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Q: What is Biochemistry? Q: Have you ever wondered about the basic chemistry of life? Q: How do our bodies make proteins? Q: How do molecules recognise each other and how are they specific? Q: How do enzymes catalyse reactions? Q: Where does the energy come from to power our cells? Q: What is Glycolysis? Q: Where does glycolysis occur? Q: What is/are the reactants/reagents necessary for glycolysis? Q: What is/are the product of glycolysis? Q: Does this process need or use oxygen? Q: How much energy does glycolysis produce? Q: What is the advantage of producing energy from glycolysis? Q: What is the Pyruvate Dehydrogenase (PDH) Complex ? Q: What are the reactants for the PDH cycle? Q: What is the product of the PDH cycle? Q: What is the advantage of using this process? Q: What is the Citrus Acid Cycle? Q: Where does the Citrus Acid Cycle occur? Q: Does the TCA Cycle need or use oxygen? Q: What is the reactant of the TCA cycle? Q: What is the product of the TCA cycle? Q: What is the advantage of the TCA cycle? Q: Why is glycolysis important? Q: Who uses glycolysis? Q: What happens to the products of glycolysis? Q: What does the term "glycolysis" mean? Q: How many stages does glycolysis have? Q: What happens in the process of glycolysis? Q: What is ATP? Q: Is alanine necessary for nutrition? Q: What is alanine? Q: Where is alanine found? Q: How is alanine used? Q: What do I need to know? Q: What is its function? Q: What is the overall reaction? Q: What are the processes involved? Q: Where does the energy come from? Q: What's the point of all the phosporylation? Q: For medical students: What is the curriculum? Q: For M.Phil. and Ph.D.: What is the curriculum? Q: What are the most common human biochemistry tests? Q: What biochemistry tests can be done at your laboratory? Q: What is the mechanism involved in each test? Q: What type of machines do you have? Q: How many people work in this laboratory? Q: Would you like your laboratory to be affiliated with Qureshi University? Q: Would you like your college to be affiliated with Qureshi University? Q: Can you start M.Phil. and Ph.D. programs in biochemistry without knowing the difference between M.Phil. and Ph.D.? Q: What is the difference between the curriculums for medical students, M.Phil. and Ph.D.? Q: Are you interested in manufacturing these products? Q: Are your M.Phil. or Ph.D. students developing these capabilities? Q: Do you want me to give them some guidance? Q: What are other similar types of work? |
| Medical Biochemistry |
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What is Biochemistry?
Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level. It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to investigate the chemistry of living systems. Anaerobic glycolysis takes a six carbon sugar (glucose), splits it into two molecules of three carbon sugar (glyceradehyde) and then rearranges the atoms (to lactate). The rearrangement of atoms provides energy to make ATP which is the principle energy 'currency' in the cell. The starting point for glycolysis is normally glucose although other monosacharides may be brought into the pathway. The end product, in anaerobic conditions, depends on the organism. In higher organisms the end product is lactate whereas in some microorganisms (for example brewers yeast) it is ethanol and carbon dioxide. 1. What is Glycolysis? Glycolysis is the sequence of reactions that converts glucose into pyruvate with the concomitant production of a relatively small amount of ATP. Glycolysis can be carried out anerobically (in the absence of oxygen) and is thus an especially important pathway for organisms that can ferment sugars. For example, glycolysis is the pathway utilized by yeast to produce the alcohol found in beer. Glycolysis also serves as a source of raw materials for the synthesis of other compounds. For example, 3 phosphoglycerate can be converted into serine, while pyruvate can be aerobically degraded by the Krebs or TCA cycle to produce much larger amounts of ATP. 2. Why do animal need glycolysis? Glycolysis is perhaps the first step in the of all energy producing. 3. Where does glycolysis occur? Glycolysis occurs in most area of the cell. 4. What is/are the reactants/reagents necessary for glycolysis? Glycolysis of requires glucose to produce energy. 5. What is/are the product of glycolysis? Glycolysis produces a net amount of 2 ATP and 2NADH 4. Does this process need or use oxygen? No it does not need large amounts of energy. 5. How much energy does glycolysis produce? Glycosis produces 2ATP and 2 NADH which then goes into the Oxidative Phosphorylation cycle which then produces more ATP. 6. What is the advantage of producing energy from glycolysis? Glycolysis, is considered as the basis for all energy processes in the cell. Althoug it only produces low levels of ATP, normally called basal levels, this process also produces large quantities of NADH which when processed by the Oxidative Phosphorylation pathway can produce large amount of energy. Glycolysis can also be carried out throughout the cell, which gives it an advantage over the TCA and Oxidative phosphorylation cycles that occur in the mitochondria. Review of Pyruvate Dehydrogenase (PDH) Complex The fate of pyruvate depends on the cell energy charge. In cells or tissues with a high energy charge pyruvate is directed toward fatty acid synthesis, but when the energy charge is low pyruvate is preferentially oxidized to CO 2 and H 2 O in the TCA cycle, with generation of 15 equivalents of ATP per pyruvate. What is the Pyruvate Dehydrogenase (PDH) Complex ? The PDH Complex is a series of biological step that prepare the pyruvate produced in glycolysis to go into the TCA cycle. These processes chemically convert pyurvate to Acetyl-CoA that can then enter the TCA cycle. What are the reactants for the PDH cycle? Pyruvate from glycolysis What is the product of the PDH cycle? Acetyl-CoA What is the advantage of using this process? This process allow for the chemical conversion of pyruvate into Acetyl-Co A which can then be inserted into the TCA cycle for processing. Review of Citrus Acid Cycle 1.What is the Citrus Acid Cycle? Krebs cycle or the citric acid cycle or tricarboxylic acid cycle is the common pathway to completely oxidize fuel molecules that mostly is acetyl CoA, the product from the oxidative decarboxylation of pyruvate. It enters the cycle and passes ten steps of reactions that yield energy and CO 2 . Where does the Citrus Acid Cycle occur? The mitochondrial membrane Does the TCA Cycle need or use oxygen? Yes. The Citrus Acid Cycle does need oxygen. How much energy does the TCA cycle produce? Per turn of the TCA cycle 3 NADH, 1 FADH 2 , and 1ATP What is the reactant of the TCA cycle? Acetyl-CoA produced from the pyruvate from glycolysis and converted by the PDH complex. Citrate is also a reactant, which can come from OAA in the citrus acid cycle. What is the product of the TCA cycle? In fact since the TCA cycle feed backs into itself there is no net products. However, TCA cycle 3 NADH, 1 FADH 2 , and 1ATP are produced each turn. What is the advantage of the TCA cycle? The advantage of the TCA cycle is that it cycles that it can cycle which means that it can repeat for several times to accumulate several products which can be either used as direct energy or put into the oxidative phosphorylation pathway which can produce large amounts of energy. Citrus Acid Cycle Steps Step 1: Reaction: Acetyl CoA+Oxaloacetate to Citrate Enzyme: Citrate synthase Reaction type: Condensation Description: Acetyl CoA condenses with oxaloacetate first,to form citryl CoA. Then citryl CoA is hydrolyzed to citrate and CoA Step 2. Reaction: Citrate to cis-Aconitate Enzyme: Aconitase Reaction Type: Dehydration Description: Citrate is isomerized to isocitrate by this first dehydration and yields cis-aconitate as an intermediate. Step 3. Reaction: cis-Aconitate to Isocitrate Enzyme: Aconitase Reaction Type: Hydration Description: Hydration of cis-aconitate gives the interchange of H atom and OH group from the step 2. Step 4. Reaction: Isocitrate to alpha-Ketoglutarate Enzyme: Isocitrate dehydrogenase Reaction Type: Oxidative decarboxylation Description: Dehydrogenation of isocitrate occurs and yields oxalosuccinate as an intermediate.Then CO 2 leaves to have alpha-ketoglutarate.This reaction gives NADH. Step 5. Reaction: alpha-Ketoglutarate to Succinyl CoA Enzyme: alpha-Ketoglutarate dehydrogenase complex Reaction Type: Oxidative decarboxylation Description: This mechanism is almost as same as the reaction of the oxidative decarboxylation of pyruvate to acetyl CoA by pyruvate dehydrogenase complex. This reaction gives one NADH. Step 6. Reaction: Succinyl CoA to Succinate Enzyme: Succinyl CoA synthetase Reaction Type: Substrate-level phosphorylation Description: The thioester bond of succinyl and CoA is an energy rich bond. Thus only this step gives a high-energy phosphate compound,GTP from the couple reactions of the thioester bond cleavage and the phosphorylation of GDP. Step 7. Reaction: Succinyl CoA to Succinate Enzyme: Succinate dehydrogenase Reaction Type: Oxidation Description: The two hydrogens of succinate leave to an acceptor, FAD. Then this reaction yields fumarate and FADH 2 . Step 8. Reaction: Succinate to Fumarate Enzyme: Succinate dehydrogenase Reaction Type: Oxidation Description: The two hydrogens of succinate leave to an acceptor, FAD. Then this reaction yields fumarate and FADH 2 . Step 9. Reaction: Fumarate to Malate Enzyme: Fumerase Reaction Type: Not described. Description: Not described. Step 10. Reaction: Malate to Oxaloacetate Enzyme: Malate dehydrogenase Reaction Type: Oxidation Description: Malate is dehydrogenated to form oxaloacetate. The hydrogen acceptor is NAD. So this reaction yields NADH. |
| Storage and Expression of Genetic Information |
| DNA Structure, Replication, and Repair |
| Gene Expression |
| Gene Regulation |
| Acid-Base Equilibria, Amino Acids, and Protein Structure/Function |
| Acid-Base Equilibria, Amino Acids, and Protein Structure |
| Protein Structure/Function |
| Intermediary Metabolism |
| Carbohydrate Metabolism |
| Bioenergetics and Energy Metabolism |
| Amino Acid, Lipid, and Nucleotide Metabolism |
| Nutrition |
| Vitamins and Minerals |
| Hormones and Integrated Metabolism |
| Inheritance Mechanisms and Biochemical Genetics |
| Inheritance Mechanisms/Risk Calculations |
| Genetic and Biochemical Diagnosis |
| Review Question |
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For medical students: What is the curriculum? For M.Phil. and Ph.D.: What is the curriculum? Q: What are the most common human biochemistry tests? A: Examination of the chemical constituents of blood can provide valuable screening and help to establish a diagnosis. With the growing automation of biochemical blood testing over the last forty years, the number of blood tests carried out on patients has increased enormously. Blood chemistry testing is generally carried out on the watery part of blood (serum or plasma) as opposed to the full blood count which looks at the number and condition of the cells in whole blood. Because of the large number of chemical constituents that can be analysed these tests are often used as a screen when the patient has symptoms that the doctor can't make sense of. Occasionally the result of a particular test will clinch a diagnosis. However this is unusual, history and clinical examination providing much of the useful information. Common Biochemical Tests There are very many substances that are tested for but those listed below are probably the most commonly requested. Electrolytes: sodium, potassium and chloride. These elements are important in maintaining fluid balance across cell membranes. They can give an indication of level of dehydration and kidney function. Heart muscle is particularly sensitive to potassium level. Calcium: this is also important in cell membrane function and correct levels are vital for proper muscle activity. Tetany – marked muscle spasm – can occur if calcium becomes too low. Calcium is also important for proper bone formation. Testing for calcium can be helpful in diagnosing kidney disease, parathyroid gland dysfunction and malabsorption problems in the gastrointestinal tract. Urea: sometimes referred to as blood urea nitrogen (BUN). This is a waste product from the metabolism of protein. The test is used as an indication of kidney efficiency. Glucose: this is the sugar that provides much of the body's energy. Its main use is as a test to diagnose and monitor diabetes. Low blood glucose levels are sometimes seen in some cancers, liver disease, alcoholism, starvation and certain hereditary disorders. Liver enzymes: liver cells contain very many enzymes to facilitate the large number of chemical processes that the liver is responsible for. If sufficient numbers of liver cells are damaged by infection or toxins for example, these enzymes will spill out into the blood and give a useful indication of the extent of liver damage. Conditions that can cause such damage are hepatitis, poisoning (paracetamol for example), excessive alcohol consumption and liver tumours. Liver enzymes are known by acronyms such as γGT, AST and ALT Cholesterol: there can't be many adults in the west who have not had a cholesterol test. High levels of cholesterol have been linked to heart disease and the advent of statins - cholesterol lowering drugs – has encouraged doctors to get their patients' cholesterol levels as low as possible. Some people who are perfectly healthy will have the occasional abnormal test result. This is because a published normal range is good for only 95% of the population. Five percent of the population will always fall outside of the normal range. Another reason is that other factors can interfere with the test result - diet or medicines for example. There can't be many people who have not had some kind of blood test, they're a normal part of the doctor's diagnostic kit. They are also frequently resorted to when the doctor hasn't a clue what's wrong. The full blood count, one of the most commonly used sets of pathology tests, uses whole blood mixed with anticoagulant to stop clot formation. This distinguishes it from biochemical testing on blood where the blood serum or plasma (the watery part of blood) is used The full blood count examines mostly the cellular components of blood whereas biochemical testing focuses on its chemical constituents. The Full Blood Count This group of tests looks directly at the cells of the blood and parameters related to them, largely involving the use of microscopes and automatic cell counters. The major tests involved are listed below. Haemoglobin (Hb): this is the red component of blood. Its function is to carry oxygen. It tends to be lower than normal after blood loss and in anaemia. Red blood cells (Rbcs):These are the cells which carry the haemoglobin. Clearly they will be reduced in any significant blood loss. The quantity, colour and shape of these cells is examined. White blood cells (Wbcs): the cells of the immune system. There are a number of different types such as neutrophils, eosinophils and basophils. From the total count of white cells and the relative numbers of the various types, it's possible get an idea of the state of the immune system. For example an increase in eosinophils suggests that an allergic reaction is taking place. A rise in the total white cell count could point to an infection. Platelets: cells that are intimately involved in the clotting process. Some illnesses and some adverse drug reaction can lower the platelet count which may result in spontaneous bleeding. Erythrocyte sedimentation rate (ESR): this is a very non-specific test but useful nonetheless. The blood sample is suspended in a thin glass tube and the rate at which the red cells separate from plasma is measured. This rate is increased when any inflammatory processes are going on within the body. This could be due to infection or any kind of autoimmune disease for example. Limitations of The Full Blood Count. It should be remembered that blood tests are not always diagnostic. In some instances a blood test can give a precise indication of what's wrong – anaemia for example where the number and condition of the red blood cells can give a very good indication of the type of anaemia the patient is suffering from. In many other cases the diagnosis is made by a combination of blood test results, the findings from clinical examination and the patient's case history. Q: What biochemistry tests can be done at your laboratory? Q: What is the mechanism involved in each test? Q: What type of machines do you have? Q: How many people work in this laboratory? Would you like your laboratory to be affiliated with Qureshi University? Would you like your college to be affiliated with Qureshi University? Q: Can you start M.Phil. and Ph.D. programs in biochemistry without knowing the difference between M.Phil. and Ph.D.? A: No. Q: What is the difference between the curriculums for medical students, M.Phil. and Ph.D.? A: A medical doctor needs to have insight of biochemistry and be able to question and correctly interpret test results to reach to a correct diagnosis and treatment as per preventive and curative concepts of medicine. An M.Phil. or Ph.D. in biochemistry should be able to manufacture: automatic clinical biochemistry analyzer, arterial blood gas analyzer, electrolyte analyzer, and an electrochemiluminiscence analyzer. He/she also should be able to troubleshoot and standardize test results, as well as detect false positive, false negative, true positive, and true negative results. Are you interested in manufacturing these products? Are your M.Phil. or Ph.D. students developing these capabilities? Q: Do you want me to give them some guidance? Q: What are other similar types of work? A: Biomedical engineer. |
| 1. Biochemistry Introduction |
| 2. Water and Mineral Salts |
| 3. Carbohydrates |
| 4. Lipids |
| 5. Protein Structure |
| 6. Enzyme Activity |
| 7. Nucleic Acids |