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Genes & Chromosomes
Part III, Chapters 24, 25
Central Dogma
• DNA replicates  more DNA for
daughters
• (Gene w/in) DNA transcribed  RNA
– Gene = segment of DNA
– Encodes info to produce funct’l biol
product
• RNA translated  protein
Genome
• Sum of all DNA
– Genes + noncoding regions
• Chromosomes
– Each w/ single, duplex DNA helix
– Contain many genes
• Historical: One gene = one enzyme
• Now: One gene = one polypeptide
• Some genes code for tRNAs, rRNAs
• Some DNA sequences (“genes”) = recognition
sites for beginning/ending repl’n, transcr’n
• Most gene products are “proteins”
– Made of aa’s in partic sequence
– Each aa encoded in DNA as 3 nucleotide seq
along 1 strand of dbl helix
– How many nucleotides (or bp’s) needed for prot
of 350 aa’s?
Prokaryotic DNA
• Viruses
– Rel small amt DNA
• 5K to 170K base pairs (bp’s)
– One chromosome
• Chromosome = “packaged” DNA
– Many circular
• Bacterial DNA -- larger than viral
– E. coli ~4.6 x 106 bp’s
– Both chromosomal, extrachromosomal
• Usually 1 chromosome/cell
• Extrachromosomal = plasmid
– 103-105 bp’s
– Replicate
– Impt to antibiotic resistance
Chromosomes Complex
Packaging reduces E.coli DNA 850x
Eukaryotic DNA
• Many
chromosomes
– Single human
cell DNA
~2m
• Must be
efficiently
packaged
Euk Chromosomes
• Prok’s – usually only 1 cy of each
gene (but exceptions)
• Euk’s (ex: human)
– Book: coding region (genes coding
for prot’s) ~ 1.5% total human genome
• Exons
• Euk’s (ex: mouse): ~30% repetitive
– “Junk”?
– Non-transcribed seq’s
• Centromeres – impt during cell division
• Telomeres – help stabilize DNA
• Introns – “intervening” seq’s
– Function unclear
– May be longer than coding seq’s (= exons)
Supercoiling
• DNA helix is coil
– Relaxed coil not bent
– BUT can coil upon itself  supercoil
• Due to packing; constraints; tension
• Superhelical turn = crossover
• Impt to repl’n, transcr’n
– Helix must relax so can open, expose bp’s
– Must unwind from supercoiling
Topoisomerases
• Enz’s in bacteria, euk’s
• Cleave phosphodiester bonds in 1/both
strands
– Where are these impt in nucleic acids?
– Type I – cleaves 1 strand
– Type II – cleaves both strands
• After cleavage, rewind DNA + reform
phosphodiester bond(s)
• Result – supercoil removed
Type I
Type II
DNA Packaging
• Chromosomes = packaged DNA
– Common euk “X”- “Y”-looking structures
– Each = single, uninterrupted mol DNA
• Chromatin = chromosomal material
– Equiv amts DNA + protein
– Some RNA also assoc’d
1st Level Pakaging in Euk’s
Around Histones
• DNA
bound
tightly to
histones
Histones
• Basic prot’s
• About 50% chromosomal mat’l
• 5 types
– All w/ many +-charged aa’s
– Differ in size, amt +/- charged aa’s
• What aa’s are + charged?
• Why might + charged prot be assoc’d w/ DNA helix?
• 1o structures well conserved across species
• Must remove 1
helical turn in
DNA to wind
around histone
– Topoisomerases
impt
• Histones bind
@ specific
locations on
DNA
– Mostly AT-rich
areas
Nucleosome
• Histone wrapped w/ DNA
–  7x compaction of DNA
• Core = 8 histones (2 copies of 4 diff histone prot’s)
• ~140 bp DNA wraps around core
• Linker region -- ~ 60 bp’s extend to next
nucleosome
• Another histone prot may“sit” outside
– Stabilizes
Chromatin
• Further-
structured
chromosomal
mat’l
• Repeating units
of nucleosomes
• “Beads on a
string”
– Flexibly jointed
chain
30 nm Fiber
• Further nucleosome packing
• ~100x compaction
• Some nucleosomes not inc’d into tight
structure
Rosettes
• Fiber loops around nuclear scaffold
– Proteins + topoisomerases incorporated
• 20-100K bp’s per loop
– Related genes in loop
• Book ex: Drosophila loop w/ complete set genes
coding for histones
• ~6 loops per rosette = ~ 450K bp’s/ rosette
• Further coiling, compaction   10,000X
compaction total
Semiconservative Replication
• 2 DNA strands/helix
• Nucleotide seq of 1 strand automatically
specifies complementary strand seq
– Base pairing rule: A w/ T and G w/ C ONLY in
healthy helix
– Each strand serves as template for partner
• “Semiconservative”
– Semi – partly
– Conserved parent strand
• DNA repl’n 
daughter cell w/
own helix
– 1 strand is
parental (served
as template)
– 2nd strand is
newly synth’d
Definitions
• Template
– DNA strand w/ precise info for synth complementary
strand
– = parental strand during repl’n
• Origin
– Unique point on DNA helix (strand) @ which repl’n
begins
• Replication Fork
– Site of unwinding of parental strand and synth of
daughter strand
• NOTE: helix unwinding crucial to repl’n success
• Repl’n Fork –
cont’d
– Bidirectional
repl’n
• 2 repl’n forks
simultaneously
synth daughter
strands
At Replication Fork
• Both parental strands serve as templates
– Simultaneous synth of daughter cell dbl helices
• Expected
– Helix unwinds  repl’n fork
– Get 2 free ends
• 1 end 5’ –PO4, 1 end 3’ –PO4
• REMEMBER: paired strands of helix antiparallel
• Expected -- cont’d
– Repl’n each strand at end of parent
• One strand will replicate 5’  3’
– Direction of active repl’n 5’  3’
– Happens @ parent strand w/ 3’ end
– Yields 2nd antiparallel dbl helix
• One strand will replicate 3’  5’
– Direction of active repl’n 3’  5’
– Happens @ parent strand w/ 5’ end
– Yields antiparallel dbl helix
• But, exper’l evidence:
– Repl’n ALWAYS 5’  3’
• Can envision at parental strand w/ 3’ end
• What happens at other parental strand??
Okazaki Fragments
• Discovered by Dr. Okazaki
– Found near repl’n fork
• Small segments daughter strand DNA synth’d
5’  3’
– Along parental template strand w/ 5’ end
• Get series small DNA segments/fragments
– So synth along this strand in opp direction of
overall replication (or of unwinding of repl’n
fork)
• “Lagging strand”
– Takes longer to synth fragments + join them
• Other parental strand, w/ continuous synth
“leading strand”
• W/ repl’n, fragments joined enzymatically 
complete daughter strand
• Overall, repl’n on both strands in 5’  3’
direction (w/ respect to daughter)
• Don’t be confused w/ bi-directional repl’n
– Bidirectional: >1 repl’n fork initiating repl’n
simultaneously
– At each fork, repl’n takes place along both
strands
– At each fork, repl’n in 5’  3’ direction ONLY
along each strand
Enz’s That Degrade DNA
• Exonucleases – degrade DNA from one
end of molecule
– Some digest one strand 3’  5’
– Some digest in 5’  3’ direction
• Endonucleases – degrade DNA from any
site