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.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’dTopoisomerases

– 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