Lecture 3
what Genes are and
What they do
Part II
Three Chapters
组别
第三讲：准备讨论内容（课堂
讨论时间5分左右）
A
P252-253： genetics and society
C
E
P268:connection
P269-26-70: Social and ethical
issues
P220:fast forwards
H
P202: genetics and society
M
P170-172: fast forwards
S
P191-192:1st part of chapter 7
D
Chapter 6 DNA
How the molecule of heredity carries,
replicates, and recombines
information
• How investigators pinpointed DNA as the
genetic material
• The elegant Watson-Crick model of DNA
structure
• How DNA structure provides for the
storage of genetic information
• How DNA structure gives rise to the
semiconservative model of molecular
replication
• How DNA structure promotes the
recombination of genetic information
• How investigators pinpointed DNA as the
genetic material
• The elegant Watson-Crick model of DNA
structure
• How DNA structure provides for the
storage of genetic information
• How DNA structure gives rise to the
semiconservative model of molecular
replication
• How DNA structure promotes the
recombination of genetic information
The
chemical
composition
of DNA
Fig. 6.2
Chemical characterization localizes DNA in
the chromosomes
• 1869 – Friedrich Meischer
extracted a weakly acidic,
phosphorous rich material
from nuclei of human white
blood cells which he named
nuclein
Are genes composed of DNA or protein?
• DNA
– Only four different subunits make up DNA
– Chromosomes contain less DNA than protein
by weight
• Protein
– 20 different subunits – greater potential
variety of combinations
– Chromosomes contain more protein than
DNA by weight
Bacterial transformation implicates DNA as
the substance of genes
• 1928 – Frederick Griffith – experiments
with smooth (S), virulent strain
Streptococcus pneumoniae, and rough (R),
nonvirulent strain
– Bacterial transformation demonstrates
transfer of genetic material
• 1944 – Oswald Avery, Colin MacLeod, and
MacIyn McCarty – determined that DNA is
the transformation material
Griffith experiment
Fig. 6.3
Griffith experiment
Fig. 6.3 b
Avery, MacLeod, McCarty
experiment
Hershey and Chase
experiments
• 1952 – Alfred Hershey and Martha Chase
provide convincing evidence that DNA is
genetic material
• Waring blender experiment using T2
bacteriophage and bacteria
• Radioactive labels 32P for DNA and 35S for
protein
Hershey and Chase Waring blender
experiment
Fig. 6.5 a,b
Hershey and Chase Waring blender
experiment
Fig. 6.5 c
• How investigators pinpointed DNA as the
genetic material
• The elegant Watson-Crick model of DNA
structure
• How DNA structure provides for the
storage of genetic information
• How DNA structure gives rise to the
semiconservative model of molecular
replication
• How DNA structure promotes the
recombination of genetic information
The Watson-Crick Model: DNA is a double
helix
• 1951 – James Watson learns about x-ray
diffraction pattern projected by DNA
• Knowledge of the chemical structure of
nucleotides (deoxyribose sugar, phosphate, and
nitrogenous base)
• Erwin Chargaff’s experiments demonstrate that
ratio of A and T are 1:1, and G and C are 1:1
• 1953 – James Watson and Francis crick
propose their double helix model of DNA
structure
X-ray diffraction patterns produced by DNA
fibers – Rosalind Franklin and Maurice
Wilkins
Fig. 6.6
Chargaff’s ratios
Complementary base pairing by formation of
hydrogen bonds explain Chargaff’s ratios
Fig. 6.8
• DNA is double helix
• Strands are antiparallele
with a sugar-phosphate
backbone on outside and
pairs of bases in the
middle
• Two strands wrap around
each other every 30
Angstroms, once every 10
base pairs
• Two chains are held
together by hydrogen
bonds between A-T and
G-C base pairs
Fig. 6.9
• Stucturally, purines (A and G )pair
best with pyrimadines (T and C)
• Thus, A pairs with T and G pairs
with C, also explaining Chargaff’s
ratios
Fig. 6.9 d
Double helix may assume alternative forms
Fig. 6.10

Some DNA molecules are circular
instead of linear
1.
 2.
 3.
 4.


Some viruses carry single-stranded
DNA


Prokaryotes
Mitochondria
Chloroplasts
Viruses
1. bacteriophages
Some viruses carry RNA

1. e.g., AIDS
• How investigators pinpointed DNA as the
genetic material
• The elegant Watson-Crick model of DNA
structure
• How DNA structure provides for the
storage of genetic information
• How DNA structure gives rise to the
semiconservative model of molecular
replication
• How DNA structure promotes the
recombination of genetic information
Four requirements for DNA to be
genetic material
• Must carry information
– Cracking the genetic code
• Must replicate
– DNA replication
• Must allow for information to change
– Mutation
• Must govern the expression of the phenotype
– Gene function
Some viruses use RNA as the repository of
genetic information
Fig. 6.13
• How investigators pinpointed DNA as the
genetic material
• The elegant Watson-Crick model of DNA
structure
• How DNA structure provides for the
storage of genetic information
• How DNA structure gives rise to the
semiconservative model of molecular
replication
• How DNA structure promotes the
recombination of genetic information
DNA replication: Copying genetic information for
transmission to the next generation
• Complementary base pairing produces
semiconservative replication
– Double helix unwinds
– Each strand acts as template
– Complementary base pairing ensures that T
signals addition of A on new strand, and G
signals addition of C
– Two daughter helices produced after
replication
Fig. 6.14
Fig. 6.15
Meselson-Stahl experiments confirm
semiconservative replication
Fig. 6.16
The mechanism of DNA replication
• Arthur Kornbuerg, a nobel prize winner
and other biochemists deduced steps of
replication
– Initiation
• Proteins bind to DNA and open up double helix
• Prepare DNA for complementary base pairing
– Elongation
• Proteins connect the correct sequences of
nucleotides into a continuous new strand of DNA
Enzymes involved in replication
• Pol III – produces new stands of complementary
DNA
• Pol I – fills in gaps between newly synthesized
Okazaki segments
• DNA helicase – unwinds double helix
• Single-stranded binding proteins – keep helix
open
• Primase – creates RNA primers to initiate
synthesis
• Ligase – welds together Okazaki fragments
Replication is bidirectional
• Replication forks move in opposite directions
• In linear chromosomes, telomeres ensure the
maintenance and accurate replication of
chromosome ends
• In circular chromosomes, such as E. coli, there
is only one origin of replication.
• In circular chromosomes, unwinding and
replication causes supercoiling, which may
impede replication
• Topoisomerase – enzyme that relaxes
supercoils by nicking strands
The bidirectional replication of a circular
chromosome
Fig. 6.18
Fig. 6.18
Cells must ensure accuracy of genetic
information
• Redunancy
– Basis for repair of errors that occur during
replication or during storage
• Enzymes repair chemical damage to DNA
• Errors during replication are rare
• How investigators pinpointed DNA as the
genetic material
• The elegant Watson-Crick model of DNA
structure
• How DNA structure provides for the
storage of genetic information
• How DNA structure gives rise to the
semiconservative model of molecular
replication
• How DNA structure promotes the
recombination of genetic information
Recombination reshuffles the information
content of DNA
• During recombination, DNA molecules
break and rejoin
• Meselson and Weigle - Experimental
evidence from viral DNA and radioactive
isotopes
• Coinfected E. coli with light and heavy
strains of virus after allowing time for
recombination
• Separated on a CsCl density gradient
Meselson and Weigle demonstrate recombination
occurs by breakage and rejoining of DNA
Fig. 6.19
Heteroduplexes mark the spot of
recombination
• Products of recombination are always in
exact register; not a single base pair is lost
or gained
• Two strands do not break and rejoin at the
same location; often they are hundreds of
base pairs apart
• Region between break points is called
heteroduplex
Heteroduplex region
Fig .6.20
In heterozygotes, mismatches within
heteroduplexes must be repaired
• Gene conversion – a deviation from
expected 2:2 segregation of alleles due to
mismatch repair.
• Studied most extensively in yeast where
tetrad analysis makes possible to follow
products of meiosis
Gene
conversion in
yeast
Mismatch leads to 3:1
ratio of a:A. Ratio of B:b
and C:c which lie outside
of heteroduplex are both
2:2, as expected.
Fig. 6.20 c
Double stranded break model of meiotic
recombination
• Homologs physically break, exchange parts, and
rejoin.
• Breakage and repair create reciprocal products
of recombination
• Recombination events can occur anywhere
along the DNA molecule
• Precision in the exchange prevents mutations
from occurring during the process
• Gene conversion can give rise to unequal yield
of two different alleles. 50% of gene
conversions are associated with crossing over of
adjacent chromosomal regions, and 50% of
gene conversions are not associate with
crossing over
Double stranded break formation
spoI protein breaks one chromatid on both strands
Fig. 6.22 step 1
Resection
5’ end on each side of break are degraded to produce two 3’ single
stranded tails
Fig. 6.22 step 2
First strand invasion
RecA binds 3’ tail and double helix allowing invasion and migration
Fig. 6.22 step 3
Formation of Holliday junctions
New DNA synthesis forms two X structures called Holliday junciions
Fig. 6.22 step 4
Branch migration
Both invading strands zip up and migrate while newly created
heteroduplex molecules rewind behind.
Fig. 6.22 step 5
The Holliday intermediate
Interlocked nonsister chromatids disenguage. Two resolutions are
possible
Fig. 6.22
step 6
Alternative resolutions
Endonuclease cuts Holliday intermediate
Probability of crossover occurring
Resolution of Holliday junction in same plan results in noncrossover chromatids.
Resolution in different planes results in crossover.
Fig. 6.22 step 8
Chapter 7
Anatomy and Function of a
Gene
Dissection through mutation
57
• What mutations are
– How often mutations occur
– What events cause mutations
– How mutations affect survival and evolution
• Mutations and gene structure
– Experiments using mutations demonstrate a gene is a
discrete region of DNA
• Mutations and gene function
– Genes encode proteins by directing assembly of amino
acids
• How do genotypes correlate with phenotypes?
– Phenotype depends on structure and amount of protein
– Mutations alter genes instructions for producing proteins
structure and function, and consequently phenotype
58
• What mutations are
– How often mutations occur
– What events cause mutations
– How mutations affect survival and evolution
• Mutations and gene structure
– Experiments using mutations demonstrate a gene is
a discrete region of DNA
• Mutations and gene function
– Genes encode proteins by directing assembly of
amino acids
• How do genotypes correlate with phenotypes?
– Phenotype depends on structure and amount of
protein
– Mutations alter genes instructions for producing
proteins structure and function, and consequently
phenotype
59
Mutations: Primary tools of genetic analysis
• Mutations are heritable changes in base
sequences that modify the information
content of DNA
– Forward mutation – changes wild-type to
different allele
– Reverse mutation – causes novel mutation to
revert back to wild-type (reversion)
60
Classification of mutations by affect on DNA
molecule
• Substitution – base is replaced by one of the
other three bases
• Deletion – block of one or more DNA pairs is lost
• Insertion – block of one or more DNA pairs is
added
• Inversion 180 rotation of piece of DNA
• Reciprocal translocation – parts of
nonhomologous chromosomes change places
• Chromosomal rearrangements – affect many
genes at one time
61
62
Spontaneous mutations influencing
phenotype occur at a very low rate
Mutation rates from wild-type to recessive alleles for five coat color
genes63in mice
Fig. 7.3 b
General observations of mutation rates
• Mutations affecting phenotype occur very
rarely
• Different genes mutate at different rates
• Rate of forward mutation is almost always
higher than rate of reverse mutation
64
Are mutations spontaneous or induced?
• Most mutations are spontaneous.
• Luria and Delbruck experiments - a simple
way to tell is mutations are spontaneous or
if they are induced by a mutagenic agent
65
Fig. 7.4
66
Chemical and Physical agents cause
mutations
• Hydrolysis of a purine
base, A or G occurs
1000 times an hour in
every cell

67
Deamination removes –
NH2 group. Can change
C to U, inducing a
substitution to and A-T
base pair after replication
• X rays break the
DNA backbone

UV light produces
thymine dimers
Fig. 7.6 c, d
68
Oxydation from free radicals formed by irradiation
damages individual bases
Fig. 7.6 e
69
Repair enzymes fix errors created by
mutation
Excision repair
enzymes
release
damaged
regions of
DNA. Repair
is then
completed by
DNA
polymerase
and DNA
ligase
70
Fig. 7.7a
Mistakes during replication alter genetic
information
• Errors during replication are exceedingly
rare, less than once in 109 base pairs
• Proofreading enzymes correct errors
made during replication
– DNA polymerase has 3’ – 5’ exonuclease
activity which recognizes mismatched bases
and excises it
– In bacteria, methyl-directed mismatch repair
finds errors on newly synthesized strands and
corrects them
71
DNA polymerase proofreading
Fig. 7.8
72
Methyldirected
mismatch
repair
Fig. 7.9
73
Unequal crossing over creates one homologous
chromosome with a duplication and the other with a
deletion
7.10 a
74
Transposable elements move around the genome
and are not susceptible to excision or mismatch
repair
Fig. 7.10 e
75
Trinucleotide instability causes mutations
• FMR-1 genes in
unaffected
people have
fewer than 50
CGG repeats.
• Unstable
premutation
alleles have
between 50 and
200 repeats.
• Disease causing
alleles have >
200 CGG
repeats.
76
Fig. B(1) Genetics and Society
Trinucleotide repeat in people with fragile X
syndrom
Fig. A, B(2) Genetics and
Society
77
Mutagens induce mutations
• Mutagens can be used to increase
mutation rates
• H. J. Muller – first discovered that X rays
increase mutation rate in fruitflies
– Exposed male Drosophila to large doses of X
rays
– Mated males to females with balancer X
chromosome (dominant Bar eyed mutation
and multiple inversions)
– Could assay more than 1000 genes at once
on the X chromosome
78
Muller’s experiment
Fig. 7.11
79
Mutagens increase mutation rate using
different mechanisms
Fig. 7.12a
80
81
82
Fig. 7.12 b
Fig. 7.12 c
83
Consequences of mutations
• Germ line mutations – passed on to next
generation and affect the evolution of
species
• Somatic mutations – affect the survival of
an individual
– Cell cycle mutations may lead to cancer
• Because of potential harmful affects of
mutagens to individuals, tests have been
developed to identify carcinogens
84
• What mutations are
– How often mutations occur
– What events cause mutations
– How mutations affect survival and evolution
• Mutations and gene structure
– Experiments using mutations demonstrate a gene is a
discrete region of DNA
• Mutations and gene function
– Genes encode proteins by directing assembly of amino
acids
• How do genotypes correlate with phenotypes?
– Phenotype depends on structure and amount of protein
– Mutations alter genes instructions for producing proteins
structure and function, and consequently phenotype
85
What mutations tell us about gene structure
• Complementation testing tells us whether
two mutations are in the same or different
genes
• Benzer’s experiments demonstrate that a
gene is a linear sequence of nucleotide
pairs that mutate independently and
recombine with each other
• Some regions of chromosomes mutate at
a higher rate than others – hot spots
86
Complementation testing
Fig. 7.15 a
87
Fig. 7.15 b,c
Five complementation groups (different genes) for eye color.
Recombination mapping demonstrates distance between genes and alleles.
88
A gene is a linear sequence of nucleotide
pairs
• Seymore Benzer mid 1950s – 1960s
– If a gene is a linear set of nucleotides,
recombination between homologous
chromosomes carrying different mutations
within the same gene should generate wildtype
– T4 phage as an experimental system
• Can examine a large number of progeny to detect
rare mutation events
• Could allow only recombinant phage to proliferate
while parental phages died
89
Benzer’s experimental
procedure
• Generated 1612 spontaneous point mutations
and some deletions
• Mapped location of deletions relative to one
another using recombination
• Found approximate location of individual point
mutations by deletion mapping
• Then performed recombination tests between all
point mutations known to lie in the same small
region of the chromosome
• Result – fine structure map of the rII gene locus
90
How recombination within a gene could
generate wild-type
Fig. 7.16
91
• What mutations are
– How often mutations occur
– What events cause mutations
– How mutations affect survival and evolution
• Mutations and gene structure
– Experiments using mutations demonstrate a gene is a
discrete region of DNA
• Mutations and gene function
– Genes encode proteins by directing assembly of amino
acids
• How do genotypes correlate with phenotypes?
– Phenotype depends on structure and amount of protein
– Mutations alter genes instructions for producing proteins
structure and function, and consequently phenotype
92
What mutations tell us about gene function
• One gene, one enzyme hypothesis: a gene
contains the information for producing a specific
enzyme
– Beadle and Tatum use auxotrophic and prototrophic
strains of Neurospora to test hypothesis
• Genes specify the identity and order of amino
acids in a polypeptide chain
• The sequence of amino acids in a protein
determines its three-dimensional shape and
function
• Some proteins contain more than one
polypeptide coded for by different genes
93
Beadle and Tatum – One gene, one enzyme
• 1940s – isolated mutagen induced mutants that
disrupted synthesis of arginine, an amino acid
required for Neurospora growth
– Auxotroph – needs supplement to grow on minimal
media
– Prototroph – wild-type that needs no supplement; can
synthesize all required growth factors
• Recombination analysis located mutations in
four distinct regions of genome
• Complementation tests showed each of four
regions correlated with different
complementation group (each was a different
gene)
94
Fig. 7.20 a
95
Fig. 7.20 b
96
Interpretation of Beadle and Tatum
experiments
• Each gene controls the synthesis of an
enzyme involved in catalyzing the
conversion of an intermediate into
arginine
97
Genes specify the identity and order of amino
acids in a polypeptide chain
• Proteins are linear polymers of amino acids
linked by peptide bonds
– 20 different amino acids are building blocks of
proteins
– NH2-CHR-COOH – carboxylic acid is acidic, amino
group is basic
– R is the side chain that distinguishes each amino acid
Fig. 7.21 a
98
R is the side group that distinguishes each
amino acid
Fig. 7.21 b
99
100
101
Fig. 7.21 b
N terminus of a protein contains a free amino group
C terminus of protein contains a free carboxylic acid group
Fig. 7.21 c
102
Genes specify the amino acid sequence of a
polypeptide – example, sickle cell anemia
Mutant b chain of
hemoglobin form
aggregates that
cause red blood
cells to sickle
103
Fig. 7.22 a
Sequence of amino acids determine a proteins
primary, secondary, and tertiary structure
104
Fig. 7.23
Some proteins are multimeric, containing
subunits composed of more than one polypeptide
Fig. 7.24
105
How do genotypes and phenotypes
correlate?
• Alteration of amino acid composition of a
protein
• Alteration of the amount of normal protein
produced
• Changes in different amino acids at
different positions have different effects
– Proteins have active sites and sites involved
in shape or structure
106
Dominance relations between alleles depend on
the relation between protein function and
phenotype
• Alleles that produce nonfunctional proteins are usually
recessive
– Null mutations – prevent synthesis of protein or promote synthesis of
protein incapable of carrying out any function
– Hypomorphic mutations – produce much less of a protein or a protein
with weak but detectable function; usually detectable only in
homozygotes
• Incomplete dominance – phenotype varies in proportion to
amount of protein
– Hypermorphic mutations – produces more protein or same amount of a
more effective protein
– Dominant negative – produces a subunit of a protein that blocks the
activity of other subunits
– Neomorphic mutations – generate a novel phenotype; example is
ectopic expression where protein is produced outside of its normal
place or time
107
Gene Expression
The Flow of Genetic Information
from DNA via RNA to Protein
• The genetic code
– How triplets of the four nucleotides unambiguously
specify 20 amino acids, making it possible to
translate information from a nucleotide chain to a
sequence of amino acids
• Transcription
– How RNA polymerase, guided by base pairing,
synthesizes a single-stranded mRNA copy of a
gene’s DNA template
• Translation
– How base pairing between mRNA and tRNAs
directs the assembly of a polypeptide on the
ribosome
• Significant differences in gene expression
between prokaryotes and eukaryotes
• How mutations affect gene information and
expression
• The genetic code
– How triplets of the four nucleotides unambiguously
specify 20 amino acids, making it possible to
translate information from a nucleotide chain to a
sequence of amino acids
• Transcription
– How RNA polymerase, guided by base pairing,
synthesizes a single-stranded mRNA copy of a
gene’s DNA template
• Translation
– How base pairing between mRNA and tRNAs
directs the assembly of a polypeptide on the
ribosome
• Significant differences in gene expression
between prokaryotes and eukaryotes
• How mutations affect gene information and
expression
The triplet codon represents each amino
acid
• 20 amino acids encoded for by 4
nucleotides
– By deduction:
• 1 nucleotide/amino acid = 41 = 4 triplet
combinations
• 2 nucleotides/amino acid = 42 = triplet
combinations
• 3 nucleotides/amino acid = 43 = triplet
combinations
– Must be at least triplet combinations that code
for amino acids
The Genetic Code: 61 triplet codons represent
20 amino acids; 3 triplet codons signify stop
Fig. 8.3
A gene’s nucleotide sequence is colinear the
amino acid sequence of the encoded polypeptide
• Charles Yanofsky – E. coli genes for a
subunit of tyrptophan synthetase
compared mutations within a gene to
particular amino acid substitutions
• Trp- mutants in trpA
• Fine structure recombination map
• Determined amino acid sequences of
mutants
Fig. 8.4
• A codon is composed of more than one
nucleotide
– Different point mutations may affect same
amino acid
– Codon contains more than one nucleotide
• Each nucleotide is part of only a single
codon
– Each point mutation altered only one amino
acid
A codon is composed of three nucleotides and the starting
point of each gene establishes a reading frame
studies of frameshift mutations in bacteriophage T4 rIIB gene
Fig. 8.5
• Most amino acids
are specified by
more than one
codon
• Phenotypic effect
of frameshifts
depends on if
reading frame is
restored
Fig. 8.6
Cracking the code: biochemical manipulations
revealed which codons represent which amino
acids
• The discovery of messenger RNAs,
molecules for transporting genetic
information
– Protein synthesis takes place in cytoplasm
deduced from radioactive tagging of amino
acids
• RNA, an intermediate molecule made in
nucleus and transports DNA information to
cytoplasm
Synthetic mRNAs and in vitro translation determines which
codons designate which amino acids
• 1961 – Marshall Nirenberg
and Heinrich Mathaei
created mRNAs and
translated to polypeptides
in vitro
• Polymononucleotides
• Polydinucleotides
• Polytrinucleotides
• Polytetranucleotides
• Read amino acid
sequence and deduced
codons
Fig. 8.7
• Ambiguities
resolved by
Nirenberg and
Philip Leder using
trinucleotide
mRNAs of known
sequence to
tRNAs charged
with radioactive
amino acid with
ribosomes
Fig. 8.8
• 5’ to 3’ direction of mRNA corresponds to N-terminal-toC-terminal direction of polypeptide
– One strand of DNA is a template
– The other is an RNA-like strand
• Nonsense codons cause termination of a polypeptide
chain – UAA (ocher), UAG (amber), and UGA (opal)
Fig. 8.9
Summary
• Codon consist of a triplet codon each of which specifies an
amino acid
– Code shows a 5’ to 3’ direction
• Codons are nonoverlapping
• Code includes three stop codons, UAA, UAG, and UGA that
terminate translation
• Code is degenerate
• Fixed starting point establishes a reading frame
– UAG in an initiation codon which specifies reading frame
• 5’- 3’ direction of mRNA corresponds with N-terminus to Cterminus of polypeptide
• Mutaiton modify message encoded in sequence
– Frameshift mutaitons change reading frame
– Missense mutations change codon of amino acid to another amino acid
– Nonsense mutations change a codon for an amino acid to a stop codon
Do living cells construct polypeptides according to
same rules as in vitro experiments?
Fig. 8.10 a
• Studies of how
mutations affect
amino-acid
composition of
polypeptides
encoded by a gene
• Missense
mutations induced
by mutagens
should be single
nucleotide
substitutions and
conform to the
code
• Proflavin treatment generates trp- mutants
• Further treatment generates trp+
revertants
– Single base insertion (trp-) and a deletion
causes reversion (trp+)
Fig. 8.10 b
Genetic code is almost universal but not
quite
• All living organisms use same basic
genetic code
– Translational systems can use mRNA from
another organism to generate protein
– Comparisons of DNA and protein sequence
reveal perfect correspondence between
codons and amino acids among all organisms
• The genetic code
– How triplets of the four nucleotides unambiguously
specify 20 amino acids, making it possible to
translate information from a nucleotide chain to a
sequence of amino acids
• Transcription
– How RNA polymerase, guided by base pairing,
synthesizes a single-stranded mRNA copy of a
gene’s DNA template
• Translation
– How base pairing between mRNA and tRNAs
directs the assembly of a polypeptide on the
ribosome
• Significant differences in gene expression
between prokaryotes and eukaryotes
• How mutations affect gene information and
expression
Transcription
• RNA polymerase catalyzes transcription
• Promoters signal RNA polymerase where
to begin transcription
• RNA polymerase adds nucleotides in 5’ to
3’ direction
• Terminator sequences tell RNA when to
stop transcription
Initiation of transcription
Fig. 8.11 a
Elongation
Fig. 8.11 b
Termination
Fig. 8.11 c
Information flow
Fig. 8.11 d
Promoters of 10 different bacterial
genes
Fig. 8.12
In eukaryotes, RNA is processed after
transcription
• A 5’ methylated cap and a
3’ Poly-A tail are added
• Structure of the methylated
cap
How Poly-A tail is added to 3’ end of mRNA
Fig. 8.14
RNA splicing removes introns
• Exons – sequences found in a gene’s
DNA and mature mRNA (expressed
regions)
• Introns – sequences found in DNA but not
in mRNA (intervening regions)
• Some eukaryotic genes have many introns
Dystrophin gene underlying Duchenne muscular
dystrophy (DMD) is an extreme example of introns
Fig. 8.15
How RNA processing splices out introns and
adjoins adjacent exons
Fig. 8.16
• Splicing is
catalyzed by
spliceosomes
– Ribozymes –
RNA molecules
that act as
enzymes
– Ensures that all
splicing
reactions take
place in concert
Fig. 8.17
• Alternative
splicing
– Different mRNAs
can be produced
by same
transcript
– Rare transplicing
events combine
exons from
different genes
Fig. 8.18
• The genetic code
– How triplets of the four nucleotides unambiguously
specify 20 amino acids, making it possible to
translate information from a nucleotide chain to a
sequence of amino acids
• Transcription
– How RNA polymerase, guided by base pairing,
synthesizes a single-stranded mRNA copy of a
gene’s DNA template
• Translation
– How base pairing between mRNA and tRNAs
directs the assembly of a polypeptide on the
ribosome
• Significant differences in gene expression
between prokaryotes and eukaryotes
• How mutations affect gene information and
expression
Translation
• Transfer RNAs (tRNAs) mediate translation of
mRNA codons to amino acids
– tRNAs carry anticodon on one end
• Three nucleotides complementary to an mRNA codon
– Structure of tRNA
• Primary – nucleotide sequence
• Secondary – short complementary sequences pair and make
clover leaf shape
• Teriary – folding into three dimensional space shape like an L
– Base pairing between an mRNA codon and a tRNA
anticodon directs amino acid incorporation into a
growing polypeptide
– Charged tRNA is covalently coupled to its amino acid
Many tRNAs contain modified
bases
Fig. 8.19 a
Secondary and tertiary structure
Fig. 8.19 b
Aminoacyl-tRNA syntetase catalyzes attachment
of tRNAs to corresponding amino acid
Fig. 8.20
Base pairing between mRNA codon and tRNA anticodon
determines where incorporation of amino acid occurs
Fig. 8.21
Wobble:
Some tRNAs
recognize
more than
one codon
for amino
acids they
carry
Fig. 8.22
Rhibosomes are site of polypeptide
synthesis
• Ribosomes
are complex
structures
composed of
RNA and
protein
Fig. 8.23
Mechanism of translation
• Initiation sets stage for polypeptide synthesis
– AUG start codon at 5’ end of mRNA
– Formalmethionine (fMet) on initiation tRNA
• First amino acid incorporated in bacteria
• Elongation during which amino acids are added
to growing polypeptide
– Ribosomes move in 5’-3’ direction revealing codons
– Addition of amino acids to C terminus
– 2-15 amino acids per second
• Termination which halts polypeptide synthesis
– Nonsense codon recognized at 3’ end of reading
frame
– Release factor proteins and halt polypeptide
synthesis
Initiation of translation
Fig. 8.24 a
Elongation
Fig. 8.24 b
Termination of translation
Fig. 8.24 c
• Posttranslatio
nal processing
can modify
polypeptide
structure
Fig. 8.25
• The genetic code
– How triplets of the four nucleotides unambiguously
specify 20 amino acids, making it possible to
translate information from a nucleotide chain to a
sequence of amino acids
• Transcription
– How RNA polymerase, guided by base pairing,
synthesizes a single-stranded mRNA copy of a
gene’s DNA template
• Translation
– How base pairing between mRNA and tRNAs
directs the assembly of a polypeptide on the
ribosome
• Significant differences in gene expression
between prokaryotes and eukaryotes
• How mutations affect gene information and
expression
Significant differences in gene expression
between prokaryotes and eukaryotes
• Eukaryotes, nuclear membrane prevents
coupling of transcription and translation
• Prokaryotic messages are polycistronic
– Contain information for multiple genes
• Eukaryotes, small ribosomal subunit binds to 5’
methylated cap and migrates to AUG start codon
– 5’ untranslated leader sequence – between 5’ cap
and AUG start
– Only a single polypeptide produced from each gene
• Initiating tRNA in prokaryotes is fMet
• Initiating tRNA in eukaryotes Met is unmodified
A computerized analysis of gene expression
in C. elegans: A comprehensive example
• Computer programs search for possible
exons by looking for strings of codons
uninterrupted by nonsense codons
• Look for splice donor and acceptor sites to
identify introns
• C. elegans genome contains roughly
19,000 genes
– 15% encode worm’s genes or proteins
Landmarks in a
callogen gene
of C. elegans
and
comparison of
DNA and
mRNA
sequences
Fig. 8.26
• The genetic code
– How triplets of the four nucleotides unambiguously
specify 20 amino acids, making it possible to
translate information from a nucleotide chain to a
sequence of amino acids
• Transcription
– How RNA polymerase, guided by base pairing,
synthesizes a single-stranded mRNA copy of a
gene’s DNA template
• Translation
– How base pairing between mRNA and tRNAs
directs the assembly of a polypeptide on the
ribosome
• Significant differences in gene expression
between prokaryotes and eukaryotes
• How mutations affect gene information and
expression
• Mutations in a gene’s coding sequence can alter the
gene product
– Silent mutations do not alter amino acid specified
– Missense mutations replace one amino acid with another
– Nonsense mutations change an amino-acid-specifying
codon to a stop codon
– Frameshift mutations result from the insertion or deletion of
nucleotides within the coding sequence
• Mutations outside of the coding sequence can
also alter gene expression
–
–
–
–
Promoter sequences
Termination signals
Splice-acceptor and splice-donor sites
Ribosome binding sites
Fig. 8.27 c
• Mutations in genes encoding the
molecules that implement expression may
affect transcription,l mRNA splicing, or
translation
– Usually lethal
– Mutations in tRNA genes can suppress
mutations in protein-coding genes
• Nonsense supressor tRNAs
• Nonsense
suppression
– (a) Nonsense
mutation that
causes incomplete
nonfunctional
polypeptide
– (b) Nonsensesuppressing
mutation causes
addition of amino
acid at stop codon
allowing production
of full length
polypeptide
Fig. 8.28