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HL TOPIC
7.1, 7.2, 7.3, 7.4
NUCLEIC ACIDS AMD PROTEIN
SYNTHESIS
• Describe the structure of DNA, including the
antiparallel strands, 3’–5’ linkages and hydrogen
bonding between purines and pyrimidines.
• Outline the structure of nucleosomes
• State that nucleosomes help to supercoil
chromosomes and help to regulate transcription.
• Distinguish between unique or single-copy genes
and highly repetitive sequences in nuclear DNA.
• State that eukaryotic genes can contain exons and
introns.
Discovery of genetic material
• In 1928 Frederict Griffith made an
experiment to understand what is genetic
material in the cell. DNA or protein?
• After these four steps of experiments,
scientists tought that there must be a factor
which transforms living R bacteria into S
bacteria. This factor should bu genetic
material.
• In 1949 Avery and Mc Carty copmleted the
experiment.
Heat-killed
S strain
Heat-killed
S strain
Protein Alive R
strain
DNA alive
R strain
Mice lived
Mice died
** They concluded that DNA fragments of dead S bacteria
transform living R bacteria into S bacteria. So, genetic material
must be DNA not protein.
DISCOVERY OF THE DNA
• In 1952, Alfred Hershey and Martha Chase used
bacteriophages to show that DNA is the genetic
material of T2, a virus that infects the bacterium
Escherichia coli (E. coli).
• Bacteriophages (or phages for short) are viruses that
infect bacterial cells.
• Phages were labeled with radioactive sulfur to detect
proteins or radioactive phosphorus to detect DNA.
• Bacteria were infected with either type of labeled phage
to determine which substance was injected into cells and
which remained outside the infected cell.
• The sulfur-labeled protein stayed with the phages outside
the bacterial cell, while the phosphorus-labeled DNA was
detected inside cells.
• Cells with phosphorus-labeled DNA produced new
bacteriophages with radioactivity in DNA but not in
protein.
Figure 10.1B
Phage
Empty
protein shell
Radioactive
protein
Bacterium
Phage
DNA
DNA
Batch 1:
Radioactive
protein
labeled in
yellow
The radioactivity
is in the liquid.
Centrifuge
Pellet
1
Batch 2:
Radioactive
DNA labeled
in green
2
3
4
Radioactive
DNA
Centrifuge
Pellet
The radioactivity
is in the pellet.
Discovery of viral genetic material
• Hershey and Chase used
radioactive labeling
method. They used
radioactive sulfur to
label protein capcid and
radioactive phosphorus
to label DNA.
Figure 11.2A
DNA double helix
(2-nm diameter)
Metaphase
chromosome
Nucleosome
(10-nm diameter)
Linker
“Beads on
a string”
Histones Supercoil
(300-nm diameter)
Tight helical
fiber (30-nm
diameter)
700 nm
Nucleosome, junk DNA
Nucleosome: coiled DNA double helix around
proteins called histone.
30 5 of the human DNA is made of genes that
we use, 70 % of the DNA we do not use. This
part is called non-sense DNA.
Figure 10.5B
3 end
5 end
P
HO
5
4
3
2
1
2
A
T
5
P
C
P
G
C
P
P
T
3 end
P
G
P
OH
3
4
1
A
P
5 end
Figure 10.3D_2
Hydrogen bond
G
T
C
A
A
C
T
G
Partial chemical
structure
Prokaryotic genetic material versus eukaryotic
genetic material
• Prokaryotic DNA is
circular DNA.
• There is no protein part
in prokaryotic genetic
material (pure DNA).
• It is found in cytoplasm
• There is no intron.
• Eukaryotic DNA is not
circular (linear)
• It is called chromatin
which is made of DNA
and protein
• It is found in nucleus,
chloroplast,
mitochondria.
• There are introns.
• Intron : A portion of mRNA, as
transcribed from the DNA of a
eukaryote, which is removed
by enzymes before it is used
for protein synthesis.
• Exon: The portions of mRNA
that remain after the excision
of the introns.
Replication of DNA
• Meselson and Stahl proved
semi-conservative replication of
DNA.
They used density
gradient centrifugation
method.
They replicated E-Coli
bacteria in 15N medium
and then they transferred
the bacteria into 14N
medium.
They extracted DNA of
bacteria and centrifuged
them.
7.2 DNA replication proceeds in two directions at many
sites simultaneously
 DNA replication begins at the origins of replication
where
• DNA unwinds at the origin to produce a “bubble,”
• replication proceeds in both directions from the origin, and
• replication ends when products from the bubbles merge
with each other.
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DNA replication proceeds in two directions at many
sites simultaneously
 DNA replication occurs in the 5 to 3 direction.
• Replication is continuous on the 3 to 5 template.
• Replication is discontinuous on the 5 to 3 template,
forming short segments.
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DNA replication proceeds in two directions at many
sites simultaneously
 Two key proteins are involved in DNA replication.
1. DNA ligase joins small fragments into a continuous chain.
2. DNA polymerase
– adds nucleotides to a growing chain and
– proofreads and corrects improper base pairings.
Animation: Origins of Replication
Animation: Leading Strand
Animation: Lagging Strand
Animation: DNA Replication Review
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DNA replication proceeds in two directions at many
sites simultaneously
 DNA polymerases and DNA ligase also repair DNA
damaged by harmful radiation and toxic chemicals.
 DNA replication ensures that all the somatic cells in a
multicellular organism carry the same genetic
information.
© 2012 Pearson Education, Inc.
Figure 10.5A
Parental
DNA
molecule
Origin of
replication
“Bubble”
Two
daughter
DNA
molecules
Parental strand
Daughter strand
Figure 10.5C
DNA polymerase
molecule
5
3
Parental DNA
Replication fork
5
3
DNA ligase
Overall direction of replication
3
5
This daughter
strand is
synthesized
continuously
This daughter
strand is
3 synthesized
5 in pieces
7.3-7.4 Transcription and Translation
 DNA specifies traits by dictating protein synthesis.
 The molecular chain of command is from
• DNA in the nucleus to RNA and
• RNA in the cytoplasm to protein.
 Transcription is the synthesis of RNA under the
direction of DNA.
 Translation is the synthesis of proteins under the
direction of RNA.
© 2012 Pearson Education, Inc.
Figure 10.6A_s3
DNA
Transcription
RNA
NUCLEUS
Translation
Protein
CYTOPLASM
One gene one enzyme hypothesis
 The connections between genes and proteins
• The initial one gene–one enzyme hypothesis was based on
studies of inherited metabolic diseases.
• The one gene–one enzyme hypothesis was expanded to
include all proteins.
• Most recently, the one gene–one polypeptide hypothesis
recognizes that some proteins are composed of multiple
polypeptides.
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Transcription
 The sequence of nucleotides in DNA provides a code
for constructing a protein.
• Protein construction requires a conversion of a nucleotide
sequence to an amino acid sequence.
• Transcription rewrites the DNA code into RNA, using the
same nucleotide “language.”
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Genetic Code, Codon
• The flow of information from gene to protein is based on a
triplet code: the genetic instructions for the amino acid
sequence of a polypeptide chain are written in DNA and
RNA as a series of three-base “words” called codons.
• Translation involves switching from the nucleotide
“language” to the amino acid “language.”
• Each amino acid is specified by a codon.
– 64 codons are possible.
– Some amino acids have more than one possible codon.
© 2012 Pearson Education, Inc.
Figure 10.7
DNA
molecule
Gene 1
Gene 2
Gene 3
DNA
A A A C C G G C A A A A
Transcription
RNA
Translation
U U
U G G C
Codon
Polypeptide
Amino
acid
C G U
U
U U
Figure 10.7_1
DNA
A A
A C
U U
U
C G G
C
A
A
A A
C G U
U
U
Transcription
RNA
Translation
Codon
Polypeptide
Amino
acid
G
G C
U
Genetic code
 Characteristics of the genetic code
• Three nucleotides specify one amino acid.
– 61 codons correspond to amino acids.
– AUG codes for methionine and signals the start of transcription.
– 3 “stop” codons signal the end of translation.
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The genetic code dictates how codons are translated into
amino acids
 The genetic code’s charecteristics
• There are more than one codon for some amino acids,
• Any codon for one amino acid does not code for any other
amino acid,
• The genetic code is shared by organisms from the simplest
bacteria to the most complex plants and animals so it is
nearly universal.
• Codons are adjacent to each other with no gaps in
between.
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Figure 10.8A
Third base
First base
Second base
Figure 10.8B_s3
Strand to be transcribed
T A C T
T
C A A A A T
C
DNA
A T G A A G T
T T
T A G
Transcription
RNA
A U G A A G U U U U A G
Translation
Start
codon
Polypeptide
Met
Stop
codon
Lys
Phe
Figure 10.8C
The mice to the left and right are engineered
to express a green fluorescence protein
obtained from a jelly (jellyfish)
Transcription
 Overview of transcription
• An RNA molecule is transcribed from a DNA template by a
process that resembles the synthesis of a DNA strand
during DNA replication.
• RNA nucleotides are linked by the transcription enzyme
RNA polymerase.
• Specific sequences of nucleotides along the DNA mark
where transcription begins and ends.
• The “start transcribing” signal is a nucleotide sequence
called a promoter.
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Transcription produces genetic messages in the form of
RNA
• Transcription begins with initiation, as the RNA polymerase
attaches to the promoter.
• During the second phase, elongation, the RNA grows longer.
• As the RNA peels away, the DNA strands rejoin.
• Finally, in the third phase, termination, the RNA polymerase
reaches a sequence of bases in the DNA template called a
terminator, which signals the end of the gene.
• The polymerase molecule now detaches from the RNA
molecule and the gene.
Animation: Transcription
© 2012 Pearson Education, Inc.
Figure 10.9A
Free RNA
nucleotides
RNA
polymerase
C C A A
A U C C A
T A G G T
Direction of
transcription
Newly made RNA
T
Template
strand of DNA
Figure 10.9B
RNA polymerase
DNA of gene
Terminator
DNA
Promoter
DNA
1
Initiation
2
Elongation
Area shown
in Figure 10.9A
3
Termination
Growing
RNA
Completed
RNA
RNA
polymerase
Eukaryotic RNA is processed before leaving the nucleus
as mRNA
 Messenger RNA (mRNA)
• encodes amino acid sequences and
• conveys genetic messages from DNA to the translation
machinery of the cell, which in
– prokaryotes, occurs in the same place that mRNA is made, but in
– eukaryotes, mRNA must exit the nucleus via nuclear pores to
enter the cytoplasm.
• Eukaryotic mRNA has
– introns, interrupting sequences that separate
– exons, the coding regions.
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Eukaryotic RNA is processed before leaving the
nucleus as mRNA
 Eukaryotic mRNA undergoes processing before leaving
the nucleus.
• RNA splicing removes introns and joins exons to produce a
continuous coding sequence.
• A cap and tail of extra nucleotides are added to the ends of
the mRNA to
– facilitate the export of the mRNA from the nucleus,
– protect the mRNA from attack by cellular enzymes, and
– help ribosomes bind to the mRNA.
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Figure 10.10
Exon Intron
Exon
Intron
Exon
DNA
Cap
RNA
transcript
with cap
and tail
Transcription
Addition of cap and tail
Introns removed
Tail
Exons spliced together
mRNA
Coding sequence
NUCLEUS
CYTOPLASM
The Role of Transfer RNA
 Transfer RNA (tRNA) molecules function as a language
interpreter,
• converting the genetic message of mRNA
• into the language of proteins.
 Transfer RNA molecules perform this interpreter task
by
• picking up the appropriate amino acid and
• using a special triplet of bases, called an anticodon, to
recognize the appropriate codons in the mRNA.
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Figure 10.11A
Amino acid
attachment site
Hydrogen bond
RNA polynucleotide
chain
Anticodon
A tRNA molecule, showing
its polynucleotide strand
and hydrogen bonding
A simplified
schematic of a tRNA
Translation
 Translation occurs on the surface of the ribosome.
• Ribosomes coordinate the functioning of mRNA and tRNA and,
ultimately, the synthesis of polypeptides.
• Ribosomes have two subunits: small and large.
• Each subunit is composed of ribosomal RNAs and proteins.
• Ribosomal subunits come together during translation.
• Ribosomes have binding sites for mRNA and tRNAs.
© 2012 Pearson Education, Inc.
Figure 10.12B
tRNA binding sites
Large
subunit
P A
site site
Small
subunit
mRNA binding site
Figure 10.12C
The next amino
acid to be added
to the polypeptide
Growing
polypeptide
mRNA
tRNA
Codons
Translation
 Translation can be divided into the same three phases
as transcription:
1. initiation,
2. elongation, and
3. termination.
• Initiation brings together
• mRNA,
• a tRNA bearing the first amino acid, and
• the two subunits of a ribosome.
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Translation
 Initiation establishes where translation will begin.
 Initiation occurs in two steps.
1. An mRNA molecule binds to a small ribosomal subunit and the
first tRNA binds to mRNA at the start codon.
– The start codon reads AUG and codes for methionine.
– The first tRNA has the anticodon UAC.
2. A large ribosomal subunit joins the small subunit, allowing the
ribosome to function.
– The first tRNA occupies the P site, which will hold the growing peptide
chain.
– The A site is available to receive the next tRNA.
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Figure 10.13A
Start of genetic message
Cap
End
Tail
Figure 10.13B
Large
ribosomal
subunit
Initiator
tRNA
P
site
mRNA
U A C
A U G
Start codon
1
Small
ribosomal
subunit
2
A
site
U A C
A U G
Translation
 Once initiation is complete, amino acids are added
one by one to the first amino acid.
 Elongation is the addition of amino acids to the
polypeptide chain.
 Each cycle of elongation has three steps.
1. Codon recognition: The anticodon of an incoming tRNA
molecule, carrying its amino acid, pairs with the mRNA
codon in the A site of the ribosome.
2. Peptide bond formation: The new amino acid is joined to
the chain.
3. Translocation: tRNA is released from the P site and the
ribosome moves tRNA from the A site into the P site.
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Translation
 Elongation continues until the termination stage of
translation, when
• the ribosome reaches a stop codon,
• the completed polypeptide is freed from the last tRNA, and
• the ribosome splits back into its separate subunits.
Animation: Translation
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Figure 10.14_s4
Polypeptide
P
site
mRNA
Amino
acid
A
site
Anticodon
Codons
1
Codon recognition
mRNA
movement
Stop
codon
2
New
peptide
bond
3
Translocation
Peptide bond
formation
CONTROL OF GENE EXPRESSION
 Gene regulation is the turning on and off of genes.
 Gene expression is the overall process of information flow
from genes to proteins.
 The control of gene expression allows cells to produce
specific kinds of proteins when and where they are
needed.
 Our earlier understanding of gene control came from the
study of E. coli.
 A cluster of genes with related functions, along with the
control sequences, is called an operon.
 With few exceptions, operons only exist in prokaryotes.
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REGULATION OF GENE IN PROKARYOTES
 When an E. coli encounters lactose, all the enzymes
needed for its metabolism are made at once using the
lactose operon.
 The lactose (lac) operon includes
1. three adjacent lactose-utilization genes,
2. a promoter sequence where RNA polymerase binds and
initiates transcription of all three lactose genes, and
3. an operator sequence where a repressor can bind and block
RNA polymerase action.
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REGULATION OF GENE IN PROKARYOTES
 Regulation of the lac operon
• A regulatory gene, located outside the operon, codes for a
repressor protein.
• In the absence of lactose, the repressor binds to the operator
and prevents RNA polymerase action.
• Lactose inactivates the repressor, so
– the operator is unblocked,
– RNA polymerase can bind to the promoter, and
– all three genes of the operon are transcribed.
© 2012 Pearson Education, Inc.
Figure 11.1B
Operon turned off (lactose is absent):
OPERON
Regulatory
gene
Promoter Operator
Lactose-utilization genes
DNA
RNA polymerase cannot
attach to the promoter
mRNA
Protein
Active
repressor
Operon turned on (lactose inactivates the repressor):
DNA
RNA polymerase is
bound to the promoter
mRNA
Translation
Protein
Lactose
Inactive
repressor
Enzymes for lactose utilization
Figure 11.1B_1
Operon turned off (lactose is absent):
OPERON
Regulatory Promoter Operator
gene
Lactose-utilization genes
DNA
RNA polymerase cannot
attach to the promoter
mRNA
Protein
Active
repressor
Figure 11.1B_2
Operon turned on (lactose inactivates the repressor):
DNA
RNA polymerase is
bound to the promoter
mRNA
Translation
Protein
Lactose
Inactive
repressor
Enzymes for lactose utilization
Environmental changes and regulation of genes
 There are two types of repressor-controlled operons.
• In the lac operon, the repressor is
– active when alone and
– inactive when bound to lactose.
• In the trp bacterial operon, the repressor is
– inactive when alone and
– active when bound to the amino acid tryptophan (Trp).
© 2012 Pearson Education, Inc.
Figure 11.1C
trp operon
lac operon
Promoter Operator Gene
DNA
Active
repressor
Active
repressor
Inactive
repressor
Lactose
Inactive
repressor
Tryptophan
Environmental changes and regulation of genes
 Another type of operon control involves activators,
proteins that turn operons on by
• binding to DNA and
• making it easier for RNA polymerase to bind to the promoter.
 Activators help control a wide variety of operons.
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Chromosome structure and chemical modifications
can affect gene expression
 Differentiation
• involves cell specialization, in structure and function, and
• is controlled by turning specific sets of genes on or off.
 Almost all of the cells in an organism contain an identical
genome.
 The differences between cell types are
• not due to the presence of different genes but instead
• due to selective gene expression.
© 2012 Pearson Education, Inc.
Chromosome structure and chemical
modifications can affect gene expression
 Eukaryotic chromosomes undergo multiple levels of
folding and coiling, called DNA packing.
• Nucleosomes are formed when DNA is wrapped around
histone proteins.
– This packaging gives a “beads on a string” appearance.
– Each nucleosome bead includes DNA plus eight histones.
– Stretches of DNA, called linkers, join consecutive nucleosomes.
• At the next level of packing, the beaded string is wrapped into a
tight helical fiber.
• This fiber coils further into a thick supercoil.
• Looping and folding can further compact the DNA.
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Chromosome structure and chemical
modifications can affect gene expression
 DNA packing can prevent gene expression by
preventing RNA polymerase and other transcription
proteins from contacting the DNA.
 Cells seem to use higher levels of packing for longterm inactivation of genes.
 Highly compacted chromatin, found in varying
regions of interphase chromosomes, is generally
not expressed at all.
Animation: DNA Packing
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Figure 11.3
Enhancers
Promoter
Gene
DNA
Activator
proteins
Transcription
factors
Other
proteins
RNA polymerase
Bending
of DNA
Transcription
Complex assemblies of proteins control eukaryotic
transcription
 Silencers are repressor proteins that
• may bind to DNA sequences and
• inhibit transcription.
 Coordinated gene expression in eukaryotes often
depends on the association of a specific combination
of control elements with every gene of a particular
metabolic pathway.
© 2012 Pearson Education, Inc.
Review: Multiple mechanisms regulate gene
expression in eukaryotes
 These controls points include:
1. chromosome changes and DNA unpacking,
2. control of transcription,
3. control of RNA processing including the
– addition of a cap and tail and
– splicing,
4. flow through the nuclear envelope,
5. breakdown of mRNA,
6. control of translation, and
7. control after translation including
– cleavage/modification/activation of proteins and
– breakdown of protein.
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