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Chapter 2
DNA, RNA, and Protein
Clark & Pazdernik
FIGURE 2.1
The Central Dogma
Cells store the genetic information to function and replicate in their DNA. When a protein is needed,
DNA is transcribed into RNA, which in turn, is translated into a protein.
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Copyright © 2012 by Academic Press. All rights reserved.
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FIGURE 2.2
The Structure of a Typical Gene
Genes are regions of DNA that are transcribed to give RNA. In most cases, the RNA is translated into
protein, but some RNA is not. The gene has a promoter region plus transcriptional start and stop
points that flank the actual message. After transcription, the RNA has a 5’ untranslated region (5’
UTR) and 3’ untranslated region (3’ UTR), which are not translated; only the ORF is translated into
protein.
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Copyright © 2012 by Academic Press. All rights reserved.
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FIGURE 2.3
RNA Polymerase Synthesizes RNA at the Transcription Bubble
RNA polymerase is a complex enzyme with two grooves. The first groove holds a single strand of
DNA, and the second groove holds the growing RNA. RNA polymerase travels down the DNA, adding
ribonucleotides that complement each of the bases on the DNA template strand.
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FIGURE 2.4
Monocistronic versus Polycistronic
Eukaryotes transcribe genes in single units, where each mRNA encodes for only one protein.
Prokaryotes transcribe genes in operons as one single mRNA, and then translate the proteins as
separate units.
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FIGURE 2.5
Eukaryotic Transcription
Many different general transcription factors help RNA polymerase II find the TATA and initiator box
region of a eukaryotic promoter.
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FIGURE 2.6
Components of the lac Operon
The lac operon consists of three structural genes, lacZYA, which are all transcribed from a single
promoter, designated lacP. The promoter is regulated by binding of the repressor at the operator,
lacO, and of Crp protein at the Crp site. Note that in reality, the operator partly overlaps both the
promoter and the lacZ structural gene. The single lac mRNA is translated to produce the LacZ, LacY,
and LacA proteins. The lacI gene that encodes the LacI repressor has its own promoter and is
transcribed in the opposite direction from the lacZYA operon.
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FIGURE 2.7
Control of Lactose Operon
The lactose operon is turned on only when glucose is absent but lactose is present. When glucose is available, the
global activator protein, Crp, does not activate binding of RNA polymerase. When there is no glucose, Crp binds to the
promoter and stimulates RNA polymerase to bind. The lack of lactose keeps LacI protein bound to the operator site and
prevents RNA polymerase from transcribing the operon. Only when lactose is present is LacI released from the DNA.
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FIGURE 2.8
Structures of Lactose, allo-Lactose, and IPTG
IPTG is a nonmetabolizable analog of the lactose operon inducer, allo-lactose. β-galactosidase cannot
break the sulfur linkage, and therefore, does not cleave IPTG in two.
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FIGURE 2.9
Model of Two-Component Regulatory System
The two-component regulatory system includes a membrane component (sensor kinase) and a cytoplasmic component
(regulator). Outside the cell, the sensor domain of the kinase detects an environmental change, which leads to
phosphorylation of the transmitter domain. The response regulator protein receives the phosphate group, and as a
consequence, changes configuration so as to bind the DNA.
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FIGURE 2.10
Transcription Factors Have Two Independent Domains
(A) One domain of the GAL4 transcription factor normally binds to the GAL4 DNA recognition
sequence and the other binds the transcription apparatus. (B) If the LexA sequence is substituted for
the GAL4 site, the transcription factor does not recognize or bind the DNA. (C) An artificial protein
made by combining a LexA binding domain with a GAL4 activator domain will not recognize the GAL4
site, but (D) will bind to the LexA recognition sequence and activate transcription. Thus, the GAL4
activator domain acts independently of any particular recognition sequence. It works as long as it is
held in close contact with the DNA.
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FIGURE 2.11
Somatic Mutations
The early embryo has the same genetic information in every cell. During division of a somatic cell, a
mutation may occur that affects the organ or tissue it gives rise to. Because the mutation was isolated
in a single precursor cell, other parts of the body and the germline cells will not contain the mutation.
Consequently, the mutation will not be passed on to any offspring.
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FIGURE 2.12
Eukaryotic Regulation of Transcription
(A) AP-1 is a eukaryotic transcription factor that consists of Fos and Jun. These two proteins interact
through their leucine zippers. (B) To activate transcription, AP-1 must itself first be activated by
phosphorylation by the kinase, JNK. Only then does Jun stimulate RNA polymerase II to transcribe the
appropriate genes.
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FIGURE 2.13
DNA Methylation Induces Gene Silencing
Gene expression in eukaryotes can be turned off by chromatin condensation. First, the area to be
silenced is methylated. The methyl groups attract methyl cytosine binding protein, which in turn
attracts histone deacetylases. Once HDAC removes the acetyl groups from the histone tails, the
histones aggregate tightly. The closeness of histones excludes any DNA binding proteins and hence
turns off gene expression in the area.
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FIGURE 2.14
Processing Eukaryotic mRNA
Eukaryotic RNA is processed before exiting the nucleus for translation into protein. A guanine with a
methyl group is added to the 5’ end of the message, a poly(A) tail is added to the 3’ end, and the
introns are spliced out. These modifications stabilize the message and make it much shorter than the
original RNA transcribed from the DNA.
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FIGURE 2.15
The Genetic Code
The 64 codons found in mRNA are shown with their corresponding amino acids. As usual, bases are
read from 5’ to 3’ so that the first base is at the 5’ end of the codon. Three codons (UAA, UAG, UGA)
have no cognate amino acid but signal stop. AUG (encoding methionine) and, much less often, GUG
(encoding valine) act as start codons. To locate a codon, find the first base in the vertical column on
the left, the second base in the horizontal row at the top, and the third base in the vertical column on
the right.
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FIGURE 2.16
Structure of tRNA Allows Wobble in the Third Position
Transfer RNA recognizes the codons along mRNA and presents the correct amino acid for each
codon. The first position of the anticodon on tRNA matches the third position of the codon.
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FIGURE 2.17
Translation in Prokaryotes
(A) Initiation of translation begins with the association of the small ribosome subunit with the Shine-Dalgarno sequence
(S-D sequence) on the mRNA. Next, the initiator tRNA that reads AUG is charged with fMet. The charged initiator tRNA
associates with the small ribosome subunit and finds the start codon. Assembly is helped by initiation factors (IF1, IF2,
and IF3)—not shown. (B) During elongation peptide bonds are formed between the amino acids at the A-site and the Psite. The movement of the ribosome along the mRNA and addition of a new tRNA to the A-site are controlled by
elongation factors (also not shown). (C) Termination requires release factors. The various components dissociate. The
completed protein folds into its proper three-dimensional shape.
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FIGURE 2.18
Translation in Eukaryotes
(A) Assembly of the small subunit plus initiator Met-tRNA involves the binding of factors eIF3 and eIF2. (B) The cap
binding protein of eIF4 attaches to the mRNA before it joins the small subunit. (C) The mRNA binds to the small subunit
via cap binding protein and the 40S initiation complex is assembled. (D) Assembly of the large subunit requires factor
eIF5. After assembly, eIF2 and eIF3 depart.
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FIGURE 2.19
Human Mitochondrial DNA
The mitochondrial DNA of humans contains the genes for ribosomal RNA (16S and 12S), some
transfer RNAs (single-letter amino acid codes mark these on the genome), and some proteins of the
electron transport chain.
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