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 10 6 bp’s –Both chromosomal and extrachromosomal Usually 1 chromosome/cell Extrachromosomal = plasmid – 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.24- 9,10) 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

1 st 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? 1 o 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 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) –2 nd 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 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’ –PO 4, 1 end 3’ –PO 4 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’ parent strand w/ 3’ end –Yields 2 nd antiparallel dbl helix One strand will replicate 3’  5’ –Direction of active repl’n 3’  5’ 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