Biochem 3 Objectives

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CircadianHomunculus
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Biochem 3 Objectives
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2013-04-03 14:47:49
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Biochem 3 Objectives
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  1. What is considered as the sum of protein synthesis + protein degradation?
    Protein turnover
  2. Amino acids released by protein break-down that can be utilized for protein synthesis efficiently refers to what process?
    Nitrogen recycling
  3. Which proteins are specifically targeted for degradation since their turnover is high? What is a result of this feature?
    • Proteins with very short half-lives.
    • They respond quickly to acute changes in protein intake.
  4. What are the two products of protein oxidation/excretion?
    • N-urea
    • N-ammonia
  5. How is the rate of protein turnover assessed non-invasively?
    With non-radioactive table isotopes (measured in urine).
  6. What is mathematically equivalent to the difference between total protein synthesis minus total protein breakdown?
    Nitrogen balance
  7. Do catabolic disorders result in increased or decreased protein breakdown?
    Increased
  8. Protein feeding for someone with a catabolic disorder results in...?
    A relative increase in protein synthesis which minimizes N losses.
  9. Protein restriction for someone with a catabolic disorder results in...?
    • Adaptation of protein metabolism (decreased protein turnover/degradation).
    • Amino acid oxidation.
  10. What are the endogenous factors that affect protein turnover?
    • Age/aging
    • Growth
    • Body composition (fat free mass, adipose)
    • Various diseases (catabolic, hypermetabolic)
    • Example: rate of protein turnover tends to decrease with age in humans.
  11. What are the exogenous factors that affect protein turnover?
    • Nutritional status (protein and energy)
    • Anabolic substances
    • Prolonged exercise
    • Recovery from malnutrition ("regrowth" in adults)
    • Example: during endurance exercise, protein utilization as a fuel increases and the net amount of whole body protein is depressed.
  12. A drop in total energy intake while keeping protein intake constant, as seen in a weight-loss diet, would cause what kind of effect?
    Increase in protein needs due to an increase in body protein loss (enhanced protein oxidation).
  13. What are the metabolic processes that require energy?
    • Protein synthesis/degradation in particular, activation of AAs and formation of peptide bonds during elongation of peptides.
    • r-RNA and t-RNA turnover
    • AA transport
    • Ion pumps and channels
    • Signal transduction and protein translocation.
    • Glucose-alanine cycle
    • Urea synthesis
  14. What is the total energy requirement for protein synthesis and protein turnover in adults and premature babies?
    • 20% of resting energy expenditure (adults)
    • 30% of resting energy expenditure (premature babies)
  15. What are the major metabolic fates of amino acids in the amino acid pool?
    • Synthesis of new endogenous proteins/other biological substances.
    • Oxidized, yielding urea, ammonia, and CO2 as terminal end-products (ureagenesis).
    • Converted into other compounds (gluconeogenesis).
  16. What are the factors that regulate catabolism of amino acids?
    Mainly regulated (short term) by substrate availability from exogenous supply (food) or endogenous mobilization in the post-absorptive state (protein breakdown).
  17. Are surplus amounts of amino acids stored?
    No. Excess AAs are used as metabolic fuel and oxidized.
  18. Where does the process of the urea cycle mainly occur in terrestrial vertebrates?
    The liver
  19. What is the biochemical role of the urea cycle in humans?
    Sole mechanism for ammonia disposal.
  20. What are the biochemical properties of urea?
    • Water soluble "waste" end product of protein metabolism.
    • Produced by the liver, excreted by kidneys in urine.
    • Safe vehicle to transport and excrete excess nitrogen.
    • Is the main nitrogen-containing substance in human urine.
  21. What is the urea salvage pathway and what is its purpose?
    • Microflora (bacteria) in the lower hind gut (colon) recycle urea by way of hydrolysis, allowing some nitrogen to be recovered.
    • This nitrogen returns to the AA pool and is retransformed into AAs in the liver.
  22. What are factors that stimulate and inhibit gluconeogenesis?
    • Stimulate: fasting diet and low carbohydrate diet (<100 g/day).
    • Inhibit: high carbohydrate diets.
    • Basically it is influenced by the nature and level of dietary intakes.
  23. Is gluconeogenesis simply a reversal of the glycolytic pathway? Why/why not?
    • No
    • The irreversible steps of glycolysis are bypassed during gluconeogenesis.
  24. What term is used to describe the simultaneous activation of glycolysis and gluconeogenesis? Why is it called this?
    • Futile cycle
    • Both processes activated at once would result in a waste of energy, therefore they are tightly regulated to prevent simultaneous activation.
  25. Although glycolysis occurs universally throughout the body, gluconeogenesis occurs in specific locations. What are they?
    Liver and kidneys
  26. What is the key hormone that regulates the metabolic transformation of amino acids into glucose in the liver and kidneys?
    Glucagon
  27. What are the roles of glucagon?
    • Stimulates gluconeogenesis (inhibits glycolysis).
    • Enhances glycogen breakdown (inhibits glycogen synthesis).
    • Allows release of free glucose into circulation to maintain glycemia.
    • Stimulates hepatic ureagenesis (hypergluconemia).
  28. What are the hormones that regulate gluconeogenesis?
    • Glucagon
    • Cortisol
  29. What are the precursors for gluconeogenesis in muscle and fat?
    • Lactate (muscle)
    • Glycerol (fat)
  30. What are two patient populations that have high protein demands and turnover rates?
    • Premature babies
    • Children recovering from malnutrition
  31. What are the sources of amino acids for the amino acid pool?
    • Exogenous proteins (digestion, absorption).
    • Tissue protein breakdown during protein turnover.
    • De novo synthesis, including AAs (and ammonia) from urea salvage.
  32. How are excess amino acids disposed of?
    • Increased oxidation
    • Enhanced ureagenesis
    • Gluconeogenesis
  33. What are the types of glycosidic linkages present in the glycogen structure?
    • α-1,4 glycosidic linkages (between glucose residues)
    • α-1,6 glycosidic linkages (branchpoints)
  34. What are the types of chains present in the glycogen structure?
    • Inner B-chains (2 branchpoints)
    • Outer A-chains (unbranched)
  35. What is the general structure of glycogen?
    • 12 tiers of chains w/ ˜55000 glucose residues
    • Molecular mass of ˜107 kDa
    • Diameter of ˜44nm
  36. What other types of molecules are present in glycogen besides glucose residues?
    • Glucosamine
    • Phosphate
  37. What enzyme is responsible for the addition of other molecules to the glycogen structure?
    Glycogen synthase
  38. What are the effects of excessive phosphorylation of glycogen?
    • Lafora disease (epilepsy)
    • Multiple cycles of expansion and contraction cause chemical/metabolic insults that can accumulate, and results in aberrant structures that sometimes escape normal metabolism and degenerate into an insoluble deposit.
  39. What are the locations of glycogen storage?
    • Skeletal muscle and liver (major deposit)
    • Other organs capable of glycogen synthesis are the kidney, heart, adipose, and brain.
  40. What are the precursors and donors used in glycogen synthesis?
    • Precursor: Glucose (carbohydrate)
    • Precursor: Lactate or alanine (gluconeogenic)
    • Donor: Activated NDP-sugar UDP-glucose
  41. What are the types of glucose transporters used in the direct pathway?
    • GLUT1 (widely distributed, basal glucose transport)
    • GLUT2 (prominent in liver and β-cells of pancreas, admits glucose based on positive glucose gradient between blood and tissue)
    • GLUT4 (up-regulated by insulin, important in insulin sensitive tissues like skeletal muscle and adipose)
  42. How are the UDP-glucose, glycogenin primer and glycogen A&B chains synthesized?
    • UTP is converted to UDP by UDP-glucose pyrophosphorylase.
    • Glycogenin self-glucosylates to form oligosaccharide primer.
    • Glycogenin interacts with glycogen synthase which forms the majority of the α-1,4 glycosidic linkages.
    • α-1,6 glycosidic branchpoints are formed by branching enzyme.
  43. What is the difference between the indirect and direct pathways for glycogen synthesis?
    • Indirect pathway=glyconeogenesis that occurs with gluconeogenic precursors (lactate, alanine, etc)
    • Direct pathway=requires transport of glucose into cells with GLUTs
  44. What are the products of glycogen degradation?
    • Glucose-1-phosphate (from α-1,4 linkages)
    • Free glucose (from α-1,6 linkages)
  45. What are the conditions that stimulate glycogen breakdown?
    • Nutritional deprivation (hepatic glycogenolysis)
    • Exercise (muscle glycogenolysis under conditions of increased cAMP and Ca2+)
  46. How is the breakdown of glycogen mediated in the first pathway?
    • Actions of glycogen phophorylase.
    • Actions of debranching enzyme AGL.
  47. How is the breakdown of glycogen mediated in the second pathway?
    Glycogen is transferred to the lysosome and hydrolyzed to glucose by lysosomal α-glucosidase.
  48. What is the biochemical function of glycogenin?
    • 1. Transfers glucose from UDP-glucose to a tyrosine residue within the protein itself.
    • 2. From there it forms α-1,4 glycosidic linkages until the oligosaccharide chain is 10-20 residues long.
  49. What are the genes that encode glycogenin and how are they expressed?
    • GYG1: widely expressed
    • GYG2: expressed in liver, heart, pancreas
  50. What type of gene mutation can cause glycogenin to be defective? What effect does this have on the patient?
    • Nonsense mutation in one allele and missense mutation (T83M) in the other which leads to inactive glycogenin-1.
    • Patient has muscle weakness and cardiac abnormalities following exercise.
  51. What is the biochemical function of glycogen synthase?
    It is responsible for the bulk synthesis of glycogen by formation of the α-1,4 linkages with UDP-glucose as the glucosyl donor.
  52. What are the genes that encode glycogen synthase in mammals and how are they expressed?
    • GYS1: expressed in skeletal muscle and most other cells capable of glycogen synthesis
    • GYS2: expression restricted to liver
  53. How is glycogen synthase regulated?
    • Phosphorylation
    • Allosteric activation by glucose-6-phosphate
  54. What are the types of glycogen synthase mutations, and what are they physiological effects on patients?
    • Mutation of GYS2 (GSD 0): causes hepatic glycogen deficiency. Patients have mild symptoms, postprandial hyperglycemia, and fasting hypoglycemia. Hepatic glycogen synthase activity is reduced.
    • Mutation of GYS1: glycogen synthase and glycogen are absent from muscle. Causes cardiac problems, and poor exercise performance. Occurs as a result of a homozygous mutation of R462X in GYS1.
  55. What are the enzymes involved in the rate-determining steps of glycogen synthesis in muscle?
    • GLUT4
    • Hexokinase
    • Glycogen synthase
  56. Name the general location of glycogen storage inside cells.
    Cytosol
  57. What is glycogen autophagy?
    • Autophagy is comprised of processes described as a mechanism for random recycling of cellular materials under conditions of nutritional deprivation.
    • The term glycogen autophagy has been applied particularly to the liver of newborns.
  58. What is the location of glycogen in liver and muscle cells?
    Close to membranes, endoplasmic reticulum (liver), sarcoplasmic reticulum (muscle).
  59. What are the causes and physiological effects of Lafora Disease?
    • 'Lafora bodies' are deposits containing poorly branched, insoluble glycogen-like carbohydrate (polyglucosan) in individuals with an autosomal recessive neurodegenerative disorder called Lafora Disease.
    • Causes progressive myoclonus epilepsy, dementia and death (within 10 years of symptoms starting).
  60. Where are Lafora bodies found in humans?
    • Brain (neurons)
    • Skeletal muscle
    • Heart
    • Liver
  61. Name the location of and substrates for laforin.
    • Skeletal muscle
    • Liver
    • Kidney
    • Heart
    • Brain
    • Tissues
    • Substrates: Lafora bodies
  62. What are the substrates for malin?
    Debranching enzyme AGL

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