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Copyright © 2007 by W. H. Freeman and Company
Berg • Tymoczko • Stryer
BiochemistrySixth Edition
Chapter 4:DNA, RNA, and the Flow of
Genetic Information
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Purine & Pyrimidine Bases
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Ribose & Deoxyribose
Note: numbers are primed on sugars but not bases
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Adenosine, a Nucleoside (base + sugar)
Anti form
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ATP, a 5′-Nucleotide (base + sugar + phosphate)
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Nucleotide Functions1. Provide energy for reactions:
ATP < === > ADP + Pi
ATP < === > AMP + PPi
2. High energy carrier moleculesUDP-glucose and CDP-diacylglycerol
3. Substrates for making DNA and RNAAll NTPs and dNTPs
4. Regulatory moleculesc-AMP and c-GMP
5. Coenzyme componentsNAD+ and NADP+ ; FMN and FAD
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Nucleotide Carrier
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Nucleotides
NAD+ (NADP+)
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A 3′-nucleotide
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Bases, Nucleosides, Nucleotides
Base nucleoside 5′-nucleotide
Adenine adenosine adenosine 5′- monophosphate or AMP or 5′- adenylic acid
Guanine guanosine guanosine 5′- monophosphate or GMP or 5′- guanylic acidCytosine cytidine cytidine 5′- monophosphate or CMP or 5′- cytidylic acidUracil uridine uridine 5′- monophosphate or UMP or 5′- uridylic acidThymine thymidine thymidine 5′- monophosphate(deoxy) or dTMP or 5′- thymidylic acid
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DNA & RNA Polymers
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Shorthand Notation for DNA
• Deoxyribose is the vertical line. The anomeric C is #1 and phosphodiester bonds link the sugars 3’-5’.
• a and b are cleavage sites for nucleases.
P PP P OHP
A G T A C
1'
3'
5' b
a
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B-DNA
DNA can exist inA, B or Z forms. B is most common, A is at low humidity, Z is left handed
Minor groove = 12 AMajor groove = 22 ADiameter = 20 A
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H-Bonding in dsDNA
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Chargaff’s Rules
Purines = Pyrimidines
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Overlap of bases in dsDNA
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Meselson & Stahl
Experiment
Beginning withDNA that containsall N15 isotope.
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Semiconservative Replication
of DNA
N15-N15
N15-N14 N14-N15
N15-N14 N14-N14 N14-N14 N14-N15
N15-N14 N14-N14 N14-N14 N14-N14 N14-N14 N14-N14 N14-N14 N14-N15
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Meselson & Stahl
Results
Replication usingNTPs that areall N14 isotope.
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Detection of DNA by
absorbance of aromatic bases at 260 nm
(Denaturing causesan increase in A260)
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DNA Melting (strand dissociation)
Tm = 69o + 0.41(%G + %C)
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Determine %G, C, A & T from Tm
Tm = 69o + 0.41(%G + %C)
Tm for 100% A:T dsDNA = 69o
Tm for 100% G:C dsDNA = 110o
Assume Tm was determined to be 98oC.
98 = 69 + 0.41(%G + %C)29 = 0.41(%G + %C)29/0.41 = 70.7 = (%G + %C) %G = %C = 70.7/2 = 35.35% %A = %T = 29.3/2 = 14.65%
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Circular Mitochondrial dsDNA
Relaxed
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Circular Mitochondrial dsDNASupercoiled
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DNA Synthesis
Addition of an AMP residue.DNA synthesis occurs from 5′ to 3′
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DNA Synthesis
Addition of a GMP residue
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DNA Coupling Mechanism
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Common Types of RNA
r-RNA, t-RNA & m-RNA
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Transcription
Synthesis of m-RNA
Template strand = antisense strandCoding strand = sense strand
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Promotor region for m-RNA
Region of DNA that controls the start of m-RNA synthesis.
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Stem-loop structure in RNA
Simple stem-loop structure in RNA.Shows short segments of base pairing in RNA.
Note the poly-U structure at the 3′ end of Ecoli m-RNA.
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Eucaryotic m-RNA
The 5′ end is capped with 7-methylG through a -ppp- bridge. Other caps are known.The 3′ end has a poly-A tail (100-200 bases).
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Reverse Transcription
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t-RNA
TC loopDHU loop
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t-RNA3′-end of t-RNA
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Formyl-Met
fMet bonds to the AUG codon and initiates translation.
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Translation Start
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Translation Start
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Splicing m-RNA
Introns = intervening sequences (excised), vary in size & number
Exons = expressed sequences
Eucaryotes have split genes
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m-RNA with no introns
Hybridization to genomic DNA is smooth
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m-RNA with introns
Hybridization to genomic DNA is looped
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Intron consensus sequence
All introns have conserved 5GU…..AG3termini and a splicing start ..PyUPuAPy…
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RecombinationExon shuffling
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End of Chapter 4
Copyright © 2007 by W. H. Freeman and Company
Berg • Tymoczko • Stryer
BiochemistrySixth Edition