Chapter 12: Molecular Structure of Chromosomes and Transpositon

chromosomes

structures within living cells that contain the genetic material

genome

all genetic material that an organism possesses

bacteria genome

a single circular chromosome

eukaryotic genome

one complete set of chromosomes that resides in the cell nucleus

DNA sequences are necessary for

• synthesis of RNA + proteins

• Replication of chromosomes 

• Proper segregation of chromosomes

• Compaction of chromosomes (so they fit in the cell)

bacterial chromosomes

circular molecule that is a few million bps long

• contains an origin of replication

• contains a few thousand protein-encoding genes

• Intergenic regions

Intergenic regions

DNA segments between genes 

protein-coding genes

nucleotide sequences that code proteins

• account for the majority of bacterial DNA

origin of replication

a nucleotide sequence functions as an initiation site for the assembly of several proteins required for DNA replication

repetitive sequences

sequences found in multiple copies, interspersed within the intergenic regions throughout the bacterial chromosome

• play role in DNA folding, gene regulation and genetic recombination

operon

a functional unit of DNA, primarily found in prokaryotes, containing a cluster of genes under the control of a single promoter

promoter

where transcription starts, regulatory region 

nucleoid

non-membrane-bound region within prokaryotic cells (bacteria and archaea) that contains the majority of the genetic material

• DNA is in direct contact w/cytoplasm

• No separation between transcription and translation (can occur simultaneously)

bacterial structural organization

must be compacted 1000-fold

micro domains

loops that emanate from the core

• 10,000 bp in length (400-500 micro domains)

macro domains

80-100 microdmains

• 800-1000 kbp in length

• recombination is much more frequent between sites within a macro domain

nucleoid-associaited proteins (NAPs)

form the micro and macro domains

• bend DNA or act as bridges between DNA regions

• Ex: histone-like nuclei structuring proteins (H-NS) and structural maintenance of chromosomes (SMC) proteins

DNA supercoiling

formation of additional coils due to twisting forces

• due to both underfunding and overwinding

topoisomers

DNA structures that differ in supercoiling

underwinding

left-handed twisting motion

• can cause fewer turns = unstable structure

• negative supercoil

overwinding

right-handed turn

• more turns —> unstable

DNA supercoiling affects chromosome function

E. coli

• One negative supercoil per 40 turns of the double helix

• Helps the compaction of the chromosome

• Creates tension that may be released by DNA strand separation 

DNA gyrase

• topoisomerase II: creates negative supercoils using energy from ATP

• Can also relax positive supercoils when they occur

• can untangle DNA molecules

DNA topoisomerase I

• relaxes negative supercoils

  • Breaks one strand and rotates the DNA

supercoiling enzymes as drug targets

DNA gyrase is crucial for bacteria to survive, drugs inhibit bacterial topoisomerase but not eukaryotic

• Quinolones and coumarins

eukaryotic chromosomes

• Eukaryotic species sets of linear chromosomes found in the nucleus

• Much bigger and contain thousands of genes (~20,000)

eukaryotic genes

•  located between the centromeric and telomeric regions along the entire chromosome 

• Simple eukaryotes (ex: yeast)

  • Genes are relatively small and have few introns

• Complex eukaryotes (ex: mammals)

  • Genes are longer and have many introns ranging from 100-10,000 bp

• have centromeres and telomeres (bacteria do not)

• more repetitive sequences

exons

• encode for amino acids

introns

• don’t encode for amino acids 

primary RNA

produced by transcription, must undergo modification to produce mature mRNA

Telomere sequences

• protects ends of the chromosome

  • Shorten every cell division as we age

  • Allow for cell division and tissue regeneration 

  • Overactive telomerase → uncontrollable cell division (act as young cells) 

chromatin compaction

Binds to proteins that allow for DNA compaction

chromatin

• DNA-protein complex

nucleosomes

•  octamers of histone proteins + DNA 

  • H2A, H2B, H3 and H4 are the core histones (2 of each) 

  • H1 is the linker histone 

histone tails are modified

• Amino acids are numbered for each histone 

• Modifications are correlated with heterochromatin or euchromatin 

• Conserved in eukaryotes 

• Location of added covalent group + specific tail → corresponds to how open/closed chromatin is around that region 

Euchromatin

•  active transcription, open, methylation

• less condensed

• 30 nm fiber in radial loops

Methylated histones

 positive → attracted to each other = more compact

Acetylated histones

negative → repeal each other = less compact 

levels of chromatin condensation

1. beads on a string

2. 30 nm fiber

beads on a string

1. Beads are nucleosome w/linker DNA connecting them 

2. 146 bp of DNA make 1.65 negative superhelical turns around the octamer

3. Linker region between nucleosomes 20-100 bp

30 nm fiber

shortens total length of DNA 7-fold

• irregular configuration where nucleosomes have little face-to-face contact

heterochromatin

tightly compacted regions of chromosomes

• transcriptionally inactive (in general)

• during cell division

chromosome territory

each chromosome in the cell nucleus is located in its own distinct region in the cell nucleus