Genes are DNA

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Chapter 1
Genes are DNA
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Figure 1.1 A brief history of genetics.
1.1 Introduction
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Genes are DNA
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Avirulent mutants of a virus have lost the
capacity to infect a host cell productively, that
is, to make more virus.Transfection of
eukaryotic cells is the acquisition of new
genetic markers by incorporation of added
DNA.Transforming principle is DNA that is taken
up by a bacterium and whose expression then
changes the properties of the recipient cell.
1.2 DNA is the genetic material
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Figure 1.2 The transforming principle is DNA.
1.2 DNA is the genetic material
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Figure 1.3 The genetic material of phage T2 is
DNA.
1.2 DNA is the genetic material
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Figure 1.4 Eukaryotic cells can acquire a new
phenotype as the result of transfection by added
DNA.
1.2 DNA is the genetic material
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Antiparallel strands of the double helix are
organized in opposite orientation, so that the 5'
end of one strand is aligned with the 3' end of
the other strand.Base pairing describes the
specific (complementary) interactions of adenine
with thymine or of cytosine with thymine in a DNA
double helix (the former is replaced by adenine
with uracil in double helical RNA).Complementary
base pairs are defined by the pairing reactions
in double helical nucleic acids (A with T in DNA
or with U in RNA, and C with G).Supercoiling
describes the coiling of a closed duplex DNA in
space so that it crosses over its own axis.
1.3 DNA is a double helix
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Figure 1.5 A polynucleotide chain consists of a
series of 5?-3? sugar-phosphate links that form a
backbone from which the bases protrude
1.3 DNA is a double helix
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Figure 1.6 The double helix maintains a constant
width because purines always face pyrimidines in
the complementary A-T and G-C base pairs. The
sequence in the figure is T-A, C-G, A-T, G-C.
1.3 DNA is a double helix
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Figure 1.7 Flat base pairs lie perpendicular to
the sugar-phosphate backbone.
1.3 DNA is a double helix
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Figure 1.8 The two strands of DNA form a double
helix.
1.3 DNA is a double helix
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DNA polymerases are enzymes that synthesize a
daughter strand(s) of DNA (under direction from a
DNA template). May be involved in repair or
replication.DNAases are enzymes that attack
bonds in DNA.Endonucleases cleave bonds within a
nucleic acid chain they may be specific for RNA
or for single-stranded or double-stranded
DNA.Exonucleases cleave nucleotides one at a
time from the end of a polynucleotide chain they
may be specific for either the 5' or 3' end of
DNA or RNA.Parental strands of DNA are the two
complementary strands of duplex DNA before
replication.
1.4 DNA replication is semicon-servative
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Replication fork is the point at which strands of
parental duplex DNA are separated so that
replication can proceed.Ribonucleases are
enzymes that degrade RNA. Exo(ribo)nucleases work
progressively, typically degrading one base at a
time from the 3' end toward the 5 ' end.
Endo(ribo)nucleases make single cuts within the
RNA chain.RNA polymerases are enzymes that
synthesize RNA using a DNA template (formally
described as DNA-dependent RNA polymerases).RNAas
es are enzymes that degrade RNA.Semiconservative
replication is accomplished by separation of the
strands of a parental duplex, each then acting as
a template for synthesis of a complementary
strand.
1.4 DNA replication is semicon-servative
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Figure 1.9 Base pairing provides the mechanism
for replicating DNA.
1.4 DNA replication is semicon-servative
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Figure 1.10 Replication of DNA is
semiconservative.
1.4 DNA replication is semicon-servative
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Figure 1.11 The replication fork is the region of
DNA in which there is a transition from the
unwound parental duplex to the newly replicated
daughter duplexes.
1.4 DNA replication is semiconservative
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Denaturation of DNA or RNA describes its
conversion from the double-stranded to the
single-stranded state separation of the strands
is most often accomplished by heating.Hybridizati
on is the pairing of complementary RNA and DNA
strands to give an RNA-DNA hybrid.Melting of DNA
means its denaturation.Melting temperature of
DNA is the mid-point of the transition when
duplex DNA to denatured by heating to separate
into single strands. Renaturation is the
reassociation of denatured complementary single
strands of a DNA double helix.
1.5 Nucleic acids hybridize by base pairing
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Figure 1.12 Base pairing occurs in duplex DNA and
also in intra- and inter-molecular interactions
in single-stranded RNA (or DNA).
1.5 Nucleic acids hybridize by base pairing
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Figure 1.13 Denatured single strands of DNA can
renature to give the duplex form.
1.5 Nucleic acids hybridize by base pairing
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Figure 1.14 Filter hybridization establishes
whether a solution of denatured DNA (or RNA)
contains sequences complementary to the strands
immobilized on the filter.
1.5 Nucleic acids hybridize by base pairing
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Background level of mutation describes the rate
at which sequence changes accumulate in the
genome of an organism. It reflects the balance
between the occurrence spontaneous mutations and
their remomval by repair systems, and is
characteristic for any species.Deletions are
generated by removal of a sequence of DNA, the
regions on either side being joined
together.result from the action of a mutagen
(which may act directly on the bases in DNA) or
indirectly, but in either case the result is a
change in the sequence of DNA. are identified by
the presence of an additional stretch of base
pairs in DNA.
1.6 Mutations change the sequence of DNA
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Leaky mutants have some residual function, either
because the mutant protein is partially active
(in the case of a missense mutation), or because
a small amount of wild-type protein is made (in
the case of a nonsense mutation).Mutagens
increase the rate of mutation by inducing changes
in DNA sequence, directly or indirectly.Point
mutations are changes involving single base
pairs.Revertants are derived by reversion of a
mutant cell or organism.Spontaneous mutations
occur as the result of natural effects, due
either to mistakes in DNA replication or to
environmental damage.
1.6 Mutations change the sequence of DNA
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Suppression describes the occurrence of changes
that eliminate the effects of a mutation without
reversing the original change in DNA.Suppressor
(extragenic) is usually a gene coding a mutant
tRNA that reads the mutated codon either in the
sense of the original codon or to give an
acceptable substitute for the original
meaning.Transition is a mutation in which one
pyrimidine is substituted by the other or in
which one purine is substituted for the
other.Transversion is a mutation in which a
purine is replaced by a pyrimidine or vice versa.
1.6 Mutations change the sequence of DNA
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Figure 1.15 Mutations can be induced by chemical
modification of a base.
1.6 Mutations change the sequence of DNA
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Figure 1.16 Mutations can be induced by the
incorporation of base analogs into DNA.
1.6 Mutations change the sequence of DNA
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Back mutation reverses the effect of a mutation
that had inactivated a gene thus it restores
wild type.Forward mutations inactivate a
wild-type gene.Hotspot is a site at which the
frequency of mutation (or recombination) is very
much increased.Modified bases are all those
except the usual four from which DNA (T, C, A, G)
or RNA (U, C, A, G) are synthesized they result
from postsynthetic changes in the nucleic
acid.Neutral substitutions in a protein are
those changes of amino acids that do not affect
activity.Silent mutations do not change the
product of a gene.
1.7 Mutations are concentrated at hotspots
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Figure 1.17 Spontaneous mutations occur
throughout the lacI gene of E. coli, but are
concentrated at a hotspot.
1.7 Mutations are concentrated at hotspots
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Figure 1.18 The deamination of 5-methylcytosine
produces thymine (causing C-G to T-A
transitions), while the deamination of cytosine
produces uracil (which usually is removed and
then replaced by cytosine).
1.7 Mutations are concentrated at hotspots
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Figure 1.15 Mutations can be induced by chemical
modification of a base.
1.7 Mutations are concentrated at hotspots
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Cistron is the genetic unit defined by the
cis/trans test equivalent to gene.Complementatio
n group is a series of mutations unable to
complement when tested in pairwise combinations
in trans defines a genetic unit (the
cistron).Gene (cistron) is the segment of DNA
involved in producing a polypeptide chain it
includes regions preceding and following the
coding region (leader and trailer) as well as
intervening sequences (introns) between
individual coding segments (exons).One gene
one enzyme hypothesis is the basis of modern
genetics that a gene is a stretch of DNA coding
for a single polypeptide chain.
1.8 A cistron is a single stretch of DNA
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Figure 1.19 Genes code for proteins dominance is
explained by the properties of mutant proteins. A
recessive allele does not contribute to the
phenotype because it produces no protein (or
protein that is nonfunctional).
1.8 A cistron is a single stretch of DNA
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Figure 1.20 The cistron is defined by the
complementation test. Genes are represented by
bars red stars identify sites of mutation.
1.8 A cistron is a single stretch of DNA
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Gain-of-function mutation represents acquisition
of a new activity. It is dominant.Leaky mutants
have some residual function, either because the
mutant protein is partially active (in the case
of a missense mutation), or because a small
amount of wild-type protein is made (in the case
of a nonsense mutation).Loss-of-function
mutation inactivates a gene. It is
recessive.Null mutation completely eliminates
the function of a gene, usually because it has
been physically deleted.Polymorphism refers to
the simultaneous occurrence in the population of
genomes showing allelic variations (as seen
either in alleles producing different phenotypes
or-for example-in changes in DNA affecting the
restriction pattern).
1.9 The nature of multiple alleles
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Figure 1.19 Genes code for proteins dominance is
explained by the properties of mutant proteins. A
recessive allele does not contribute to the
phenotype because it produces no protein (or
protein that is nonfunctional).
1.9 The nature of multiple alleles
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Figure 1.21 The w locus has an extensive series
of alleles, whose phenotypes extend from
wild-type (red) color to complete lack of
pigment.
1.9 The nature of multiple alleles
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Figure 1.22 The ABO blood group locus codes for a
galactosyltransferase whose specificity
determines the blood group.
1.9 The nature of multiple alleles
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Bivalent is the structure containing all four
chromatids (two representing each homologue) at
the start of meiosis.Breakage and reunion
describes the mode of genetic recombination, in
which two DNA duplex molecules are broken at
corresponding points and then rejoined crosswise
(involving formation of a length of heteroduplex
DNA around the site of joining).Chiasma (pl.
chiasmata) is a site at which two homologous
chromosomes appear to have exchanged material
during meiosis.Crossing-over describes the
reciprocal exchange of material between
chromosomes that occurs during meiosis and is
responsible for genetic recombination.Hybrid DNA
is another term for heteroduplex DNA.
1.10 Recombination occurs by physical exchange of
DNA
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Figure 1.23 Chiasma formation is responsible for
generating recombinants.
1.10 Recombination occurs by physical exchange of
DNA
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Figure 1.24 Recombination involves pairing
between complementary strands of the two parental
duplex DNAs.
1.10 Recombination occurs by physical exchange of
DNA
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Figure 1.13 Denatured single strands of DNA can
renature to give the duplex form.
1.10 Recombination occurs by physical exchange of
DNA
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Codon is a triplet of nucleotides that represents
an amino acid or a termination signal.Frameshift
mutation results from an insertion or deletion
that changes the phase of triplets, so that all
codons are misread after the site of
mutation.Genetic code is the correspondence
between triplets in DNA (or RNA) and amino acids
in protein.Initiation codon is a special codon
(usually AUG) used to start synthesis of a
protein.ORF is an open reading frame presumed
likely to code for a protein.gtReading frame is
one of three possible ways of reading a
nucleotide sequence as a series of
triplets.Suppressor (extragenic) is usually a
gene coding a mutant tRNA that reads the mutated
codon either in the sense of the original codon
or to give an acceptable substitute for the
original meaning.Termination codon is one of
three (UAG, UAA, UGA) that causes protein
synthesis to terminate.
1.11 The genetic code is triplet-- Key terms
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Figure 1.25 Frameshift mutations show that the
genetic code is read in triplets from a fixed
starting point.
1.11 The genetic code is triplet
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Figure 1.26 An open reading frame starts with AUG
and continues in triplets to a termination codon.
Blocked reading frames may be interrupted
frequently by termination codons.
1.11 The genetic code is triplet
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Coding region is a part of the gene that
represents a protein sequence.Leader of a
protein is a short N-terminal sequence
responsible for passage into or through a
membrane.RNA splicing is the process of excising
the sequences in RNA that correspond to introns,
so that the sequences corresponding to exons are
connected into a continuous mRNA.Trailer is a
nontranslated sequence at the 3 end of an mRNA
following the termination codon.Transcription is
synthesis of RNA on a DNA template.Translation
is synthesis of protein on the mRNA template.
1.12 The relationship between coding sequences
and proteins
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Figure 1.27 The recombination map of the
tryptophan synthetase gene corresponds with the
amino acid sequence of the protein.
1.12 The relationship between coding sequences
and proteins
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Figure 1.28 RNA is synthesized by using one
strand of DNA as a template for complementary
base pairing.
1.12 The relationship between coding sequences
and proteins
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Figure 1.29 The gene may be longer than the
sequence coding for protein.
1.12 The relationship between coding sequences
and proteins
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Figure 1.30 Gene expression is a multistage
process.
1.12 The relationship between coding sequences
and proteins
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Figure 2.10 Interrupted genes are expressed via a
precursor RNA. Introns are removed when the exons
are spliced together. The mRNA has only the
sequences of the exons.
1.12 The relationship between coding sequences
and proteins
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Figure 5.16 Eukaryotic mRNA is modified by
addition of a cap to the 5? end and poly(A) to
the 3? end.
1.12 The relationship between coding sequences
and proteins
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cis- configuration describes two sites on the
same molecule of DNA.Trans- configuration of two
sites refers to their presence on two different
molecules of DNA (chromosomes).
1.13 cis-acting sites and trans-acting molecules
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Figure 1.20 The cistron is defined by the
complement-ation test. Genes are represented by
bars red stars identify sites of mutation.
1.13 cis-acting sites and trans-acting molecules
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Figure 1.31 Control sites in DNA provide binding
sites for proteins coding regions are expressed
via the synthesis of RNA.
1.13 cis-acting sites and trans-acting molecules
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Figure 1.32A cis-acting site controls the
adjacent DNA but does not influence the other
allele.
1.13 cis-acting sites and trans-acting molecules
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Figure 1.33 A trans-acting mutation in a protein
affects both alleles of a gene that it controls.
1.13 cis-acting sites and trans-acting molecules
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Central dogma describes the basic nature of
genetic information sequences of nucleic acid
can be perpetuated and interconverted by
replication, transcription, and reverse
transcription, but translation from nucleic acid
to protein is unidirectional, because nucleic
acid sequences cannot be retrieved from protein
sequences.Prion is a proteinaceous infectious
agent, which behaves as an inheritable trait,
although it contains no nucleic acid. Examples
are PrPSc, the agent of scrapie in sheep and
bovine spongiform encephalopathy, and Psi, which
confers an inherited state in yeast.Reverse
transcription is synthesis of DNA on a template
of RNA accomplished by reverse transcriptase
enzyme.Scrapie is a infective agent made of
protein.Virion is the physical virus particle
(irrespective of its ability to infect cells and
reproduce).Viroid is a small infectious nucleic
acid that does not have a protein coat.
1.14 Genetic informationcan be provided by DNA or
RNA
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Figure 1.34 The central dogma states that
information in nucleic acid can be perpetuated or
transferred, but the transfer of information into
protein is irreversible.
1.14 Genetic information can be provided by DNA
or RNA
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Figure 1.35 Double-stranded and single-stranded
nucleic acids both replicate by synthesis of
complementary strands governed by the rules of
base pairing.
1.14 Genetic information can be provided by DNA
or RNA
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Figure 1.36 The amount of nucleic acid in the
genome varies over an enormous range.
1.14 Genetic information can be provided by DNA
or RNA
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Figure 1.37 PSTV RNA is a circular molecule that
forms an extensive double-stranded structure,
interrupted by many interior loops. The severe
and mild forms differ at three sites.
1.14 Genetic information can be provided by DNA
or RNA
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1. Two classic experiments proved that DNA is the
genetic material. 2. DNA is a double helix
consisting of antiparallel strands in which the
nucleotide units are linked by 5?3 phosphodiester
bonds. 3. A stretch of DNA may code for
protein.4. A chromosome consists of an
uninterrupted length of duplex DNA that contains
many genes. 5. A gene may have multiple alleles.
Recessive alleles are caused by a
loss-of-function.
1.15 Summary
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6. A mutation consists of a change in the
sequence of AT and GC base pairs in DNA. 7.
The natural incidence of mutations is increased
by mutagens. 8. Forward mutations occur at a
rate of 106 per locus per generation back
mutations are rarer. 9. Although all genetic
information in cells is carried by DNA, viruses
have genomes of double-stranded or
single-stranded DNA or RNA.
1.15 Summary