Gene Expression

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Gene Expression

• How proteins are made.

2
W O R K T O G E T H E R

• what monomers make up proteins?
• what monomers make up nucleic acids (DNA and RNA)?

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Nucleic Acids
Proteins
Primarily DNA, RNA
Thousands of different proteins
Made up of four different bases
Made up of more than than 20 amino acids
So, how does relatively simple-sounding DNA
contain the information for building thousands of
different proteins?
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Codons
A codon is a sequence of three bases in DNA and
RNA. Each codon codes for a different amino acid.
This mRNA strand
codes for these amino acids
met
cys
glu
leu
trp
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The Genetic Code
All 20 amino acids are coded for. Redundancy of
codes is one protection against mutations.
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The Gene Concept

• A gene is a segment of DNA that codes for a
  specific protein.
• Only one side of the DNA double-helix (the
  sense or coding strand) contains the actual
  gene.
• Genes are defined by promotor and terminator
  sequences in the DNA.

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Eukaryotic gene structure
exons
DNA
introns
promoter
A typical eukaryotic gene consists of sequences
of DNA called exons, which code for the amino
acids of a protein (medium blue), and intervening
sequences called introns (dark blue), which
do not. The promoter (light blue) determines
where RNA polymerase will begin transcription.
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A small protein is 30 amino acids long. How many
nucleotides are needed to code for it?

1. 30
2. 60
3. 90
4. Depends on which amino acids.

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The same protein that is 30 amino acids long
needs how many codons to code for it?

1. 30
2. 60
3. 90
4. Depends on the amino acids it is made of.

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Transcription

• DNA stays in the nucleus.
• To get information out of one gene on a strand of
  DNA, the gene must be transcribed.
• An mRNA copy of a gene leaves the nucleus, so the
  original information (DNA) remains intact in the
  nucleus.

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RNA

• RNA is a single-stranded nucleic acid.
• RNA contains the bases adenine, uracil, guanine,
  and cytosine.
• RNA contains the sugar ribose in its
  sugar-phosphate backbone.

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(No Transcript)
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W O R K T O G E T H E R

• Which of these is TRUE about RNA
• RNA has uracil instead of thymine.
• RNA is a protein.
• RNA is a single strand instead of a double-helix.
• RNA never leaves the nucleus.

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gene
DNA
Transcription of the gene produces an mRNA with
a nucleotide sequence complementary to one of the
DNA strands.
(nucleus)
(cytoplasm)
(a) Transcription
messenger RNA
Notice that transcription takes place in the
nucleus.
ribosome
protein
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(a) Initiation
DNA
gene 1
gene 2
gene 3
RNA polymerase
DNA
promoter
RNA polymerase binds to the promoter region of
DNA near the beginning of a gene, separating the
double helix near the promoter.
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(b) Elongation
RNA
DNA template strand
RNA polymerase travels along the DNA template
strand (blue), catalyzing the addition of ribose
nucleotides into an RNA molecule (pink). The
nucleotides in the RNA are complementary to the
template strand of the DNA.
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(c) Termination
termination signal
At the end of a gene, RNA polymerase encounters a
DNA sequence called a termination signal. RNA
polymerase detaches from the DNA and releases the
mRNA molecule.
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(d) Conclusion of transcription
mRNA
After termination, the DNA completely rewinds
into a double helix. The RNA molecule is free to
move from the nucleus to the cytoplasm for
translation, and RNA polymerase may move
to another gene and begin transcription once
again.
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RNA synthesis and processing in eukaryotes
DNA
transcription
initial RNA transcript
add RNA cap and tail
cap
tail
introns cut out and broken down
RNA splicing
completed mRNA
to cytoplasm for translation
RNA polymerase transcribes both the exons and
introns, producing a long RNA molecule. Enzymes
in the nucleus then add further nucleotides at
the beginning (cap) and end (tail) of the RNA
transcript. Other enzymes cut out the RNA introns
and splice together the exons to form the true
mRNA, which moves out of the nucleus and is
translated on the ribosomes.
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gene
RNA molecules
DNA
direction of transcription
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Transcription begins when

1. RNA polymerase finds a start codon
2. RNA polymerase finds a promoter sequence
3. RNA polymerase finds a ribosome

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Base-pair matching, DNA mRNA
DNA (ns) DNA (sense) mRNA
A
G
T
A
C
G
T
T
A
C
G
A
U
T
A
G
C
C
G
A
U
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W O R K T O G E T H E R

• The enzyme that assembles RNA bases to make mRNA
  is _________________
• This enzyme begins reading DNA at the
  ____________ sequence of a gene and ends at the
  ___________ sequence.
• True or False The entire DNA strand must be
  unzipped for transcription to take place.

RNA Polymerase
promoter
terminator
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Translation

• Once the gene has been transcribed into mRNA, the
  message must be translated to build a protein.
• Ribosomes (made of rRNA) read the mRNA message
  and use the information to assemble amino acids.

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gene
Notice that translation takes place outside the
nucleus, at the ribosomes.
DNA
(nucleus)
(cytoplasm)
messenger RNA
Translation of the mRNA produces a
protein molecule with an amino acid sequence
determined by the nucleotide sequence in the mRNA.
(b) Translation
ribosome
protein
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The players

• mRNA Carries the encoded instructions for
  building a protein.
• Ribosome (rRNA protein structures) these act
  like enzymes to catalyze protein assembly.
• tRNA Transport RNA molecules that carry amino
  acids from the cytoplasm to the ribosome.

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To what class of molecules does tRNA belong?

1. Proteins
2. Carbohydrates
3. Lipids
4. Nucleic acids
5. Depends on which amino acid it carries.

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W O R K T O G E T H E R

• What other molecule have we encountered has
  active sites and acts as a catalyst? How is a
  ribosome like this molecule? How is it different?

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Initiation
amino acid
met
methionine tRNA
initiation complex
small ribosomal subunit
A tRNA with an attached methionine amino acid
binds to a small ribosomal subunit, forming an
initiation complex.
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Initiation
met
tRNA
mRNA
The initiation complex binds to an mRNA
molecule. The methionine (met) tRNA anticodon
(UAC) base-pairs with the start codon (AUG) of
the mRNA.
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Initiation
second tRNA binding site
catalytic site
met
first tRNA binding site
large ribosomal subunit
The large ribosomal subunit binds to the small
subunit. The methionine tRNA binds to the first
tRNA site on the large subunit.
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Elongation
catalytic site
met
val
The second codon of mRNA (GUU) base-pairs with
the anticodon (CAA) of a second tRNA carrying the
amino acid valine (val). This tRNA binds to the
second tRNA site on the large subunit.
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Elongation
met
peptide bond
val
The catalytic site on the large subunit catalyzes
the formation of a peptide bond linking the amino
acids methionine and valine. The two amino acids
are now attached to the tRNA in the second
binding position.
Is this hydrolysis or dehydration synthesis?
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Elongation
catalytic site
met
initiator tRNA detaches
val
ribosome moves one codon to right
The empty tRNA is released and the ribosome
moves down the mRNA, one codon to the right. The
tRNA that is attached to the two amino acids is
now in the first tRNA binding site and the second
tRNA binding site is empty.
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Elongation
catalytic site
met
his
val
The third codon of mRNA (CAU) base-pairs with
the anticodon (GUA) of a tRNA carrying the amino
acid histidine (his). This tRNA enters the second
tRNA binding site on the large subunit.
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Elongation
met
val
his
The catalytic site forms a new peptide bond
between valine and histidine. A three-amino-acid
chain is now attached to the tRNA in the second
binding site. The tRNA in the first site leaves,
and the ribosome moves one codon over on the mRNA.
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Termination
met
val
his
arg
completed peptide
arg
stop codon
ile
This process repeats until a stop codon is
reached the mRNA and the completed peptide are
released from the ribosome, and the subunits
separate.
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The ribosome has just bonded a series of amino
acids into a chain. What has it built?

1. An amino acid.
2. A protein.
3. A nucleic acid.
4. Impossible to tell at this point.

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W O R K T O G E T H E R

• When a tRNA leaves the ribosome, it goes off and
  finds another amino acid in the cell. Where do
  amino acids in human cells originally come from?
  Where do they come from in plant cells?

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gene
(a) DNA
etc.
complementary DNA strand
template DNA strand
etc.
codons
(b) mRNA
etc.
anticodons
(c) tRNA
etc.
amino acids
(d) protein
etc.
methionine
glycine
valine
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direction of transcription
RNA polymerase
DNA
mRNA
protein
ribosome
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DNA to mRNA to Protein
DNA (Sense) mRNA Amino Acids
T
A
C
G
G
T
A
G
A
A
methionine (start)
U
G
C
C
proline
A
U
C
serine
U
U
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DNA to mRNA to Protein
DNA (Sense) mRNA (sense) Amino Acids
C
A
A
T
G
A
A
C
T
G
valine
U
U
A
threonine
C
U
U
stop codon
G
A
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Practice Transcription and Translation http//le
arn.genetics.utah.edu/content/begin/dna/transcribe
/
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Translation begins when

1. The ribosome finds a promoter sequence.
2. The ribosome finds a start codon.
3. The ribosome breaks apart.

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The role of the ribosome is

1. Interpret mRNA and build proteins.
2. Construct mRNA.
3. Replicate DNA.
4. Facilitate cell division.

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The role of tRNA is

1. Transcribe DNA and move mRNA out of the nucleus.
2. Bind to the ribosome and mRNA chain together.
3. Carry amino acids to the ribosome.
4. Replace T with U when transcribing mRNA.

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If genes code for proteins, what codes for
enzymes?

1. Genes
2. Non-coding DNA
3. Other proteins
4. Nothing. Theyre manufactured in the smooth ER.

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W O R K T O G E T H E R

• Write out the mRNA strand that would be formed
  from this DNA segmentC A T A T G G G C T T A T
  A C
• If the segment doesnt include the start or stop
  codon, how many amino acids does it code for?

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W O R K T O G E T H E R

• Suppose a segment of DNA contains the triplet
  ACG, and a mutation changes it to ACT. Would that
  cause a change in the resulting amino acid chain?
  Use your knowledge of transcription and
  translation to find the answer.

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Gene Regulation

• All cells in the human body have the same DNA and
  the same set of genes, yet different cells look
  different and do different jobs.
• Cells have systems to regulate which genes are
  turned on (transcribed) and which are not.

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Cells can control the frequency of transcription.
DNA
1 transcription
Different mRNAs may be produced from a single
gene.
pre-mRNA
tRNA
rRNA proteins
2 mRNA processing
Cells can control the stability and rate
of translation of particular mRNAs.
mRNA
tRNA
ribosomes
amino acids
If the active protein is an enzyme, it will
catalyze a chemical reaction in the cell.
3 translation
inactive protein
Cells can regulate a proteins activity by
degrading it.
4 modification
substrate
active protein
Cells can regulate a proteins activity by
modifying it.
product
5 degradation
amino acids
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(a) Structure of the lactose operon
operator repressor protein binds here
codes for repressor protein
R
P
O
gene 1
gene 2
gene 3
promoter RNA polymerase binds here
structural genes that code for enzymes of lactose
metabolism
The lactose operon consists of a regulatory gene,
a promoter, an operator, and three structural
genes that code for enzymes Involved in lactose
metabolism. The regulatory gene codes for
a protein, called a repressor, which can bind to
the operator site under certain circumstances.
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(b) Lactose absent
RNA polymerase
transcription blocked
R
P
gene 1
gene 2
gene 3
repressor protein bound to operator, overlaps
promoter
free repressor proteins
When lactose is not present, repressor proteins
bind to the operator of the lactose operon. When
RNA polymerase binds to the promoter, the
repressor protein blocks access to the
structural genes, which therefore cannot be
transcribed.
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(c) Lactose present
RNA polymerase binds to promoter,
transcribes structural genes
R
O
gene 1
gene 2
gene 3
lactose- metabolizing enzymes synthesized
lactose bound to repressor proteins
When lactose is present, it binds to the
repressor protein. The lactose-repressor complex
cannot bind to the operator, so RNA polymerase
has free access to the promoter. The
RNA polymerase transcribes the three structural
genes coding for the lactose-metabolizing enzymes.
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Recap

• Transcription moves coded information from DNA to
  the ribosome by creating an mRNA copy of a gene.
• In translation, a ribosome reads the mRNA code
  and uses the information to assemble a chain of
  amino acids to make a protein.