Chapter 9

From DNA to Protein

BIO 121
Instructor: Dr. Marisa Khoo
 Chapter 9: Big Ideas

• Introducing Gene Expression.

• Transcription: DNA to RNA.
• RNA and the Genetic Code.
• Translation: RNA to Protein.
• Consequences to Mutations.
 Introducing gene expression
• The DNA of a gene—a linear sequence of
many nucleotides—is transcribed into RNA,
which is translated into a polypeptide.
• Transcription is the synthesis of RNA under
the direction of DNA.
• Translation is the synthesis of proteins under
the direction of RNA.
 Introducing gene expression
• Currently, a gene is defined as a region of DNA
that can be expressed to produce a functional
product that is either a polypeptide or an RNA
molecule.
 Introducing gene expression
• DNA to RNA (transcription)
– The DNA sequence of a gene encodes (contains
instructions for building) an RNA or protein
product
– Converting the information encoded by a gene
into a product starts with transcription (RNA
synthesis)
– During transcription, enzymes use the gene’s DNA
sequence as a template to assemble a strand of
RNA
 Introducing gene expression
• RNA to protein (translation)
– An mRNA’s protein-building message is encoded
by sets of three nucleotides
– By the process of translation, the protein-building
information in an mRNA molecule is decoded
(translated) into a sequence of amino acids
• Results in a polypeptide chain that twists and folds into
a protein
 Introducing gene expression
• Transcription and translation are part of gene
expression:
– Multistep process by which information encoded
in a gene guides the assembly of an RNA or
protein product
– Information flows from DNA to RNA to protein
 DNA
molecule

Gene 1

Gene 2

Gene 3

DNA
A A A C C G G C A A A A

Transcription

RNA U U U G G C C G U U U U

Translation Codon

Polypeptide
Amino acid
 DNA
A A A C C G G C A A A A
Transcription

RNA U U U G G C C G U U U U

Translation Codon

Polypeptide

Amino acid
Introducing gene expression
The flow of genetic information in a eukaryotic cell

DNA

Transcription

RNA
NUCLEUS

CYTOPLASM
Translation

Protein
 Introducing gene expression
• Checkpoint question In a eukaryotic cell,
where do the processes of transcription and
translation occur, and which molecule is
produced in each process?

• Transcription occurs in the nucleus, where an

RNA is made using DNA as a template.
Translation occurs in the cytoplasm and
produces a polypeptide using RNA as template
 RNA
• RNA is composed of a single-strand chain of
nucleotides
• An RNA nucleotide has three phosphate
groups, a sugar, and one of four bases
– Unlike DNA, the sugar is a ribose
– RNA contains three of the same bases found in
DNA (adenine, cytosine, and guanine)
– RNA’s fourth base is uracil, not thymine (as found
in DNA)
 DNA vs. RNA
DNA RNA
• Double stranded • Single stranded
• Deoxyribose sugar • Ribose sugar
• Bases: C,G A,T • Bases: C,G,A,U

Both contain a sugar, phosphate, and base.

 RNA

A RNA nucleotides (ribonucleotides) have a hydroxyl group (in red) at the 2′ carbon of the
sugar. This is uridine triphosphate, one of the four nucleotides in RNA. The other three differ
only in their component bases (adenine, cytosine, or guanine).
B DNA nucleotides (deoxyribonucleotides) have a hydrogen atom (in red) at the 2′ carbon of
the sugar. This is deoxythymidine triphosphate, one of the four nucleotides in DNA. The other
three differ only in their component bases (adenine, cytosine, or guanine).
 Types of RNA
• Three types
– Ribosomal RNA (rRNA): the main component of
ribosomes, which assemble amino acids into
polypeptide chains
– Transfer RNA (tRNA): delivers amino acids to a
ribosome during protein synthesis
– Messenger RNA (mRNA): contains the protein-
building message; specifies amino acid sequence
 Transcription: DNA to RNA
• In the nucleus, the DNA helix unzips, and RNA
nucleotides line up and RNA polymerase joins
them along one strand of the DNA, following the
base-pairing rules.
• The same base-pairing rules for DNA also govern
RNA synthesis in transcription
– An RNA strand is so similar to a DNA strand that the
two can base-pair if their nucleotide sequences are
complementary
– G pairs with C, and A pairs with U (uracil)
Transcription: DNA to RNA

Base-Pairing
 Transcription: DNA to RNA (1)
• The enzyme RNA polymerase adds
nucleotides to the end of a growing RNA
molecule
• In contrast to DNA replication, transcription
produces a single strand of RNA (mRNA)
• In eukaryotic cells, transcription occurs in the
nucleus; in prokaryotes, it occurs in cytoplasm
 Transcription: DNA to RNA (2)
• Transcription begins when RNA polymerase
and regulatory proteins attach to a DNA site
called a promoter
– RNA polymerase moves over a gene region and
unwinds the double helix a bit so it can “read” the
base sequence of the DNA strand
– The polymerase joins free RNA nucleotides into a
chain (at 3′ end of strand), in the order dictated by
that DNA sequence
 Transcription: DNA to RNA (3)
• When the polymerase reaches the end of the
gene region (terminator region), it releases
the DNA and the new RNA
• Typically, many polymerases transcribe a
particular gene region at the same time, so
many new RNA strands can be produced very
quickly
Figure 9.3 Process of Transcription.
By this process, a strand of RNA is assembled from
nucleotides. A gene region in the DNA serves as
the template for RNA synthesis.
1. The enzyme RNA polymerase binds to a
promoter in the DNA. The binding positions the
polymerase near a gene. Only the DNA strand
complementary to the gene sequence will be
transcribed into RNA.
2. RNA polymerase begins to move along the gene
and unwind the DNA. As it does, it links RNA
nucleotides in the order specified by the base
sequence of the complementary DNA strand.
The DNA winds up again after the polymerase
passes.
3. Zooming in on the site of transcription, we can
see that RNA polymerase covalently bonds
successive nucleotides into an RNA strand. The
base sequence of the new RNA strand is
complementary to the base sequence of its DNA
template strand, so it is an RNA copy of the
gene.
Post-transcriptional modifications

• Primary transcript is
not mature mRNA
• DNA sequence has
coding regions (exons)
and non-coding regions
(introns)
• Introns must be
removed.
• The process of
removing introns is
called as alternative
splicing.
 Post-transcriptional modifications
• Further modifications of mRNA include:
– A modified guanine “cap” is added to the 5′ end
(helps mRNA bind to a ribosome)
– A poly-A tail (multiple adenines) are added to the
3′ end (enables exportation from the nucleus)
Post-transcriptional modifications
 Post-transcriptional modifications
Checkpoint question Explain why most
eukaryotic genes are longer than the mRNA that
leaves the nucleus.

These genes have introns, noncoding sequences

of nucleotides that are spliced out of the initial
RNA transcript to produce mRNA.
 RNA and The Genetic Code
• The genetic code is the set of rules that
dictates the amino acid translations of each of
the mRNA nucleotide triplets.
• Nearly all organisms use an identical genetic
code to convert the mRNA codons transcribed
from a gene to the amino acid sequence of a
polypeptide.
 RNA and The Genetic Code
• Characteristics of the genetic code
• Triplet: Three nucleotides specify one
amino acid
• AUG codes for methionine and signals the
start of transcription
• 3 “stop” codons signal the end of translation
– UAA and UAG (thyrosine), UGA (cysteine)
 RNA and The Genetic Code
• Redundant: More than one codon for some
amino acids
• Unambiguous: Any codon for one amino acid
does not code for any other amino acid
• Does not contain spacers or punctuation:
Codons are adjacent to each other with no
gaps in between
• Nearly universal (for all living organism)
RNA and The Genetic Code
Figure 9.6 The genetic code.
A Codon table. Each codon in
mRNA is a set of three nucleotide
bases. A codon’s first base is given
to the left of the table; its second,
in the top row; and its third, to the
right of the table.
Sixty-one of the triplets encode
amino acids; one of those, AUG,
both codes for methionine and
serves as a signal to start
translation. Three codons are
signals that stop translation.
Correspondence Between DNA, RNA,
and Protein

Example of the
correspondence between
DNA, RNA, and protein. A
gene region in a strand of
chromosomal DNA is
transcribed into an
mRNA, and the codons of
the mRNA specify a chain
of amino acids—a
protein.
 The Translators: rRNA and tRNA
• Ribosomes
- Translation occurs on the surface of the
ribosome
– Ribosomes have two subunits: small and large
– Each subunit is composed of ribosomal RNA
(rRNA) and proteins and
– Ribosomal subunits come together during
translation
– have binding sites for tRNAs and mRNA.
 Growing tRNA binding sites
tRNA polypeptide Exit tunnel
molecules

Ribosome
Large P A
subunit site site

Small
subunit
mRNA binding site

Growing The next amino

polypeptide acid to be added
exits via to the polypeptide
the tunnel

mRNA tRNA

Codons

Figure: A ribosome with occupied binding sites.

This figure shows that one of the tRNA binding sites (P site) holds the growing peptide chain while the
adjacent site (A site) holds the tRNA carrying the next amino acid to be added to the chain.
 The Translators: rRNA and tRNA
• A ribosome attaches to the mRNA and
translates its message into a specific
polypeptide, aided by transfer RNAs (tRNAs).
• Each tRNA is a folded molecule bearing a base
triplet called an anticodon on one end and a
specific amino acid attachment site at the
other end.
 Amino acid
3′ attachment
Amino acid A site
C
attachment C
site A 5′
C G
G C
C G
U G
Chemically
U A modified
A U base
U C A U
* C A C AG U A G *
A C U C
G *
C G U G U* C G A G G
* * C A G G
U *
*GA
G C
G C
U A
* G
* A RNA polynucleotide
A C Hydrogen bonds chain
* U
A G
A

Anticodon
A flattened view of the RNA
nucleotides that make up a Anticodon
tRNA, with specially modified
bases marked with asterisks A tRNA molecule, showing its A simplified
folded polynucleotide strand representation
and the hydrogen bonds that of a tRNA, showing
hold it in shape its overall shape
 Translation: RNA to Protein
• Steps of translation
– Translation begins in the cytoplasm when a small
ribosomal subunit binds to the mRNA
– Next, the anticodon of a special tRNA called an
initiator base pairs with the first AUG codon of the
mRNA
– A large ribosomal subunit joins the small subunit,
and the intact ribosome begins to assemble a
polypeptide chain as it moves along the mRNA
 Translation: RNA to Protein
• Steps of translation (cont’d.)
– Initiator tRNAs carry methionine
• The first amino acid of all new polypeptide chains
– Another tRNA joins the complex when its anticodon
base-pairs with the second codon
– The ribosome catalyzes formation of a peptide bond
between first two amino acids
– As the ribosome moves to the next codon, it releases
the first tRNA
– Elongation of polypeptide continues until a stop
codon reaches the ribosome’s A site.
Translation: RNA to Protein
 Translation: RNA to Protein
Zooming in on translation. Ribosomal subunits and an initiator tRNA converge
on an mRNA. Then, tRNAs deliver amino acids in the order dictated by
successive codons in the mRNA. As the ribosome moves along the mRNA, it
links the amino acids together via peptide bonds, so a polypeptide forms and
elongates. Translation ends when the ribosome reaches a stop codon.
1 Ribosomal subunits and an initiator tRNA converge on an mRNA. A second
tRNA binds to the second codon.
2 A peptide bond forms between the first two amino acids.
3 The first tRNA is released and the ribosome moves to the next codon. A third
tRNA binds to the third codon.
4 A peptide bond forms between the second and third amino acids.
5 The second tRNA is released and the ribosome moves to the next codon. A
fourth tRNA brings the next amino acid to be added to the polypeptide chain.
6 The process repeats until the ribosome encounters a stop codon. Then, the
new polypeptide is released and the ribosome subunits separate.
DNA Transcription

1 mRNA is transcribed
mRNA from a DNA template.
RNA
polymerase

Amino acid Translation

Each amino acid
2
attaches to its proper
Enzyme tRNA with the help of a
specific enzyme and
ATP.

ATP
tRNA

Anticodon

Initiator Large Figure:

ribosomal 3 Initiation of
tRNA
subunit polypeptide synthesis
Summary of
The mRNA, the first
tRNA, and the ribosomal
transcription
Start Codon
sub-units come together. and translation.
Small
mRNA ribosomal
subunit
 New peptide
Growing bond forming
polypeptide

4 Elongation
A succession of tRNAs
add their amino acids
to the polypeptide chain
as the mRNA is moved
through the ribosome,
Codons one codon at a time.
mRNA

Polypeptide

5 Termination
The ribosome Figure:
recognizes a stop
codon. The polypeptide Summary of
is terminated and
Stop codon released. transcription
and translation.
 RNA Transcription NUCLEUS
polymerase

DNA 1 Transcription
mRNA

Translation CYTOPLASM

Amino acid
2 Amino acid
attachment
Enzyme
tRNA

ATP

Initiator Anticodon
tRNA Large
ribosomal 3 Initiation of
UAC
subunit polypeptide
AUG synthesis
Start codon Small
mRNA ribosomal
subunit
Growing
polypeptide New peptide
bond forming

4 Elongation
Codons
mRNA

Polypeptide

5 Termination
Stop codon
Review: The flow of genetic information in
the cell is DNA  RNA  protein
• Checkpoint question Which of the types of
nucleic acids you’ve learned about does not
participate directly in translation?

• DNA
 Consequences to Mutations
• Mutations are changes in the genetic information
of a cell or virus, caused by errors in DNA
replication or recombination, or by physical or
chemical agents called mutagens.
• Substituting, inserting, or deleting nucleotides
alters a gene, with varying effects.
• When a mutation does occur in a protein-coding
region, the redundancy of the genetic code offers
a margin of safety
– Example: a mutation that changes a CCC codon to CCG
may not have further effects, because both of these
codons specify the amino acid serine
 Consequences to Mutations
• Base substitutions: replacement of one nucleotide
with another
– Effect depends on whether there is an amino acid
change that alters the function of the protein
• Deletions or insertions
– Alter the reading frame of the mRNA, so that
nucleotides are grouped into different codons
– Lead to significant changes in amino acid
sequence downstream of mutation
– Cause a nonfunctional polypeptide to be
produced
 Consequences to Mutations
Normal hemoglobin DNA Mutant hemoglobin DNA

C T T C A T

mRNA mRNA

G A A G U A

Normal hemoglobin Sickle-cell hemoglobin

Glu Val

The molecular basis of sickle-cell disease

Normal T A C T T C A A A C C G C G T
gene A U G A A G U U U G G C G C A
mRNA
Protein Met Lys Phe Gly Ala

Nucleotide A U G A A G U U U A G C G C A
substitution
Met Lys Phe Ser Ala

Deleted

Nucleotide A U G A A G U U G G C G C A
deletion
Met Lys Leu Ala

Inserted

Nucleotide A U G A A G U U U G G C G C
insertion
Met Lys Leu Trp Arg