Chapter 10- Chromosome Organization & Molecular Structure
nucleoid-associated proteins (NAPs) 4 functions
-facilitate chromosome compaction and organization -bend the DNA or act as bridges for DNA to bind to other DNA regions -facilitate chromosome segregation -play a role in gene regulation
unique or repetitive sequences (3)
-found once or a few times in the genome -includes protein-encoding genes and intergenic regions -makes up 41% of the genome in humans
three features of bacterial and eukaryotic chromosomes
-general organization of functional sites on a chromosome -transposition -molecular mechanisms of chromosome compaction
DNA gyrase (topoisomerase II) 3 functions
-introduces negative supercoils using energy from ATP -relax positive supercoils when they occur using energy from ATP -can untangle intertwined DNA molecules
key features of bacterial chromosomes (5)
-most but not all bacterial species contain circular chromosomal DNA -most bacterial species contain a single type of chromosome, but it may be present in multiple copies -a typical chromosome is a few million base pairs in length -one O.O.R is required to initiate DNA replication -repetitive sequences may be interspersed throughout the chromosome
DNA sequences are necessary for (4):
-synthesis of RNA and cellular proteins -replication of chromosomes -proper segregation of chromosomes -compaction of chromosomes
8 key features of eukaryotic chromosomes
-usually linear -occur in sets. many species are diploid, so somatic cells contain 2 sets of chromosomes -typical chromosome is tens of millions to hundreds of millions of bp in length -genes are interspersed throughout the chromosomes. a typical chromosome contains between a few hundred and several thousand different genes -each chromosome contains many origins of replication that are interspersed every 100,00 base pairs -each chromosome contains a centromere that forms a recognition site for the kinetochore proteins; required for chromosome sorting during mitosis and meiosis -telomeres contain specialized sequences located at both ends of the linear chromosome -repetitive sequences are commonly found near centromeric and telomeric regions but they may also be interspersed throughout the chromosome
2 main classes of drugs that inhibit gyrase (topoisomerase II) and other bacterial topoisomerases
1. Quinolones 2. Coumarins
2 major effects of negative supercoiling
1. helps in compaction of the chromosome 2. in localized regions, creates tension that may be released by DNA strand separation
3 main types of repetitive sequences
1. unique or non-repetitive 2. moderately repetitive 3. highly repetitive
negative supercoil DNA has ____ bp per turn plus 1 negative supercoil
10
normal DNA has ____ bp per turn
10
positive supercoil DNA has ____ bp per turn plus 1 positive supercoil
10
loop domains within a bacterial chromosome: -to fit within a bacterial cell, chromosomal DNA must be compacted ________-fold -involves formation of loop domains (____________) which are typically 10,000 bp -number of loops varies according to __________ of the bacterial chromosome and ___________ -E.coli= ______-______ microdomains -adjacent microdomains are further organized into macrodomains of 800-1000kbp (each with 80-100 microdomains)
1000 microdomains size, species 400-500
unstable DNA (left-handed twist) has ____ bp per turn
12.5
nuclear genome in humans
22 autosomes, X chromosome, Y chromosome
how many base pairs is bacterial chromosomal DNA?: E. coli= H. influenza=
4.6 mil 1.8 mil
chromosomal DNA in bacteria is negatively supercoiled -in E.coli, one negative supercoil per _____ turns of the double helix
40
unstable DNA (right-handed twist) has ____ bp per turn
8.3
intron length range
<100 to >10,000 bp
example of a quinolone
Ciprofloxacin (Cipro)
topoisomers
DNA conformations that differ with regard to supercoiling, differ based on a turn that either unwinds or overwinds the helix
DNA topoisomerase II aka?
DNA gyrase
control of supercoiling in bacteria is accomplished by what 2 main enzymes?
DNA gyrase (DNA topoisomerase II) DNA topoisomerase I
what further compacts bacterial chromosomes?
DNA supercoiling
relaxes negative supercoils
DNA topisomerase I
causes negative supercoils
DNA topoisomerase II
nucleoid-associated proteins (NAPs)
DNA-binding proteins that help compact/hold DNA in place, allows certain portions of the chromosome to readily go through transcription
2 ways bacterial chromosomes become more compact
NAPs DNA supercoiling
DNA sequences are necessary for: -synthesis of _________ and cellular proteins -__________ of chromosomes -proper ___________ of chromosomes -___________ of chromosomes
RNA replication segregation compaction
plants tolerate changes in chromosomal organization better than animals T or F
T
there is a two-fold difference in the genome size in two closely related salamander species (P. larselli is 2x larger than P. richmondi), what is this difference due to?
accumulation of repetitive DNA sequences that do not encode proteins NOT due to extra genes
genome
all the genetic material an organism possesses
where are telomeres located?
both ends of linear chromosomes
loop domains
chromosomal segments that are folded into loops
what does DNA supercoiling influence?
chromosome function
key features of bacterial chromosome: -most but not all bacterial species contain ___________ chromosomal DNA -most bacterial species contain a _________ type of chromosome, but it may be present in _________ copies -a typical chromosome is a few ___________ base pairs in length -____________ origin of replication (OOR) is required to initiate DNA replication -__________ sequences may be interspersed throughout the chromosome
circular single, multiple million one repetitive
bacterial chromosomal DNA is usually a ___________ molecule that is a few ___________ nucleotides in length
circular, million
2 major effects of negative supercoiling: 1. helps in the ____________ of the chromosome 2. in localized regions, creates ___________ that may be released by DNA strand separation
compaction tension
nucleoid-associated proteins (NAPs): -facilitate chromosome ___________ and ____________ -_________ the DNA or act as ___________ for DNA to bind to other DNA regions -facilitate chromosome ____________ -play a role in ___________ regulation
compaction, organization bend, bridges segregation gene
chromosomes
complexes of DNA and proteins that contain genetic material
benefit to blocking the function of DNA gyrase
cures or alleviates bacterial diseases
what does compaction do to the chromosome?
decreases its size
3 types of DNA sequences required for eukaryotic chromosomal replication and segregation: telomeres -specialized regions at the __________ of chromosomes -important in replication for _____________
ends stability
Quinolones and Coumarins do not inhibit __________ topoisomerases
eukaryotic
DNA given a turn that UNWINDS the helix can cause ___________ turns OR the formation of a ___________ supercoil
fewer, negative
three features of bacterial and eukaryotic chromosomes: -general organization of ___________ sites on a chromosome -__________- short segments of DNA, calls transposable elements (TEs), can move to different sites within chromosomes -molecular mechanisms of chromosome ____________
functional transposition compaction
the completing action of DNA gyrase (DNA topoisomerase II) and DNA topoisomerase I
governs the overall supercoiling of bacterial DNA
-the total amount of DNA in eukaryotic species is much ___________ than that in bacterial cells because it contains many ___________ genes -eukaryotic genomes vary substantially in size --in many cases, this variation in size is NOT related to the ___________ of the species
greater, more complexity
3 types of DNA sequences required for eukaryotic chromosomal replication and segregation: origins of replication -chromosomal sites necessary to __________ DNA replication -eukaryotic chromosomes contain _________ origins
initiate many
what ability of DNA gyrase is crucial for bacteria to survive?
introducing negative supercoils into DNA
eukaryotic species contain one or more sets of chromosomes: -each set is composed of several different __________ chromosomes -humans have 2 sets of ____ chromosomes
linear 23
key features of eukaryotic chromosomes: -eukaryotic chromosomes are usually __________ -eukaryotic chromosomes occur in ________. many species are DIPLOID, meaning that somatic cells contain 2 sets of chromosomes -a typical chromosome is _______ of millions to ________ of millions of base pairs in length -genes are interspersed throughout the chromosomes. a typical chromosome contains between a few __________ and several __________ different genes -each chromosome contains many origins of replication that are interspersed about every __________ base pairs -each chromosome contains a ___________ that forms a recognition site for the kinetochore proteins; required for chromosome sorting during meiosis and mitosis -__________ contain specialized sequences located at both ends of the linear chromosome -repetitive sequences are commonly found near ___________ and ___________ regions, but they may also be intersper
linear sets tens, hundreds hundred, thousand 100,000 centromere telomeres centromeric, telomeric
in complex eukaryotes such as mammals and flowering plants: -genes are __________
long
microdomains
loops of bacterial chromosomal DNA that emanate from the central core and are 10kp (10,000bp) in length
eukaryotic chromosome contains a single, linear molecule of DNA: -typically tens to hundreds of ___________ of base pairs -typically a few __________ to several __________ genes
millions hundred, thousand
eukaryotes posses a ____________ genome plants also have a ___________ genome
mitochondrial chloroplast
DNA given a turn that OVERWINDS the helix can cause __________ turns OR the formation of a ____________ supercoil
more, positive
how many O.O.R do eukaryotes have?
multiple
DNA gyrase (topoisomerase II) -introduces __________ supercoils using energy from ATP -can also relax ___________ supercoils when they occur -can __________ intertwined DNA molecules
negative positive untangle
chromosomal DNA in bacteria is ___________ supercoiled
negatively
nucleoid
non-membrane bound region in a prokaryotic cell where the bacterial DNA is found and is in direct contact with the cytoplasm
introns
noncoding interval sequences
bacterial chromosome: what is found between adjacent genes?
nontranscribed DNA
intergenic regions
nontranscribed regions of DNA located between adjacent genes
bacterial chromosome is highly compacted and found in the ___________
nucleoid
what do bacteria use to form microdomains and macrodomains?
nucleoid-associated proteins
unique or non-repetitive sequences: useful -found ________ or a few times in the genome -includes ____________ genes as well as _________ regions -in humans, make up 41% of the genome --protein-encoding regions of genes (exons)=____% --introns= ____% --unique regions not found within genes=____%
once protein-encoding, intergenic 2, 24, 15
how many O.O.R do bacteria have?
one
eukaryote genome
one complete set of nuclear chromosomes
eukaryotic species contain how many sets of chromosomes?
one or more
3 types of DNA sequences required for eukaryotic chromosomal replication and segregation
origins of replication centromeres telomeres
right handed twist
overwining
topoisomerase
prevents DNA from overwinding during DNA replication
bacterial chromosome: what accounts for the majority of bacterial DNA?
protein-encoding genes
genetic material stores information via....
protein-encoding genes
what do centromeres form?
recognition site for kinetochore proteins that is required for chromosome sorting during mitosis and meiosis
centromeres
regions of DNA located in the center of the chromosome that holds hold the chromatids together in a chromosome and play a role in segregation of chromosomes
DNA topoisomerase I
relaxes negative supercoils
repetitive sequences
segments of DNA repeated multiple times in a genome
3 types of DNA sequences required for eukaryotic chromosomal replication and segregation: centromeres -regions that play a role in ___________ of chromosomes during mitosis and meiosis
segregation
in simpler eukaryotes such as yeast: -genes are relatively __________ (several hundred bp long)
short
transposition
short segments of DNA (transposable elements) can move to different sites within chromosomes and accumulate in large numbers
transposable elements (TEs)
short segments of DNA that have the ability to move within a genome
bacteria genome
single circular chromosome
each eukaryotic chromosome contains what kind of DNA molecule?
single, linear
origins of replication
sites where the replication of a DNA molecule begins
telomeres
specialized DNA regions at the ends of chromosomes that are important in replication and for stability
DNA gyrase (topoisomerase II)
temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix
what happens to the circular chromosome in bacteria when there is DNA strand separation?
tension in a localized region becomes released which enhances genetic activities such as replication and transcription that require DNA to be separated
what does sequence complexity refer to?
the number of times a particular base sequence appears in the genome
why are genes in complex eukaryotes longer than in simpler eukaryotes?
they have many introns
a typical bacterial chromosome contains a few ___________ different genes
thousand
main function of genetic material
to store information in DNA required to produce traits of an organism
DNA supercoiling
two strands of DNA that already coil around each other with the formation of additional coils due to twisting forces (over or under coiling)
left handed twist
underwinding
both ___________ and __________ of the DNA double helix can cause supercoiling
underwinding, over-winding
360-degree left-handed twist of the DNA can result in what 2 conformations?
unstable negative supercoil
360-degree right-handed twist of the DNA can result in what 2 conformations?
unstable positive supercoil
Ciprofloxacin (Cipro)
used in treatment of anthrax
