1. Gene Expression: From Gene to Protein14
Gene Expression: From Gene to Protein

2. Overview: The Flow of Genetic Information
The information content of genes is in the form of specific sequences of nucleotides in DNA
The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins
Proteins are the links between genotype and phenotype
Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation 2 2

3. Basic Principles of Transcription and Translation
RNA is the bridge between DNA and protein synthesis
RNA is chemically similar to DNA, but RNA has a ribose sugar and the base uracil (U) rather than thymine (T)
RNA is usually single-stranded
Getting from DNA to protein requires two stages: transcription and translation 3 3

4. Transcription is the synthesis of RNA using information in DNA
Transcription produces messenger RNA (mRNA)
Translation is the synthesis of a polypeptide, using information in the mRNA
Ribosomes are the sites of translation 4 4

5. In prokaryotes, translation of mRNA can begin before transcription has finished
In eukaryotes, the nuclear envelope separates transcription from translation
Eukaryotic RNA transcripts are modified through RNA processing to yield the finished mRNA
Eukaryotic mRNA must be transported out of the nucleus to be translated 5 5

6. Nuclear envelope DNA TRANSCRIPTION Pre-mRNA RNA PROCESSING mRNA DNA
Figure 14.4
Nuclear
envelope
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
mRNA
DNA
TRANSCRIPTION
mRNA
Ribosome
TRANSLATION
Ribosome
Figure 14.4 Overview: the roles of transcription and translation in the flow of genetic information
TRANSLATION
Polypeptide
Polypeptide
(a) Bacterial cell
(b) Eukaryotic cell 6

7. The Genetic Code
How are the instructions for assembling amino acids into proteins encoded into DNA?
There are 20 amino acids, but there are only four nucleotide bases in DNA
How many nucleotides correspond to an amino acid? 7 7

8. Codons: Triplets of Nucleotides
The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide words
The words of a gene are transcribed into complementary nonoverlapping three-nucleotide words of mRNA
These words are then translated into a chain of amino acids, forming a polypeptide 8 8

9. DNA template strand 3 5 A C C A A A C C G A G T T G G T T T G G C T
Figure 14.5
DNA
template
strand 3 5 A C C A A A C C G A G T T G G T T T G G C T C A 5 3
TRANSCRIPTION U G G U U U G G C U C A
mRNA 5 3
Codon
Figure 14.5 The triplet code
TRANSLATION
Protein
Trp
Phe
Gly
Ser
Amino acid 9

10. The template strand is always the same strand for any given gene
During transcription, one of the two DNA strands, called the template strand, provides a template for ordering the sequence of complementary nucleotides in an RNA transcript
The template strand is always the same strand for any given gene 10 10

11. During translation, the mRNA base triplets, called codons, are read in the 5 to 3 direction
Each codon specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide 11 11

12. Cracking the Code All 64 codons were deciphered by the mid-1960s
Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation
The genetic code is redundant: more than one codon may specify a particular amino acid
But it is not ambiguous: no codon specifies more than one amino acid 12 12

13. Codons are read one at a time in a nonoverlapping fashion
Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced
Codons are read one at a time in a nonoverlapping fashion 13 13

14. First mRNA base (5 end of codon) Third mRNA base (3 end of codon)
Figure 14.6
Second mRNA base U C A G
UUU
UCU
UAU
UGU U
Phe
Tyr
Cys
UUC
UCC
UAC
UGC C U
Ser
UUA
UCA
UAA
Stop
UGA
Stop A
Leu
UUG
UCG
UAG
Stop
UGG
Trp G
CUU
CCU
CAU
CGU U
His
CUC
CCC
CAC
CGC C C
Leu
Pro
Arg
CUA
CCA
CAA
CGA A
Gln
CUG
CCG
CAG
CGG G
First mRNA base (5 end of codon)
Third mRNA base (3 end of codon)
AUU
ACU
AAU
AGU U
Asn
Ser
AUC
IIe
ACC
AAC
AGC C A
Thr
Figure 14.6 The codon table for mRNA
AUA
ACA
AAA
AGA A
Lys
Arg
AUG
Met or
start
ACG
AAG
AGG G
GUU
GCU
GAU
GGU U
Asp
GUC
GCC
GAC
GGC C G
Val
Ala
Gly
GUA
GCA
GAA
GGA A
Glu
GUG
GCG
GAG
GGG G 14

15. Evolution of the Genetic Code
The genetic code is nearly universal, shared by the simplest bacteria and the most complex animals
Genes can be transcribed and translated after being transplanted from one species to another 15 15

16. Concept 14.2: Transcription is the DNA-directed synthesis of RNA: a closer look
Transcription is the first stage of gene expression 16 16

17. Molecular Components of Transcription
RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and joins together the RNA nucleotides
RNA polymerases assemble polynucleotides in the 5 to 3 direction
However, RNA polymerases can start a chain without a primer
Animation: Transcription Introduction 17 17

18. Completed RNA transcript
Figure
Promoter
Transcription unit 5 3 3 5
Start point
RNA polymerase 1
Initiation 5 3 3 5
Unwound
DNA
RNA
transcript
Template strand of DNA 2
Elongation
Rewound
DNA 5 3 3 3 5 5
Figure The stages of transcription: initiation, elongation, and termination (step 3)
Direction of
transcription
(“downstream”)
RNA
transcript 3
Termination 5 3 3 5 5 3
Completed RNA transcript 18

19. The stretch of DNA that is transcribed is called a transcription unit
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 19 19

20. Synthesis of an RNA Transcript
The three stages of transcription
Initiation
Elongation
Termination 20 20

21. RNA Polymerase Binding and Initiation of Transcription
Promoters signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point
Transcription factors mediate the binding of RNA polymerase and the initiation of transcription 21 21

22. The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex
A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes 22 22

23. DNA TRANSCRIPTION Pre-mRNA RNA PROCESSING mRNA Ribosome TRANSLATION
Figure 14.UN02
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
mRNA
Figure 14.UN02 In-text figure, transcription, p. 275
Ribosome
TRANSLATION
Polypeptide 23

24. Several transcription factors bind to DNA. 3 5
Figure 14.9
Promoter
Nontemplate strand
DNA 5 T A T A A A A 3 3 A T A T T T T 5 1
A eukaryotic
promoter
TATA box
Start point
Template
strand
Transcription
factors 5 3 2
Several transcription
factors bind to DNA. 3 5
RNA polymerase II
Transcription
factors 3
Transcription
initiation
complex forms.
Figure 14.9 The initiation of transcription at a eukaryotic promoter 5 3 3 3 5 5
RNA transcript
Transcription initiation complex 24

25. Elongation of the RNA Strand
As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time
Transcription progresses at a rate of 40 nucleotides per second in eukaryotes
A gene can be transcribed simultaneously by several RNA polymerases 25 25

26. Direction of transcription Template strand of DNA
Figure 14.10
Nontemplate
strand of DNA
RNA nucleotides
RNA
polymerase T C C A A A 3 T 5 U C T
3 end T G U A G A C C A U C C A C A 5 A 3 T A G G T T
Figure Transcription elongation 5
Direction of transcription
Template
strand of DNA
Newly made
RNA 26

27. Termination of Transcription
The mechanisms of termination are different in bacteria and eukaryotes
In bacteria, the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification
In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10–35 nucleotides past this polyadenylation sequence 27 27

28. Concept 14.3: Eukaryotic cells modify RNA after transcription
Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm
During RNA processing, both ends of the primary transcript are altered
Also, usually some interior parts of the molecule are cut out and the other parts spliced together 28 28

29. Alteration of mRNA Ends
Each end of a pre-mRNA molecule is modified in a particular way
The 5 end receives a modified G nucleotide 5 cap
The 3 end gets a poly-A tail
These modifications share several functions
Facilitating the export of mRNA to the cytoplasm
Protecting mRNA from hydrolytic enzymes
Helping ribosomes attach to the 5 end 29 29

30. DNA TRANSCRIPTION Pre-mRNA RNA PROCESSING mRNA Ribosome TRANSLATION
Figure 14.UN03
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
mRNA
Figure 14.UN03 In-text figure, RNA processing, p. 277
Ribosome
TRANSLATION
Polypeptide 30

31. Polyadenylation signal
Figure 14.11
50–250 adenine
nucleotides added
to the 3 end
A modified guanine
nucleotide added to
the 5 end
Polyadenylation
signal
Protein-coding segment 5 3 G P P P
AAUAAA
AAA …
AAA
Start
codon
Stop
codon
5 Cap
5 UTR
3 UTR
Poly-A tail
Figure RNA processing: addition of the 5' cap and poly-A tail 31

32. Split Genes and RNA Splicing
Most eukaryotic mRNAs have long noncoding stretches of nucleotides that lie between coding regions
The noncoding regions are called intervening sequences, or introns
The other regions are called exons and are usually translated into amino acid sequences
RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence 32 32

33. exons spliced together
Figure 14.12
Pre-mRNA
Intron
Intron
5 Cap
Poly-A tail
1–30
31–104
105–
146
Introns cut out and
exons spliced together
mRNA
5 Cap
Poly-A tail
1–146
Figure RNA processing: RNA splicing
5 UTR
3 UTR
Coding
segment
AAUAAA 33

34. This process is called alternative RNA splicing
Many genes can give rise to two or more different polypeptides, depending on which segments are used as exons
This process is called alternative RNA splicing
RNA splicing is carried out by spliceosomes
Spliceosomes consist of proteins and small RNAs 34 34

35. Spliceosome Small RNAs 5 Pre-mRNA Exon 1 Exon 2 Intron Spliceosome
Figure 14.13
Spliceosome
Small RNAs 5
Pre-mRNA
Exon 1
Exon 2
Intron
Figure A spliceosome splicing a pre-mRNA
Spliceosome
components
mRNA
Cut-out
intron 5
Exon 1
Exon 2 35

36. Ribozymes Ribozymes are RNA molecules that function as enzymes
RNA splicing can occur without proteins, or even additional RNA molecules
The introns can catalyze their own splicing 36 36