Chapter 810 Questions

1
Chapter 8-10 Questions

• Chapter 8
• 1, 2, 4, 5-10, 12-15, 18-24, 34-36
• Chapter 9
• 1-6, 9. 10, 12, 14-20, 21, 25, 29, 30, 43
• Chapter 10
• 1, 4, 5, 15, 21, 23, 49

2
Can you draw/diagram

• Thymine diamer
• GC or AT H-bonding
• Tautomerization of bases
• Polymerization of nucleotides (5-3 addition)
• mRNA synthesis from template/coding strands

3

• Chapter 9
• Biosynthesis of Nucleic Acids Replication

4
Central Dogma of Molecular Biology
Transcription
Translation
PROTEIN
DNA
RNA
Replication
5
Nucleotides and Nucleic Acids

• Replication Terms
• Leading Lagging Strands
• Primase
• Polymerase III Polymerase d
• RNase H, Ligase
• Okazaki fragments (10x longer in Prokaryotes)
• Replisome 2 polymerases leading lagging
• Gyrases/topoisomerase helicases
• SSB Single-Stranded Binding Proteins
• Teleomerase/reverse transcriptase - CCCUAA

6
Nucleotides and Nucleic Acids

• Repair Terms
• 3?5 Exonuclease - repair
• 5?3 Exonuclease primer repl.
• Why is Repair Needed?
• Mismatch repair during synthesis before
  methylation Pol III
• Chemical mod./oxidation - glycosylase apurinic
  endonuclease Pol I
• UV damage pyrimidine diamer repair Pol I
• Recombinant/Crossover Repair

7

• Chapter 10
• Transcription of the Genetic Code The
  Biosynthesis of RNA

8
Points to Understand

• Transcription vs Replication
• Prokaryotic
• Eukaryotic
• DNA binding proteins regulation of Txn
• Lac Operon as a model
• DNA-protein Interactions

9
RNA Synthesis

• DNA-dependent-RNA polymerase
• A, G, U, C and Mg
• No primer needed
• 5?3 synthesis with ppp _at_ 5
• Reads DNA in 3 ?5 direction
• Template/antisense/- strand
• Coding/sense/ strand

10
Prokaryote RNA Synthesis

• RNA Polymerase Holoenzyme
• Promotor recognition s-subunit binding
• -40 to -60 UP promotor
• -35 region core promotor (GC rich)
• -10 region Pribnow box (TA rich)
• 1 TSS - Txn start
• pppA most often first
• Topoisomerases before and after
• Termination
• Intrinsic GC-rich inverted repeats and U series

11
Prokaryotic RNA Synthesis
Topoisomerase for overwound DNA
Topoisomerase for underwound DNA
5
3
p
5
3
p
RNA Polymerase ? s Opens complex (melting)
a-a ß-ß SS Binding
ppp
5
? factor termination when catches polymerase
at hairpin
Different s units may attach to RNA pol to
initiate promotion at different sites
12
Prokaryotic RNA Synthesis
REGULATION Initiation Elongation Attenuation
Secondary RNA structures Termination Encoded
sites AAAGGCUCCUUUUGGAGCCUUUUUUUU
13
Prokaryotic RNA Synthesis

• Procaryote Regulation the lac operon (lactose
  gal-glu)
• Repressor, Promotor, Operator, ß-galactosidase,
  permease, transacetylase
• Negative regulation constitutive repressor
  (tetramer) _at_ O blocked by Inducerlactose
• Catabolite repression catabolite activator
  protein cAMP required for good Pol binding to
  promotor (enhancer)
• Secondary RNA structures hairpin loops

lacI
O
LacZ
lacY
lacA
Plac
14
Eukaryotic RNA Synthesis

• Pol I (rRNA), Pol II (mRNA), Pol III (tRNA)
• Pol II 12 subunits binding regulated by
• Upstream Elements GC box (GGGCGG) (-40) and CAAT
  (GGCCAATCT) (-100) box
• TATA box (TATAA) (-25)
• YYCAYYYYY TSS (1)
• Downstream regulator
• Transcription factors 6 general (GTFs ABDEFH)
• Pol CTD (C-terminal domain) phosphorylation
  activates POL

15
Eukaryotic RNA Synthesis

• Enhancers, Silencers Response Elements
• DNA Binding Motifs
• Helix-turn-helix 20 aa helices in major
  groove often diamers Gln-A Arg-G
• Zinc Fingers 30 aa C,C,H,H bind Zn below 12 aa
  finger
• Basic Region-Leucine Zipper K, R, H L every 7
  residues
• PROTEIN Binding Domains
• Acidic Domain
• Gln-rich Domain (39 out of 143)
• Pro-rich Domain (19 out of 84)

16
Helical Wheel Diagram
b
a
c
d
e
f
g
e
b
a
f
d
c
Leu
17
Post-Transcriptional Modifications

• tRNA, rRNA
• Next Chapter - Tln
• mRNA
• Eukaryotic
• 5-methyl G cap, 3-poly A (100-200)
• Eucaryotic
• Splicing by snRNP (snurps) in nucleus 50S
  particule spliceosome
• Alternate Splicing Ab diversity enzyme
  isomers Tau protein

18
mRNA SPLICING

• Alternate Splicing
• Isozymes
• Antibodies

AGGU
AGG
INTRON
EXON
Lariat structure 2 OH of A starts nucleophilic
attack
A