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Exam 1, 2, and 3 Review Guides

by: Shannon Kilfoy

Exam 1, 2, and 3 Review Guides BMS 9265 - 0001

Shannon Kilfoy

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About this Document

Basically a condensed version of slides and info we need to know for the exam!
Darla McCarthy, Rosa Huang
Study Guide
biochemistry, Science, Chemistry, Biology, DNA, Cell, metabolism
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This 58 page Study Guide was uploaded by Shannon Kilfoy on Monday March 14, 2016. The Study Guide belongs to BMS 9265 - 0001 at University of Missouri - Kansas City taught by Darla McCarthy, Rosa Huang in Spring 2016. Since its upload, it has received 46 views. For similar materials see Biochemistry in General Science at University of Missouri - Kansas City.

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Date Created: 03/14/16
Test 1 Study Guide 08/22/2013 Metabolic Fuels 1. describe the general metabolic routes for dietary components in the body. a. Intake (Macronutrients: Fats, Carbs & proteins, Micro: vitamins, minerals, water, Xenobiotics: not natural) b. Digestion (of macronutrients to smaller molecules), absorption (of micro & xenobiotics) c. Compounds transported into cells d. 4 typical pathways in cells: i. Used for energy production ii. Biosynthetic pathways iii. Fuels Stores iv. Waste products (most xeno & vitamins) 2. identify dietary fuels (including their calorie contents and food sources) and body fuel stores. a. Dietary Fuels: i. Carbs = 4kcal/g (starch, glucose, lactose, sucrose, fructose) ii. Fats = 9 kcal/g  TG can be sat (LDL = bad), mono-un-sat, or poly-un-sat (HDL = good) iii. Proteins = 4 kcal/g (vegetarians need good balance of essential AA) 3. calculate/estimate the following: a. calorie intake (in kcal) = (g of proteins)*4 + (g of fats)*9 + (g of carbs)*4 b. basal metabolic rate = 8.7*(kg body weight) + 829 c. daily energy expenditure = (# of hours)*(DEE )/24 af d. body mass index (and know the categories and risk levels) = kg/m 2 i. 4. Explain the dietary requirements and guidelines for macronutrients. a. Fats should make up about 20-35% of daily calorie intake (sat fats should only be about 10% or less) b. Proteins intake should equal about 0.8g/kg body weight per day c. Carbs should come from 1’ whole foods & refine sugar intake should be limited 5. list the essential fatty acids and amino acids, and explain the concept of nitrogen balance. a. Essential FA: i. a-linoleic acid ii. a-linolenic acid iii. eicosapentaenoic acid (EPA) iv. docosahexaenoic acid (DHA) b. Essential AA (PVT TIM HaLL has a CAT that says ARGGG!): i. P = phenylalanine, V= valine, T= threonine ii. T = tryptophan, I = isoleucine, M = methionine iii. H= histidine*, L = leucine, L= lysine, 1. Conditional: Cysteine, Arginine, Tyrosine c. Nitrogen Balance = Nitrogen intake – Nitrogen excretion  0.8/kg body weight/day Vitamins, Fed State 1. prepare a table or chart identifying the dietary vitamins and essential minerals, their general biological roles, dietary sources, and the names of diseases associated with their deficiencies. a. 2. describe the digestion and absorption of macro- nutrients, including the names of key digestive enzymes. a. Carbs: a-amylases digest starches  oligosaccharides  hydrolyzed by maltase (lactase/sucrase) b. Fats: TGs solubilized by bile salts  hydrolyzed by lipases  free FA + monosaccharides i. In intestine they are reformed & packages w/ cholesterols into chylomicrons c. Proteins cleaved  AA (stomach: pepsin, intestine: trypsin, chymotrypsin, elastase, carboxypeptidase, aminopeptidase, dipeptidase, tripeptidase) 3. explain the fates of glucose, triglycerides, and amino acids after a meal (if you can reproduce Figure 2.2, and narrate the scheme to a friend, you’ll be “golden” for the quiz next week). a. Fed State Diagram 4. name the processes (summarized in Figure 2.2) that are stimulated by insulin, and explain how those processes help to maintain glucose homeostasis in the blood. a. Fed State diagram Fasting 1. explain how the body maintains glucose homeostasis during a short term fast (basal state) and during a long term fast (fasting state). a. Basal/Fasted State diagrams 2. predict changes in serum and/or urine levels of ketone bodies, urea, creatinine, and albumin as a function of changes in metabolic state. a. KB = increase in basal and fasted states b. Urea = increase in basal, less increase in fasted c. Creatinine = decrease in basal, less decrease in fasted d. Albumin = decrease in basal, less decrease in basal Diseases of Macronutrient Malnutrition 1. recognize the symptoms and causes of obesity, anorexia nervosa, kwashiorkor, and marasmus. a. Obesity = caused by consumption of excessive calories and/ lack of physical activity i. Can lead to: metabolic disease, type 2 DM, CVD, gallstones, osteoarthritis, some cancers b. Anorexia nervosa = protein & caloric malnutrition due to self induced restriction of food intake i. Patients are usually female, early teens deny low body weight, have fear of being overweight 1. At risk for osteoporosis & heart/kidney damage c. Kwashikor = protein malnutrition w/ adequate/slightly depleted calorie consumption i. Body stays in fed/basal state  wasting of muscle, edema, etc. d. Marasmus = prolonged protein & calorie malnutrition 2. list the constellation of symptoms associated with metabolic syndrome. a. Increased waist circumference b. Elevated TG c. Reduced HDL d. Elevated BP e. Elevated fasting glucose Water, Acids, and Bases 1. explain the chemical bases for the important physiological roles of water as a solvent and thermal regulator. a. Solvent  water is polar so it can form H-bonds (important releasing energy property) & interact w/ ions (electrolyte concentration gradients) b. Thermo Regulator  H-bonds = high heat capacity which can readily dissipate heat of metabolic reactions 2. identify conjugate acid/base pairs, and recognize names of carboxylic acids and their carboxylate ions, as well as amines and their conjugate acids. a. Acid = H+ donor, Base = H+ acceptor: HA + H2O  A- + H3O+ b. Carboxylic acid = OH (protonated), Carboxylate ion = O- (deprotonated) c. Amine = NH2 (deprotonated), Ammonium ion = NH3+ (protonated) 3. use the Henderson-Hasselbach equation to calculate pH, [A-], or [HA]; and pKa and pH to estimate relative quantities of acid and conjugate base and the net charge on a molecule. a. b. Buffers 1. explain the function and importance of biological buffers. a. Buffer (WA and it’s CB) prevents large changes in pH – usually from acids produced in metabolic reactions 2. describe the properties of an effective buffer. a. Effective buffer range: pH = pKa +/- 1  buffering capacity is greatest when you have equal [] of acid & CB b. 2 main effectiveness factors: its pKa relative to the pH of the solution and its concentration. 3. list the major buffer systems in the body, and the specific locations in which they can be found. a. Bicarbonate-carbonic acid  all ECF b. Hemoglobin buffer system  RBCs c. Pi buffer system  ICF d. General protein buffer sytsems  ICF & blood plasma 4. describe the serum bicarbonate buffering system and predict the effects of acids, bases, and altered PCO2 on serum pH, and how the body will compensate for that change. a. Bicarbonate Buffer System  buffers serum & ECF, solubilizes CO2 for elimination by respiration & can be manipulated by the respiratory & renal systems (compensation) b. Effects on pH by: i. Acid  shifts rxn cat by carbonic anhydrase toward CO2 & water (respiration by lungs can alter [CO2]) 1. (Excretion or replacement by kidneys can alter [H+] or [HCO3-]) ii. Base  Absorbs extra protons iii.PCO2  High = increases respiration, Low = decreases respiration Organic Chemistry Review, and Monosaccharide Structure 1. recognize the major functional groups found in biological molecules and identify the reactants and products of common biochemical condensation and oxidation/reduction reactions. a. Fx groups: b. c. Condensation rxns: d. e. Oxidation = loss of H/gain of O, Reduction = gain of H/loss of O 2. identify simply biochemical molecules if given a common name, and determine if a biomolecule will be chiral. a. Naming: Greek (alpha, beta, gamma, delta), Carbon numbering (form-, acet-, prop-, but-) b. Chiral = 4 different fx groups on a single carbon 3. predict whether a given biological compound will be non- polar, polar, or charged, and whether it will be water-soluble. a. Soluble: (-) @ physiological pH = carboxylate, phosphate, sulfate, (+) = amines b. Insoluble: high hydrocarbon surface area, low # of polar fx groups (ex. cholesterol) 4. identify linear and cyclic carbohydrate structures, as well as epimers, anomers, substituted sugars, and oxidized or reduced sugars. a. Linear  D = right, L = left, Anomers = a or B, Epimer = chiral center differs at 1 C b. Substituted sugar  substituted w/ phosphate, sulfate, amino, or N-acetyl groups c. Oxidized ( carboxylic acids), Reduced (deoxy-sugars/alcohol) 5. draw Hayworth projections of the two anomeric forms of glucose, galactose, mannose, and fructose. a. Glucose = B – D glucopyranose (alternating OH groups) b. Galactose = epimer of glu @ C4 c. Fructose = a – D – fructofuranose Biomolecular Structures 1. draw glycosidic bonds and recognize the structures of sucrose, lactose, starch, glycogen, and cellulose a. Glycogen = a (14) linkages w/ a (16) branches & Starch similar (less branching) b. Cellulose = B (14) linkages 2. distinguish between reducing and non-reducing sugars a. Reducing = anomeric carbon on 1 molecule in sugar is still free to make new linkages b. Non –reducing = both anomeric carbons in a sugar are participating in the glycosidic bond 3. use the standard and w-systems to describe fatty acid chains a. w-system: start numbering form methyl end (opposite of carboxyl end) 4. recognize the structures of triglycerides, glycerophospholipids, sphingolipids, and cholesterol and its derivatives; bile salts and steroid hormones. a. TG = glycerol backbone w/ 3 FA (long hydrocarbon chain – sat/unsat) attached via ester linkage b. Glycerophospholipids = glycerol backbone w/ 2 FA & phosphate c. Sphingolipids = sphingosome backbone d. Cholesterol = 4 ring core w/ hydrocarbon chains i. Bile Salts = sterol (cholesterol derivative) w/ OH groups & carboxylic acid chain ii. Steroid = sterol w/ OH groups Glycerophospholipid example  5. recognize the structures of amino acids purines, pyrimidines, and pyrines. Exam  2  Review  Guide     Chapter  10:  Relationship  Between  Cell  Biology  and  Biochemistry     Basic  structure  and  function  of  eukaryotic  cells     Membrane  lipids  and  proteins     Lipids   • Glycerol  lipids:  glycerol  backbone,  ester  bonds,  2  FA  chains,  phosphate  group   o Phosphatidylcholine  (PC)   § Most  abundant   o Phosphatidylethanolamine  (PE)   o Phosphatidylserine  (PS)   o Phosphoinositol  (PI)   • Glycoshpingolipid:  sphingosine  backbone,  amide  bond,  2  acyl  chains,  phosphate   group   o Sphingomyelin   • Arrangement   o Outer  leaflet  à  PC,  sphingomyelin   o Inner  leaflet  à  PS,  PE,  PI     Proteins   • Integral:  embedded  in  the  membrane   o Hydrophobic  interaction,  need  detergent  to  separate  from  membrane   • Peripheral:  at  surface;  does  not  penetrate  membrane   o Non-­‐covalent  interaction  with  membrane   • Lipid-­‐bound:  protein  is  anchored  by  a  FA  tail     Fluidity  and  mobility  of  membrane     é  Fluidity   • Cholesterol   • Short  FA  chains   • Cis  double  bonds,  unsaturated     Mobility   • Lateral  movement   • Transverse  movement   o More  difficult,  require  enzyme  (flipase)   • Rotation   • Flexing  of  hydrocarbon  chains     Transport  mechanisms     Passive   • Simple  Diffusion:  no  protein  needed;  let  gases  (O2,  CO2,  and  NO2)  and  small   hydrophobic  molecules  through;  rate  of  diffusion  is  linear   • Facilitative  Diffusion:  bind  to  substrates;  more  likely  to  bind  (cooperative   binding)  until  Vmax  is  reached     o Pore:  always  open   o Gated  channel:  sometimes  open   § Voltage  gated   § Ligand  gated   § Phosphorylation  gated   § Pressure  gated   o Carrier  protein     Active  Transport   • Primary  carrier:  directly  uses  ATP  as  energy  source   o Ex:  Na/K  ATPase   • Secondary  carrier:  uses  potential  energy  from  a  primary  carrier  to  drive  reaction   o Ex:  Na/glucose  cotransporter     CFTR  (Cystic  Fibrosis  Transmembrane  conductase  Regulator)   • Has  2  binding  domains,  controlling  open/close  of  channel   o ABD  (adenosine  binding  domain)   o R  (regulatory  domain)   • Steps   o Phosphorylation  of  R  causes  shape  change   o Change  allows  ATP  to  bind  to  ABD   o Hydrolysis  of  bound  ATP  à  open  channel     Chapter  12:  Structure  of  Nucleic  Acids     Central  Dogma   • DNA  à  RNA  à  protein     Structure  of  Nitrogen  molecules   • Nitrogenous  Bases:  nonpolar,  aromatic,  planar  molecules   o Purines:  A,  G   o Pyrimidines:  T,  C   • Nucleosides:  base  +  sugar   o N-­‐glycosidic  bond  made  at  1’  Carbon   • Nucleotides:  base  +  sugar  +  phosphate   • Nucleic  Acids:  larger  polymers  (DNA  and  RNA)     Difference  between  ribonucleotides  and  deoxyribonucleotides     • 2’  OH  in  ribose  sugar  vs.  2’  H  in  deoxyribose  sugar     Chemistry  behind  polymers  of  DNA   • Nucleotides  linked  together  by  phosphodiester  bonds   • Antiparallel  structure   • Bases  pair  through  H-­‐bonding   o G  and  C  form  stronger  bonds     Structures  and  properties  of  double  helical  DNA   • Negative  charged  phosphates  on  outside   • Many  interactions  (hydrophobic,  Van  der  Waals,  H-­‐bonds)   • 3  types  of  helical  structures   o B:  right,  normal   § Most  common   o A:  right,  short  and  fat   o Z:  left,  skinny,  no  grooves   § Transient  within  a  cell   • Environmental  change   o Denaturation:  achieved  in  vitro  by  raising  temperature  or  raising  pH   o Tm:  temperature  at  which  50%  of  DNA  is  melted   o Hybridization:  renaturation;  if  temperature  is  slowly  decreased,  strands   can  realign  and  reform  the  original  DNA     Packaging  of  chromosomes     Nucleosomes   • Histones   o 4  types:  H2A,  H2B,  H3,  H4   o Contain  a  large  amount  of  Arg  and  Lys   § Positive  charge  binds  to  negative  AA   • Polynucleosome:  “beads  on  a  string”   o H1  binds  to  linker  DNA/stabilizes  30  nm  structure   • Regulation   o Acetylation:  relaxed,  easier  transcription   o Deactylation:  tighter  conformation,  transcription  repressor     Chromosomes   • Coiled  and  supercoiled  polynucleosomes   • Associated  with  histone/other  chromosomal  proteins  during  interphase   • Organized  before  mitosis  during  metaphase   • Human  cells  contain  23  pairs  of  chromosomes   o Each  are  longer  than  the  diameter  of  the  nucleus  à  must  be  packaged   • Each  chromosome  has  a  centromere,  2  telomeres,  and  sequences  for  origins  of   replication     Structures  and  properties  of  RNA     mRNA   • Structure   o 5’  cap  made  of  7-­‐methylguanosine  linked  by  5’-­‐5’  triphosphate  bridge  to   a  2’  C-­‐methylribonucleoside   § Initiates  ribosomal  entry   o Start  codon  (AUG  à  Met)   o Stop  codon   o PolyA  tail  on  3’  end   § Stabilizes  mRNA   • Properties   o Eukaryotes  à  only  codes  for  one  polypeptide,  monocistronic   o Prokaryotes  à  may  code  for  many,  polycistronic     rRNA   • Structure   o Eukaryotes   § Small  40S  subunit  =  18S  rRNA  +  33  other  proteins   § Large  60S  subunit  =  28S  +  5.85S  +  5S  rRNA  +  50  proteins   o Prokaryotes   § Small  30S  subunit  =  16S  rRNA  +  21  proteins   § Large  50S  subunit  =  5S  +23S  rRNA  +  34  proteins   o Highly  folded   § More  stable  than  mRNA   § Lost  of  modification   • Properties   o Makes  up  80%  of  all  RNA   o Assembled  in  80S  eukaryotic  ribosome   o Catalyzes  translation   o S:  how  fast  a  structure  will  sediment   § é  size,  é  S     tRNA   • Structure   o Small  structure  (smallest  ~  80  nucleotides  long)   o “Cloverleaf”  structure   o 4  loops   o 5’  end  linked  to  sequence  close  to  3’  end   o 3’  end  carries  AA   o 10-­‐20%  of  nucleotides  are  modified   • Properties   o 15%  of  RNA   o Covalently  activates  AA  for  protein  synthesis   o Recognizes  complimentary  codon   o Cells  contain  at  least  20  different  tRNA  molecules     Life  cycle  of  a  retrovirus  (See  below!)     Chapter  8:  Enzymes  and  Catalysts     Enzyme  function   • Biological  catalyst,  faster  reaction  rate   • Stabilizes  transition  state  à  lowers  activation  energy   • Does  not  alter  thermodynamics,  favorability  of  reaction  never  changes     Classification  of  enzymes  “Over  The  HILL”   1. Oxidoreductase:  electron  transfer/redox  reactions;  requires  reducing  and   oxidizing  agents   a. Dehydrogenase,  hydroxylase,  oxidase,  oxygenase   2. Transferase:  transfer  of  one  functional  group  from  one  molecule  to  another   a. Kinase,  glycosyltransferase,  acyltransferase,  transaminase,   aminotransferase,  synthase   3. Hydrolase:  breaking/lysis  of  bonds  via  addition  of  H2O;  hydrolysis  reaction   4. Isomerase:  rearrangement  of  existing  atoms;  creating  isomers   5. Ligase:  join  carbon  atoms  using  energy;  formation  of  C-­‐C  bond  coupled  with  ATP   hydrolysis   a. Synthetase   6. Lyase:  Lysis  of  bonds  by  means  other  than  hydrolysis  or  oxidation   a. Aldolase,  decarboxylase,  thiolase,  dehydratase,  synthase     5  methods  of  enzyme  catalysis   1. General  electrostatic  interactions   • Method  used  by  ALL  enzymes   • Partial  charges  are  stabilized  by  dipole-­‐dipole,  H-­‐bonding,  or  ion-­‐ dipole  interactions  of  functional  groups  in  the  active  site   2. Orientation/proximity   • Enzyme  active  site  is  complimentary  to  the  shape  of  the  transition   state   • Enzymes  place  molecules  in  optimal  orbital  overlap   3. General  acid/base  catalysis   • AA  in  active  site  accepts  or  donates  proton  from  the  reactant  in  the   transition  state   o Most  common:  Glu,  Asp,  His   o Sometimes:  Lys,  Ser,  Tyr,  Cys,  Arg   4. Metal  ion  catalysis   • Metals  with  (+)  can  stabilize  (-­‐)  in  the  transition  state   • Facilitate  electron  transfer  in  redox  reactions   5. Covalent  catalysis   • Enzyme  or  coenzyme  forms  intermediate  with  the  substrate  à   stability   o Covalent  AA:  His  Lys,  Ser,  Cys   • Can  isolate  this  intermediate  structure     Remember:  CAMEO     Coenzymes     Activation-­‐transfer   • Covalent  bond  à  activation  of  substrate  à  transfer/other  reaction   • Most  a  derived  from  vitamins   • Many  types   o Thiamine  phosphate:  transfer  carbonyl   § From  B1   o Biotin:  binds  CO2,  transfers  it  as  carboxylate   § From  B7   o Pyridoxal  phosphate:  transfers  aminos   § From  B6   o Coenzyme  A:  transfers  acyl  groups   § From  B5   o Lipoic  acid:  transfers  acyl  groups   § From  B5   o Cobalamin:  transfers  methyl  groups   § From  B12   o Tetrahydrofolate:  transfers  single  carbons   § From  B9     Oxidation-­‐reduction   • Redox  reaction  require  reducing  and  oxidizing  agents   o NADH/NAD+   o FADH2/FAD   o Ascorbate  and  dehydroascorbate     Drug  applications     Aspirin   • Covalent  inhibitor   • Covalent  acetylation  of  serine  residue  on  cyclooxygenase  (COX  enzyme)   o Prevent  prostaglandin  (causes  pain  and  swelling)  production     Organophosphates   • Covalent  inhibitor   • Makes  covalent  bond  with  ACHesterase   o Enzyme  cannot  degrade  neurotransmitter     Penicillin   • Suicide  inhibitor   • Binds  to  glycopeptidyl  transferase  à  partial  catalysis  of  penicillin  creates   irreversible  covalent  bond   o Bacteria  can’t  build  cell  wall  without  enzyme     Allopurinol   • Suicide  inhibitor   • Xanthine  oxidase  oxidizes  the  drug  to  form  oxypurinol  à  binds  very  tightly  to   the  active  site     o Inhibits  urate  prodution     Effect  of  pH  and  temperature  on  enzymes     pH   • Require  (+)  and  (-­‐)  to  stabilize  the  transitional  substrate  and  overall  enzyme   structure   • Change  in  pH  may  cause  protonation/deprotonation,  changing  the  ionization   states  of  given  functional  groups     Temperature   • Rising  temperature  =  higher  energy   • Optimal  temperature   • Above  optimal  =  protein  denaturation     Chapter  9:  Regulation  of  Enzymes       Rate  dependence  on  [S]   • Velocity  is  relative  to  [ES]   • Rate  graph  shows  slope  as  [S]/unit  of  time     o [S]  decreases  over  time  because  it  is  being  converted  into  [P]   o As  time  increases,  rate  decreases   o Rate  decreases  until  equilibrium  is  reached     Rate  dependence  on  [E]   • More  enzyme  =  faster  rate   • Easy  to  regulate   o Upregulation/synthesis  of  more  enzyme   o Degradation  by  capsases  and  proteasomes   o Enzyme  concentration  generally  does  not  change  under  physiologic   conditions   § Not  used  up  in  the  reaction     Michaelis-­‐Menton  equation     Vo  =  (Vmaz  x  [S])/(Km  +  [S])     Kinetic  parameters     Km  =  (K2  +  K3)/K1   • Michaelis  constant     • Can  be  thought  of  as  the  “off”  rates/“on”  rates   • Estimate  à  Km  =    [S]  where  Vi  =  Vmax/2   • Km  is  associated  with  Kd   o Lower  Km  is  ideal  for  an  active  enzyme     When  [S]  <<  Km,  equation  can  be  simplified  to  Vo  =  Vmax/Km.   When  [S]  >>  Km,  equation  can  be  simplified  to  Vo  =  Vmax.     Vmax   • Maximum  velocity   • Even  when  [S]  reaches  high  levels,  the  rate  maxes  out     Ki   • Inhibition  constant   • Effectiveness  of  the  inhibitor   • Found  in  the  equation  for  α  (see  more  below)     Transferase  Kinase   • Transfer  phosphate  from  ATP  to  glucose  to  produce  glucose-­‐6-­‐phosphate   • 2  important  types   o Hexokinase   § Found  in  RBCs   § Has  a  low  Km   § Always  working  at  max  velocity   o Glucokinase   § Found  in  the  liver   § Has  a  higher  Km   § Only  working  when  glucose  concentrations  are  high   • Slow  in  fasted  stated   • Speed  up  in  fed  state     Estimate  Vmax  and  Km  from  Michaelis-­‐Menton  and  Lineweaver-­‐Burk  plot     Michaelis-­‐Menton   • Vmax  =  where  curve  flattens   • Km  =  [S]  where  Vi  =  Vmax/2     Lineweaver-­‐Burk   • Double  reciprocal  of  M-­‐M  equation…  1/Vo  =  (Km/Vmax)(1/[S])  +  (1/Vmax)   o Look  familiar?  y  =  mx  +  b   o Vmax  =  y-­‐intercept   o Km/Vmax  =  slope     Types  of  reversible  inhibition     Competitive  inhibition   • Inhibitor  “competes”  with  substrate  for  active  site   o Resembling  substrate,  transition  state,  or  product   • Inhibitor  can  be  outcompeted  if  [S]  is  high  enough   • Vmax  remains  the  same,  Km  increases   o Lines  intercept  will  always  intercept  at  y-­‐axis   • Changes  by  a  factor  of  α   o α  =  1  +  ([I]/Ki)   o Vo  =  (Vmaz  x  [S])/(αKm  +  [S])   o 1/Vo  =  (αKm/Vmax)(1/[S])  +  (1/Vmax)   • Example:  Statins   o Inhibits  HMG-­‐CoA  reductase  –  controls  cholesterol  production  in  liver   o Resembles  mevalonate  –  product  of  HMG-­‐CoA  reductase   o Used  to  lower  cholesterol  levels     Uncompetitive  inhibition   • Binds  to  ES  complex,  not  at  active  site   • Usually  changes  the  conformation  of  the  active  site   • Vmax  decreases,  Km  remains  the  same   o Lines  are  always  parallel   • Changes  by  a  factor  of  α   o α’  =  1  +  ([I]/Ki’)   o Vo  =  (Vmaz  x  [S])/(Km  +  α’[S])   § Really  high  [S]  à  Vmax/   o 1/Vo  =  (Km/Vmax)(1/[S])  +  (α’/Vmax)     Mixed  (noncompetitive)  inhibition   • May  bind  to  either  the  enzyme  or  the  ES  complex   • Mixture  of  properties  from  competitive  and  uncompetitive   o Pure  noncompetitive:  inhibitor  has  the  same  affinity  for  enzyme  and  ES   complex;  Ki  =  Ki’   • Vmax  decreases,  Km  may  or  may  not  change   o Lines  will  intercept  to  the  left  of  y-­‐axis   o Pure  à  lines  will  intercept  on  the  x-­‐axis   • Changes  by  α  and  α’   o Vo  =  (Vmaz  x  [S])/(αKm  +  α’[S])   § Really  high  [S]  à  Vmax/   o 1/Vo  =  (αKm/Vmax)(1/[S])  +  (α’/Vmax)     Allosteric  activation/inactivation   • Hemoallosteric:  exhibit  cooperative  substrate  binding   • Heteroallosteric:  exhibit  cooperative  substrate  binding  and  respond  to  regulators   that  bind  to  regulatory  sites   • Taut  vs.  relaxed  state     Modificaiton   • ATP,  ADP,  and  AMP  allosteric  modifiers   o Good  indicators  of  cell’s  energy  state   • Reversible  covalent  modification:  allows  rapid  activation/inactivation  of   regulatory  proteins  à  coordinated  responses     Glycogen  Phosphorylase   • Catalyzes  first  step  in  glycogenolysis   • Has  both  allosteric  effector  and  reversible  covalent   o Activated  when…   § AMP  binds  =  low  in  energy   § Phosphorylation,  stimulated  by  adrenaline  =  extra  work     Control  of  metabolic  pathways     Specific  proteins   • Kinase   o Phosphorylation  à  activate/inactivate   o May  be  dedicated:  only  act  on  one  type  of  protein   o Or  act  on  many  types  (ex:  PKA,  PKB,  PKC)   • Calmodulin   o Protein-­‐protein  interaction  à  conformational  change  which  will   activate/inactivate  other  proteins   o Calmodulin  activated  after  binding  Ca2+  and  activated  other  enzymes   o Ex:  Glycogen  phosphorylase  activated  by  calmodulin,  thus  is  stimulated   by  increase  in  Ca2+  à  glycogenolysis   • G-­‐proteins   o Protein-­‐protein  interaction   o GTP  binds  to  G-­‐protein  to  activate   o Activated  G-­‐protein  can  act  on  target  proteins   • Proteolytic  cleavage   o Produce  inactive  proteins  =  zymogen   o Zymogen  is  cleaved  and  then  activated   o Ex:  chymotrypsin  is  produced  in  pancreas,  activated  one  it  enters   intestine     General  regulation   • Feedback  inhibition:  inhibition  of  early  reaction  by  later  product   • Feedforward  activation:  activation  of  later  reaction  by  early  product   • Counterregulation:  regulation  by  another  pathway   • Compartmentation:  enzymes  have  compartments/organelles  to  control   substrate  levels     Important  steps  of  metabolic  pathways   • Rate-­‐limiting  step:  slowest  step;  generally  irreversible   • Committed  step:  first  irreversible  pathway  unique  to  pathway     Chapter  13:  Synthesis  of  DNA     Basics  of  DNA  replication   • Semiconservative   • Synthesized  by  DNA  Pol  from  5’  to  3’   o Need  3’  OH  to  bind  to  5’  Phosphate   o Leading  vs.  lagging  strands   • Eukaryotes   o Multiple  origins,  replication  bubbles  eventually  merge   • Prokaryotes   o Circular  DNA  à  single  origin     Properties  of  prokaryotic  polymerases   • Pol  1   o Removal  of  RNA  primer  and  filling  in  the  gap   § May  work  with  RNAse  H  to  remove  primer   o DNA  Repair   • Pol  2   o DNA  Repair  –  can  bypass  damaged  region   • Pol  3   o Replication;  synthesis  of  DNA     Properties  of  eukaryotic  polymerases   • Pol  α   o Replication  –  helps  primase  create  RNA  primer   o DNA  repair   • Pol  δ   o Replication  –  synthesis  of  lagging  strand   o DNA  repair   • Pol  ε   o Replication  –  synthesis  of  leading  strand   o DNA  repair     Other  major  proteins   • Primase:  synthesizes  RNA  primers   • Helicase:  separate  parental  strands   • SSB:  prevent  stands  from  re-­‐associating   • Topoisomerase:  can  break  and  rejoin  phosphodiester  bonds  à  relieve   supercoiling   • Enzymes  that  remove  primers   o RNAse  H:  hydrolyzes  RNA   o Flap  endonuclease  1  (FEN1):  recognizes  “flap  near  5’  end  of  primer   • DNA  ligase:  joins  Okazaki  fragments   • Proliferating  cell  nuclear  antigen  (PCNA):  can  bind  to  many  proteins  at  the   replication  fork;  coordinates  proteins     Telomeres  and  telomerase     Telomerase   • Prevent  chromosome  shortening  by  adding  DNA  to  telomeres   • Structure   o Protein  portion   o RNA  template   • Telomeres  are  associated  with  aging   o Mutagens  and  carcinogens  (ex:  smoking  and  UV  light)  can  also  contribute   to  aging  à  damage  DNA  by  distorting  structure   § UV  light  causes  thymine  dimers   § Smoke  causes  benzopyrene  to  disrupt  G/C  H-­‐bonding  by   covalently  attaching  to  G     DNA  Repair     Base  Excision  Repair   • Damage  to  single  base   • Glycosylase  cleaves  glycosidic  bonds  between  altered  base  and  sugar  at  AP  site     Nucleotide  Excision  Repair   • Bulky  DNA  distortions/lesions   o Thymine  dimers   o Benzopyrene   • Repair  endonucleases  cleave  distorted  chain   • Xeroderma  Pigmentosum     Mismatch  Repair   • Mismatched  bases   • Usually  fixed  during  replication   • Post-­‐replicational  à  replace  unmethylated  daughter  strand     Genetic  Rearrangement   • Double  stranded  DNA  breaks   o Translocations   o Chromosomal  rearrangement   • Recombination:  homologous  chromosomes  exchange  information   o Endonuclease  creates  nicks   o Free  3’  ends  switch  à  ligation   o Form  X  structure  (holliday  complex)  and  can  migrate   § Structure  is  cleaved  to  produce  final  recombinant     Life  cycle  of  a  retrovirus   • Enter  cell  with  RNA  and  reverse  transcriptase   • Reverse  transcriptase  decodes  the  RNA  into  double  stranded  DNA  (cDNA)   • Integrase  cleaves  3’  ends  of  viral  DNA  and  inserts  it  into  cellular  DNA   • Undergoes  transcription  and  translation  à  send  off  viral  proteins  to  other  cells     Drugs  used  to  treat  AIDS   • ZDV:  analog  of  deoxythiymidine   o Terminates  DNA  synthesis  because  there  is  not  a  free  3’  OH  group   • Dideoxynucleoside     Chapter  14:  Transcription     Eukaryotic  RNA  polymerases   • RNA  Pol  1  à  rRNA   • RNA  Pol  2  à  mRNA  and  miRNA   • RNA  Pol  3  à  tRNA  and  other  small  RNAs     RNA  polymerase  function   • Polymerization  of  nucleotides  5’  à  3’     • Base  pair  with  template  strand,  other  strand  is  coding  strand   o Coding  strand  and  new  mRNA       Antibiotic  sensitivity  (prokaryotes)   • Rifampicin   o Yes   o Inhibits  initiation  step   • Actinomycin   o Yes   o Inhibits  elongation  step   • α-­‐Amanitin   o Not  effective  for  prokaryotes   o Inhibitor  of  eukaryotic  RNA  Pol  2,  lethal  to  humans     Promoters   • Binding  of  RNA  polymerase  and  initiation  of  transcription   • Many  consensus  sequences   o The  more  consensus  sequences  à  the  stronger  the  promoter   o Prokaryotes   § Common  sequence  TATAAT  =  TATA  box     • Recognized  by  σ   • In  12.5%  of  promoters   § TTGACA  sequence   • Where  RNA  Pol  binds   o Eukaryotes   § PPE   § BRE   § Inr   § MTE   § DPE   • Repressors  bind  to  the  operator  and  prevent  RNA  Pol  binding   • Activators  bind  to  spot  >  -­‐35  and  facilitate  RNA  Pol  binding     Eukaryotic  promoter   1. Enhancer   2. Promoter  proximal  elements:  other  regulatory  parts;  gene-­‐specific  (-­‐100   to  -­‐200)   • Sites  for  TFs  to  bind   3. BRE:  TF2B  recognition  element   • G/C  rich   • In  15%  of  promoters   4. TATA  box  (-­‐10)   5. Cap  site   6. Initiator  (+1)   7. MTE:  motif  ten  element  (-­‐10)   8. DPE:  downstream  promoter  element   • In  15%  of  promoters     Prokaryotic  promoter   1. TTGACA  sequence  (-­‐35)   2. TATA  box  (-­‐10)       Transcription     Prokaryotes   • Form  promoter  complex,  recognize  promoter  through  σ-­‐factor   • Open  10-­‐20  base  pairs  of  DNA   • Form  first  few  bonds   • Release  σ-­‐factor  when  chain  is  10  bases  long   • Translocation  of  RNA  Pol  to  continue  transcription   • Termination     *  process  for  eukaryotes  is  similar  but  more  complex     Formation  of  transcription  apparatus   1. TBP  (component  of  TF2  D  along  with  other  co-­‐activators)  binds  to  TATA  box   2. TF2  A  and  B  bind  to  TBP   3. RNA  Pol  binds   4. Then  TF2  E,  F,  and  H  bind  à  complex  may  now  transcribe     Cap  and  tail     5’  cap   • Stabilizes  mRNA,  helps  mRNA  bind  to  ribosome   • Co-­‐transcriptional  modification   • Steps   1. Triphosphate  on  5’  end  loses  a  Phosphate   2. Diphosphate  attacks  GTP  to  form  5’-­‐5’  linkage   3. N-­‐7  nitrogen  of  terminal  guanine  is  methylated  by  SAM  to  form  Cap  0   à  may  be  additionally  methylated  to  form  Cap  1  or  2     3’  polyA  tail   • Stabilize  mRNA   • Post-­‐transcriptional   • Steps   1. Endonuclease  recognizes  AAUAAA  sequence  and  cleaves  after   2. PolyA  polymerase  adds  250  residues  to  3’  end     Splicing  introns   • Cleavage  and  ligation  occurs  in  spliceosome,  which  contains  snRNPs   • Slice  portion  between  GU  (5’  end)  and  AG  (3’  end)   o 3’  end  of  A  and  Phosphate  of  G  covalently  bind     Other  RNA     rRNA   • About  1000  genes  in  nucleolus   • Large  45S  subunit  coded  by  RNA  Pol  1  inside  nucleolus   o Generate  granular  regions  of  nucleolus   o Lots  of  processing     • Small  produced  by  RNA  Pol  3  outside  nucleolus  à  migrates  to  nucleolus     tRNA   • Synthesized  by  RNA  Pol  3   • Precursor  à  modifications/cleavage  by  RNAse  P   • Mature  tRNA  migrates  to  cytoplasm     Distribution  of  repetitivity   • 64%  are  unique   o Only  about  10%  is  actually  made  into  product   • 25%  are  moderately  repetitive   • 10%  are  highly  repetitive       Exam 3 Review    Chapter 22 Carbohydrate Structure & Intro to Glycolysis    Objectives  1. Identify linear and cyclic carbohydrate structures, as well as epimers, anomers, substituted  sugars, and oxidized or reduced sugars.    General formula Cn(H2O)n   ● Glucose C6(H2O)6 == C6H12C6   ○ hydrated carbon chain   ● Polyhydroxy aldehydes or ketones: all of the carbons have a hydroxyl group and one carbon has  a ketone  ○ Aldoses: an aldehyde with a terminal ketone  ○ Ketoses: ketone with a carbonyl on C2   ● Saccharides or sugars   ● # of carbons 3‐7, prefix aka 5 = pent    Chirals   ● Epimers: stereoisomers with multiple chiral  centers that differ in the chirality at only one  carbon  ● Enantiomers: mirror image structures   ○ D ‐ the OH projects to the right   ○ L ‐ the OH projects to the left   ■ Bottom OH on right = D, bottom OH on left = L   ● Cyclic structures ‐ form in aqueous solutions if long enough   ○ Generates a new stereocenter at the anomeric carbon (C‐1)   ○ Anomer: type of epimer, one of two stereoisomers of a cyclic saccharide differs in  configuration at the anomeric carbon(C‐1); alpha vs beta   ○ Cyclization is reversible  ■ Can form two different anomers   ● B‐anomer : OH group above plane of ring : cis   ● a‐anomer : OH group below plane of ring : trans  ○ Flipped for initials, B ‐ above A‐ below   ○ Always true for D sugars   ■ Interconversion between A and B anomers called mutarotation catalyzed by  mutarotase enzymes   ○ Cyclic monosaccharides:   ■ 6 membered rings = pyranoses   ■ 5 = furanoses   ● Sugar derivatives:   ○ Common substitutes: phosphates, sulfates, aminos, N‐acetyl groups   ■ Glucose 6‐Phosphate: glucose → G‐6‐P ; P added at C‐6 OH, catalyzed by  hexokinase(first enzyme in glycolytic pathway) with Mg2+, ATP‐> ADP,  phosphorylation  ■ N‐acetyl‐B‐D‐glucosamine: OH of C‐2 replaced with Nitrogen (make amine),  acetylated,   ■ Glycosaminoglycan: epimer at C‐4 = galactose, sulfated, ‐O3SO at C4,   ○ Oxidized to acids, reduced to deoxy sugars or sugar alcohols   ■ B‐D‐glucuronate: oxidize terminal hydroxyl to carboxylic acid  ■ D‐ gluconate: oxidize C1 hydroxyl group to carboxylic acid   ■ D‐ sorbitol: reduce aldehyde to an alcohol at terminal end  ● not metabolized in the human body but tastes sweet ‐ processed foods  and sugar free gum   ■ Deoxyribose: OH → H     2. Draw Hayworth projections of the two anomeric forms of glucose, galactose, mannose, and  fructose.    Hayworth projections:   ● Fructose is the keto isomer of glucose at C‐2         3. Draw glycosidic bonds and recognize the structures (and know dietary sources/functions) of  sucrose, lactose, starch, glycogen, and cellulose.    Glycosidic Bonds ‐ connect monosaccharides to form polysaccharides   ● Take OH of anomeric carbon → link to another OH group of another sugar   ○ Condensation reaction → product of H2O and bond between sugars   ○ 2 ethers now attached to anomeric carbon ‐ can no longer break open the ring,  locked in, stuck, cannot mutarotate   ○ B(1 → 4) : link C‐1 (anomeric carbon) or one sugar to C‐4 of another      Structures   Dietary Sources   Functions   Sucrose   table sugar       glucose a(1 ← → 2) fructose   *double arrow because the link is  between two anomeric carbons   Lactose   milk sugar       galactose B(1 → 4) glucose   Starch  less extensively branched than  fuel storage in    glycogen   plants   Glycogen   fuel storage in    animals     large polymers   >10^5 glucose molecules   glucopyranose linked a(1 → 4)           branched a(1 → 6)   Cellulose   plant structural polymer   grass and twigs  vertebrates lack digestive  only B(1→ 4) linkages   ‐ we can’t  enzymes (cellulases) to  digest it  cleave these linkages;  acts as fiber in  vertebrates like cows are  human   rumbinantes ‐‐ have  bacteria that digest the  cellulose in their stomachs     4. Distinguish between reducing and non‐reducing sugars.    Reducing sugars  ● Aldehydes can be oxidized to a carboxylic acid  ○ The oxidizing agent is reduced  ■ Reducing sugar test: use an oxidant like Cu+2 that changes color when it is  reduced, detects sugars in the urine  ● Must be a linear carb  ○ Any aldose (some ketoses ‐ keto can isomerize to aldehyde) that can linearise is called a  reducing sugar   ● Must have an open hemi‐acetal group ‐ aka a free anomeric carbon     Non reducing sugar  ● Add a glycosidic bond in a reducing sugar that locks the anomeric carbon → forms a  non‐reducing sugar     Lactose = reducing sugar (reducing end is glucose, non‐reducing end is galactose)  Sucrose = non‐reducing sugar     5. Recite the intermediates, enzymes, and cofactors used in the glycolytic pathway.    Glycolysis  ● Anaerobic   ○ Glucose → Pyruvate  (ByProducts: NADH, ATP) →  Lactate  ● Oxygen present  ○ Pyruvate *→ Acetyl CoA (BP:  NADH) → TCA   ■ * Pyruvate  dehydrogenase complex     Glycolytic Pathway   ● Phase I: Preparative/Investing Phase   ○ Glucose + 2ATP → Fructose  1,6‐bis‐P   ● Phase II: ATP‐Generating phase   ○ F 1,6‐BP → 2 triose phosphate +  (NAD+, ADP, Pi) → 2 Pyruvate  (2 NADH, 2ATP, 2ATP)   ● Net Reaction: Glucose + 2 NAD+ + 2Pi +  2 ADP → 2 pyruvate + 2 NADH +4H‐  +2ATP +2H2O   ○ 1 Glucose | 2 Pyruvate     Reactions of Glycolysis   ● Glucose/hexokinase → Glucose  6‐phosphate   ○ Irreversible  ○ Phosphorylation   ● G6P ← phosphoglucose isomerase → Fructose 6‐phosphate   ● F6P (a ketone) + phosphofructokinase‐1 (PFK‐1) → Fructose 1,6‐Bisphosphate   ○ Committed step   ○ Irreversible   ○ Phosphorylation   ● F1,6BP + aldolase (aldol cleavage) →   ○ Produces dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3‐phosphate (GAP)  ○ Isomerized by triose phosphate isomerase → reaction driven by equilibrium   ● GAP ← glyceraldehyde 3‐phosphate dehydrogenase → 1,3‐Bisphosphoglycerate (1,3 BPG)  +NADH  ○  1,3BPG has high E acyl‐P  ● 1,3 BPG + ADP + phosphoglycerate kinase → 3‐Phosphoglycerate (3PG) +ATP   ● 3PG + phosphoglyceromutase → 2‐phosphoglycerate (2PG)   ● 2PG enolase → H2O + Phosphoenol‐pyruvate (PEP)   ○ PEP has high E enolic P   ○ Dehydration reaction   ● PEP + ADP + pyruvate kinase → ATP + pyruvate  ○ Irreversible  ○ Important in gluconeogenesis regulation   ○ Why do long chain FA’s inhibit pyruvate kinase?      Chapter 23 Transport, Activation, and B‐oxidation of Fatty Acids    Objectives  1. Describe how fatty acids are transported in the serum and from the serum into cells.    Transportation of FAs  ● In Serum: insoluble in water so bound to serum albumin (binds up to 6 FA chains)   ○ Serum albumin can also bind some hormones/drugs   ● Into cell:  saturable binding proteins, free diffusion   ● In cell: fatty‐acid binding protein that facilitates transport into mitochondria/ER/Perox     2. Draw a diagram showing the intracellular activation and mitochondrial transport of fatty acids,  including names of key enzymes and transporters, and describe how the transport process is  regulated.    Intracellular Activation ‐‐ to acyl‐CoA derivatives * catalyzed by acyl CoA synthetase   ● Acyl CoA synthetase ‐ has 4 isoforms each with specific affinity for various FAs in different  membranes   ● Generates AMP and PPi hydrolyzed ‐ uses equiv of 2 ATP   ○ Hydrolysis of PPi has negative delta G and drives the rxn forward   ● Fates:   ○ Energy → B‐oxidation ketogenesis → mitochondria and peroxisomes   ○ Membrane lipids → phospholipids sphingolipids → ER   ○ Storage → triacylglycerols → ER     Mitochondrial transport of FAs   ● Key Enzymes, transporters, regulation  ○ Carnitine: forms fatty acylcarnitine   ■ CPT I or CPT II ‐ primary carnitine deficiency ‐ defect in transport of carnitine  into muscle cripples FA metabolism  ● Carnitine is found in many dietary sources and can be synthesized from  lysine so a dietary deficiency is rare   ○ Basically if there is a deficiency it’s CPT I/II   ■ CPT I on OMM  ● Carnitine palmitoyltransferase I   ● Adds carnitine and removes CoA   ● CPT I deficiency → elevated FA‐CoA in serum   ■ CPT II on IMM  ● Carnitine palmitoyltransferase II   ● Removes carnitine and adds CoA   ○ Fatty acyl CoA → B‐oxidation   ● CPT II deficiency → the acylcarnitine will build up and leak back into the  serum causing elevated blood acylcarnitine levels    ■ Carnitine acylcarnitine translocase on IMM   ● Antiport   ??


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