Chapter 12

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HOW GENES WORK
CHAPTER 12
THE CENTRAL DOGMA
• The path of information is often referred to
as the central dogma.
DNA  RNA  protein
THE CENTRAL DOGMA
• The use of information in DNA to direct the
production of particular proteins is called
gene expression, which takes place in two
stages.
• Transcription is the process when a messenger
RNA (mRNA) is made from a gene within the DNA.
• Translation is the process of using the mRNA to
direct the production of a protein.
TRANSCRIPTION
• The information contained in DNA is stored
in blocks called genes.
• The genes code for proteins.
• The proteins determine what a cell will be like.
TRANSCRIPTION
• The DNA stores
this information
safely in the
nucleus where it
never leaves.
• Instructions are
copied from the
DNA into messages
comprised of RNA.
• These messages
are sent out into
the cell to direct
the assembly of
proteins.
Nucleus
DNA
Transcription
mRNA
Nuclear
envelope
Protein
Cytoplasm
Translation
TRANSCRIPTION
• A protein called RNA polymerase
produces the mRNA copy of DNA during
transcription.
• It first binds to one strand of the DNA at a site
called the promoter and then moves down
the DNA molecule and assembles a
complementary copy of RNA
• RNA uses uracil (U) instead of thymine (T)
TRANSCRIPTION
Coding strand
Unwinding Template
strand
3′
5′
A
T
T
T
A
A
G
C
T
A
C
G
A
C
A
G
T
G
A
C
T
C
G
T
3′
A
T
U
G
C
U
A
C
A
C
G
A
T
G
G
C
T
A
A
C
T
G
3′
A
G
Rewinding
U
C
A
RNA-DNA
hybrid helix
5′
G
T
RNA
polymerase
http://www.dnalc.org/resources/3d/12-transcription-basic.html
5′
mRNA
DNA
GENE EXPRESSION
• The prokaryotic gene is an uninterrupted
stretch of DNA nucleotides that corresponds
to proteins.
• In eukaryotes, the coding portions of the
DNA nucleotide sequence are interrupted
by noncoding sections of DNA.
• The coding portions are known as exons while the
noncoding portions are known as introns.
GENE EXPRESSION
• When a eukaryotic cell first transcribes a
gene, it produces a primary RNA transcript
of the entire gene.
• The primary transcript is then processed in the
nucleus.
• Enzyme-RNA complexes cut out the introns and
join together the exons to form a shorter mRNA
transcript.
• The sequences of the introns (90% of typical
human gene) are not translated.
• A 5’ cap and a 3’ poly-A tail are also added.
GENE EXPRESSION
Exon
(coding region)
DNA
5′ cap
Primary
RNA
transcript
Mature mRNA
transcript
Intron
(noncoding region)
1
2
3
4
5
6
Transcription
Introns are cut out and
coding regions are
spliced together
http://www.dnalc.org/resources/3d/rna-splicing.html
7
3′ poly-A tail
TRANSLATION
• To correctly read a gene, a cell must
translate the information encoded in the
DNA (nucleotides) into the language of
proteins (amino acids).
• Translation follows rules set out by the genetic
code.
• The mRNA is “read” in three-nucleotide units
called codons.
• Each codon corresponds to a particular
amino acid.
TRANSLATION
• The genetic code was determined from trialand-error experiments to work out which
codons matched with which amino acids.
• The genetic code is universal and employed
by all living things.
THE GENETIC CODE (RNA CODONS)
The Genetic Code
Second Letter
First
Letter
U
C
A
G
U
C
A
UUU
Phenylalanine
UUC
UUA
Leucine
UUG
UCU
UCC
UCA
UCG
UAU
UAC
UAA
UAG
CUU
CUC
Leucine
CUA
CUG
CCU
CCC
CCA
CCG
AUU
AUC
AUA
AUG
ACU
ACC
ACA
ACG
Isoleucine
Methionine; Start
GUU
GUC
Valine
GUA
GUG
GCU
GCC
GCA
GCG
Serine
Proline
Threonine
Alanine
CAU
CAC
CAA
CAG
AAU
AAC
AAA
AAG
GAU
GAC
GAA
GAG
Third
Letter
G
Tyrosine
Stop
Stop
Histidine
Glutamine
Asparagine
Lysine
Aspartate
Glutamate
UGU
UGC
UGA
UGG
CGU
CGC
CGA
CGG
AGU
AGC
AGA
AGG
GGU
GGC
GGA
GGG
Cysteine
Stop
Tryptophan
Arginine
Serine
Arginine
Glycine
There are 64 different codons in the genetic code.
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
TRANSLATION
• Translation occurs in ribosomes, which are
the protein-making factories of the cell
• Each ribosome is a complex of proteins and
several segments of ribosomal RNA (rRNA).
• Ribosomes are comprised of two subunits:
• Small subunit
• Large subunit
TRANSLATION
• The small subunit has a short sequence of
rRNA exposed that is identical to a leader
sequence that begins all genes.
• mRNA binds to the small subunit.
TRANSLATION
Large
• The large RNA
subunit has three subunit
binding sites for
transfer RNA (tRNA)
located directly
Small
subunit
adjacent to the
exposed rRNA
sequence on the
small subunit.
Large ribosomal
subunitP site
E site
A site
E
P
A
mRNA
binding
site
Small ribosomal
subunit
• These binding sites are called the A, P, and E sites.
• It is the tRNA molecules that bring amino acids to
the ribosome to use in making proteins.
TRANSLATION
• The structure of a tRNA molecule is
important to its function.
• It has an amino acid attachment site at one
end and a three-nucleotide sequence at the
other end.
TRANSLATION
• This threenucleotide
sequence is called
the anticodon and
is complementary
to 1 of the 64
codons of the
genetic code.
• Activating
enzymes match
amino acids with
their proper tRNAs.
3′
OH
Amino acid
attaches here
5′
5′
3′
Anticodon
Anticodon
TRANSLATION
• Once an mRNA molecule has bound to the
small ribosomal subunit, the other larger
ribosomal subunit binds as well, forming a
complete ribosome.
• During translation, the mRNA threads through the
ribosome three nucleotides at a time.
• A new tRNA holding an amino acid to be added
enters the ribosome at the A site.
TRANSLATION
• Before a new tRNA can be added, the previous
tRNA in the A site shifts to the P site.
• At the P site, peptide bonds form between the
incoming amino acid and the growing chain of
amino acids.
• The now empty tRNA in the P site eventually shifts to
the E site where it is released.
KEY BIOLOGICAL PROCESS:
TRANSLATION
1
2
Amino acid
Met
3
4
Leu
Asn
tRNA
P site
Met
Met Leu
A site
Leu Asn
Anticodon
E site
U A C
A U G C U G A A U
Met Leu
mRNA
Ribosome
The initial tRNA occupies
the P site on the ribosome.
Subsequent tRNAs with
bound amino acids first
enter the ribosome at the
A site.
U A C G A C
A U G C U G A A U
A C
U A C G
G A A U
A U G C U
G A C U U A
A U G C U G A A U
Codon
The tRNA that binds to the
A site has an anticodon
complementary to the
codon on them RNA.
The ribosome moves three
nucleotides to the right as
the initial amino acid is
transferred to the second
amino acid at the P site.
http://www.dnalc.org/resources/3d/15-translation-basic.html
The initiating tRNA leaves
the ribosome at the E site,
and the next tRNA enters
at the A site.
TRANSLATION
• Translation
continues until a
“stop” codon is
encountered that
signals the end of
the protein.
• The ribosome then
falls apart and the
newly made
protein is released
into the cell.
Growing
polypeptide
chain
Amino
acid
tRNA
5′
Ribosome
mRNA
3′
GENE EXPRESSION
• Gene expression works the same way in all
organisms.
DNA Replication
Key starting materials
Process
Key end product
DNA polymerase
Two DNA
duplexes
DNA
Helicase
Ligase
Transcription
Key starting materials
Process
Key end product
DNA
mRNA
RNA polymerase
Translation
Key starting materials
Process
Key end product
tRNA
Amino
acids
mRNA
Ribosome
Polypeptide
GENE EXPRESSION
• In prokaryotes, a gene
can be translated as it
is transcribed.
• In eukaryotes, a
nuclear membrane
separates the
processes of
transcription and
translation, making
protein synthesis much
more complicated.
Amino
acid
6
The amino acid chain
grows until the polypeptide
is completed.
Completed
polypeptide
5′
Ribosome moves
toward 3′ end
Cytoplasm
5
tRNAs bring their amino acids
in at the A site on the ribosome.
Peptide bonds form between
amino acids at the P site,and
tRNAs exit the ribosome from
the E site.
Ribosome
4
tRNA molecules
become attached to
specific amino acids
with the help of
activating enzymes.
Amino acids are
brought to the
ribosome in the
order directed by the
mRNA.
Nuclear
membrane
DNA
3′
3′
RNA
polymerase
In the cell nucleus, RNA
polymerase transcribes RNA
from DNA.
3′
5′
Primary
RNA transcript
ribosomal
subunit
5′
3′
Exons
Poly-A
tail
Introns
3′
Cap
Cap
Nuclear
pore Small
5′
1
5′
3′
mRNA
Large
ribosomal
subunit
Poly-A
tail
5′
mRNA
2
Introns are excised from the RNA
transcript, and the remaining exons
are spliced together, producing mRNA.
3
mRNA is transported out
of the nucleus. In the
cytoplasm, ribosomal
subunits bind to the mRNA
TRANSCRIPTIONAL CONTROL IN
PROKARYOTES
RNA
• An operon is a segment of DNA
Repressor
polymerase
containing a cluster of genes
P
O
that are all transcribed as a unit.
Promoter Operator
• The lac operon in E. coli
(a) lac operon is "repressed"
contains genes that code for
Allolactose
(inducer)
RNA
enzymes that break down the
polymerase
sugar lactose.
P
O
Promoter
Operator
• The operon contains
(b) lac operon is "induced"
regulatory elements: the
operator and promoter
• Lactose affects a repressor
mRNA
protein and causes it to fall
off the operator, allowing
transcription.
lac
lac
Protein 1 Protein 2 Protein 3
TRANSCRIPTIONAL CONTROL IN
EUKARYOTES
• Gene regulation in
eukaryotes is geared
toward the whole
organism, not the
20 nm
individual cell.
DNA
• Eukaryotic DNA is
Core complex
packaged around
of histones
Exterior
histone proteins to form
histone
nucleosomes, which are
further packaged into
higher-order
chromosome structures.
• This structure of the chromosomal material
(chromatin) affects the availability of DNA for
transcription.
COMPLEX REGULATION OF GENE
EXPRESSION
• Gene expression in eukaryotes is controlled
in many ways
•
•
•
•
•
•
Chromatin structure
Initiation of transcription
Alternative splicing
RNA interference
Availability of translational proteins
Post-translation modification of protein products
DNA tightly
packed
DNA available
for transcription
1. Chromatin
structure
Access to many
genesis affected
by the packaging
of DNA and by
chemically
altering the
histone proteins.
2. Initiation of
transcription
Most control of
gene expression is
achieved
by regulating
the frequency
of transcription
initiation.
RNA
polymerase
DNA
3′
Histones
Primary RNA transcript
5′
Exon
Intron
Cut
intron
5′ cap
3′ poly-A tail
3. RNA splicing
Gene expression
can be controlled
by altering the
rate of splicing in
eukaryotes.
Alternative splicing
can produce
multiple mRNAs
from one gene.
Mature RNA transcript
Dicer enzyme
RNA hairpins
4. Gene silencing
Cell scan silence
genes with siRNAs,
which are cut from
inverted sequences
that fold into
double-stranded
loops. siRNAs bind to
mRNAs and block
their translation.
siRNA
Completed
polypeptide
chain
6. Post-translational
modification
Phosphorylation or
other chemical
modifications can
alter the activity of
a protein after it is
produced.
5„
3„
5. Protein synthesis
Many proteins
take part in the
translation process,
and regulation of
the availability of
any of them alters
the rate of gene
expression by
speeding or slowing
protein synthesis.

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