L9-11 - L8 start here Berg Tymoczko Stryer Biochemistry...

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1 1 Biochemistry Sixth Edition Chapter 4: DNA, RNA, and the Flow of Genetic Information Berg • Tymoczko • Stryer 2 The central dogma DNA mRNA Proteins Transcription Translation Replication DNA mRNA Proteins Transcription Translation Replication 1.) The old view 2.) The new view Functional RNAs: splicing, regulation, editing, catalysis, gene silencing (ribozyme, introns, miRNA, gRNA, riboswitches, rRNA, tmRNA, U6RNA. ..) All functions No function (passive intermediary) Most functions Reverse Transcription 3 Gene expression in action Zinc-finger protein dsDNA (the gene) •A Zn-finger protein helps ‘express’ the ‘gene’ (which is encoded in DNA).
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2 4 DNA--An introduction •Some of already covered in Chpt 1 notes (you should review that material) A nucleotide (nt) (the monomer of DNA) 5’ 3’ 5 RNA differs from DNA in two ways: 1.) 2’O on the sugar The 2’-OH (also pronounced and written “2’-hydroxyl”) is: •A good nucleophile (why RNA can be an enzyme) •A source of instability •Why DNA is the genetic material (more stable than RNA) 6 Two ester linkages in DNA and RNA (DNA is a phosphodi ester) .. H - O B: RNA hydrolysis mechanism: •negative charge repels OH - leads to overall stability
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3 7 RNA differs from DNA in two ways: 2.) RNA has U, DNA has T. •Bases are nitrogenous heterocycles •In DNA, Watson-Crick (WC) base pairs (bp) are A-T, G-C •In RNA, have WC bp, and MANY non-WC bp (structural diversity=functional diversity) 8 C1’ N9 (N6 in pyrimidines) 9 ATP is the major ‘currency’ of energy in the body ( i.e. can save energy and spend it in ATP) nucleotides nucleoside nucleobase
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4 10 Nucleotides can have 3’-phosphates and deoxyribose sugars too 11 Example of a trinucleotide (aka ‘oligonucleotide’, or ‘oligo’) Sequence is ‘pApCpG’, or ‘pACG’, or ‘ACG’ ( GCA) my favorite notation 12 Genomes are composed of very long pieces of DNA Organism Genome size polyoma virus 5.1 Kb E. coli 4.6 Mb human 3,000 Mb (kb=kilobases, Mb=megabases) •Electron micrograph of a lysed E. coli showing large amounts of DNA
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5 13 Fiber diffraction of DNA This ‘X’-shape is a characteristic of X-ray diffraction patterns of dsDNA. This spacing is the rise/bp 14 Space-filling structure of DNA strands are antiparallel bp are nearly planar (2.4 o inclination) 20 Å diameter purine (5+6 membered rings) pyrimidine (6 membered ring) DNA helix is inside-out of α -helix: •Sidechains on inside •Backbone on outside 15 End-on view of dsDNA •Stacking of bp1 on bp2 on bp3 is depicted •Note the extensive overlap of the bases: •Stacking is from London and permanent dipole-permanent dipole interactions
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6 16 Watson-Crick base pairs •3 H-bonds •2 H-bonds •Tend to be weaker than GC
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This note was uploaded on 07/23/2008 for the course CHEM 476 taught by Professor Bevilacqua,philip during the Fall '07 term at Pennsylvania State University, University Park.

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L9-11 - L8 start here Berg Tymoczko Stryer Biochemistry...

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