1. Chapter 17 201 From Gene to Protein
In 1909, Archibald Garrod, a British physician, hypothesized that inherited diseases are caused by the patient’s inability to produce certain enzyme. Alkaptonuria patients have dark red urine as they are not able to produce an enzyme to metabolize alkapton, which becomes dark when exposed to air.

2. 201
In 1950s, George Beadle and Edward Tatum exposed the orange red mold Neurospora to X-rays, and then cultivated the mold from the individual ascospores in minimal media containing different amino acid supplements. They discovered that some fungi had undergone mutation which required nutritional suppliments. These mutant strains are known as auxotrophs. The wild-type or normal strains can grow in minimal medium without nutritional supplements. They hypothesized that the mutant strains had defective genes due to radiation, and were not able to synthesize the necessary enzymes. They formulated one-gene-one–enzyme hypothesis which states that the function of a gene is to produce one specific enzyme.

3. EXPERIMENT RESULTS CONCLUSION Fig. 17-2
Growth:
Wild-type
cells growing
and dividing
No growth:
Mutant cells
cannot grow
and divide
Minimal medium
RESULTS
Classes of Neurospora crassa
Wild type
Class I mutants
Class II mutants
Class III mutants
Minimal
medium
(MM)
(control)
MM +
ornithine
Condition
MM +
citrulline
MM +
arginine
(control)
Figure 17.2 Do individual genes specify the enzymes that function in a biochemical pathway?
CONCLUSION
Class I mutants
(mutation in
gene A)
Class II mutants
(mutation in
gene B)
Class III mutants
(mutation in
gene C)
Wild type
Precursor
Precursor
Precursor
Precursor
Gene A
Enzyme A
Enzyme A
Enzyme A
Enzyme A
Ornithine
Ornithine
Ornithine
Ornithine
Gene B
Enzyme B
Enzyme B
Enzyme B
Enzyme B
Citrulline
Citrulline
Citrulline
Citrulline
Gene C
Enzyme C
Enzyme C
Enzyme C
Enzyme C
Arginine
Arginine
Arginine
Arginine

4. EXPERIMENT Growth: Wild-type cells growing and dividing No growth:
Fig. 17-2a
EXPERIMENT
Growth:
Wild-type
cells growing
and dividing
No growth:
Mutant cells
cannot grow
and divide
Figure 17.2 Do individual genes specify the enzymes that function in a biochemical pathway?
Minimal medium

5. RESULTS Classes of Neurospora crassa Wild type Minimal medium (MM)
Fig. 17-2b
RESULTS
Classes of Neurospora crassa
Wild type
Class I mutants
Class II mutants
Class III mutants
Minimal
medium
(MM)
(control)
MM +
ornithine
Condition
MM +
citrulline
Figure 17.2 Do individual genes specify the enzymes that function in a biochemical pathway?
MM +
arginine
(control)

6. CONCLUSION Wild type Precursor Precursor Precursor Precursor Gene A
Fig. 17-2c
CONCLUSION
Class I mutants
(mutation in
gene A)
Class II mutants
(mutation in
gene B)
Class III mutants
(mutation in
gene C)
Wild type
Precursor
Precursor
Precursor
Precursor
Gene A
Enzyme A
Enzyme A
Enzyme A
Enzyme A
Ornithine
Ornithine
Ornithine
Ornithine
Gene B
Enzyme B
Enzyme B
Enzyme B
Enzyme B
Citrulline
Citrulline
Citrulline
Citrulline
Gene C
Figure 17.2 Do individual genes specify the enzymes that function in a biochemical pathway?
Enzyme C
Enzyme C
Enzyme C
Enzyme C
Arginine
Arginine
Arginine
Arginine

7. 201 Protein Synthesis: Transcription Translation DNA RNA Protein
Central dogma of molecular biology

8. Fig. 17-3
DNA
TRANSCRIPTION
mRNA
Ribosome
TRANSLATION
Polypeptide
(a) Bacterial cell
Nuclear
envelope
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information
mRNA
TRANSLATION
Ribosome
Polypeptide
(b) Eukaryotic cell

9. DNA TRANSCRIPTION mRNA (a) Bacterial cell Fig. 17-3a-1
Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information
(a) Bacterial cell

10. DNA TRANSCRIPTION mRNA Ribosome TRANSLATION Polypeptide
Fig. 17-3a-2
DNA
TRANSCRIPTION
mRNA
Ribosome
TRANSLATION
Polypeptide
Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information
(a) Bacterial cell

11. Nuclear envelope DNA TRANSCRIPTION Pre-mRNA (b) Eukaryotic cell
Fig. 17-3b-1
Nuclear
envelope
DNA
TRANSCRIPTION
Pre-mRNA
Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information
(b) Eukaryotic cell

12. Nuclear envelope DNA TRANSCRIPTION Pre-mRNA mRNA (b) Eukaryotic cell
Fig. 17-3b-2
Nuclear
envelope
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
mRNA
Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information
(b) Eukaryotic cell

13. Animation: Transcription
The DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator
The stretch of DNA that is transcribed is called a transcription unit
Animation: Transcription
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

14. Completed RNA transcript
Fig. 17-7
Promoter
Transcription unit 5 3 3 5
DNA
Start point
RNA polymerase 1
Initiation
Elongation
Nontemplate
strand of DNA
RNA nucleotides 5 3
RNA
polymerase 3 5
RNA
transcript
Template strand
of DNA
Unwound
DNA 3 2
Elongation
3 end
Rewound
DNA 5 5 3 3 3 5 5
Figure 17.7 The stages of transcription: initiation, elongation, and termination 5
Direction of
transcription
(“downstream”)
RNA
transcript
Template
strand of DNA 3
Termination
Newly made
RNA 5 3 3 5 5 3
Completed RNA transcript

15. Several transcription factors must bind to the DNA before RNA
Fig. 17-8 1
A eukaryotic promoter
includes a TATA box
Promoter
Template 5 3 3 5
TATA box
Start point
Template
DNA strand 2
Several transcription factors must
bind to the DNA before RNA
polymerase II can do so.
Transcription
factors 5 3 3 5 3
Additional transcription factors bind to
the DNA along with RNA polymerase II,
forming the transcription initiation complex.
Figure 17.8 The initiation of transcription at a eukaryotic promoter
RNA polymerase II
Transcription factors 5 3 3 5 5
RNA transcript
Transcription initiation complex

16. Nuclear envelope DNA TRANSCRIPTION Pre-mRNA mRNA TRANSLATION Ribosome
Fig. 17-3b-3
Nuclear
envelope
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
mRNA
Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information
TRANSLATION
Ribosome
Polypeptide
(b) Eukaryotic cell

17. Gene 2 Gene 1 Gene 3 DNA template strand mRNA Codon TRANSLATION
Fig. 17-4
Gene 2
DNA
molecule
Gene 1
Gene 3
DNA
template
strand
TRANSCRIPTION
Figure 17.4 The triplet code
mRNA
Codon
TRANSLATION
Protein
Amino acid

18. First mRNA base (5 end of codon) Third mRNA base (3 end of codon)
Fig. 17-5
Second mRNA base
First mRNA base (5 end of codon)
Third mRNA base (3 end of codon)
Figure 17.5 The dictionary of the genetic code

19. 203 RNA polymerase: Sigma factor: Aminoacyl synthetase:
Peptidyl transferase:
Release factor:

20. Figure 17.14 The structure of transfer RNA (tRNA)3
Amino acid
attachment site 5
Hydrogen
bonds
Anticodon
(a) Two-dimensional structure 5
Amino acid
attachment site 3
Figure The structure of transfer RNA (tRNA)
Hydrogen
bonds 3 5
Anticodon
Anticodon
(c) Symbol used
in this book
(b) Three-dimensional structure

21. (a) Two-dimensional structure
Fig a 3
Amino acid
attachment site 5
Hydrogen
bonds
Figure The structure of transfer RNA (tRNA)
Anticodon
(a) Two-dimensional structure

22. (b) Three-dimensional structure
Fig b
Amino acid
attachment site 5 3
Hydrogen
bonds
Figure The structure of transfer RNA (tRNA) 3 5
Anticodon
Anticodon
(c) Symbol used
in this book
(b) Three-dimensional structure

23. Aminoacyl-tRNA Amino acid synthetase (enzyme) tRNA Aminoacyl-tRNA
Fig
Aminoacyl-tRNA
synthetase (enzyme)
Amino acid P P P
Adenosine
ATP P
Adenosine
tRNA P P i
Aminoacyl-tRNA
synthetase P i P i
tRNA
Figure An aminoacyl-tRNA synthetase joining a specific amino acid to a tRNA P
Adenosine
AMP
Computer model
Aminoacyl-tRNA
(“charged tRNA”)

24. 203
In eukaryotes, before a mRNA leaves the nucleus, it is tagged with 7-methylguanosine at the 5’ end (to protect the mRNA from hydrolytic enzymes), and 50 to 250 adenine (A) to the 3’ end to form a poly-A tail. The tail helps prevent degradation of the RNA.

25. Protein-coding segment Polyadenylation signal 5 3
Fig. 17-9
Protein-coding segment
Polyadenylation signal 5 3 G P P P
AAUAAA
AAA …
AAA
5 Cap
5 UTR
Start codon
Stop codon
3 UTR
Poly-A tail
Figure 17.9 RNA processing: addition of the 5 cap and poly-A tail

26. exons spliced together Coding segment
Fig 5
Exon
Intron
Exon
Intron
Exon 3
Pre-mRNA
5 Cap
Poly-A tail 1 30 31
104
105
146
Introns cut out and
exons spliced together
Coding
segment
mRNA
5 Cap
Poly-A tail 1
146
Figure RNA processing: RNA splicing
5 UTR
3 UTR

27. 204 Heterogenous nuclear RNA (hnRNA) or primary transcript
The small nuclear RNA (snRNA) together with small nuclear ribonucleoproteins (snRNPS) form spliceosome: removes introns and splices the exons.

28. RNA transcript (pre-mRNA) 5 Exon 1 Intron Exon 2
Fig
RNA transcript (pre-mRNA) 5
Exon 1
Intron
Exon 2
Protein
Other
proteins
snRNA
snRNPs
Figure The roles of snRNPs and spliceosomes in pre-mRNA splicing

29. RNA transcript (pre-mRNA) 5 Exon 1 Intron Exon 2
Fig
RNA transcript (pre-mRNA) 5
Exon 1
Intron
Exon 2
Protein
Other
proteins
snRNA
snRNPs
Spliceosome 5
Figure The roles of snRNPs and spliceosomes in pre-mRNA splicing

30. RNA transcript (pre-mRNA) 5 Exon 1 Intron Exon 2
Fig
RNA transcript (pre-mRNA) 5
Exon 1
Intron
Exon 2
Protein
Other
proteins
snRNA
snRNPs
Spliceosome 5
Figure The roles of snRNPs and spliceosomes in pre-mRNA splicing
Spliceosome
components
Cut-out
intron
mRNA 5
Exon 1
Exon 2

31. The Functional and Evolutionary Importance of Introns
Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing.
Such variations are called alternative RNA splicing.
Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes.
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

32. Exon shuffling may result in the evolution of new proteins.
Proteins often have a modular architecture consisting of discrete regions called domains.
In many cases, different exons code for the different domains in a protein.
Exon shuffling may result in the evolution of new proteins.
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

33. Gene DNA Exon 1 Intron Exon 2 Intron Exon 3 Transcription
Fig
Gene
DNA
Exon 1
Intron
Exon 2
Intron
Exon 3
Transcription
RNA processing
Translation
Domain 3
Figure Correspondence between exons and protein domains
Domain 2
Domain 1
Polypeptide

34. (b) Schematic model showing binding sites
Fig b
P site (Peptidyl-tRNA
binding site)
A site (Aminoacyl-
tRNA binding site)
E site
(Exit site) E P A
Large
subunit
mRNA
binding site
Small
subunit
(b) Schematic model showing binding sites
Growing polypeptide
Amino end
Next amino acid
to be added to
polypeptide chain
Figure The anatomy of a functioning ribosome E
tRNA
mRNA 3
Codons 5
(c) Schematic model with mRNA and tRNA

35. Translation initiation complex
Fig
Large
ribosomal
subunit 3 U C 5 A
P site
Met 5 A
Met U G 3
Initiator
tRNA
GTP
GDP E A
mRNA 5 5 3 3
Start codon
Figure The initiation of translation
Small
ribosomal
subunit
mRNA binding site
Translation initiation complex

36. Amino end of polypeptide E 3 mRNA 5 Fig. 17-18-1 P A site site
Figure The elongation cycle of translation

37. GDP Amino end of polypeptide E 3 mRNA 5 E P A Fig. 17-18-2 P A site
GTP
GDP E P A
Figure The elongation cycle of translation

38. GDP Amino end of polypeptide E 3 mRNA 5 E P A E P A Fig. 17-18-3 P A
site A
site 5
GTP
GDP E P A
Figure The elongation cycle of translation E P A

39. GDP GDP Amino end of polypeptide E 3 mRNA Ribosome ready for
Fig
Amino end
of polypeptide E 3
mRNA
Ribosome ready for
next aminoacyl tRNA P
site A
site 5
GTP
GDP E E P A P A
Figure The elongation cycle of translation
GDP
GTP E P A

40. Release factor 3 5 Stop codon (UAG, UAA, or UGA) Fig. 17-19-1
Figure The termination of translation

41. Release factor Free polypeptide 3 3 2 5 5 Stop codon
Fig
Release
factor
Free
polypeptide 3 3 2 5 5
GTP
Stop codon
(UAG, UAA, or UGA)
2 GDP
Figure The termination of translation

42. Release factor Free polypeptide 5 3 3 3 2 5 5 Stop codon
Fig
Release
factor
Free
polypeptide 5 3 3 3 2 5 5
GTP
Stop codon
(UAG, UAA, or UGA)
2 GDP
Figure The termination of translation

43. Amino acids tRNA with amino acid attached Ribosome tRNA Anticodon 5
Fig
Amino
acids
Polypeptide
tRNA with
amino acid
attached
Ribosome
Trp
Phe
Gly
Figure Translation: the basic concept
tRNA
Anticodon 5
Codons 3
mRNA

44. Completed polypeptide Growing polypeptides Incoming ribosomal subunits
Fig
Completed
polypeptide
Growing
polypeptides
Incoming
ribosomal
subunits
Polyribosome
Start of
mRNA
(5 end)
End of
mRNA
(3 end)
(a)
Ribosomes
Figure Polyribosomes
mRNA
(b)
0.1 µm

45. Ribosome mRNA Signal peptide ER membrane Signal peptide removed
Fig
Ribosome
mRNA
Signal
peptide ER
membrane
Signal
peptide
removed
Signal-
recognition
particle (SRP)
Protein
CYTOSOL
Translocation
complex
Figure The signal mechanism for targeting proteins to the ER
ER LUMEN
SRP
receptor
protein

46. Fig
DNA
TRANSCRIPTION 3
Poly-A
RNA
polymerase 5
RNA
transcript
RNA PROCESSING
Exon
RNA transcript
(pre-mRNA)
Intron
Aminoacyl-tRNA
synthetase
Poly-A
NUCLEUS
Amino
acid
AMINO ACID ACTIVATION
CYTOPLASM
tRNA
mRNA
Growing
polypeptide
Cap 3 A
Activated
amino acid
Poly-A P
Ribosomal
subunits
Figure A summary of transcription and translation in a eukaryotic cell E
Cap 5
TRANSLATION E A
Anticodon
Codon
Ribosome

47. 207 Differences in transcription: Eukaryotes Prokaryotes
Only one gene is Several genes are
transcribed at a time transcribed together.
2. Splicing of exons No splicing
after introns have been
removed.
5’ end is tagged with No modification
7-methylguanosine.
4. 3’ end is tagged with No modification
adenines.
Movement of the No ( no nuclear
functional RNA membrane)
(the final transcript)
through the nuclear
membrane.

48. 208 Mutation: Point mutation (Base substitution): Silent mutation:
Nonsense mutation:
Missense mutation:
Addition mutation:
Deletion mutation:
Frame-shift mutation:

49.
Mutagens:
UV light:
Nitrous acid (HNO2): changes cytosine to uracil
5-Bromouracil: it pairs with guanine (G) intead of adenine (A)
Transposon (jumping gene) can cause addition or deletion of DNA when it jumps from one chromosome to another.

50. 209
Ames Test:
It is used to detect the mutagenicity of a chemical. It was developed by Bruce Ames of U.C. Berkeley in 1965.
Mutant strain of Salmonella typhimurium together with rat liver extract is mixed with the test chemical. The mutant strain is not able to grow in medium without histidine, which is an amino acid.
The mixture is plated onto the histidine-free medium. Rat liver extract is used to simulate the body conditions. It contains enzymes, which may convert a harmless chemical to a carcinogen.

51. 209
3. A control plate is similarly prepared but without the inclusion of the chemical.
The culture plates are incubated at 37oC for 2 days.
If a significant number of colonies appears on the agar plate with the suspected chemical compared to the control plate. It indicates that a reverse mutation has taken place. It implies that the chemical causes mutation. Any chemical that can cause mutation may also cause cancer.

52. 209
What is a gene?
A unit of inheritance that is responsible for a trait.
A specific locus on chromosome.
A region of specific nucleotide sequence that includes thousands of genes.
A DNA sequence that codes for a specific polypeptide.
A region of DNA that codes for the production of a RNA molecule.