12 HOW GENES WORK
CHAPTER OUTLINE
From Gene To Protein (p. 236)
12.1
12.2
12.3
The Central Dogma (p. 236; Fig. 12.1)
A. The so called “Central Dogma”
B. The four kinds of RNA used in DNA synthesis
C. The two stages of gene expression
D. The location and function of the promoter site
Transcription (p. 237; Figs. 12.2, 12.3)
A. DNA contains the genetic message, but is kept protected; instead copies of the DNA are sent
out to direct the production of proteins.
B. The working copies of genes are made of ribonucleic acid (RNA), and the path of
information from DNA to RNA to protein is called the central dogma of gene expression.
C. Transcription is the process whereby a messenger RNA (mRNA) molecule is synthesized
from a portion of the DNA molecule in the nucleus; transcription is the first step in gene
expression.
D. The second step, called translation, occurs when the mRNA leaves the nucleus of the cell and
directs the production of a protein molecule.
E. The Transcription Process
1. Transcription uses an enzyme called RNA polymerase that binds to the DNA molecule at
a specific site called the promoter and then moves along the DNA molecule.
2. A strand of mRNA is produced whose nucleotide sequence is complementary to that of
the DNA.
3. RNA uses uracil (U) in place of thymine (T).
Translation (p. 238; Figs. 12.4, 12.5, 12.6, 12.7)
A. The Genetic Code
1. In translation, the order of nucleotides in mRNA is converted into the order of amino
acids in a protein according to the genetic code.
2. In the genetic code, each three-nucleotide sequence codes for a given amino acid; a
three-nucleotide sequence on the mRNA is called a codon.
3. There are 64 different possible codons in the genetic code, and the same genetic code is
employed, for the most part, by every living creature.
B. Translating the RNA Message into Proteins
1. In translation, organelles called ribosomes use the mRNA transcript to direct the
synthesis of a protein.
C. The Protein-Making Factory
1. Translation occurs in the cytoplasm in conjunction with ribosomes, which are made up
of proteins and ribosomal RNA (rRNA).
2. Ribosomes hold the mRNA in position.
D. The Key Role of tRNA
1. A third type of RNA, called transfer RNA (tRNA), brings amino acids to the ribosome.
2. On one end of the tRNA is an anticodon sequence, which is a sequence of three
nucleotides complementary to an mRNA codon.
3. On the other end of the tRNA molecule is a binding site for the amino acid that
corresponds to the anticodon.
4. Special activating enzymes match amino acids in the cytoplasm with their tRNAs.
E. Making the Protein
1. After mRNA attaches to a ribosome, codons are positioned in each of three sites on the
ribosome: the A, P, and E sites.
2. The mRNA passes through the ribosome three-nucleotides at a time, exposing each
codon at the A site, where tRNA molecules can bind.
3.
12.4
tRNAs whose anticodons match the exposed mRNA codon bring their amino acids in
and bind at the A site on the ribosome.
4. As the ribosome proceeds along the mRNA, the old tRNA is moved to the P site, where
peptide bonds form between the incoming amino acid and the growing polypeptide
chain; at the same time, a new codon is exposed at the A site, and a new tRNA binds
with its corresponding amino acid.
5. As the ribosome proceeds again, the tRNA at the P site moves to the E site, where it is
released.
6. As the process continues, more amino acids are brought in and added to the chain.
7. When a “stop” codon is encountered, the process is finished, the ribosome complex falls
apart, and the completed protein is released into the cell.
Gene Expression (p. 241; Figs. 12.8, 12.9, 12.10)
A. Architecture of the Gene
1. Prokaryotic DNA is made up of a continuous sequence of genes with no interruptions.
2. Eukaryotic DNA is constructed differently because it possesses gene sequences that
code for amino acids, called exons, plus intervening, nonusable sequences of
nucleotides, called introns.
3. In eukaryotes, transcription first produces a primary RNA transcript; a 5´ cap and a 3´
poly-A tail are added to the primary transcript to protect it from degradation.
4. Enzymes complexes then remove the introns and join the remaining exons to form the
mature mRNA.
5. Alternative splicing allows the exons to be joined in different orders, producing many
possible different mRNAs.
B. Protein Synthesis
1. In prokaryotes, there is no nucleus and no barrier between transcription and translation;
mRNA can be translated as it is being transcribed.
2. In eukaryotes, transcription and RNA processing take place in the nucleus, and then the
mRNA travels to the cytoplasm for translation.
Regulating Gene Expression in Prokaryotes (p. 244)
12.5
How Prokaryotes Control Transcription (p. 244; Figs. 12.11-12.14)
A. Cells must also have the ability to regulate which genes will be expressed and how often
expression occurs.
B. How Prokaryotes Turn Genes Off and On
1. Prokaryotes use regulatory proteins to control when genes are transcribed.
2. When genes are transcribed, RNA polymerase binds to the DNA at a site called the
promoter.
3. Repressors
a. Proteins called repressors can bind to the DNA at a site called the operator and block
the promoter; RNA polymerase then cannot begin transcribing the genes.
b. When the gene needs to be transcribed, a signal molecule can bind to the repressor
causing it to change shape so that it can no longer prevent gene expression.
4. In the lac operon (a set of genes in the bacterium E. coli), a repressor blocks the
transcription of three genes that allow the breakdown of the sugar lactose.
5. When lactose is encountered, a signal molecule binds to the repressor; the repressor falls
off the DNA, and transcription of the genes can proceed.
6. Activators
a. Proteins called activators can bind to the DNA and make the promoter more accessible
to RNA polymerase.
7. In the lac operon, gene transcription cannot proceed unless the activator CAP is bound to
the DNA; CAP can only bind when its signal molecule cAMP binds and the CAP/cAMP
complex forms.
8. With regulatory proteins providing precise control, the transcription of genes at the lac
operon only proceeds when needed, such as when lactose is present but glucose is not.
Regulating Gene Expression in Eukaryotes (p. 246)
12.6
12.7
12.8
12.9
Transcriptional Control in Eukaryotes (p. 246; Fig. 12.15)
A. Turning Genes Off and On in Eukaryotes
1. Gene regulation in eukaryotes serves the needs of the entire organism, rather than
responding only to the cell’s immediate environment as in prokaryotic gene regulation.
B. The Structure of Chromosomes Can Affect Eukaryotic Gene Expression
1. Eukaryotic DNA is packaged around histone proteins to form nucleosomes, which are
further packaged into higher-order chromosome structures.
2. Modifying histones to result in greater condensation of the chromatin (chromosomal
material) makes promoters less accessible for gene transcription.
3. Methylation of the DNA can ensure that “turned-off” genes stay off.
4. Proteins called coactivators can methylate histones and disrupt chromatin coiling,
making the DNA more accessible; or corepressors can remove methyl groups from
histones and cause tighter coiling of chromatin and less accessibility to the DNA.
Controlling Transcription at a Distance (p. 247; Figs. 12.16, 12.17, 12.18)
A. Transcription is much more complex in eukaryotes than in prokaryotes.
B. Eukaryotic Transcription Factors
1. In addition to RNA polymerase, eukaryotic transcription requires proteins called
transcription factors.
2. Basal transcription factors come together to form an initiation complex and recruit RNA
polymerase to the promoter.
3. A wide variety of other proteins called specific transcription factors can also bind and
will affect the rate at which genes are transcribed.
C. Enhancers
1. Activator proteins can bind to distant sites called enhancers; the DNA can then loop to
bring the activator in contact with RNA polymerase and the initiation complex.
2. In addition, coactivator and mediator proteins can bind to transcription factors and affect
transcription.
3. All the factors together form a transcription complex and allow for flexibility in the
control of gene expression in eukaryotes.
RNA-Level Control (p. 249; Fig. 12.19)
A. Some controls of gene expression in eukaryotes act after transcription.
B. Discovery of RNA Interference
1. Researchers found that double-stranded RNA molecules could block the transcription of
genes whose sequence was complimentary to that of the double-stranded RNA.
2. This effect is called gene silencing or RNA interference.
C. How RNA Interference Works
1. Small fragments of RNA have been found in a wide range of organisms.
2. Single strands of RNA can fold back and form hairpin loops; areas with complementary
base-pairs can become double-stranded.
3. An enzyme called dicer can recognize double-stranded RNA and cut it into smaller bits
called siRNAs (small interfering RNAs).
4. siRNA then associates with proteins and forms a complex called RISC.
5. This complex unwinds the siRNA to produce single-stranded RNA, which can bind to
mRNAs complementary to it.
6. Genes are then silenced because the mRNA cannot be translated or because the mRNA
is destroyed.
Complex Regulation of Gene Expression (p. 251; Fig. 12.20)
A. In eukaryotes, a variety of factors can influence what genes are expressed and when:
1. Chromatin structure
2. Initiation of transcription
3. Alternative splicing
4. RNA interference
5. Availability of translational proteins
6. Post-translation modification of protein products