Chromosomes, Genomes, and DNA Structure in Bacteria and Eukaryotes
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124 Terms
Chromosome
A DNA-protein structure that contains genetic material
Genome
All genetic material possessed by an organism
Typical bacterial genome
Usually one circular chromosome with a few million base pairs
Eukaryotic nuclear genome
One complete set of nuclear chromosomes
Additional eukaryotic genomes
Mitochondria contain a genome and plants also contain a chloroplast genome
Four DNA sequence requirements
RNA and protein synthesis / chromosome replication / chromosome segregation / chromosome compaction
Structural gene
A gene that encodes a protein
Intergenic region
A nontranscribed DNA region between adjacent genes
Typical bacterial chromosome gene content
A few thousand genes with protein-coding genes making up most of the DNA
E. coli chromosome size
About 4.6 million base pairs
Haemophilus influenzae chromosome size
About 1.8 million base pairs
Bacterial origin of replication
A chromosomal site where DNA replication begins
Typical number of bacterial replication origins
One per chromosome
Nucleoid
The non-membrane-bound region containing a bacterial chromosome
Bacterial nucleoid versus eukaryotic nucleus
A nucleoid lacks a surrounding membrane so its DNA directly contacts the cytoplasm
Bacterial chromosome compaction requirement
About 1000-fold
Loop domain or microdomain
A loop of bacterial chromosomal DNA that contributes to compaction
Loop domains in E. coli
About 50 to 100 loops with roughly 40000 to 80000 base pairs per loop according to the lecture
DNA supercoiling
Additional coiling caused by twisting a DNA double helix
Underwinding right-handed DNA
Can reduce helical turns or produce negative supercoils
Overwinding right-handed DNA
Can add helical turns or produce positive supercoils
Topoisomers
DNA molecules with the same sequence but different degrees of supercoiling
Usual supercoiling state of bacterial DNA
Negative supercoiling
Negative supercoiling frequency in E. coli
About one negative supercoil per 40 turns of the double helix
Two major effects of negative supercoiling
Chromosome compaction and promotion of DNA strand separation
Why negative supercoiling promotes DNA function
Its stored tension makes strand separation easier during processes such as replication and transcription
DNA gyrase
ATP-dependent bacterial topoisomerase II that introduces negative supercoils
Additional functions of DNA gyrase
Relaxes positive supercoils and untangles intertwined DNA molecules
DNA topoisomerase I
Relaxes negative supercoils
Control of bacterial supercoiling
The opposing activities of DNA gyrase and topoisomerase I determine the overall level
Basic mechanism of DNA gyrase
Gyrase cuts both strands of one DNA segment / passes another segment through the break / rejoins the cut DNA
Why DNA gyrase is a useful drug target
Negative supercoiling is essential for bacterial survival and bacterial gyrase differs from eukaryotic topoisomerases
Two drug classes that inhibit bacterial gyrase
Quinolones and coumarins
Ciprofloxacin
A quinolone antibiotic that inhibits bacterial topoisomerases and can treat anthrax
Typical eukaryotic chromosome shape
Linear
Chromosome sets in eukaryotes
Eukaryotic chromosomes occur in sets and many species are diploid
Diploid
A cell or organism with two sets of chromosomes
Human chromosome complement
Two sets of 23 chromosomes in typical somatic cells
DNA molecules per unreplicated eukaryotic chromosome
One linear DNA molecule
Typical eukaryotic chromosome size
Tens to hundreds of millions of base pairs
Typical genes per eukaryotic chromosome
A few hundred to several thousand
Genes in lower eukaryotes
Usually small with few short introns
Genes in higher eukaryotes
Usually longer with many noncoding introns
Three essential eukaryotic chromosome sites
Origins of replication / centromere / telomeres
Eukaryotic origins of replication
Sites that initiate DNA replication and occur many times along each chromosome
Approximate spacing of eukaryotic replication origins
About every 100000 base pairs according to the lecture
Centromere
Chromosomal region that forms the recognition site for kinetochore proteins and enables chromosome segregation
Telomeres
Specialized sequences at both ends of a linear chromosome that support end replication and chromosome stability
Location of many repetitive sequences
Common near centromeres and telomeres but also found throughout chromosomes
C-value paradox or genome-size paradox
Genome size does not reliably correspond to organismal complexity
Main cause of genome-size differences among related eukaryotes
Different amounts of repetitive non-protein-coding DNA rather than simply more genes
Sequence complexity
The number of times a particular base sequence occurs in a genome
Three sequence-complexity classes
Unique DNA / moderately repetitive DNA / highly repetitive DNA
Unique or nonrepetitive DNA
Sequences present once or only a few times in a genome
Examples of unique DNA
Structural genes and some intergenic regions
Unique DNA in the human genome
Roughly 41 percent according to the lecture
Moderately repetitive DNA
Sequences found from a few hundred to several thousand times
Examples of moderately repetitive DNA
rRNA genes / histone genes / regulatory sequences / transposable elements
Highly repetitive DNA
Short sequences repeated tens of thousands to millions of times
Two arrangements of repetitive DNA
Interspersed copies throughout the genome or tandem arrays of adjacent repeats
Alu family
An interspersed human repeat about 300 base pairs long
Abundance of Alu repeats
About 10 percent of the human genome with a copy roughly every 5000 to 6000 base pairs
Tandem array
Many copies of a short sequence repeated directly next to one another
Example of tandemly repeated DNA
AATAT and AATATAT repeats in Drosophila centromeric regions
Chromatin
The DNA-protein complex that makes up eukaryotic chromosomes
Why chromatin compaction is necessary
A human chromosome set would exceed 1 meter if stretched out but must fit inside a microscopic nucleus
Nucleosome
The repeating structural unit of chromatin consisting of DNA wrapped around a histone octamer
Histone octamer
Two copies each of H2A / H2B / H3 / H4
DNA in a nucleosome core particle
146 base pairs wrapped around the octamer
DNA turns around a histone octamer
About 1.65 negative superhelical turns
Approximate nucleosome diameter
11 nanometers
Why histones bind DNA
Their positively charged lysine and arginine residues interact with negatively charged DNA phosphates
Histone structure
A globular domain plus a flexible charged amino-terminal tail
Core histones
H2A / H2B / H3 / H4
Linker histone
H1
Function of histone H1
Binds linker DNA and helps compact adjacent nucleosomes
Core histones versus H1
Core histones form the octamer and bind DNA tightly while H1 binds linker DNA less tightly
Linker DNA
DNA between neighboring nucleosome core particles
Beads-on-a-string structure
Nucleosomes connected by linker DNA with relatively little higher-order compaction
Kornberg nucleosome model
A 1974 model proposing that chromatin consists of repeating nucleosome units
Evidence used by Kornberg
Biochemical experiments / X-ray diffraction / electron microscopy
Purpose of Noll's experiment
To test the beads-on-a-string model by digesting chromatin with DNase I
Why DNase I preferentially cuts linker DNA
Linker DNA is more exposed than DNA wrapped around core histones
Prediction of Noll's experiment
DNase I should produce DNA fragments in units of about 200 base pairs if nucleosomes repeat regularly
Noll result at low DNase I concentration
Only some linkers are cut so longer fragments appear in multiples of about 200 base pairs
Noll result at high DNase I concentration
Nearly all linker regions are cut and most fragments are about 200 base pairs
Conclusion from Noll's experiment
Chromatin contains repeating DNA-protein units separated by accessible linker DNA
30-nm fiber
A higher-order chromatin structure formed by associations among nucleosomes
Role of H1 in the 30-nm fiber
H1 promotes interactions that compact neighboring nucleosomes
Effect of removing H1
Chromatin adopts a less compact beads-on-a-string appearance
Compaction produced by the 30-nm fiber
About seven-fold beyond the nucleosome level
Two proposed 30-nm fiber models
Solenoid model and three-dimensional zigzag model
Solenoid model
Nucleosomes form a compact helical arrangement
Zigzag model
Linker DNA crosses the fiber so nucleosomes alternate back and forth
Approximate compaction from DNA through the 30-nm fiber
About 50-fold total according to the lecture
Nuclear matrix
A proposed protein network that helps organize and compact chromosomes
Two components of the nuclear matrix
Nuclear lamina lining the inner nuclear membrane and internal matrix proteins filling the nucleus
Radial loop domain
A loop of the 30-nm fiber attached to the nuclear matrix or chromosome scaffold
Typical radial loop size
About 25000 to 200000 base pairs
MAR or SAR
A matrix-attachment region or scaffold-attachment region that anchors a radial loop