What is the flow of information through the cell?

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What is the flow of information through the cell?
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Double helix - antiparallel polymers
Major groove Minor groove
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5 3
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Purine Pyrimidine
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(No Transcript)
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06_12_asymmetrical.jpg
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(No Transcript)
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• Transcription
• dsDNA template
• Nucleotides (ACGU) make ssRNA
• Need to separate strands.
• Nucleotides added to free 3 OH (5?3)

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Classes of RNA
mRNA
rRNA
tRNA
also snRNA and microRNA
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Prokaryotes
untranslated regions 5 UTR
3 UTR
coding sequence
promoter (not transcribed)
DNA
mRNA
RNA Polymerase Ribosome
polypeptide
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Eukaryotes
untranslated regions 5 URT
3 UTR
promoter (not transcribed)
coding sequence
DNA
pre mRNA
mRNA
RNA Polymerase Ribosome
polypeptide
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Bacterial Promoter Elements

• Transcription start 1
• Consensus sequence 35 TTGACA, recognized by
  ?
• Pribnow box -10, TATAAT determines 1
• Terminator sequence where polymerase stops

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(No Transcript)
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Initiation of transcription in prokaryotes
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Initiation of eukaryotic transcription by RNA
Pol II (mRNA) TF transcription factor (compare
with prokaryotic sigma factor)
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• Eukaryotic mRNA
• 5 cap,
• 5 UTR
• coding region
• 3 UTR
• 3 poly-A tail

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mRNA processing in Eukaryotes 5 cap
added Remove 3 end Poly-A tail
added Introns removed Exons joined
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Gene cloning - making lots of copies...
1. Make a library of small pieces of DNA (2
types) 2. Find the one piece you want 3. Insert
it into a vector 4. Grow it in a new organism
(bacteria, euk. cells)
Isolate DNA, fragment with RE
Isolate mRNA, convert to cDNA with reverse
transcriptase
Genomic library
cDNA library
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(No Transcript)
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07_37_Protein.produc.jpg
Overview of gene expression in eukaryotes
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07_28_ribosome.jpg
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07_26_2_adaptors.jpg
Two adapters link an amino acid to a codon
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07_32_initiation.jpg
Intiation of translation in Eukaryotes
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07_33_mRNA.encode.jpg
Intiation of translation in Prokaryotes
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07_30_3_step_cycle.jpg
Elongation of proteins
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5
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07_34_stop codon.jpg
Termination of translation
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Mutations

• Frameshift Adding or removing 1 or 2 nucleotides
  results in changes the reading frame from that
  point on.
• Nonsense Changing an amino acid codon to a stop
  codon results in truncated proteins
• Missense Changing an amino acid codon to one
  encoding a different amino acid - effect depends
  on type of amino acid and where in the protein.

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(No Transcript)
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04_03_20 amino acids.jpg
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Side chains interact via all of the noncovalent
bonds
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Primary structure (1) of a protein Arabidopsis
?-glucosidase (single letter codes) MSSLHWFPNIFIV
VVVFFSLRSSQVVLEEEESTVVGYGYVVRSVGVDSNRQVLTAKLDLIKPS
SVYAPDIKSLNLHVSLETSERLRIRITDSSQQRWEIPETVIPRAGNHSPR
RFSTEEDGGNSPENNFLADPSSDLVFTLHNTTPFGFSVSRRSSGDILFDT
SPDSSDSNTYFIFKDQFLQLSSALPENRSNLYGIGEHTKRSFRLIPGETM
TLWNADTGSENPDVNLYGSHPFYMDVRGSKGNEEAGTTHGVLLLNSNGMD
VKYEGHRITYNVIGGVIDLYVFAGPSPEMVMNQYTELIGRPAPMPYWSFG
FHQCRYGYKNVSDLEYVVDGYAKAGIPLEVMWTDIDYMDGYKDFTLDPVN
FPEDKMQSFVDTLHKNGQKYVLILDPGIGVDSSYGTYNRGMEADVFIKRN
GEPYLGEVWPGKVYFPDFLNPAAATFWSNEIKMFQEILPLDGLWIDMNEL
SNFITSPLSSGSSLDDPPYKINNSGDKRPINNKTVPATSIHFGNISEYDA
HNLYGLLEAKATHQAVVDITGKRPFILSRSTFVSSGKYTAHWTGDNAAKW
EDLAYSIPGILNFGLFGIPMVGADICGFSHDTTEELCRRWIQLGAFYPFA
RDHSSLGTARQELYLWDSVASSARKVLGLRMRLLPHLYTLMYEAHVSGNP
IARPLFFSFPQDTKTYEIDSQFLIGKSIMVSPALKQGAVAVDAYFPAGNW
FDLFNYSFAVGGDSGKHVRLDTPADHVNVHVREGSIVAMQGEALTTRDAR
KTPYQLLVVASRLENISGELFLDDGENLRMGAGGGNRDWTLVKFRCYVTG
KSVVLRSEVVNPEYASKMKWSIGKVTFVGFENVENVKTYEVRTSERLRSP
RISLIKTVSDNDDPRFLSVEVSKLSLLVGKKFEMRLRLT
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Secondary structure (2) ?-helix H-bonds
between CO and N-H of backbone. (No R-groups
involved)
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Secondary structure ?-sheet H-bonds between
CO and N-H of backbone. (No R-groups involved)
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Tertiary structure - the entire polypeptide
?-helix
?-sheet
loops and turns disulfide bridge
ribonuclease
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Quaternary structure - multiple subunits
e.g. hemoglobin
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04_20_protein domains.jpg
lactic (lactate) dehydrogenase
immunoglobulin light chain
cytochrome b562
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Domains - discrete modules within tertiary
structure that fold independently and have a
specific function. 4 domains of phospholipase C
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Motif - a recurring substructure ?/? barrel
e.g. ?-amylase
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Motif - a recurring substructure coiled coil
e.g. myosin
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How do proteins get to their folded state?
unfolded
native conformation
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04_21_Serine proteases.jpg
Proteins with different functions may have
similar shape - members of a family with a common
ancestor.
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04_22_protein subunit.jpg