BIO130H1 Chapter Notes - Chapter 4: Noncoding Dna
What is a genome:
- The complete set of genes or genetic material
present in a cell or organism
Denaturing DNA
- once DNA strands have been separated the
hydrophobic interactions that results from base
stacking has decreased which changes the
chemical nature of the bases and increases their
absorbance of ultraviolet radiation
- Melting temperature (Tm): the temperature in
which the shift of absorbance is half completed
… higher the GC content (G%+ %C) then higher
the Tm
DNA Renaturation
- if you cooled the DNA that has been separated
the DNA regains the properties of the double
helix
- it absorbed less ultraviolet light and once again
behave like genetic material
- Renaturation or reannealing: complementary
base pairs being able to reassociate back into
the double helix formation and continue its
function after being denatured
- reannealing ha sled to the development of
methodology called nucleic acid hybridization:
complementary base strands of nucleic acids
from different source can mix and form double
stranded (hybrid) molecules)
Viral and Bacterial Genomes
- Factors that determine the rate of renaturation:
1. the ionic strength go the solution
2. the incubation temperature
3. the concentration of DNA
4. the period of incubation
5. the size of the interacting molecules
Comparing DNAs with these factors in mind
- the reaction molecules must be of
equivalent length
NOTE: the small the genome size= the great the
number of genomes present in a given weight of
DNA ad the great the chance of collision
between complementary fragments
Eukaryotic Genomes
- Bacterial and viral renaturation occurs along
single, symmetrical curves
- it occurs in these curved because all of the
sequences are present at the same
concentration therefore any nucleotide sequence
in the population can more than likely find a
partner
- Mammalian renaturation occur at different rates
- this means that DNA fragments are present
in a population a different concentrations
- this is one example that eukaryotic DNA is
not a simple progression of one gene after
another but has a complex organization
- Reanneal curves have three more or less
distinct steps which correspond to the
reannealing of three broad classes of DNA
sequences
- the three classes reanneal at different rates
because they differ as to the number of times
their nucleotide sequence is repeated within the
population of fragments
- The three classes are termed:
1. The highly repeated fraction
2. the moderately repeated fraction
3. the non repeated fraction
Highly repeated DNA sequences
- constitutes anywhere form about 1 - 10 percent
of the total DNA
- typically short
- present in clusters
- the given sequence repeats itself over and over
again without interruption
- tandem: a sequence arranged in end to end
manner
- falls into overlapping categories:
satellite DNAs,
minisatilite DNAs,
microsatelite DNAs
Satellite DNA
- consist of short sequences that from
very large clusters
- each contain up to several million
base pairs of DNA
- the base composition is sufficiently
different than the build of the DNA
- fragments containing the sequence
can be separated into distinct “satellite” band
during density gradient centrifugation
- Satellite DNA tend to evolve
rapidlycausing the sequences of these genomic
elements to vary even between closely related
species
Minisatellite DNAs
- shortest sequences (1 to 9 base pairs
long)
- present in clusters of 10 to 40 base
pairs in length
- scattered evenly through the genome
- DNA replicating enzymes have trouble
copying regions of the genome that contain
these small repetitive sequences
- which causes the DNA to change in
length through the generations
In situ hybridization
- DNA of the chromosomes is kept in place while
it is allowed to react with a particular preparation
of labeled DNA
- FISH: Fluorescence in situ hybridization:
- DNA can be detected by being radioactively
labeled and was localized by autoradiography
- use fluorescent dye and then the DNA is
localized with a fluorescence microscope
- the process: both interactants (DNA) must
be single stranded (by treating the chromosomes
with a hot salt solution which causes the strands
to separate and remain apart
- denatured chromosomes ar incubated
with a solution of biotin- labeled, single-
stranded satellite DNA, which binds selectively
to the complementary strands of immobilized
satellite DNA located in the chromosomes
- following the incubation period, the
soluble, unhybridized satellite DNA is washed
away or digested, and has the sites of the
bound, labeled DNAs revealed
Moderately Repeated DNA sequences
- vary about 20 to more than 80 percent of the
total DNA (depending on the organism)
- sequences repeated anywhere from a few
times to tend of thousands of times
- included are sequences that code for known
gene products, either RNAs or proteins, and
those that lack a coding function
Repeated DNA sequences with
Coding Functions
DNA that codes for ribosomal
RNA, important group of
chromosomal proteins, the
histones
the repeated sequences are
typically identical to one
another an located in tandem
array
Repeated DNAs that Lack
Functions
the build of the moderately
repeated DNA fraction does
not encode any type of
product
the members are scattered
throughout the genomes
can by grouped int two
classes: SINEs (short
interspersed elements) or
LINEs (long intersperse
elements)
Non repeated DNA sequences
when DNA is denature and
reanneals it takes a slow time
to find its partner… so slow
that the presume to be
present in a single copy per
genome
This fraction comprises the
non repeated (or single-
copy) DNA sequences, which
includes the genes that
exhibit Mendelian patterns of
inheritance
Non repeated genes localized
in a particular site on a
particular chromosome
Contains the greatest amount
of of genetic information
included DNA
sequenced that code
for virtually all proteins
other than histones
FACT: genes that code
polypeptides are
usually members of a
family of related genes
Fact: 1.5% of the human genome encodes the
amino acids of our proteins
The Stability of the Genome
Diploid: 2 sets of chromosomes: one from
mother and one from father
- having homologous chromosomes
Polyploidization (or whole genome
duplication)
- it is an even in which offspring are produces
that have twice the number chromosomes in
each cell as their diploid parent
- therefore the offspring has 4 homologues of
each chromes rather than two
- occurs in two ways:
1) two released spiced mate to from a hybrid
organism that contains combine chromosomes
from both parents (occurs most often in plants)
2) a singled celled embryo undergoes
chromosome duplication but the duplicates,
rather than being separated into two separate
cells, are retained in a single cell that developed
a viable embryo. (occurs most often in animals)
doubling f chromosomes gives the organisms an
evolutionary advantage
- can result in the production of new species that
has a great deal of “extra” genetic information
- extra copied can be:
- lost by deletion
- render inactive by deleterious
mutations,
- evolve into new genes that possess
new functions
THE HUMAN GENOME
- Only 1.5% of your genome encodes protein
- only 50% of your genome is repetitive DNA
unique sequences: non repeating sequences
repeated sequences: highly to moderately
repeated
red/ orange region: Irons, protein- coding
regions —> 1.5%
Green: the non repetitive DNA that is neither
introns or codons —> ex promoter and
regulatory regions
- yellow: histones, rRNA (near 50)
- Brown to brown region: Transposons—
repeated genes, they are mobile, can move
around the genome
- Greyretroviral: not active genes
- brown: thousands of repeats… long
repeated sequences
- green: tens of repeats.. shorter
- black: simple sequence repeats :
microsatilites
- Yellow: segmental duplications
NOT JUNK DNA
- some of these are not even sequence yet
because it hard to sequence highly receptive
stuff
What is a genome:
- The complete set of genes or genetic material
present in a cell or organism
Denaturing DNA
- once DNA strands have been separated the
hydrophobic interactions that results from base
stacking has decreased which changes the
chemical nature of the bases and increases their
absorbance of ultraviolet radiation
- Melting temperature (Tm): the temperature in
which the shift of absorbance is half completed
… higher the GC content (G%+ %C) then higher
the Tm
DNA Renaturation
- if you cooled the DNA that has been separated
the DNA regains the properties of the double
helix
- it absorbed less ultraviolet light and once again
behave like genetic material
- Renaturation or reannealing: complementary
base pairs being able to reassociate back into
the double helix formation and continue its
function after being denatured
- reannealing ha sled to the development of
methodology called nucleic acid hybridization:
complementary base strands of nucleic acids
from different source can mix and form double
stranded (hybrid) molecules)
Viral and Bacterial Genomes
- Factors that determine the rate of renaturation:
1. the ionic strength go the solution
2. the incubation temperature
3. the concentration of DNA
4. the period of incubation
5. the size of the interacting molecules
Comparing DNAs with these factors in mind
- the reaction molecules must be of
equivalent length
NOTE: the small the genome size= the great the
number of genomes present in a given weight of
DNA ad the great the chance of collision
between complementary fragments
Eukaryotic Genomes
- Bacterial and viral renaturation occurs along
single, symmetrical curves
- it occurs in these curved because all of the
sequences are present at the same
concentration therefore any nucleotide sequence
in the population can more than likely find a
partner
- Mammalian renaturation occur at different rates
- this means that DNA fragments are present
in a population a different concentrations
- this is one example that eukaryotic DNA is
not a simple progression of one gene after
another but has a complex organization
- Reanneal curves have three more or less
distinct steps which correspond to the
reannealing of three broad classes of DNA
sequences
- the three classes reanneal at different rates
because they differ as to the number of times
their nucleotide sequence is repeated within the
population of fragments
- The three classes are termed:
1. The highly repeated fraction
2. the moderately repeated fraction
3. the non repeated fraction
Highly repeated DNA sequences
- constitutes anywhere form about 1 - 10 percent
of the total DNA
- typically short
- present in clusters
- the given sequence repeats itself over and over
again without interruption
- tandem: a sequence arranged in end to end
manner
- falls into overlapping categories:
satellite DNAs,
minisatilite DNAs,
microsatelite DNAs
Satellite DNA
- consist of short sequences that from
very large clusters
- each contain up to several million
base pairs of DNA
- the base composition is sufficiently
different than the build of the DNA
- fragments containing the sequence
can be separated into distinct “satellite” band
during density gradient centrifugation
- Satellite DNA tend to evolve
rapidlycausing the sequences of these genomic
elements to vary even between closely related
species
Minisatellite DNAs
- shortest sequences (1 to 9 base pairs
long)
- present in clusters of 10 to 40 base
pairs in length
- scattered evenly through the genome
- DNA replicating enzymes have trouble
copying regions of the genome that contain
these small repetitive sequences
- which causes the DNA to change in
length through the generations
In situ hybridization
- DNA of the chromosomes is kept in place while
it is allowed to react with a particular preparation
of labeled DNA
- FISH: Fluorescence in situ hybridization:
- DNA can be detected by being radioactively
labeled and was localized by autoradiography
- use fluorescent dye and then the DNA is
localized with a fluorescence microscope
- the process: both interactants (DNA) must
be single stranded (by treating the chromosomes
with a hot salt solution which causes the strands
to separate and remain apart
- denatured chromosomes ar incubated
with a solution of biotin- labeled, single-
stranded satellite DNA, which binds selectively
to the complementary strands of immobilized
satellite DNA located in the chromosomes
- following the incubation period, the
soluble, unhybridized satellite DNA is washed
away or digested, and has the sites of the
bound, labeled DNAs revealed
Moderately Repeated DNA sequences
- vary about 20 to more than 80 percent of the
total DNA (depending on the organism)
- sequences repeated anywhere from a few
times to tend of thousands of times
- included are sequences that code for known
gene products, either RNAs or proteins, and
those that lack a coding function
Repeated DNA sequences with
Coding Functions
DNA that codes for ribosomal
RNA, important group of
chromosomal proteins, the
histones
the repeated sequences are
typically identical to one
another an located in tandem
array
Repeated DNAs that Lack
Functions
the build of the moderately
repeated DNA fraction does
not encode any type of
product
the members are scattered
throughout the genomes
can by grouped int two
classes: SINEs (short
interspersed elements) or
LINEs (long intersperse
elements)
Non repeated DNA sequences
when DNA is denature and
reanneals it takes a slow time
to find its partner… so slow
that the presume to be
present in a single copy per
genome
This fraction comprises the
non repeated (or single-
copy) DNA sequences, which
includes the genes that
exhibit Mendelian patterns of
inheritance
Non repeated genes localized
in a particular site on a
particular chromosome
Contains the greatest amount
of of genetic information
included DNA
sequenced that code
for virtually all proteins
other than histones
FACT: genes that code
polypeptides are
usually members of a
family of related genes
Fact: 1.5% of the human genome encodes the
amino acids of our proteins
The Stability of the Genome
Diploid: 2 sets of chromosomes: one from
mother and one from father
- having homologous chromosomes
Polyploidization (or whole genome
duplication)
- it is an even in which offspring are produces
that have twice the number chromosomes in
each cell as their diploid parent
- therefore the offspring has 4 homologues of
each chromes rather than two
- occurs in two ways:
1) two released spiced mate to from a hybrid
organism that contains combine chromosomes
from both parents (occurs most often in plants)
2) a singled celled embryo undergoes
chromosome duplication but the duplicates,
rather than being separated into two separate
cells, are retained in a single cell that developed
a viable embryo. (occurs most often in animals)
doubling f chromosomes gives the organisms an
evolutionary advantage
- can result in the production of new species that
has a great deal of “extra” genetic information
- extra copied can be:
- lost by deletion
- render inactive by deleterious
mutations,
- evolve into new genes that possess
new functions
THE HUMAN GENOME
- Only 1.5% of your genome encodes protein
- only 50% of your genome is repetitive DNA
unique sequences: non repeating sequences
repeated sequences: highly to moderately
repeated
red/ orange region: Irons, protein- coding
regions —> 1.5%
Green: the non repetitive DNA that is neither
introns or codons —> ex promoter and
regulatory regions
- yellow: histones, rRNA (near 50)
- Brown to brown region: Transposons—
repeated genes, they are mobile, can move
around the genome
- Greyretroviral: not active genes
- brown: thousands of repeats… long
repeated sequences
- green: tens of repeats.. shorter
- black: simple sequence repeats :
microsatilites
- Yellow: segmental duplications
NOT JUNK DNA
- some of these are not even sequence yet
because it hard to sequence highly receptive
stuff
What is a genome:
- The complete set of genes or genetic material
present in a cell or organism
Denaturing DNA
- once DNA strands have been separated the
hydrophobic interactions that results from base
stacking has decreased which changes the
chemical nature of the bases and increases their
absorbance of ultraviolet radiation
- Melting temperature (Tm): the temperature in
which the shift of absorbance is half completed
… higher the GC content (G%+ %C) then higher
the Tm
DNA Renaturation
- if you cooled the DNA that has been separated
the DNA regains the properties of the double
helix
- it absorbed less ultraviolet light and once again
behave like genetic material
- Renaturation or reannealing: complementary
base pairs being able to reassociate back into
the double helix formation and continue its
function after being denatured
- reannealing ha sled to the development of
methodology called nucleic acid hybridization:
complementary base strands of nucleic acids
from different source can mix and form double
stranded (hybrid) molecules)
Viral and Bacterial Genomes
- Factors that determine the rate of renaturation:
1. the ionic strength go the solution
2. the incubation temperature
3. the concentration of DNA
4. the period of incubation
5. the size of the interacting molecules
Comparing DNAs with these factors in mind
- the reaction molecules must be of
equivalent length
NOTE: the small the genome size= the great the
number of genomes present in a given weight of
DNA ad the great the chance of collision
between complementary fragments
Eukaryotic Genomes
- Bacterial and viral renaturation occurs along
single, symmetrical curves
- it occurs in these curved because all of the
sequences are present at the same
concentration therefore any nucleotide sequence
in the population can more than likely find a
partner
- Mammalian renaturation occur at different rates
- this means that DNA fragments are present
in a population a different concentrations
- this is one example that eukaryotic DNA is
not a simple progression of one gene after
another but has a complex organization
- Reanneal curves have three more or less
distinct steps which correspond to the
reannealing of three broad classes of DNA
sequences
- the three classes reanneal at different rates
because they differ as to the number of times
their nucleotide sequence is repeated within the
population of fragments
- The three classes are termed:
1. The highly repeated fraction
2. the moderately repeated fraction
3. the non repeated fraction
Highly repeated DNA sequences
- constitutes anywhere form about 1 - 10 percent
of the total DNA
- typically short
- present in clusters
- the given sequence repeats itself over and over
again without interruption
- tandem: a sequence arranged in end to end
manner
- falls into overlapping categories:
satellite DNAs,
minisatilite DNAs,
microsatelite DNAs
Satellite DNA
- consist of short sequences that from
very large clusters
- each contain up to several million
base pairs of DNA
- the base composition is sufficiently
different than the build of the DNA
- fragments containing the sequence
can be separated into distinct “satellite” band
during density gradient centrifugation
- Satellite DNA tend to evolve
rapidlycausing the sequences of these genomic
elements to vary even between closely related
species
Minisatellite DNAs
- shortest sequences (1 to 9 base pairs
long)
- present in clusters of 10 to 40 base
pairs in length
- scattered evenly through the genome
- DNA replicating enzymes have trouble
copying regions of the genome that contain
these small repetitive sequences
- which causes the DNA to change in
length through the generations
In situ hybridization
- DNA of the chromosomes is kept in place while
it is allowed to react with a particular preparation
of labeled DNA
- FISH: Fluorescence in situ hybridization:
- DNA can be detected by being radioactively
labeled and was localized by autoradiography
- use fluorescent dye and then the DNA is
localized with a fluorescence microscope
- the process: both interactants (DNA) must
be single stranded (by treating the chromosomes
with a hot salt solution which causes the strands
to separate and remain apart
- denatured chromosomes ar incubated
with a solution of biotin- labeled, single-
stranded satellite DNA, which binds selectively
to the complementary strands of immobilized
satellite DNA located in the chromosomes
- following the incubation period, the
soluble, unhybridized satellite DNA is washed
away or digested, and has the sites of the
bound, labeled DNAs revealed
Moderately Repeated DNA sequences
- vary about 20 to more than 80 percent of the
total DNA (depending on the organism)
- sequences repeated anywhere from a few
times to tend of thousands of times
- included are sequences that code for known
gene products, either RNAs or proteins, and
those that lack a coding function
Repeated DNA sequences with
Coding Functions
DNA that codes for ribosomal
RNA, important group of
chromosomal proteins, the
histones
the repeated sequences are
typically identical to one
another an located in tandem
array
Repeated DNAs that Lack
Functions
the build of the moderately
repeated DNA fraction does
not encode any type of
product
the members are scattered
throughout the genomes
can by grouped int two
classes: SINEs (short
interspersed elements) or
LINEs (long intersperse
elements)
Non repeated DNA sequences
when DNA is denature and
reanneals it takes a slow time
to find its partner… so slow
that the presume to be
present in a single copy per
genome
This fraction comprises the
non repeated (or single-
copy) DNA sequences, which
includes the genes that
exhibit Mendelian patterns of
inheritance
Non repeated genes localized
in a particular site on a
particular chromosome
Contains the greatest amount
of of genetic information
included DNA
sequenced that code
for virtually all proteins
other than histones
FACT: genes that code
polypeptides are
usually members of a
family of related genes
Fact: 1.5% of the human genome encodes the
amino acids of our proteins
The Stability of the Genome
Diploid: 2 sets of chromosomes: one from
mother and one from father
- having homologous chromosomes
Polyploidization (or whole genome
duplication)
- it is an even in which offspring are produces
that have twice the number chromosomes in
each cell as their diploid parent
- therefore the offspring has 4 homologues of
each chromes rather than two
- occurs in two ways:
1) two released spiced mate to from a hybrid
organism that contains combine chromosomes
from both parents (occurs most often in plants)
2) a singled celled embryo undergoes
chromosome duplication but the duplicates,
rather than being separated into two separate
cells, are retained in a single cell that developed
a viable embryo. (occurs most often in animals)
doubling f chromosomes gives the organisms an
evolutionary advantage
- can result in the production of new species that
has a great deal of “extra” genetic information
- extra copied can be:
- lost by deletion
- render inactive by deleterious
mutations,
- evolve into new genes that possess
new functions
THE HUMAN GENOME
- Only 1.5% of your genome encodes protein
- only 50% of your genome is repetitive DNA
unique sequences: non repeating sequences
repeated sequences: highly to moderately
repeated
red/ orange region: Irons, protein- coding
regions —> 1.5%
Green: the non repetitive DNA that is neither
introns or codons —> ex promoter and
regulatory regions
- yellow: histones, rRNA (near 50)
- Brown to brown region: Transposons—
repeated genes, they are mobile, can move
around the genome
- Greyretroviral: not active genes
- brown: thousands of repeats… long
repeated sequences
- green: tens of repeats.. shorter
- black: simple sequence repeats :
microsatilites
- Yellow: segmental duplications
NOT JUNK DNA
- some of these are not even sequence yet
because it hard to sequence highly receptive
stuff
31
BIO130H1 Full Course Notes
Verified Note
31 documents
Document Summary
The complete set of genes or genetic material present in a cell or organism. Once dna strands have been separated the hydrophobic interactions that results from base stacking has decreased which changes the chemical nature of the bases and increases their absorbance of ultraviolet radiation. Melting temperature (tm): the temperature in which the shift of absorbance is half completed. Higher the gc content (g%+ %c) then higher the tm. If you cooled the dna that has been separated the dna regains the properties of the double helix. It absorbed less ultraviolet light and once again behave like genetic material behave like genetic material. Renaturation or reannealing: complementary base pairs being able to reassociate back into the double helix formation and continue its function after being denatured. Reannealing ha sled to the development of methodology called nucleic acid hybridization: complementary base strands of nucleic acids from di erent source can mix and form double stranded (hybrid) molecules)
