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CH. 17:
PROTEIN
FROM GENE TO
DNA, RNA, and the Flow of
Information
 The expression of a gene takes place in two
steps:
 Transcription makes a single-stranded RNA copy
of a segment of the DNA.
 Translation uses information encoded in the RNA
to make a polypeptide.
DNA, RNA, and the Flow of
Information
 RNA (ribonucleic acid) differs from DNA in
three ways:
 RNA consists of only one polynucleotide strand.
 The sugar in RNA is ribose, not deoxyribose.
 RNA has uracil instead of thymine.
 RNA can base-pair with single-stranded DNA
(adenine pairs with uracil instead of thymine)
and also can fold over and base-pair with
itself.
DNA, RNA, and the Flow of
Information
 Francis Crick’s central dogma stated that
DNA codes for RNA, and RNA codes for
protein.
 How does information get from the nucleus
to the cytoplasm?
 What is the relationship between a specific
nucleotide sequence in DNA and a specific
amino acid sequence in protein?
Figure 17.2 The Central Dogma
DNA, RNA, and the Flow of
Information
 Messenger RNA, or mRNA moves from
the nucleus of eukaryotic cells into the
cytoplasm, where it serves as a template
for protein synthesis.
 Transfer RNA, or tRNA, is the link between
the code of the mRNA and the amino acids
of the polypeptide, specifying the correct
amino acid sequence in a protein.
Figure 17.3 From Gene to Protein
DNA, RNA, and the Flow of
Information
 Certain viruses use RNA rather than DNA as their
information molecule during transmission.
 These viruses transcribe from RNA to RNA; they
make a complementary RNA strand and then
use this “opposite” strand to make multiple
copies of the viral genome by transcription.
 HIV and certain tumor viruses (called
retroviruses) have RNA as their infectious
information molecule; they convert it to a DNA
copy inside the host cell and then use it to make
more RNA.
Transcription: DNA-Directed
RNA Synthesis
 In normal prokaryotic and eukaryotic cells,
transcription requires the following:
 A DNA template for complementary base pairing
 The appropriate ribonucleoside triphosphates
(ATP, GTP, CTP, and UTP) to act as substrates
 The enzyme RNA polymerase
Transcription: DNA-Directed
RNA Synthesis
 Just one DNA strand (the template strand) is
used to make the RNA.
 For different genes in the same DNA
molecule, the roles of these strands may be
reversed.
 The DNA double helix partly unwinds to serve
as template.
 As the RNA transcript forms, it peels away,
allowing the already transcribed DNA to be
rewound into the double helix.
Transcription: DNA-Directed
RNA Synthesis
 The first step of transcription, initiation, begins
at a promoter, a special sequence of DNA.
 There is at least one promoter for each gene to
be transcribed.
 The RNA polymerase binds to the promoter
region when conditions allow.
 The promoter sequence directs the RNA
polymerase as to which of the double strands is
the template and in what direction the RNA
polymerase should move.
Figure 17.4 (Part 1) DNA is Transcribed in RNA
Transcription: DNA-Directed
RNA Synthesis
 After binding, RNA polymerase unwinds the
DNA about 20 base pairs at a time and reads
the template in the 3-to-5 direction
(elongation).
 The new RNA elongates from its 5 end to its
3 end; thus the RNA transcript is antiparallel
to the DNA template strand.
 Transcription errors for RNA polymerases are
high relative to DNA polymerases.
Figure 17.4 (Part 2) DNA is Transcribed in RNA
Transcription: DNA-Directed
RNA Synthesis
 Particular base sequences in the DNA specify
termination.
 Gene mechanisms for termination vary:
 For some, the newly formed transcript simply falls
away from the DNA template.
 For other genes, a helper protein pulls the
transcript away.
 In prokaryotes, translation of the mRNA often
begins before transcription is complete.
Figure 17.4 (Part 3) DNA is Transcribed in RNA
The Genetic Code
 A genetic code relates genes (DNA) to mRNA
and mRNA to the amino acids of proteins.
 mRNA is read in three-base segments called
codons.
 The number of different codons possible is 64
(43), because each position in the codon can
be occupied by one of four different bases.
 The 64 possible codons code for only 20
amino acids and the start and stop signals.
Figure 17.5 The Universal Genetic Code
The Genetic Code
 After subtracting start and stop codons, the
remaining 60 codons code for 19 different amino
acids.
 This means that many amino acids have more
than one codon. Thus the code is redundant.
 However, the code is not ambiguous. Each
codon is assigned only one amino acid.
 Except for a few very minor exceptions, the code
is universal. It is one of the strongest pieces of
evidence for evolution from a common ancestor.
The Genetic Code
 In the early 1960s, molecular biologists
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broke the genetic code.
Nirenberg prepared an artificial mRNA in
which all bases were uracil (poly U).
When incubated with additional
components, the poly U mRNA led to
synthesis of a polypeptide chain consisting
only of phenylalanine amino acids.
UUU appeared to be the codon for
phenylalanine.
Other codons were deciphered from this
starting point.
Figure 17.6 Deciphering the Genetic Code
Preparation for Translation:
Linking RNAs, Amino Acids,
and Ribosomes
 The molecule tRNA is required to assure
specificity in the translation of mRNA into
proteins.
 The tRNAs must read mRNA correctly.
 The tRNAs must carry the correct amino
acids.
Preparation for Translation:
Linking RNAs, Amino Acids,
and Ribosomes
 The codon in mRNA and the amino acid in a
protein are related by way of an adapter—a
specific tRNA molecule.
 tRNA has three functions:
 It carries an amino acid.
 It associates with mRNA molecules.
 It interacts with ribosomes.
Preparation for Translation:
Linking RNAs, Amino Acids,
and Ribosomes
 A tRNA molecule has 75 to 80 nucleotides and
a three-dimensional shape (conformation).
 The shape is maintained by complementary
base pairing and hydrogen bonding.
 The three-dimensional shape of the tRNAs
allows them to combine with the binding
sites of the ribosome.
Figure 17.7 Transfer RNA
Preparation for Translation:
 At the 3 end of every tRNA molecule is a
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site to which its specific amino acid binds
covalently.
Midpoint in the sequence are three bases
called the anticodon.
The anticodon is the contact point between
the tRNA and the mRNA.
The anticodon is complementary (and
antiparallel) to the mRNA codon.
The codon and anticodon unite by
complementary base pairing.
Preparation for Translation:
 Each ribosome has two subunits: a large one and
a small one.
 In eukaryotes the large one has three different
associated rRNA molecules and 45 different
proteins. (60S)
 The small subunit has one rRNA and 33 different
protein molecules.(40s)
 When they are not translating, the two subunits
are separate. When translating they are 80S
 Prokaryotic ribosomes are also two subunits of
50S and 30S. When translating they are 70S.
Figure 12.9 Ribosome Structure
Preparation for Translation:
Linking RNAs, Amino Acids,
and Ribosomes
 The proteins and rRNAs are held together by
ionic bonds and hydrophobic forces.
 The large subunit has four binding sites:
 The T site where the tRNA first lands
 The A site where the tRNA anticodon binds to the
mRNA codon
 The P site where the tRNA adds its amino acid to the
polypeptide chain
 The E site where the tRNA goes before leaving the
ribosome
Translation: RNA-Directed
Polypeptide Synthesis
 Translation begins with an initiation complex: a
charged tRNA with its amino acid and a small
subunit, both bound to the mRNA.
 This complex is bound to a region upstream of
where the actual reading of the mRNA begins.
 The start codon (AUG) designates the first
amino acid in all proteins.
 The large subunit then joins the complex.
 The process is directed by proteins called
initiation factors.
Figure 17.10 The Initiation of Translation
Translation: RNA-Directed
Polypeptide Synthesis
 Ribosomes move in the 5-to-3 direction
on the mRNA.
 The peptide forms in the NH–to–COOH
direction.
 The large subunit catalyzes two reactions:
 Breaking the bond between the tRNA in the P
site and its amino acid
 Peptide bond formation between this amino
acid and the one attached to the tRNA in the A
site
Figure 12.11 Translation: The Elongation Stage
Translation: RNA-Directed
Polypeptide Synthesis
 After the first tRNA releases methionine, it
dissociates from the ribosome and returns to the
cytosol.
 The second tRNA, now bearing a dipeptide,
moves to the P site.
 The next charged tRNA enters the open A site.
 The peptide chain is then transferred to the P
site.
 These steps are assisted by proteins called
elongation factors.
Translation: RNA-Directed
Polypeptide Synthesis
 When a stop codon—UAA, UAG, or UGA—
enters the A site, a release factor and a water
molecule enter the A site, instead of an amino
acid.
 The newly completed protein then separates
from the ribosome.
Figure 12.12 The Termination of Translation
Regulation of Translation
 Antibiotics are defensive molecules produced
by some fungi and bacteria, which often
destroy other microbes.
 Some antibiotics work by blocking the
synthesis of the bacterial cell walls, others by
inhibiting protein synthesis at various points.
 Because of differences between prokaryotic
and eukaryotic ribosomes, the human
ribosomes are unaffected.
Regulation of Translation
 Polysomes are mRNA molecules with more
than one ribosome attached.
 These make protein more rapidly, producing
multiple copies of protein simultaneously.
Figure 17.13 A Polysome (Part 1)
Figure 17.13 A Polysome (Part 2)
Posttranslational Events
 Two posttranslational events can occur after
the polypeptide has been synthesized:
 The polypeptide may be moved to another
location in the cell, or secreted.
 The polypeptide may be modified by the addition
of chemical groups, folding, or trimming.
Figure 12.14 Destinations for Newly Translated Polypeptides in a Eukaryotic Cell
Posttranslational Events
 Most proteins are modified after translation.
 These modifications are often essential to the
functioning of the protein.
 Three types of modifications:
 Proteolysis (cleaving)
 Glycosylation (adding sugars)
 Phosphorylation (adding phosphate groups)
Figure 12.16 Posttranslational Modifications to Proteins
Mutations: Heritable Changes
in Genes
 All mutations are alterations of the DNA
nucleotide sequence and are of two types:
 Point mutations are mutations of single
genes.
 Chromosomal mutations are changes in the
arrangements of chromosomal DNA segments.
Mutations: Heritable Changes
in Genes
 Point mutations result from the addition or
subtraction of a base or the substitution of
one base for another.
 Point mutations can occur as a result of
mistakes during DNA replication or can be
caused by environmental mutagens.
 Because of redundancy in the genetic code,
some point mutations, called silent
mutations, result in no change in the
amino acids in the protein.
Silent Mutation
Mutations: Heritable Changes
in Genes
 Some mutations, called missense mutations,
cause an amino acid substitution.
 An example in humans is sickle-cell anemia, a
defect in the b-globin subunits of
hemoglobin.
 The b-globin in sickle-cell differs from the
normal by only one amino acid.
 Missense mutations may reduce the
functioning of a protein or disable it
completely.
Missense mutation
Figure 12.17 Sickled and Normal Red Blood Cells
Mutations: Heritable Changes
in Genes
 Nonsense mutations are base substitutions
that substitute a stop codon.
 The shortened proteins are usually not
functional.
Nonsense mutation
Mutations: Heritable Changes
in Genes
 A frame-shift mutation consists of the
insertion or deletion of a single base in a
gene.
 This type of mutation shifts the code,
changing many of the codons to different
codons.
 These shifts almost always lead to the
production of nonfunctional proteins.
Frame-shift mutation
Mutations: Heritable Changes
in Genes
 Spontaneous mutations are permanent
changes, caused by any of several
mechanisms:
 Nucleotides occasionally change their structure
(called a tautomeric shift).
 Bases may change because of a chemical reaction.
 DNA polymerase sometimes makes errors in
replication which can escape being repaired.
 Meiosis is imperfect. Nondisjunction and
translocations can occur.
Mutations: Heritable Changes
in Genes
 Induced mutations are permanent changes
caused by some outside agent (mutagen).
 Mutagens can alter DNA in several ways:
 Altering covalent bonds in nucleotides
 Adding groups to the bases
 Radiation damages DNA:
 Ionizing radiation (X rays) produces free radicals.
 Ultraviolet radiation is absorbed by thymine and
causes interbase covalent bonds to form.
Figure 17.19 Spontaneous and Induced Mutations (Part 1)
Figure 17.19 Spontaneous and Induced Mutations (Part 2)
Mutations: Heritable Changes
in Genes
 Mutations have both benefits and costs.
 Germ line mutations provide genetic
diversity for evolution, but usually produce
an organism that does poorly in its
environment.
 Somatic mutations do not affect offspring,
but can cause cancer.
Mutations: Heritable Changes
in Genes
 Mutations are rare events and most of them
are point mutations involving one nucleotide.
 Different organisms vary in mutation
frequency.
 Mutations can be detrimental, neutral, or
occasionally beneficial.
 Random accumulation of mutations in the
extra copies of genes can lead to the
production of new useful proteins.