Download Biochemistry Lecture 20

Genes & Chromosomes
Chapter 24
Central Dogma (p.906)
• DNA replicates  more DNA for
daughters
• (Genes of) DNA transcribed  RNA
– Gene = segment of DNA
– Encodes info to produce funct’l biol.
product
• RNA translated  protein
Genome
• Sum of all DNA
• Viruses (Table 24-1)
– Rel small amt DNA
• 5K to 182K base pairs (bp’s)
– One chromosome
• Chromosome = “packaged” DNA
– Many circular
Genome – cont’d
• Bacterial DNA -- larger than viral
– E. coli -- ~4.6 x 106 bp’s
– Both chromosomal and extrachromosomal
• Usually 1 chromosome/cell
• Extrachromosomal = plasmid
– 103-105 bp’s
– Replicate
– Impt to antibiotic resistance
• Eukaryotes – many chromosomes
– Single human cell DNA ~ 2 m
• Must be efficiently packaged
Chromosomes
• Each has single, duplex DNA helix
• Contains 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
Chromosomes – cont’d
• 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?
Fig.24-2
Euk Chromosomes Complex
• Prok’s – usually only 1 cy of each gene
(but exceptions)
• Euk’s (ex: mouse): ~30% repetitive
– “Junk”?
– Non-trascribed seq’s
• Centromeres – impt during cell division (24-3)
• Telomeres – help stabilize DNA
• Introns – “intervening” seq’s (24-4)
– Function unclear
– May be longer than coding seq’s (= exons)
Fig.24-3
Fig.24-4
Supercoiling
• DNA helix is coil
– Relaxed coil is not bent
– BUT can coil upon itself  supercoil (Fig.249,10)
• Occur due to packing; constraints;
tension
• Superhelical turn = crossover
• Impt to repl’n, transcr’n (Fig.24-11)
– Helix must be relaxed so it can open, expose
bp’s
– Must be able to unwind from supercoiling
Fig.24-9
Fig.24-10
Fig.24-11
Fig.24-13
Supercoiling – cont’d
Topoisomerases
– Enz’s found in bacteria, euk’s
– Cleave phosphodiester bonds in 1 or 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
DNA Packaging
• Chromosomes = packaged DNA
– Common euk “X” “Y” type structures
– Comprised of single, uninterrupted mol of
DNA
– Table 24-2 – Chromosome #
• Chromatin = chromosomal material
– Equiv amts DNA + protein
– Some RNA also assoc’d
Fig.24-7
1st Level Pakaging in Euk’s
Is Around Histones
• DNA
bound
tightly to
histones
(24-24)
Histones – cont’d
• Basic prot’s
• About 50% of chromosomal mat’l
• 5 types all w/ many +-charged aa’s (Table
24-3)
– 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
Histones – cont’d
• Must remove 1 helical turn in DNA to wind
around histone (24-25)
– Topoisomerases impt
Histones – cont’d
• Histones bind
@ specific
locations on
DNA (24-26)
– Most contact
between
DNA/histones:
AT-rich areas
Nucleosome
• Histone w/ DNA wrapped around it
– Yields 7x compaction of DNA
• Core = 8 histones (2 copies of 4 diff histone
prot’s)
• ~140 bp length of DNA wraps around core
• Linker region -- ~ 60 bp’s extend to next
nucleosome
• May be another histone prot “sits” at outside
– Stabilizes
Fig.24-24
Chromatin
• Repeating
units of
nucleosomes
(24-23)
• “Beads on a
string”
– Flexibly
jointed chain
30 nm Fiber
• Further nucleosome packing (24-27)
• Yields ~100x compaction
• Some nucleosomes not inc’d into tight structure
Rosettes
• Fiber loops around nuclear scaffold
(24-29)
– Proteins + topoisomerases incorporated
• ~75K bp’s per loop
• ~6 loops per rosette = ~ 450K bp’s/
rosette
• Further coiling, compaction   10,000X
compaction total (24-30)
Fig.24-29
Fig.24-30
Semiconservative Replication
• 2 DNA strands/helix
• Nucleotide seq of 1 strand automatically
specifies seq of complementary strand
– Base pairing rule: A w/ T and G w/ C ONLY in
healthy helix
– Each strand can serve as template for its partner
• “Semiconservative”
– Semi – partly
– Conserved parent strand
Semiconservative Rep’n-cont’d
• DNA repl’n 
daughter cell
w/ own helix
(25-2)
– 1 strand is
parental
(served as
template)
– 2nd strand is
newly synth’d
Definitions
• Template
– DNA strand providing 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: Unwinding of helix is crucial to repl’n success
Definitions – cont’d
• Replication
Fork – cont’d
– Bidirectional
repl’n (25-3)
• 2 repl’n forks
simultaneously
synth daughter
strands
At the 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 are
antiparallel
At the Repl’n Fork – cont’d
• Expected -- cont’d
– Repl’n of 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
At the Repl’n Fork – cont’d
• But, exper’l evidence
– Showed repl’n ALWAYS 5’  3’
• Easy to 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 of daughter strand DNA
synth’d 5’  3’
– Along parental template strand w/ 5’ end
• Get series of small DNA
segments/fragments
– So synthesis along this strand takes place in
opposite direction of overall replication (or of
unwinding of repl’n fork)
Okazaki Fragments—cont’d
• Called “lagging strand”
– Takes longer to synth fragments + join them
• Other parental strand, w/ continuous
synth, called “leading strand”
• As repl’n proceeds, fragments are joined
enzymatically  complete daughter
strand
• Overall, repl’n on both strands happens in
5’  3’ direction (w/ respect to daughter)
Fig.25-4
Okazaki Fragments—cont’d
• Don’t be confused w/ bi-directional repl’n
– Bidirectional refers to >1 repl’n fork initiating
repl’l 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