12
Gene Expression
Lecture Outline
I.
II.
Most genes carry information for making proteins
A. In 1908, Archibald Garrod proposed that genes are responsible for enzymes,
while studying a rare genetic disease, alkaptonuria
1. Book: "Inborn Errors of Metabolism"
2. Sumner, in 1926, purified a different enzyme and found it to be a protein
(Nobel Prize in 1946)
B. In the 1940s, George Beadle and Edward Tatum worked on Neurospora (a
mold)
1. 1 mutant gene affected 1 single step in a metabolic pathway
2. The "one gene, one enzyme" hypothesis
a) It's now known that some genes encode proteins that are not enzymes;
based on the work of Pauling and others
b) It's also know that one gene is responsible for one polypeptide chain,
and that some proteins have more than one chain
c) Used the term "wild type," meaning the organism with the normal
phenotype; does not imply dominant or recessive, just the normal
3. The "one gene, one polypeptide" hypothesis
DNA is transcribed to form RNA; RNA is translated to form a polypeptide
A. RNA (ribonucleic acid) is used as an intermediary between DNA and proteins
1. RNA is a single-stranded, uncoiled nucleotide polymer (although some
areas may be folded)
2. The sugar in RNA is ribose, and uracil substitutes for thymine
a) Uracil is a pyrimidine and forms two bonds with adenine
B. A copy of the DNA is made in the form of messenger RNA (mRNA) in
transcription
C. Translation involves mRNA, tRNA (transfer RNA), and rRNA (ribosomal
RNA) coordinating to produce proteins
1. mRNA has sequences of 3 nucleotides called codons
a) Codons are read in sequences of 3; this is called the triplet code
b) Codons are written in a 5’ to 3’ fashion
c) Each codon codes for 1 amino acid
d) 4 bases can combine in 43 combinations—more than enough to code
for the 20 naturally occurring amino acids
2. Each tRNA molecule has a sequence of 3 nucleotides—the anticodon
a) Anticodons base pair with the codon in a complimentary way via
hydrogen bonds
b) Anticodons are written in a 3’ to 5’ fashion
III.
IV.
3. Ribosomes are composed of proteins and rRNA
Biologists cracked the genetic code in the 1960s
A. In 1961 Crick and colleagues determined that the code was read in a
nonoverlapping sequence of bases, forming a 3-base reading frame
1. 1 nucleotide code for 1 amino acid? No, 4 bases, 20 amino acids
2. 2 nucleotides code for 1 amino acid? No, not enough combinations
3. 3 nucleotides code for 1 amino acids? Yes, 64 possible combinations
B. Sidney Brenner, in 1961, concluded from experiments that it was a
nonoverlapping triplet code; established the "reading frame"
C. Nirenberg and Matthaei produced experimental evidence that began
assigning mRNA to base sequences
1. First was poly-U (phenylalanine = UUU)
2. In 1968 Nirenberg received the Nobel Prize
3. Further found that UAA, UGA, and UAG did not code for any amino acid;
they are stop codons
4. By 1967, code was completely "cracked"
5. Remember that the code is in mRNA code
6. The genetic code of all 64 possible codons has been found to be nearly
universal
7. The genetic code is redundant
a) Redundant codons have similar base sequences
b) Only methionine and tryptophan have single triplet codes
D. The wobble hypothesis, proposed by Crick, suggests that the third nucleotide
of the tRNA anticodon can bind with more than one nucleotide of the mRNA
codon, as cells typically produce only about 40 different tRNA molecules
Transcription is the synthesis of RNA from a DNA template
A. RNA is synthesized by DNA-dependent RNA polymerases, which are similar
to DNA polymerases
B. Like DNA replication, the reactions are exergonic and require an input of ATP
C. Messenger RNA contains base sequences that code for protein
1. Transcription does not involve a primer; it begins at a promoter sequence
on the template strand (the promotor is not transcribed)
2. RNA synthesis proceeds in a 5’3’ direction (copying the DNA from the 3’
 5’)
a) Upstream refers to sections toward the 5’ end of the mRNA sequence
b) Downstream refers to sections toward the 3’ end of the mRNA
sequence
D. Synthesis of mRNA includes initiation, elongation, and termination
1. In both prokaryotes and eukaryotes, RTNA polymerases move past the
promoter to begin transcription of DNA
2. Bacterial promoters are about 40 bases long and are located in the DNA,
just upstream from the starting point
3.
4.
Unlike DNA synthesis, RNA synthesis does not require a primer
In elongation, nucleotides are added in a complementary way with the
input of energy
5. Elongation continues until RNA polymerases recognize a stop signal
6. At the stop signal, the process differs in prokaryotes and eukaryotes
a) In prokaryotes, transcription stops immediately
b) In eukaryotes, RNA polymerase continues to add new nucleotides for
about 10-15 nucleotides past the stop
7. Typically only one strand of the DNA is transcribed—the template strand
a) In a single DNA molecule, some of the template sections are on one
strand, others are on the other strand
E. Messenger RNA contains base sequences that do not directly code for protein
1. mRNA has a noncoding leader sequence at the 5’ end, important in
binding to the ribosome during translation
2. The start codon begins the coding sequences that follow the leader
sequence
3. Coding sequences are followed by a stop codon (UAA, UAG, and UGA),
and may be followed by variable noncoding 3’ trailing sequences
V.
During translation, the nucleic acid message is decoded
A. An amino acid is attached to tRNA before becoming incorporated into a
polypeptide
1. To form a polypeptide chain, the amino and carboxyl groups of amino
acids are joined by peptide bonds
2. The specific sequence of the amino acids (primary structure) is dictated by
the sequence of codons of the mRNA
3. tRNA molecules are produced from tRNA genes
a) tRNA is linked to amino acids by aminoacyl-tRNA synthetases,
forming aminoacyl-tRNAs
b) This is an energy-requiring process
B. tRNA molecules have specialized regions with specific functions
1. tRNA molecules have attachment sites for amino acids
2. tRNA molecules have anticodons that will bind to complementary codons
of the mRNA
3. tRNA molecules must be recognized by both the specific aminoacyl-tRNA
synthetase and the ribosome and have recognition sites for each
4. tRNA molecules are approximately 70 nucleotides long, with some generic
sections and some unique sections
5. The nucleotide chain is folded back upon itself to form 3 or more loops,
with unpaired nucleotides exposed to form the recognition or attachment
sites
C. The components of the translational machinery come together at the
ribosomes
1.
Ribosomes are composed of two subunits
a) In E. coli, the small subunit is composed of 21 proteins and 1 RNA
molecule; the large subunit is composed of 35 proteins and 2 RNA
molecules
b) The large subunit has a groove into which the small subunit fits
c) Ribosomes are transcribed from DNA, but do not carry information—
rather they function as the physical site of translation and as a catalyst
d) The A (aminoacyl) site of the ribosome is where the aminoacyl-tRNA
binds
e) The P (peptidyl) site of the ribosome is where the tRNA holding the
polypeptide chain is positioned
f) The E (exit) site is where the tRNAs that have delivered the amino
acids to the growing polypeptide chain exit the ribosome
D. Translation includes initiation, elongation, and termination
1. Initiation is the first step
a) Initiation factors (proteins) move an initiation tRNA onto the small
ribosomal subunit
b) The codon for the initiation is AUG, which codes for the amino acid
methionine (met), although the methionine is often removed later
c) The initiation complex binds to ribosome-recognition sequences on the
mRNA and aligns the anticodon of the tRNA with the codon of the
mRNA
d) The large ribosomal subunit then binds, forming the functional
ribosome or initiation complex
e) In eukaryotes, the methionine of the initiator tRNA is unmodified;
there is no leader sequence, but a start codon is embedded in a short
sequence; and lastly, the initiation complex is more complex
2. Elongation is the addition of new amino acids to the growing protein
a) As the initiator, tRNA is bound to the P site of the ribosome; the A site
is unoccupied until the next aminoacyl-tRNA moves in
b) The energy for this binding process comes from guanosine
triphosphate(GTP)
c) Peptide bond formation takes place between the amino group of the
new amino acid and the carboxyl group of the amino acid bound in
the preceding reaction
d) The tRNA molecule is released from the P site
(1) This reaction requires the ribozyme, peptidyl transferase
(2) This ribozyme is not a protein, but is a rRNA portion of the large
ribosomal subunit
e) Protein synthesis always proceeds from the amino end to the carboxyl
end
f) Translocation is the movement of the growing polypeptide chain from
the A site to the P site
(1) Energy for translocation comes from GTP
g) The tRNA, without an attached amino acid, now moves from the P to
the E site
h) This tRNA then leaves the ribosome and becomes part of the tRNA
pool in the cytosol
i)Translation of the mRNA proceeds from a 3’ to a 5’ direction, which is the
same as the direction of transcription
j) Termination occurs when the mRNA presents the codons UAA, UGA,
or UAG, as there is no tRNA that is complementary to them
(1) Release factors recognize these codons, and a bond between the
tRNA in the P site and its amino acid breaks
(2) The ribosome dissociates into the 2 subunits, and the newly
produced polypeptide chain dissociates from the ribosome
E.
VI.
A polyribosome is a complex of one mRNA and many ribosomes
1. In prokaryotes, transcription and translation occur simultaneously
2. The half-life of the mRNA molecules in bacteria is about 2 minutes
Transcription and translation are more complex in eukaryotes than in prokaryotes
A. Eukaryotic mRNA molecules are processed after transcription; prokaryotic
mRNAs are used immediately without processing
1. Processing begins in the nucleus; 5’ cap is added to the 5’ end
a) The cap is 7-methylguanylate, which is GMP and a methyl group
added
b) The cap is necessary for binding to ribosomes
2. Capping may protect mRNA from degradation; half-lives of eukaryotic
mRNA molecules are as long as 24 hours
3. At the 3’ end of the molecule, a sequence is added that acts as a signal for
the subsequent addition of a tail
4. Enzymes recognize the signal and add 100-250 adenines (the poly-A tail)
B. Both noncoding sequences and coding sequences are transcribed from
eukaryotic genes
1. Genes of most eukaryotes have interrupted coding sequences
a) Coding sequences are exons (expressed sequences); noncoding
sequences are introns (intervening sequences)
b) A typical eukaryotic gene has multiple exons and introns, with
variable numbers of each
2. This terminology refers to sequences in both DNA and mRNA
3. Precursor mRNA (pre-mRNA) contains both introns and exons
4. Small nuclear ribonucleoprotein complexes (snRNPs) may bind to the
introns and catalyze excision and splicing
a) To be functional, it must be capped and have a poly-a tail added
5. RNA may also act as a self-acting enzyme and excise and splice without
the intervention of protein enzymes
C. The evolution of eukaryotic gene structure is not completely understood
1. In the 1980s, Gilbert proposed that exons are nucleotides that code for
protein domains
2. Protein domains are regions of protein tertiary structure with specific
functions
3. New proteins with new functions emerge rapidly when genetic
recombination produces new combinations of exons, and therefore novel
proteins
4. This may lead to evolution by exon shuffling
5. One hypothesis states that introns may have evolved from transposons
VII. There are exceptions to the usual direction of flow of genetic information
A. In 1964, Temin discovered that some viruses use reverse transcriptase (an
RNA directed DNA polymerase) to transcribe DNA from an RNA template
B. Viruses, called retroviruses, use reverse transcriptase
C. HIV-1, which causes AIDS, is the best known retrovirus
D. Reverse transcriptase is a very important research tool for molecular
biologists
VIII. Mutations are changes in the nucleotide sequence of DNA
A. Base substitution mutations involve the exchange of one base for another
1. Due to redundancy of the code, this may not alter the product
2. Missense mutations result in the substitution of 1 amino acid for another
a) The resulting protein may be nonfunctional, or the mutation may have
no effect on the organism (a silent mutation)
3. Nonsense mutations result in a stop codon
B. Frameshift mutations involve insertion or deletion of a base pair
1. Frameshift mutations result in an entirely different sequence of amino
acids (they change the reading frame)
2. These usually result in a non-functional protein
C. Transposons, or transposable genetic elements, are movable sequences of
DNA that may move into another area of DNA
1. Transposons may disrupt genes, but may also activate some genes
2. Transposons were discovered by Barbara McClintock, in corn, in the 1950s
(she received the Nobel Prize in 1983)
3. Transposons have some similarities to retroviruses; most are
retrotransposons
D. Hot spots are regions of DNA more likely to undergo mutations, and are often
share regions of repeated nucleotides, causing the polymerases to slip during
DNA replication
E. Mutagens are agents that cause mutations, including various types of
radiation and chemicals
1. Mutations in somatic cells are not passed on to the next generation
2. Some somatic mutagens are also carcinogens
IX.
A gene is defined as a functional unit
A. A gene is a transcribed nucleotide sequence that yields a product
Research and Discussion Topics

Research how McClintock’s pioneering work on transposons at the Cold Spring
Harbor Lab in New York led to her Nobel Prize in 1983 at the age of 81. How was
corn involved in her research?

Discuss the mutagenic effects of x-rays and UV radiation. What do they do at the
molecular level?

Each year, more and more chemicals, particularly organic chemicals, are identified
as mutagenic, carcinogenic, and/or teratogenic. Define these terms. How do they
affect the genetic material? Give examples of organic chemicals that cause this type
of genetic damage.

Discuss the characteristics of retroviruses. How do they act? How is their action
different from normal transcription? Give examples of retroviruses.

Describe pseudogenes. What is their probable origin?