuts, beans or chocolate food stuffs (which are all native to S. America) and was introduced to the rest of the world after the discovery of the New World). Cimmyt is the CGIAR centre with responsibility for maize. Explore its website and note that a lot of its work is on improving maize protein content! http://www.cimmyt.org/ Wheat (Triticum aestivum): Domesticated in the near east (now, with gene mapping, domestication has been located to eastern Turkey about 6000BC) and initially used with chickpeas and lentils (which are all native to the near east) but now used with beans in S. America, and many pulses in India for example. Cimmyt also carries out research on wheat. http://www.cimmyt.org/ Rice (Oryza sativa): Domesticated in China and possibly India. Classically accompanied by soya products in China and chickpeas/lentils in India. About 450 million tonnes on world markets each year - this is a lot considering most rice is eaten by the person who grew it and doesn't even get on to world markets! Sorghum (Sorghum bicolor): Sorghum was domesticated in Africa but is now grown around the world. It is the most drought tolerant of the major cereals and is the most important cereal in much of the semi-arid tropics. It is one of the ICRISAT mandate crops and you can find out more about it from the ICRISAT website http://www.icrisat.org/ 2 Protein extraction method • • • • • You are supplied with seeds of a species of legume or cereal in a glass boiling tube. Exactly 1 gram dry weight has been measured for you then soaked overnight. Pour off the excess water from the seeds using the gauze supplied. Using a 10 mL glass pipette and pi pump add 8mL of Tris extraction buffer (50 mM Tris- HCl, pH 7.5) and then grind the seeds using the Ultra Turrax homogeniser. Transfer all the liquid and ground material to a 15 mL plastic centrifuge tube. You have a few extra mL to play with so use extra Tris buffer to rinse out all the bits from the boiling tube and into the centrifuge tube. Label your centrifuge tube with your name (not on the lid) and take it to the centrifuge where it will be spun at full speed for 10 minutes. Retrieve your centrifuge tube then measure and record the volume (V) of the supernatant (the liquid left above the solid pellet) by pouring it into a 25 mL measuring cylinder. This supernatant contains your extracted protein, so don't throw it away but, pour it into a small conical flask. Plant cells typically contain many compounds, such as lipids, that interfere with protein quantification assays. Consequently, the proteins in your extract will need to be precipitated to separate them from these compounds prior to assay. • • • • Using a micropipette fitted with a blue tip, set at 1000 microlitres (1 mL) transfer 1 mL of the extract to a micro-centrifuge tube (it's the small transparent tube with a snap lid attached). Change the volume setting of your micropipette accordingly and add 0.35 mL of 20% (w/v) trichloracetic acid (TCA), close the lid tightly and mix well by inverting the tube a few times. Label the lid of the tube then stand the tube in an ice bath for at least 10 min. Remember TCA is harmful. After 10 minutes, take your tube to the micro centrifuge and spin at 1500 × g for 10 min. This time the protein is in the pellet at the bottom, so discard the supernatant and re-suspend the pellet in 1mL of 1% (w/v) TCA. You will need to resuspend the pellet completely by stirring with a glass pipette with a squeezy bulb attached. Centrifuge again for 10 minutes and discard the supernatant. Transfer the pellet into a glass boiling tube using 5 mL of Tris extraction buffer. In order to resuspend it completely, use the Turrax homogeniser again. However, to avoid cross contamination, ensure that it is completely clean and dry before inserting into your sample. Protein determination This method is based on protein binding to the dye Coomasie Brilliant Blue G250 (Bradford, 1976). Bradford, M.M. (1976) A Rapid and Sensitive Method for the Quantification of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding Analytical Biochemistry 72(1–2), pp. 248–254. 3 Standard Curve: A standard curve must be constructed before the protein content of your extracts can be determined. This can be done at any time during the practical class. You will add different volumes of a pre-determined protein standard to deionised water, giving you concentrations from zero to 40 μg mL-1. You will then add Bradford Reagent to develop a colour whose strength is related to the concentration of protein. To do this, to six glass test tubes add the following using the micropipettes: Reagent Tube Tube Tube Tube Tube Tube 1 2 3 4 5 6 Vol. 40 μg mL-1 BSA* (mL) 0 0.1 0.25 0.5 0.75 1.0 Vol. deionised H2O (mL) 1.0 0.9 0.75 0.5 0.25 0 Final conc. BSA (μg mL-1) 0 4 10 20 30 40 *BSA is Bovine Serum Albumin - a reference protein from cow serum Add 2 mL of Bradford reagent (see below) to each of the tubes and mix well. Allow the blue colour to develop for 10 minutes and then determine the absorbance of the mixture from each tube at 595nm. How to use the Spectrophotometer: • • • • • ● Turn on and let the spectrophotometer warm up for 30 minutes Select absorbance function (ABS) using left and right arrows. Adjust wavelength to 595 nm using up and down arrows Lift lid, insert the blank (your deionized water with Bradford Reagent - Tube 1 mixture) in a 3mL cuvette (ensure clear window of the cuvette is in the correct orientation), close the lid and press CAL Spectrophotometer will calibrate to zero Remove blank and insert samples in 3mL cuvettes to be read Do not press CAL again or your results will be wrong Plotting the standard curve Use μg protein mL-1 on the horizontal x-axis (independent variable) and absorbance at 595nm on the vertical y-axis (dependent variable) and plot a graph with a line of best fit. This is not 'join the dots' but a prediction of what you think the underlying relationship to be. It will not be linear, so draw a smooth curve. Measuring Protein Concentration in Your Extract Your sample extracts will probably require considerable dilution before their protein content can be determined using the Bradford reagent and your standard curve. The dilution factor necessary (D) can only be worked out empirically, but we will suggest a starting dilution depending on which species' seeds you have extracted. When you have made a suitable dilution: • • Transfer 1.0 mL of your diluted seed protein extract to a 3 mL cuvette. Add 2.0 mL of Bradford Reagent and mix well. After 10 minutes determine the absorbance at 595 nm using the same spectrophotometer as you used to make your standard curve. The Bradford Protein Reagent: This is already made up. Briefly: 100mg of Coomasie Brilliant Blue G-250 were dissolved in 50 mL of 95% (v/v) ethanol. 100 mL of 85% (w/v) phosphoric acid were then added and the solution diluted to 1 litre with distilled water. The solution was left overnight and filtered to remove un-dissolved solids. Results Plot the standard curve and use it to determine the protein concentration in your diluted samples. From these data, calculate the protein concentration in the TCA-precipitated sample and then in the initial extract. Finally, calculate the protein content of the seed tissue in mg g¹. This is how to do the calculation: From the absorbance you obtained from your Bradford's reading of your diluted protein extract read off its protein concentration from the standard curve = X μg mL-1 Multiply by your dilution factor (D) = DX (μg mL-1) Multiply by 5 (because you also diluted the samples by a factor of 5 at the TCA stage) = 5DX (μg mL-1) Multiply by the volume of the initial extract (V) in mL = V5DX (µg) Divide by the weight of seed tissue extracted (W) in g = V5DX (µg g‍¹) W Enter your data on the class sheet in mg g‍1 (i.e. divide by 1000) and think about any differences there are between the seed protein contents of the different species. Keep your Bradford's standard curve. It will be useful as a guide when you come to do the coursework. 5See Answer
Q20: Km Vmax calculation exercise Kindly solve the following question via Excel sheet and submit your trial: - Individual submission Refer to topic 4.Enzymes to solve the question. The initial rate of conversion of fumarate to L-malate using the enzyme fumarase was recorded at different fumarate concentrations. Inhibitors A, B and C were added. By using the data below, answer the following: 1.What is the Km and Vmax of the reaction without inhibitors? 2.What type of inhibitors were they? Fumarate [S] Rate of product formation With A (MM) (mmol l-1 min-1) (mmol l-1 min-1 2 2.5 2 3.3 3.1 2.7 5 3.6 3.1 10 4.2 3.9 2.What type of inhibitors were they? Fumarate [S] (mM) Rate of product formation With A With B With C (mmol l-1 min-1) (mmol 1-1 min-1) (mmol l-1 min-1) (mmol I-1 min-1) 2 2.5 2 2 1.4 3.3 3.1 2.7 2.35 1.7 5 3.6 3.1 2.6 2 10 4.2 3.9 3.1 2.35See Answer

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