1.6 Mutations change the sequence of DNA

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Chapter 1

Genes are DNA

DNA
是遗传物质

DNA
为双螺旋

DNA
的复制是半保留的

通过碱基配对进行核酸杂交

突变改变了
DNA
的序列

突变集中于热点

顺反子是单个
DNA
片断

多重等位基因的种类

DNA
的物理交换导致重组

遗传密码是三联体

细菌的基因和蛋白是共线性的

顺式作用点和反式作用分子

遗传信息可由
DNA
或者
RNA
提供









Figure 1.1 A brief
history of genetics.

1.1
Introduction

Genes are DNA

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

Figure 1.2 The transforming
principle is DNA.

1.2 DNA is the
genetic material

Figure 1.3 The genetic
material of phage T2 is DNA.

1.2 DNA is the
genetic material

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


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


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


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


Figure 1.7 Flat base
pairs lie perpendicular
to the sugar
-
phosphate
backbone.

1.3 DNA is a
double helix

Figure 1.8 The two
strands of DNA form a
double helix.

1.3 DNA is a
double helix

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

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).

RNAases

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

Figure 1.9 Base pairing
provides the
mechanism for
replicating DNA.

1.4 DNA
replication is
semicon
-
servative

Figure 1.10
Replication of DNA is
semiconservative.

1.4 DNA
replication is
semicon
-
servative

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

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.

Hybridization

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

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

Figure 1.13 Denatured
single strands of DNA
can renature to give the
duplex form.

1.5

Nucleic acids
hybridize by
base pairing

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

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

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

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

Figure 1.15 Mutations
can be induced by
chemical modification
of a base.

1.6 Mutations
change the
sequence of
DNA

Figure 1.16 Mutations
can be induced by the
incorporation of base
analogs into DNA.

1.6 Mutations
change the
sequence of
DNA

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

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

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

Figure 1.15 Mutations
can be induced by
chemical modification
of a base.

1.7 Mutations
are
concentrated
at hotspots

Cistron

is the genetic unit defined by the cis/trans test; equivalent to
gene
.

Complementation 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

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

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

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

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

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

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

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

Figure 1.23 Chiasma
formation is
responsible for
generating
recombinants.

1.10
Recombination
occurs by physical
exchange of DNA

Figure 1.24
Recombination
involves pairing
between
complementary strands
of the two parental
duplex DNAs.

1.10
Recombination
occurs by physical
exchange of DNA

Figure 1.13 Denatured
single strands of DNA
can renature to give the
duplex form.

1.10
Recombination
occurs by physical
exchange of DNA

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.>

Reading 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

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

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

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

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

Figure 1.28
RNA is
synthesized
by using one
strand of
DNA as a
template for
complementa
ry base
pairing.

1.12 The relationship between coding sequences and proteins

Figure 1.29
The gene
may be
longer than
the sequence
coding for
protein.

1.12 The relationship between coding sequences and proteins


Figure 1.30

Gene expression is a
multistage process.

1.12

The relationship
between coding
sequences and
proteins

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



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

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

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

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

Figure 1.32

A
cis
-
acting site
controls the
adjacent DNA but
does not influence
the other allele.

1.13
cis
-
acting
sites and
trans
-
acting molecules

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

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 PrP
Sc
, 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

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

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


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


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

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


6. A mutation consists of a change in the sequence of A∙T
and G∙C base pairs in DNA.


7. The natural incidence of mutations is increased by
mutagens.

8. Forward mutations occur at a rate of ~10
6

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