IGenetics, Chapter 2 - Russel

Peter J.
Russell
CHAPTER 2
DNA: The Genetic Material
edited by Yue-Wen Wang Ph. D.

Dept. of Agronomy,台大農藝系
NTU 遺傳學 601 20000 Chapter 2 slide 1
The Search for the Genetic Material
• 1. Some substance must be responsible for

passage of traits from parents to offspring. For a
substance to do this it must be:
• a. Stable enough to store information for long periods.
• b. Able to replicate accurately.
• c. Capable of change to allow evolution.
台大農藝系遺傳學 601 20000 Chapter 2 slide 2

The Search for the Genetic Material
• 2. In the early 1900s, chromosomes were

shown to be the carriers of hereditary information.
In eukaryotes they are composed of both DNA
and protein, and most scientists initially believed
that protein must be the genetic material.

Chromosome theory of inheritance
• The transmission and behavior of the abstract

factors of Mendel and the physical behavior of
chromosomes in mitosis, meiosis, and fertilization
led Sutton, Roux and Boveri proposed the
chromosome theory of inheritance.

Genetic Materials
• Chromosome consists of protein and nucleic acid

• Candidate: Protein v.s. nucleic acid
• Protein: 20 kinds of amino acid
• Nucleic acid: 4 kinds of nucleotides
• Complexity of life  very complicated  protein
or nucleic acid to account for the level of
complexity?

Griffith’s Transformation Experiment
• 1. Frederick Griffith’s 1928 experiment with

Streptococcus pneumoniae bacteria in mice
showed that something passed from dead bacteria
into nearby living ones, allowing them to change
their cell surface.
• 2. He called this agent the transforming
principle, but did not know what it was or how it
worked.

Fig. 2.2 Griffith’s transformation experiment

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
Avery’s Transformation Experiment
• Animation: DNA as Genetic Material: The Avery Experiment

• 1. In 1944, Avery, MacLeod and McCarty published results of a study
that identified the transforming principle from S. pneumoniae. Their
approach was to break open dead cells, chemically separate the
components (e.g., protein, nucleic acids) and determine which was
capable of transforming live S. pneumoniae cells.
• 2. Only the nucleic acid fraction was capable of transforming the
bacteria.
• 3. Critics noted that the nucleic acid fraction was contaminated with
proteins. The researchers treated this fraction with either RNase or
protease and still found transforming activity, but when it was treated
with DNase, no transformation occurred, indicating that the
transforming principle was DNA.

Fig. 2.3 Experiment that showed that DNA, not RNA, was the transforming principle

The Hershey-Chase Bacteriophage Experiment
• Animation: DNA as Genetic Material: The Hershey-Chase Experiment

• 1. More evidence for DNA as the genetic material came in 1953 with
Alfred Hershey and Martha Chase’s work on E. coli infected with
bacteriophage T2.
• 2. In one part of the experiment, T2 proteins were labeled with 35S, and
in the other part, T2 DNA was labeled with 32P. Then each group of
labeled viruses was mixed separately with the E. coli host. After a short
time, phage attachment was disrupted with a kitchen blender, and the
location of the label determined.
• 3. The 35S-labeled protein was found outside the infected cells, while
the 32P-labeled DNA was inside the E. coli, indicating that DNA carried
the information needed for viral infection. This provided additional
support for the idea that genetic inheritance occurs via DNA.

Fig. 2.4 Bacteriophage T2

Fig. 2.5 Lytic life cycle of a virulent phage, such as T2

Fig. 2.6 Hershey-Chase experiment demonstrating DNA is genetic material

The Discovery of RNA as Viral Genetic Material
• TMV ( tobacco mosaic virus)

• 1956, A. Gierer and G. Schramm
• Infected tobacco plant with purified RNA  typical virus-
infected lesion
• RNA treated with RNAase then injected into tobacco  not
lesion
• 1957 Heinz Fraenkel-Conrat and B. Singer reconstitue the
RNA of one type with the protein of the other type and
vice versa and injected to two tobacco plants  the
progeny viruses isolated from the resulting lesion were
the type specified by the RNA, not by the protein.

Fig. 2.7 Typical tobacco mosaic virus (TMV) particle

Fig. 2.8 Demonstration that RNA is the genetic material in tobacco mosaic virus (TMV)

The Composition and Structure of DNA and
RNA
• 1. DNA and RNA are polymers composed of monomers
called nucleotides.
• 2. Each nucleotide has three parts:
• a. A pentose (5-carbon) sugar.
• b. A nitrogenous base.
• c. A phosphate group.
• 3. The pentose sugar in RNA is ribose, and in DNA it’s
deoxyribose. The only difference is at the 29 position,
where RNA has a hydroxyl (OH) group, while DNA has
only a hydrogen.

Figs. 2.9 Structures of deoxyribose and ribose in DNA and RNA

RNA
• 4. There are two classes of nitrogenous bases:
• a. Purines (double-ring, nine-membered structures)
include adenine (A) and guanine (G).
• b. Pyrimidines (one-ring, six-membered structures)
include cytosine (C), thymine (T) in DNA and uracil
(U) in RNA.

Figs. 2.10 Structures of the nitrogenous bases in DNA and RNA

RNA
• 5. The structure of nucleotides has these features:
• a. The base is always attached by a covalent bond between the 1′
carbon of the pentose sugar and a nitrogen in the base (specifically, the
nine nitrogen in purines and the one nitrogen in pyrimidines).
• b. The sugar-base combination is a nucleoside. When a phosphate is
added (always to the 5′ carbon of the pentose sugar), it becomes a
nucleoside phosphate, or simply nucleotide.
• c. Nucleotide examples are shown in Figure 2.11, and naming
conventions are given in Table 2.1.
• 6. Polynucleotides of both DNA and RNA are formed by stable
covalent bonds (phosphodiester linkages) between the phosphate group
on the 5′ carbon of one nucleotide, and the 3′ hydroxyl on another
nucleotide. This creates the “backbone” of a nucleic acid molecule.
• 7. The asymmetry of phosphodiester bonds creates 3′-5′ polarity within
the nucleic acid chain.

Fig. 2.11 Chemical structures of DNA and RNA

The Discovery of the DNA Double Helix
• 1. James Watson and Francis Crick published the famous
double-helix structure in 1953. When they began their
work, it was known that DNA is composed of
nucleotides, but how the nucleotides are assembled into
nucleic acid was unknown. Two additional sources of
data assisted Watson and Crick with their model:
• a. Erwin Chargaff’s ratios obtained for DNA derived from a
variety of sources showed that the amount of purine always
equals the amount of pyrimidine, and further, that the amount of
G equals C, and the amount of A equals T.
• b. Rosalind Franklin’s X ray diffraction images of DNA showed
a helical structure with regularities at 0.34 nm and 3.4 nm along
the axis of the molecule (Figure 8.9).

Fig. 2.13b X-ray diffraction analysis of DNA

Fig. 2.14 Molecular structure of DNA

The Discovery of the DNA Double Helix
• 2. Watson and Crick’s three-

dimensional model (Figure 2.14)
has these main features:
• a. It is two polynucleotide chains
wound around each other in a
right-handed helix.
• b. The two chains are antiparallel.
• c. The sugar-phosphate backbones
are on the outside of the helix, and
the bases are on the inside,
stacked perpendicularly to the
long axis like the steps of a spiral
staircase.

• d. The bases of the two strands
are held together by hydrogen
bonds between complementary
bases (two for A-T pairs and
three for G-C pairs). Individual
H-bonds are relatively weak
and so the strands can be
separated (by heating, for
example). Complementary
base pairing means that the
sequence of one strand dictates
the sequence of the other
strand.

• e. The base pairs are 0.34 nm apart, and one full turn of the DNA
helix takes 3.4 nm, so there are 10 bp in a complete turn. The
diameter of a dsDNA helix is 2 nm.
• f. Because of the way the bases H-bond with each other, the
opposite sugar-phosphate backbones are not equally spaced,
resulting in a major and minor groove. This feature of DNA
structure is important for protein binding.
• 3. The 1962 Nobel Prize in Physiology or Medicine was
awarded to Francis Crick, James Watson and Maurice
Wilkins (the head of the lab in which Franklin worked).
Franklin had already died, and so was not eligible.

Different DNA Structures
• X ray diffraction studies show that DNA can exist in
different forms (Figure 2.16).
• a. A-DNA is the dehydrated form, and so it is not usually found
in cells. It is a right-handed helix with 10.9 bp/turn, with the
bases inclined 13° from the helix axis. A-DNA has a deep and
narrow major groove, and a wide and shallow minor groove.
• b. B-DNA is the hydrated form of DNA, the kind normally
found in cells. It is also a right-handed helix, with only 10.0
bp/turn, and the bases inclined only 2° from the helix axis. B-
DNA has a wide major groove and a narrow minor groove, and
its major and minor grooves are of about the same depth.
• c. Z-DNA is a left-handed helix with a zigzag sugar-phosphate
backbone that gives it its name. It has 12.0 bp/turn, with the
bases inclined 8.8° from the helix axis. Z-DNA has a deep minor
groove, and a very shallow major groove. Its existence in living
cells has not been proven.
DNA in the Cell
• All known cellular DNA is in the B form.

• A-DNA would not be expected because it is
dehydrated and cells are aqueous.
• Z-DNA has never been found in living cells,
although many organisms have been shown to
contain proteins that will bind to Z-DNA.

• iActivity: Cracking the Viral Code

The Organization of DNA in Chromosomes
• 1. Cellular DNA is organized into

chromosomes. A genome is the chromosome or
set of chromosomes that contains all the DNA of
an organism.
• 2. In prokaryotes the genome is usually a
single circular chromsome. In eukaryotes, the
genome is one complete haploid set of nuclear
chromosomes; mitochondrial and chloroplast
DNA are not included.
Viral Chromosomes
• 1. A virus is nucleic acid surrounded by a
protein coat. The nucleic acid may be dsDNA,
ssDNA, dsRNA or ssRNA, and it may be linear or
circular, a single molecule or several segments.
• 2. Bacteriophages are viruses that infect
bacteria. Three different types that infect E. coli
are good examples of the variety of chromosome
structure found in viruses.

T-even phage
• 3. The T-even phages (T2, T4 and T6) have

similar structures (Figure 2.4); all have dsDNA
genomes composed of a one linear DNA molecule
surrounded by a protein coat. The genomes of
these viruses show circular permutation, meaning
that the starting point of each is different, because
these viruses package slightly more than 100% of
a genome length of DNA when they form.

Fig. 2.17 Circularly permuted and terminally redundant double-stranded DNA molecules

Fig. 2.17 Circularly permuted and terminally redundant double-stranded DNA molecules

ΦX174 phage
• 4. ΦX174 is a small, simple virus with one
short ssDNA chromosome
• Fig. 2-18

• In 1959, Robert Sinsheimer found that the DNA
of ΦX174 has a base composition that does not fit
the complementary base-pair-rules.  single
strand DNA rather than dsDNA

λ phage
• Bacteriophage λ is somewhat like the T-even

phages in structure. However, its chromosome
changes form. A linear molecule of dsDNA is
packaged inside the protein head (Fig. 2.19), but
after the virus infects its host the chromosome
becomes circular due to base-pairing of
complementary 12-base single-stranded regions at
the ends of the linear molecule (Fig. 2.20).

Fig. 2.19 Bacteriophage 

Fig. 2.20  chromosome structure varies at stages of lytic infection of E. coli

Prokaryotic Chromosomes
• 1. The typical prokaryotic genome is one circular dsDNA

chromosome, but some prokaryotes are more exotic, with
a main chromosome and one or more smaller ones. When
a minor chromosome is dispensable to the life of the cell,
it is called a plasmid. Some examples:
• a. Borrelia burgdorferi (Lyme disease in humans) has a 0.91-Mb
linear chromosome, plus an additional 0.53-Mb of DNA in 17
different linear and circular molecules.
• b. Agrobacterium tumefaciens (crown gall disease of plants) has
a 3.0-Mb circular chromosome and a 2.1-Mb linear one.

• 2. Archaebacteria also vary in chromosomal
organization, but only circular forms have been found.
Examples:
• a. Methanococcus jannaschii has three chromosomes of 1.66-
Mb, 58-kb and 16-kb.
• b. Archaeoglobus fulgidus has one 2.2-Mb circular chromosome.
• 3. Both Eubacteria and Archaebacteria lack a membrane-

bounded nucleus, hence their classification as
prokaryotes. Their DNA is densely arranged in a
cytoplasmic region called the nucleoid.

DNA Supercoiling
• 4. In an experiment where E. coli is gently

lysed, it releases one 4.6-Mb circular
chromosome, highly supercoiled. A 4.6-Mb
double helix is about 1 mm in length, about 103
times longer than an E. coli cell. DNA
supercoiling helps it fit into the cell.
• Animation: DNA supercoiling

Fig. 2.22 Illustration of DNA supercoiling

• 5. Both positive and negative supercoiling will
condense DNA.
• 6. All organisms contain topoisomerase enzymes to
supercoil their DNA.
• 7. Prokaryotes also organize their DNA into looped
domains, with the ends of the domains held so that each is
supercoiled independently (Figure 2.23). The compaction
factor for looped domains is about 10-fold.
• 8. The number of looped domains is species-specific
and depends on genome size. In E. coli there are about
100 domains of about 40 kb each.

Fig. 2.24 Model for the structure of a bacterial chromosome

Eukaryotic Chromosomes
• 1. The genome of most prokaryotes consists of

one chromosome, while most eukaryotes have a
diploid number of chromosomes.
• 2. A genome is the information in one complete
haploid chromosome set. The total amount of
DNA in the haploid genome of a species is its C
value (Table 2.4). The structural complexity and
the C value of an organism are not related,
creating the C value paradox.
C value paradox

• 3. Eukaryotic chromosomes are linear dsDNA,
and by weight contain about twice as much
protein as DNA. The DNA-protein complex is
called chromatin, and it is highly conserved in all
eukaryotes.

Chromatin Structure
• 1. Both histones and non-histones are involved in
physical structure of the chromosome.
• 2. Histones are abundant, small proteins with a net (+)
charge. The five main types are H1, H2A, H2B, H3 and
H4. By weight, chromosomes have equal amounts of
DNA and histones.
• 3. Histones are highly conserved between species (H1
less than the others).
• 4. Non-histone is a general name for other proteins
associated with DNA. This is a big group, with some
structural proteins, and some that bind only transiently.
Non-histone proteins vary widely, even in different cells
from the same organism. Most have a net (-) charge, and
bind by attaching to histones. HMG (high mobility group)
proteins are a well-studied example of non-histone
proteins. 台大農藝系遺傳學 601 20000 Chapter 2 slide 56
• 5. Chromatin formation involves histones, and
condenses the DNA so it will fit into the cell.
Chromatin formation has two components:
• a. Two molecules each of histones H2A, H2B,
H3 and H4 associate to form a nucleosome core,
and DNA wraps around it 1 3⁄4 times for a 7-fold
condensation factor. Nucleosome cores are about
11 nm in diameter (Figures 2.25 and 2.27).

Fig. 2.25 A possible nucleosome structure

• b. H1 serves as the linker histone, connecting
nucleosomes to create chromatin with a diameter
of 30 nm, for an additional 6-fold
• condensation. The exact mechanism used by H1 is
unknown (Figures 2.26 and 2.28).

Fig. 2.26 Nucleosomes connected together by linker DNA and H1 histone to produce
the “beads-on-a-string” extended form of chromatin

Fig. 2.28b Packaging of nucleosomes into the 30-nm chromatin fiber

• 6. Chromatin is arranged in looped domains of
DNA similar to those formed in prokaryotic
chromosomes. Loops are anchored to the nuclear
matrix at DNA sequences called MARs (matrix
attachment regions). An average human
chromosome has about 2,000 looped domains.
Looped domains may be important in regulating
transcription and replication (Fig. 2.30 and
overview in Figure 2.31).

Fig. 2.29 Model for the organization of 30-nm chromatin fiber into looped domains
that are anchored to a nonhistone protein chromosome scaffold

Fig. 2.31 The many different orders of chromatin packing that give rise to the highly
condensed metaphase chromosome

Euchromatin and Heterochromatin
• 1. The cell cycle affects DNA packing, with DNA condensing for
mitosis and meiosis, and decondensing during interphase.
Chromosomes are most condensed at metaphase, when the looped
domains are further coiled and the chromatic has a diameter of about
700 nm. Non-histone proteins form the scaffold for this additional
condensation.
• 2. Staining of chromatin reveals two forms:
• a. Euchromatin condenses and decondenses with the cell cycle. It is
actively transcribed, and lacks repetitive sequences. Euchromatin
accounts for most of the genome in active cells.
• b. Heterochromatin remains condensed throughout the cell cycle. It
replicates later than euchromatin, and is transcriptionally inactive.
There are two types based on activity:
• i. Constituitive heterochromatin occurs at the same sites in both
homologous chromosomes of a pair, and is mostly repetitive DNA
(e.g., centromeres).
• ii. Facultative heterochromatin varies between cell types or
developmental stages or even between homologous chromosomes.
It contains condensed, and thus inactive, euchromatin (e.g., Barr
bodies) 台大農藝系遺傳學 601 20000 Chapter 2 slide 65
Centromeric and Telomeric DNA
• 1. Centromeres and telomeres are eukaryotic

chromosomal regions with special functions.
• 2. Centromeres are the site of the kinetochore, where
spindle fibers attach during mitosis and meiosis. They are
required for accurate segregation of chromatids.
• 3. Yeast (Saccharomyces cerevisiae) centromeres are
well-studied. Called CEN regions, their sequence and
organization are similar, but not identical, between the
chromosomes. Other eukaryotes have different
centromere sequences, so while function is conserved, it
is not due to a single type of DNA sequence. (Fig. 2-32)

Fig. 2.32 Consensus sequence for centromeres of the yeast Saccharomyces cerevisiae

• Proteins interact with the centromere and the
spindle mircrotubule to form the kinetchore
structure (Fig. 2-33)

Fig. 2.33 Hypothetical model for the kinetochore of yeast, showing the relationship of
the spindle fiber microtubule to the centromere DNA elements

• 4. Telomeres are needed for chromosomal replication and stability.
Generally composed of heterochromatin, they interact with both the
nuclear envelope and each other. All telomeres in a species have the
same sequence.
• a. Simple telomeric sequences are short, species-specific and tandemly
repeated. (Examples: Tetrahymena is 59-TTGGGG-39, and human is
59-TTAGGG-39.) A new model suggests that the single-stranded end
of the chromosome folds back to form a t-loop and then invades the
double-stranded region to form a D-loop (Figure 2.34).
• b. Telomere-associated sequences are internal to the simple telomeric
sequences. These complex repetitive sequences may extend many kb
into the chromosome.
• c. Drosophila is unusual in having telomeres composed of transposons,
rather than the short repeats seen in most eukaryotes.

Fig. 2.34 Telomeres

Unique-Sequence and Repetitive-Sequence
DNA
• 1. Sequences vary widely in how often they occur within a genome.
The categories are:
• a. Unique-sequence DNA, present in one or a few copies.
• b. Moderately repetitive DNA, present in a few to 105 copies.
• c. Highly repetitive DNA, present in about 105–107 copies.
• 2. Prokaryotes have mostly unique-sequence DNA, with repeats only of
sequences like rRNAs and tRNAs. Eukaryotes have a mix of unique
and repetitive sequences.
• 3. Unique-sequence DNA includes most of the genes that encode
proteins, as well as other chromosomal regions. Human DNA contains
about 65% unique sequences.

• 4. Repetitive-sequence DNA includes the moderately and highly
repeated sequences. They may be dispersed throughout the genome, or
clustered in tandem repeats.
• 5. Dispersed repetitive sequences occur in families that have a
characteristic sequence. Often the same few sequences are highly
repeated, and comprise most of the dispersed repeats in the genome.
Little is known of their function, or indeed whether they actually serve
a function. There are two types of interspersion patterns found in all
eukaryotic organisms:
• a. SINEs (short interspersed repeated sequences) with 100–500 bp
sequences. An example is the Alu repeats found in some primates,
including humans, where these 200–300 bp repeats make up 9% of the
genome.
• b. LINEs (long interspersed repeated sequences) with sequences of 5
kb or more. The common example in mammals is LINE-1, with
sequences up to 7 kb in length.
• 6. Tandemly repetitive sequences are common in eukaryotic genomes,
ranging from very short (1–10 bp) sequences to genes and even longer
sequences. This group includes centromere and telomere sequences,
and rRNA and tRNA genes.

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Peter J.

edited by Yue-Wen Wang Ph. D.

• 1. Some substance must be responsible for

台大農藝系 遺傳學 601 20000 Chapter 2 slide 2

• 2. In the early 1900s, chromosomes were

台大農藝系 遺傳學 601 20000 Chapter 2 slide 3

• The transmission and behavior of the abstract

台大農藝系 遺傳學 601 20000 Chapter 2 slide 4

• Chromosome consists of protein and nucleic acid

台大農藝系 遺傳學 601 20000 Chapter 2 slide 5

• 1. Frederick Griffith’s 1928 experiment with

台大農藝系 遺傳學 601 20000 Chapter 2 slide 6

台大農藝系 遺傳學 601 20000 Chapter 2 slide 7

• Animation: DNA as Genetic Material: The Avery Experiment

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台大農藝系 遺傳學 601 20000 Chapter 2 slide 9

• Animation: DNA as Genetic Material: The Hershey-Chase Experiment

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• TMV ( tobacco mosaic virus)

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• 2. Watson and Crick’s three-

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• All known cellular DNA is in the B form.

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• 1. Cellular DNA is organized into

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• 3. The T-even phages (T2, T4 and T6) have

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• Bacteriophage λ is somewhat like the T-even

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• 1. The typical prokaryotic genome is one circular dsDNA

台大農藝系 遺傳學 601 20000 Chapter 2 slide 47

• 3. Both Eubacteria and Archaebacteria lack a membrane-

台大農藝系 遺傳學 601 20000 Chapter 2 slide 48

• 4. In an experiment where E. coli is gently

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• 1. The genome of most prokaryotes consists of

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