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biochem 2 study guide 4

by: ChasePrater

biochem 2 study guide 4 4510

Marketplace > Middle Tennessee State University > 4510 > biochem 2 study guide 4
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50 questions over test 4 material
Biochemistry II
Dr. Ooi
Study Guide
biochemistry, Nuceotide, DNA, metabolism
50 ?




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This 4 page Study Guide was uploaded by ChasePrater on Saturday April 23, 2016. The Study Guide belongs to 4510 at Middle Tennessee State University taught by Dr. Ooi in Spring 2016. Since its upload, it has received 18 views.


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Date Created: 04/23/16
Exam  4  Study  Guide   1. what  is  the  difference  between  a  nucleotide  and  nucleoside?   -­‐ nucleotides  have  nitrogenous  base,  a  sugar,  and  a  phosphate  group   -­‐ nucleosides  only  have  sugar  and  nitrogenous  base   2. How  can  tautormerization  be  a  bad  thing?   -­‐ if  it  happens  right  before  replication  it  can  mess  up  base  pairing   3. what  are  the  2  forms  of  uracil  and  guanine?   -­‐ Uracil:  Lactam  (normal  form)  and  Lactim  form   -­‐ Guanine:  Keto  (normal  form)  and  enol  form   4. What  are  the  functions  of  mononucleotides  and  polynucleotides?   -­‐ Mononucleotides:  regulate  metabolism  (  cAMP  and  cGMP),  source  of   chemical  energy     -­‐ Polynucleotides:  building  blocks  of  nucleic  acids  ribose  and  deoxyribose.   5. When  is  ATP  and  GTP  used?   -­‐ ATP  is  used  in  majority  of  metabolic  processes   -­‐ GTP  is  used  in  protein  synthesis   6. What  is  a  function  of  the  base  portion  of  nucleotides?   -­‐ signaling   7. Is  there  a  phosphate  group  at  both  ends  of  a  strand  of  DNA  or  RNA?   -­‐ No,  only  the  5’  end  has  a  phosphate  group,  the  3’  end  is  a  hydroxyl  group   of  the  sugar   8. What  are  the  3  conformations  of  DNA,  and  what  is  special  about  each?   -­‐ A  conformation:  base  pairs  are  not  perpendicular  to  the  axis  of  the  helix,   larger  diameter  of  26A,  and  11  base  pairs  per  turn.  Formed  from  B-­‐DNA   in  dehydrated  conditions.     -­‐ B  conformation:  most  common  form;  bases  are  perpendicular  towards   axis  of  helix,  10  BP  per  turn,  20A  diameter.   -­‐ Z  conformation:  Left  handed,  12  BP  per  turn,  narrow  diameter  of  18A,   relevance  is  unknown.   9. What  is  a  palindrome,  and  how  do  they  affect  DNA  structure?   -­‐ they  are  inverted  repeats  in  the  sequence,  and  they  cause  cruciform   tertiary  structure,  which  is  less  stable  than  normal  DNA.   10  .  What  are  Topoisomerases?   -­‐ enzymes  that  change  the  topological  state  of  DNA,  and  control   supercoiling     -­‐ Topoisomerase  I:  (nicking  closing  enzyme)  breaks  1  strand     -­‐ Topoisomerase  II:  cleaves  both  strands  of  DNA,  and  require  ATP.     -­‐   Eukaryotes:  relax  neg  and  positively  supercoiled  DNA.   -­‐   Prokaryotes:  relax  only  negatively  supercoiled  DNA   -­‐ Gyrases:  introduces  negatively  supercoiling  in  circular  DNA.     10.What  is  a  centromere?   -­‐ constricted  region  on  a  chromosome  that  attches  to  cell’s  spindle  fibers  in   division.  They  are  rich  in  As  and  Ts   11.  What  is  a  Telomer?   -­‐ CCCA  repetitive  regions  of  DNA  that  occur  at  the  end  of  chromosomes   that  prevent  unraveling  of  DNA   12.  What  are  Histones?     -­‐  small  basic  proteins,  they  are  rich  in  lysine.     -­‐ 5    classes:  H1,  H2A,  H2B,  H3,  and  H4.  (2  copies  of  each  in  each   nucleosome,  but  only  one  H!  per  nucleosome)   -­‐ H1  is  on  the  outside  of  the  wrap.   -­‐ They  are  positively  charged  proteins.     -­‐ When  they  bind  to  DNA  they  form  nucleosomes,  which  have  an  octameric   structure  that  DNA  winds  around.     13.  What  is  the  hyperchromic  effect?   -­‐ As  DNA  become  denatured,  it  absorbs  40%  more  light  than  it  does  when   in  the  native  conformation.     14.  What  is  the  melting  point  of  DNA?   -­‐ The  temp  at  the  midpoint  of  the  increase  of  absorbance  on  an  Absorbance   vs.  Temperature  graph.   -­‐ This  value  depends  on  the  amount  of  G-­‐C  base  pairs,  ion  concentration,   and  pH.     -­‐ More  salt  increases  the  MP,  and  more  G-­‐C  pairs  increases  MP.   15.  How  can  DNA  renature?     -­‐  Can  partially  re-­‐nature  if  cooled  below  its  Tm  value.     -­‐  Some  regions  can  completely  re-­‐nature  if  it  is  left  at  25  degrees  C  below  its     Tm  value.   16.  How  are  nucleic  acids  stabilized?   -­‐ Base  Pairing  (  H-­‐bonds)   -­‐ Stacking  Interactions:  are  a  type  of  van  der  Waals  forces  that  result  from   the  hydrophobic  effect.  They  are  interactions  between  adjacent   nucleotides  on  the  same  strand,  and  G-­‐C  interactions  are  greater  than  A-­‐T.       -­‐ Cations  shield  neg  P  groups  on  the  backbone  and  reduce  the  electrostatic   repulsion.  Divalent  cations  like  Mg,  Mn,  and  Co  are  shielding  agents.  Mg  is   also  important  is  stabilizing  RNA.   17.    What  is  the  function  of  mRNA  and  when  is  it  synthesized?   -­‐ Made  during  DNA  transcription.     -­‐ It  carries  the  sequence  info  for  protein  synthesis.     18.  What  are  three  examples  of  intercalating/  stain  agents  used  in  DNA  purification?     -­‐  Ethidium,  proflavin,  and  acridine  orange.   19.  What  are  causes  of  spontaneous  mutations?   -­‐ Transition  mutations:  tautomerization  of  purines  causes  incorrect  base   pairing.  Trades  a  purine  for  another  purine,  or  a  pyrimidine  for  another   pyrimidine.     -­‐ Hydrolytic  Reactions:  1)  Depurination,  in  which  glycolase  cleaves  a   purine  base  off  a  sugar.  2)  Deamination  reactions     20.  What  are  external  factors  that  can  cause  mutation?   -­‐ ionizing  radiation,  xenobiotics,  alkylating  agents,  nonalkylating  agents,   and  intercalating  agents.     21.  Explain  differences  in  ionizing  radiation.   -­‐ X-­‐rays,  and  gamma  rays  can  break  strands  and  cause  cross-­‐linking.  UV   can  only  cause  cross-­‐linking.     22.  What  are  xenobiotics?   -­‐ Base  analogs  that  look  a  lot  like  nucleosides,  and  can  be  incorrectly   incorporated  into  DNA.     23.  What  bases  are  more  susceptible  to  alkylating  agents?   -­‐ Adenine  and  guanine   24.  What  can  cause  deamination?     -­‐  Nonalkylating  agents  such  as  nitrous  acid,  nitrosamine,  and  other  nitrates.     25.  How  do  intercalating  agents  work?   -­‐ They  insert  themselves  between  strands  of  DNA.   26.  Where  can  cross-­‐linkages  occur?   -­‐ between  bases  in  same  or  opposite  strands,  and  also  between  the  DNA   and  proteins  such  as  histones.     27.  What  are  the  two  types  of  substitution  mutations?     -­‐  Transition:  change  purine  for  purine  and  pyrimidine  for  pyrimidine.     -­‐  Transversion:  change  purine  for  pyrimidine  and  vice  versa>     -­‐  these  are  the  least  dangerous  mutations   28.  What  does  it  mean  to  say  that  DNA  replication  is  semiconservative?   -­‐ it  means  that  the  original  strand  of  DNA  is  made  of  two  parent  strands,   and  after  replication  there  is  two  double  helices  each  containing  1  new   daughter  strand  and  1  old  parent  strand.   29.  During  replication  the  lagging  strand  is  made  discontinuously  in  short  pieces,   that  are  these  pieces  called?       -­‐  Okazaki  fragments   30.  What  is  the  function  of  helicase?   -­‐ it  unwinds  the  DNA  by  breaking  h-­‐bonds  of  base  pairs,  it  allows  DNA   polymerase  to  get  the  single  strand  that  it  needs.   31.  What  do  DNA  binding  proteins  do?   -­‐ Binds  to  single  stranded  DNA  to  stabilize  and  prevent  renaturation.   32.  What  does  Gyrase  (Topoisomerase  II)do?     -­‐  moves  ahead  of  replication  fork  and  prevents  tangling.   33.  Which  prokaryotic  enzyme  contains  3’-­‐5’  endonuclease  activity,  and  what  does   this  activity  allow  it  to  do?     -­‐  Pol  I,  Pol  II,  &Pol  III.  It  allows  the  enzyme  to  proof-­‐read  and  correct  errors.     34.  Which  enzyme  removes  primer  and  fills  the  gaps?     -­‐  Pol  I   35.    Which  enzyme  has  the  largest  processivity?     -­‐  Pol.  III   36.  Which  eukaryotic  enzyme  initiates  replication?     -­‐  Pol-­‐alpha   37.  What  is  the  common  precursor  for  AMP  &  GMP?     -­‐  IMP   38.  What  is  the  starting  material  for  the  de  vovo  synthesis  of  Purines  and  where   does  it  come  from?     -­‐  ribose-­‐5-­‐phosphate,  and  comes  from  pentose  phosphate  pathway.   39.  Where  to  the  nitrogens  and  carbons  come  from  during  IMP  synthesis?     -­‐  Nitrogen  donors:  glycine,  aspartate,  and  glutamine.     -­‐  Carbon  donors:  bicarbonate  and  2  fumarates   40.  What  are  the  energy  carriers  for  AMP  and  GMP  synthesis?     -­‐  GTP  used  for  AMP  synthesis     -­‐  ATP  used  for  GMP  synthesis.     -­‐  This  is  one  way  levels  of  nucleotides  are  kept  equal  and  regulated.   41.  What  must  happen  before  AMP  GMP  can  be  used  in  nucleic  acids?     -­‐  they  must  be  converted  to  triphosphates.   42.  Are  Nucleoside  monophosphate  kinases  specific  or  nonspecific?     -­‐  they  are  specific  to  either  AMP  or  GMP   43.  Are  nucleoside  diphosphates  specific  or  nonspecific?     -­‐  they  are  nonspecific,  and  will  accept  purines  and  pyrimidines.   44.  How  is  Purine  synthesis  regulated?     -­‐  PRPP  synthetase  is  inhibited  by  ADP  and  GDP     -­‐  amidophosphoribosyl  transferase  has  2  regulatory  sites.  One  for  ATP,  ADP,     &  AMP.  The  other  is  for  GTP,  GDP,  &  GMP.  Maximum  inhibition  is  reached     when  both  sites  are  filled.       -­‐  Stimulated  by  PRPP   45.  What  is  the  precursor  for  CMP?     -­‐  UMP   46.  What  are  the  nitrogen  and  carbon  donors  for  pyrimidine  synthesis?     -­‐  Carbon  donors:  bicarbonate  and  aspartate     -­‐  Nitrogen  donors:  glutamine   47.  What  is  the  reducing  agent  in  the  conversion  of  ribonucleotides  to   deoxyribonucleotides?     -­‐  thioredoxin   48.  What  is  the  end  product  of  UMP,  CMP,  and  TMP  catabolism?     -­‐  UMP  &  CMP  breakdown  into  malonyl  CoA  or  acetyl  CoA     -­‐  TMP  is  broken  down  into  succinyl  CoA   49.  How  does  the  purine  nucleotide  cycle  aid  in  skeletal  muscle  metabolism?     -­‐  When  muscles  are  active  the  TCA  cycle  speeds  up.  The  nucleotide  cycle     produces  fumarate  that  can  then  enter  the  TCA  cycle.  This  shows  that     breakdown  of  nucleotides  does  not  DIRECTLY  produce  ATP.     50.  What  base  is  used  in  IMP?     -­‐  hypoxanthine                  


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