Chapter 10: From DNA to Protein – Gene Expression
Vocabulary:
mRNA- serves as a template for protein synthesis; messenger DNA
rRNA- a molecular component of a ribosome, the cell's essential protein factory. Strictly
speaking, ribosomal RNA (rRNA) does not make proteins. It makes polypeptides (assemblies of
amino acids) that go to make up proteins.
tRNA- transfer RNA. Small RNA molecules that carry amino acids to the ribosome for
polymerization into a polypeptide
codon- a sequence of three nucleotides that together form a unit of genetic code in a DNA or
RNA molecule.
Anticodon- a sequence of three nucleotides forming a unit of genetic code in a transfer RNA
molecule, corresponding to a complementary codon in messenger RNA
microRNA- a cellular RNA fragment that prevents the production of a particular protein by
binding to and destroying the messenger RNA that would have produced the protein.
Polysome- a cluster of ribosomes held together by a strand of messenger RNA that each
ribosome is translating
Transcription- the process by which genetic information represented by a sequence of DNA
nucleotides is copied into newly synthesized molecules of RNA, with the DNA serving as a
template
Translation- the process by which a sequence of nucleotide triplets in a messenger RNA
molecule gives rise to a specific sequence of amino acids during synthesis of a polypeptide or
protein
Initiation- involves the small subunit of the ribosome binding to the 5' end of mRNA with the
help of initiation factors
Elongation- The tRNA transfers an amino acid to the tRNA corresponding to the next codon.
Termination- a specific sequence in DNA at which the RNA polymerase and the newly made
RNA transcript are released from their DNA association
Point mutation- a mutation affecting only one or very few nucleotides in a gene sequence
1.
2. mRNA: When a particular gene is expressed, one of the two DNA strands in the gene is
transcribed to guide the synthesis of a complementary RNA strand, which is then cut up
and reassembled: introns stay “in” the nucleus, exons “exit” the nucleus, after being
spliced together to produce an mRNA. The mRNA exits the nucleus to the cytoplasm,
where it serves a guide that is translated to guide the synthesis of a polypeptide: the
nucleotide sequence of the mRNA determines the ordered sequence of amino acids on the
polypeptide chain which is built by a ribosome.
rRNA: Ribosomes are often called “protein synthesis factories.” They are made up of
multiple proteins and several ribosomal RNAs. One of the rRNAs in the ribosome
catalyzes the formation of the peptide bond linking a newly delivered amino acid to the
“growing” protein as it is synthesized.
MicroRNA: MicroRNA is a small, noncoding RNA molecule, typically about 21 bases
long. When a microRNA bind to an mRNA, the mRNA-microRNA complex that is
formed cannot be translated. MicroRNAs thus exert regulation of gene expression in this
manner.
tRNA: Each specific tRNA molecule transports a specific amino acid to the ribosome.
Each specific tRNA molecule also has triplet of nucleotides (the anticodon) that binds to
a specific triplet of nucleotides (the codon) in mRNA. Thus the codon in mRNA specifies
the tRNA molecule that associates with mRNA in the ribosome, and thus determines
which amino acid is peptide-bonded to the growing polypeptide chain. In this manner, the
sequence of codons in mRNA determines the sequence of amino acids in proteins.
3. This characterization is inaccurate, because genes code for proteins, and these proteins
then determine phenotypes. In other words, genes provide the roadmap for the synthesis
of proteins, including enzymes, which influence many metabolic processes, including the
production of hormones. Low levels of cortisol could result from a mutation in a gene
that codes for an enzyme essential for the synthesis of cortisol.
4. Sickle-cell anemia is a heritable blood disorder caused by a point mutation that occurs in
people who carry two copies of the sickle allele of the gene for human β-globin (a subunit
of hemoglobin, the blood protein in humans that carries oxygen). The sickle allele differs
from the normal allele by just one base pair, resulting in a polypeptide that differs by just
one amino acid from the normal protein. People who are homozygous for this recessive
allele have defective, sickle-shaped red blood cells, especially when oxygen levels are
reduced in the blood. These deformed blood cells can block narrow capillaries, which
result in extremely painful tissue damage. Heterozygous individuals are usually
asymptomatic, with the only significant manifestation being urinary tract issues.
Surprisingly, heterozygous individuals are also resistant to malaria, given an advantage to
having one copy of the mutated β-globin gene.
5. A mutation in the stop codon of a gene could result in the transcription process
continuing past the original gene, and it could also prevent the release of the completed
polypeptide from the translation complex. Assuming the DNA eventually included
another stop codon, the results of the mutation could include much longer than normal
RNA and a much longer than normal protein.
6. A eukaryotic gene may contain noncoding sequences called introns (intervening regions)
that interrupt the coding region. These regions are called exons (expressed regions). Both
introns and exons appear in the primary mRNA (pre-mRNA) transcript, but the introns
are removed by the time the mature mRNA exits the nucleus. Pre-mRNA processing
involves cutting introns out of the transcript and splicing together the exon transcripts.
Introns stay “in” the nucleus, exons “exit” the nucleus.
7. While pre-mRNA is still in the nucleus it undergoes two processing steps, one at each
end of the molecule. First the 5’ cap (or G cap) is added to the 5’ end of the pre-mRNA
as it is transcribed. The cap is a chemically modified GTP molecule that helps bind the
mRNA to the ribosome for translation and protects it from being digested by
ribonucleases. The poly-A tail is added to the 3’ end of the pre-mRNA at the end of
transcription aids in export of mRNA from the nucleus. The poly-A tail also enhances
stability.
8. The polypeptide product’s start codon is methionine, followed by phenylalanine,
glutamine, arginine, glycine, and ending with a stop codon.
9. UUG is leucine, so the second codon would replace phenylalanine with leucine.
10. The fragment shown above only has 18 bases, so a 19th base would be an addition, not a
substitution. Since a codon is composed of three nucleotides that direct the placement of
amino acids into a polypeptide chain, a single “A” at the end of this sequence would not
provide sufficient information for translation process to continue. Furthermore, the
addition this particular 19th base follows a stop codon, so translation of this particular
amino acid sequence would have already been completed.
11. The code for serine can be specified by six difference sequences that are redundant but
not ambiguous. Serine can be produced in response to any of these six codons, but each
of these codons only encodes one amino acid. An ambiguous codon would be one that
specified two or more different amino acids.
12. The genetic code is considered to be universal because it is used by all species on our
planet. This provides strong evidence that the code is an ancient one that has been
maintained intact throughout the evolution of living organisms. “Nearly” implies life
forms not yet discovered might use a different code.
13. The E. coli bacterium can be manipulated to produce human insulin by introducing the
human gene for insulin into the bacteria through the use of plasmids. The process by
which this takes place is called recombinant DNA technology. The “universal genetic
code” for all species is the underlying reason why a process like this is possible. The
actual details for the two peptides needed for this hormone is beyond the scope of the
course.
14. Silent mutations can occur because of the redundancy of the genetic code. Even though a
mutation may change the code, this change may also translate to the production of the
same amino acid, and there would be no phenotypic difference. Nonsense mutations
could result in a premature stop codon. In this case, the polypeptide chain would be
shorter than the original protein.
15. At about the midpoint on the tRNA polynucleotide chain, there is a triplet of bases called
the anticodon. This region binds to its complementary codon in mRNA. Like the two
strands of DNA, the codon and anticodon bind together via hydrogen bonds; this binding
is associated with the “delivery” of the amino-acid “cargo” on the tRNA molecule. In this
way, mRNA determines which amino acid is at which location on a new protein. The
codons on mRNA are, of course, determined by the DNA sequence.
16. The ribosome is the molecular workbench where the translation of mRNA occurs. Like
transcription, translation is a three step process involving initiation, elongation, and
termination. The ribosome contains a large subunit where interactions with tRNA
anticodons take place. At the A site, the charged tRNA anticodon binds to the mRNA
codon. The P site is where the tRNA adds its amino acid to the growing polypeptide
chain. Finally, the tRNA is released at the E site. Polyribosomes allow more than one
ribosome to move along a strand of mRNA at one time.
17. The next anticodon will be UAC, which is the amino acid tyrosine.
18. RNA polymerase is an enzyme that catalyzes the formation of RNA from a DNA
template. This enzyme is necessary for the creation of RNA chains using the DNA
genetic code as a template in the process of transcription. RNA carries the genetic code or
“instructions” from the nucleus of the cell to the ribosomes and the ribosomes then carry
out the actual synthesis of amino acids, in accordance with these instructions through the
process of translation. RNA functions, e.g., rRNA, mRNA, tRNA, µRNA, etc. have been
discussed earlier.
19. Secreted proteins, including hormones, interact with rough endoplasmic reticulum (RER)
and Golgi apparatus (or lysosome or plasma membrane). If a newly formed polypeptide
contains a signal sequence, a short stretch of amino acids with instructions for its
destination in the organism, it will bind to a signal recognition particle. Then both bind to
a receptor protein in the membrane of the RER, and translation proceeds. The signal
sequence is removed by an enzyme in the lumen of RER. The polypeptide continues to
elongate until translation terminates. The ribosome is then released, and the protein folds
inside the RER. Next the protein may move elsewhere within the endomembrane system,
such as the Golgi apparatus, lysosome, or plasma membrane. If it lacks specific signals
for destination within the endomembrane system, it will usually be secreted from the
vesicles that fuse with the plasma membrane.
20. A gene contains the entire nucleic acid sequence necessary for the synthesis of any given
protein, such as insulin in this case. Therefore, the gene likely includes more than just the
nucleotides necessary to encode the amino acid sequence, or the coding region. The gene
must also include all the DNA sequences needed for the transcription process, including
non-coding regions such as enhancers, cleavage specifications, poly A sites, splicing
instructions, and all other non-coding instructions necessary for insulin to be produced,
packaged, and delivered for suitable functioning in the cell. Directly relevant to the size
of the insulin protein is the fact that it is synthesized as a much larger protein called prepro-insulin, which is cleaved to yield the active 51-amino-acid active hormone.
21.
22. A. 5’-CCU-CCU-AAA-AAA-AAA-CGU-AAA-GUU-3’
B. 24
C. Methionine has the codon AUG, which is the “start” codon or message for a ribosome
that signals the initiation of protein translation from mRNA.
D. 3’-AAC-TTT-ACG-TTT-TTT-TTT-AGG-AGG-5’
E. No, the codons in this peptide chain have between two and four redundant codons that
would produce the same amino acids.
23. A. A cytosolic protein bound to NLS peptide will be found in the nucleus. This is because
the nuclear localization signal involves a localization signal or tag, which is a specific
amino acid sequence that interacts with a receptor protein on the surface of the organelle,
in this case the nucleus, that is the correct “destination.”
B. The nuclear protein will remain in the cytoplasm, because the codon for the NLS is
incomplete. The correct signal sequence is necessary for it to bind to the receptor
protein at the surface of the nucleus. Without the proper signal sequence, a channel
will not form, and the targeted protein is unable to move into the nucleus.
C. This DNA sequence contains two “start” codons, one at the beginning of the sequence
and another two codons before “stop.” This mutation renders the NLS ineffective
because it lacks the proper sequence or specificity to provide a signal for it to bind to
the receptor protein on the surface of the nucleus. Therefore, this protein will remain
in the cytoplasm.