Lecture 2 Properties of DNA
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Transcript of Lecture 2 Properties of DNA
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Lecture 2 Properties of DNA
Reference:Chapter 28: Biochemistry by Voet and Voet
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C-value paradoxC-value paradox
Gene size, genome sizeGene size, genome size
Topology of DNA Topology of DNA
Denaturation and renaturation of DNADenaturation and renaturation of DNA
Lecture 2: Outline
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gene sizes Largest known mammalian gene is
DMD gene 2.5 Mbp (0.1% of the genome)
Causes Duchenne’s muscular dystrophy (DMD)
characterized by rapid progression of muscle degeneration which occurs early in life.
‘scoliosis’
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DMDMDDDMD gene maps to
chromosome Xp21DMD affects mainly malesMutations in DMD gene lead to non functional dystrophin protein
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genome sizes
organism Number of base pairs (kb)
virusesLambda bacteriophage ( λ) 48.6
bacteriaEschericia coli 4,640
eukaryotesYeast 13,500Drosophila 165,000Human 3.3 x 106
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Does size matter? C-value Does size matter? C-value paradoxparadox
mountain grasshopper Podisma pedestrisGenome size: 18 Gbp
protozoan Amoeba dubiaGenome size: 670Gbp
Boa constrictorGenome size: 2.1 Gbp
Homo sapiens sapiensGenome size: 3.2 Gbp
C value: DNA content of a haploid cellC value: DNA content of a haploid cell
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CComparatiomparative genome ve genome sizessizes
Why is there a discrepancy between genome size and genetic complexity?
C-value paradox
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Due to the presence of repetitive (junk?) DNA
Repetitive DNA families constitute nearly one-half of genome (~45%)
Protein domains contribute to organism complexity
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Topology of DNA
DNA supercoiling: coiling of a coil
Important feature in all chromosomes
Supercoiled DNA moves faster than relaxed DNA
Allows packing / unpacking of DNA
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negatively supercoiled (right handed)•Results from under or unwinding•Important in DNA packing/unpacking e.g during replication/transcription
positively supercoiled (left handed)•Results from overwinding•Also packs DNA but difficult to unwind
Supercoiling topologySupercoiling topology
No supercoiling (left) to tightly supercoiled (right)
Analogy = phone cord
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Supercoiling takes 2 forms Supercoiling takes 2 forms toroidal (DNA around histones) or toroidal (DNA around histones) or
interwound (bacterial chromosomes)interwound (bacterial chromosomes)
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Supercoiled DNA needs to be Supercoiled DNA needs to be unwound /wound when necessary unwound /wound when necessary Unwound during transcription/replicationWound before cell division
Supercoils can be relaxed by Single strand nicks (topoisomerase I) Double strand breaks (toposiomerase II)
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Topoisomerase I
Cause temporary single strand breaks in DNA Allows free rotation of helixActs by breaking phosphodiester linkage via tyrosine active site
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Topoisomerase II (DNA gyrase)
ATP hydrolysis mediated double strand breakInhibitors are effective antibiotics and cancer chemotherapy agents
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supercoiled
Relaxed circle
Full length linear
Why does a plasmid (circular DNA) that has never been cut give more than one band on a gel?
EBr
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Denaturation and Denaturation and renaturation of DNArenaturation of DNA
Applications in polymerase chain reaction (PCR)
http://www.dnai.org/b/index.html
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Denaturation of DNA
Also called melting
Occurs abruptly at certain temperatures
Tm – temp at which half the helical structure is lost
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DNA melting curve
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Tm varies according to the GC content
High GC content - high Tm
GC rich regions tend to be gene rich
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Renaturation of DNA
Also called annealing
Occurs ~ 25oC below Tm
Property used in PCR and hybridisation techniques
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