Genetics 10
HC 5-6-7
10.1
Chromosomes are located within the nucleus of living cells and are the structures that
contain the genetic material of an organism, whilst the genome is the entire genetic
material in the chromosomes. The genome of bacteria is a single, circular chromosome,
whereas eukaryotes have a single, linear, haploid set of 23 different chromosomes. The
primary function of the genetic material is to store information needed to produce
characteristics of an organism. Chromosomal sequences for this purpose feature four
important processes: RNA and protein synthesis; replication of chromosomes; proper
segregation of chromosomes and the compaction of chromosomes. The last indicates the
notion that your genome, or DNA, is never ‘naked’ but always associated with proteins, for
stability, packaging and hence regulation of gene expression. And no matter on what level,
even small virus genomes (DNA/RNA) are associated with proteins. Viruses are small
infectious particles containing nucleic acid surrounded by a capsid, which infect host cells
and rely on their host cells for replication. They do stick to a specific type of host’ they have
a limited host range. Their genome can be either DNA or RNA, single or double-stranded,
circular or linear. One example of proteins associated with the genome are chaperone
proteins, who help the viral assembly by creating the protein coat around the DNA/RNA. To
cut a long story short, there is also a virus genome, but it is relatively small and packaged
into the capsid/protein coat via an assembly process with which proteins can be associated.
Bacterial chromosomal DNA is mainly circular and contain just a single type of chromosome,
found in the nucleoid of the cell, a region that is not membrane bound so it is in direct
contact with the cytoplasm. However, they do have multiple copies of that single
chromosome. On that chromosome though, there are a few thousand genes, of which the
majority is protein-coding DNA. Non-transcribed regions between adjacent genes (similar to
introns in eukaryotic cells) are intergenic regions. Moreover, the chromosome has one
origin of replication which is a sequence that carries the initiation site for the assembly of
proteins needed for DNA replication. Contrastingly with eukaryotes, which have multiple
replication start sites, purely for a higher efficiency due to the higher number of
chromosomes. Lastly, bacterial chromosomes have several repetitive sequences scattered
within the intergenic regions, which do have a function: they play a role in DNA replication,
folding, gene regulation and gene recombination.
10.2
So, the bacterial chromosome is – highly compacted – found in the nucleoid of the cell and
suppose it has some copies of that chromosome, each copy resides in its own nucleoid,
directly exposed to the cytoplasm. But how does an entire chromosome fit inside the
nucleoid? This is not fully understood yet and differs per species. E. coli for example has a
mechanism by which the chromosomal DNA is compacted by forming many loops,
emanating from a central core, which makes up the chromosome. The loops, microdomains,
are dynamic and change in length and boundaries based on the environment. To form these
domains, a set of proteins are needed: nucleoid-associated proteins, such as structural
maintenance of chromosome proteins (SMCs), which thus facilitate chromosome
compaction and packaging.
, Because DNA is a long, thin molecule, twisting of it can change its conformation, both in
bacteria but as well in eukaryotes. Like a rubber band, when twisted it will eventually bulge
out and twist around itself. And because DNA is already in a double helix and coils around
each other, the additional coils caused by twisting is referred to as DNA supercoiling. When
you have a double helix of B DNA with 10 bp/turn and its ends fixed, and you give it a left-
handed twist, underwinding it, two things can happen. It either becomes an unstable
structure of 12.5 bp/turn or it can form a negative supercoil. The opposite, if you give it a
right-handed turn, overwinding it, it can have 8.3 bp/turn or form a positive supercoil. DNA
conformations of the negative or positive supercoil are topo-isomers of each other, they
only differ in the supercoil, but the rest is the same. Most of the bacterial chromosome is
negatively supercoiled.
The effect of supercoiling is that it is an important way to compact the bacterial
chromosome, so it decreases its size. Moreover, it affects DNA functioning, since it creates
tension on the DNA strands that may be released by their separation; it thus promotes
strand separation needed for replication. DNA gyrase in bacteria, or topoisomerase II in
eukaryotes, is an enzyme with four subunits that introduces negative supercoils (or relaxes
positive ones) through ATP-energy and can cleave both DNA strands. This is desirable for
greater compaction/condensation of the chromosome. DNA gyrase can as well ‘unknot’
intertwined DNA molecules after DNA replication.
Topoisomerase I cleaves only one DNA strand and introduces positive supercoils/relaxes
negative ones. It can thus bind to a negative supercoil, break one DNA strand, so it can
rotate and release the tension; untangle ‘knotted’ DNA. Introducing negative supercoils via
DNA gyrase for bacteria is critical for survival, since it regulates replication, so antibacterial
drugs aim at inhibiting the functioning of this enzyme. Because topoisomerase I unwinds
DNA, it is essential for replication because without it, the knotted DNA would not be
accessible; this makes it an interesting target in cancer cells, because would it be inhibited,
so would DNA replication be stopped, causing (cancer) cell death.
10.3
Eukaryotic cells have one or more sets of chromosomes composed of different linear
chromosomes, which in turn contains a long, linear DNA molecule. Humans, e.g., have two
sets of 23 chromosomes (diploid); the total amount of DNA is greater than in bacterial cells.
The chromosomes are located in the nucleus, wherein they fit thanks to several protein-
interactions and a DNA-protein complex named chromatin. In general, protein-encoding
genes in complex eukaryotes are long due to introns (noncoding intervening sequences)
whereas only the exons account for RNA structure.
There are three types of DNA sequences required for chromosomal replication and
segregation:
- Origin of replication chromosomal sites needed to initiate DNA replication
- Centromeres a site for the formation of kinetochores, which assemble before and
during mitosis and meiosis. Kinetochores are composed of proteins that ensure
proper linkage of the centromere to the spindle apparatus for the good segregation
of the chromosome during mitosis/meiosis in each daughter cell. Centromeres in
complex eukaryotes have such repetitive DNA sequences.
- Telomeres found at the end of linear chromosomes, they play a role I the
replication and stability of the chromosome. They prevent translocations and
chromosome shortening.
HC 5-6-7
10.1
Chromosomes are located within the nucleus of living cells and are the structures that
contain the genetic material of an organism, whilst the genome is the entire genetic
material in the chromosomes. The genome of bacteria is a single, circular chromosome,
whereas eukaryotes have a single, linear, haploid set of 23 different chromosomes. The
primary function of the genetic material is to store information needed to produce
characteristics of an organism. Chromosomal sequences for this purpose feature four
important processes: RNA and protein synthesis; replication of chromosomes; proper
segregation of chromosomes and the compaction of chromosomes. The last indicates the
notion that your genome, or DNA, is never ‘naked’ but always associated with proteins, for
stability, packaging and hence regulation of gene expression. And no matter on what level,
even small virus genomes (DNA/RNA) are associated with proteins. Viruses are small
infectious particles containing nucleic acid surrounded by a capsid, which infect host cells
and rely on their host cells for replication. They do stick to a specific type of host’ they have
a limited host range. Their genome can be either DNA or RNA, single or double-stranded,
circular or linear. One example of proteins associated with the genome are chaperone
proteins, who help the viral assembly by creating the protein coat around the DNA/RNA. To
cut a long story short, there is also a virus genome, but it is relatively small and packaged
into the capsid/protein coat via an assembly process with which proteins can be associated.
Bacterial chromosomal DNA is mainly circular and contain just a single type of chromosome,
found in the nucleoid of the cell, a region that is not membrane bound so it is in direct
contact with the cytoplasm. However, they do have multiple copies of that single
chromosome. On that chromosome though, there are a few thousand genes, of which the
majority is protein-coding DNA. Non-transcribed regions between adjacent genes (similar to
introns in eukaryotic cells) are intergenic regions. Moreover, the chromosome has one
origin of replication which is a sequence that carries the initiation site for the assembly of
proteins needed for DNA replication. Contrastingly with eukaryotes, which have multiple
replication start sites, purely for a higher efficiency due to the higher number of
chromosomes. Lastly, bacterial chromosomes have several repetitive sequences scattered
within the intergenic regions, which do have a function: they play a role in DNA replication,
folding, gene regulation and gene recombination.
10.2
So, the bacterial chromosome is – highly compacted – found in the nucleoid of the cell and
suppose it has some copies of that chromosome, each copy resides in its own nucleoid,
directly exposed to the cytoplasm. But how does an entire chromosome fit inside the
nucleoid? This is not fully understood yet and differs per species. E. coli for example has a
mechanism by which the chromosomal DNA is compacted by forming many loops,
emanating from a central core, which makes up the chromosome. The loops, microdomains,
are dynamic and change in length and boundaries based on the environment. To form these
domains, a set of proteins are needed: nucleoid-associated proteins, such as structural
maintenance of chromosome proteins (SMCs), which thus facilitate chromosome
compaction and packaging.
, Because DNA is a long, thin molecule, twisting of it can change its conformation, both in
bacteria but as well in eukaryotes. Like a rubber band, when twisted it will eventually bulge
out and twist around itself. And because DNA is already in a double helix and coils around
each other, the additional coils caused by twisting is referred to as DNA supercoiling. When
you have a double helix of B DNA with 10 bp/turn and its ends fixed, and you give it a left-
handed twist, underwinding it, two things can happen. It either becomes an unstable
structure of 12.5 bp/turn or it can form a negative supercoil. The opposite, if you give it a
right-handed turn, overwinding it, it can have 8.3 bp/turn or form a positive supercoil. DNA
conformations of the negative or positive supercoil are topo-isomers of each other, they
only differ in the supercoil, but the rest is the same. Most of the bacterial chromosome is
negatively supercoiled.
The effect of supercoiling is that it is an important way to compact the bacterial
chromosome, so it decreases its size. Moreover, it affects DNA functioning, since it creates
tension on the DNA strands that may be released by their separation; it thus promotes
strand separation needed for replication. DNA gyrase in bacteria, or topoisomerase II in
eukaryotes, is an enzyme with four subunits that introduces negative supercoils (or relaxes
positive ones) through ATP-energy and can cleave both DNA strands. This is desirable for
greater compaction/condensation of the chromosome. DNA gyrase can as well ‘unknot’
intertwined DNA molecules after DNA replication.
Topoisomerase I cleaves only one DNA strand and introduces positive supercoils/relaxes
negative ones. It can thus bind to a negative supercoil, break one DNA strand, so it can
rotate and release the tension; untangle ‘knotted’ DNA. Introducing negative supercoils via
DNA gyrase for bacteria is critical for survival, since it regulates replication, so antibacterial
drugs aim at inhibiting the functioning of this enzyme. Because topoisomerase I unwinds
DNA, it is essential for replication because without it, the knotted DNA would not be
accessible; this makes it an interesting target in cancer cells, because would it be inhibited,
so would DNA replication be stopped, causing (cancer) cell death.
10.3
Eukaryotic cells have one or more sets of chromosomes composed of different linear
chromosomes, which in turn contains a long, linear DNA molecule. Humans, e.g., have two
sets of 23 chromosomes (diploid); the total amount of DNA is greater than in bacterial cells.
The chromosomes are located in the nucleus, wherein they fit thanks to several protein-
interactions and a DNA-protein complex named chromatin. In general, protein-encoding
genes in complex eukaryotes are long due to introns (noncoding intervening sequences)
whereas only the exons account for RNA structure.
There are three types of DNA sequences required for chromosomal replication and
segregation:
- Origin of replication chromosomal sites needed to initiate DNA replication
- Centromeres a site for the formation of kinetochores, which assemble before and
during mitosis and meiosis. Kinetochores are composed of proteins that ensure
proper linkage of the centromere to the spindle apparatus for the good segregation
of the chromosome during mitosis/meiosis in each daughter cell. Centromeres in
complex eukaryotes have such repetitive DNA sequences.
- Telomeres found at the end of linear chromosomes, they play a role I the
replication and stability of the chromosome. They prevent translocations and
chromosome shortening.
