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 has 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 and

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 ~ 2 m

• 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 codinng

for prot’s) ~ 1.5% total human genome•Exons

• Euk’s (ex: mouse): ~30% repetitive– “Junk”?– Non-trascribed 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 is 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” type 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

• 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

Histones

• Must remove 1 helical turn in DNA to wind around histone – Topoisomeras

es 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)

• Called “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 occurs 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