CELL PROTEIN SYNTHESIS
1 . Compare RNA and DNA in terms of chemical composition, base-pairing properties,
and overall structure.
● Chemical Composition:
○ DNA: Contains deoxyribonucleic acid, with a sugar backbone of deoxyribose
(lacking one oxygen atom compared to ribose). Its bases are adenine (A),
thymine (T), cytosine (C), and guanine (G).
○ RNA: Contains ribonucleic acid, with a sugar backbone of ribose. Its bases are
adenine (A), uracil (U) (replacing thymine), cytosine (C), and guanine (G).
● Base-Pairing Properties:
○ DNA: A pairs with T, C pairs with G.
○ RNA: A pairs with U, C pairs with G.
● Overall Structure:
○ DNA: Double-stranded, helical structure, forming a double helix.
○ RNA: Single-stranded, typically linear but can form secondary structures like
hairpins.
2 . Write the sequence of an mRNA from a double-strand DNA. Identify the coding and
non-coding strands.
Given a double-stranded DNA:Coding strand (sense strand): 5’–ATGCGTAC–3’
Non-coding strand (antisense strand): 3’–TACG CATG–5’
hemRNAis synthesized from thenon-coding strand(antisense strand), which will be
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complementary to it:mRNA sequence: 5’–AUGCGAUC–3’
oding strand: The DNA strand whose sequence matches the mRNA sequence (except that
C
thymine is replaced by uracil in RNA).
Non-coding strand: The DNA strand that is used as a template to produce the mRNA.
3 . Compare the reactions catalyzed by RNA and DNA polymerases in terms of
templates, substrates, directionality, and sources of energy that drive these reactions.
● RNA polymerase:
○ Template: Uses one strand of DNA as a template to synthesize RNA.
○ Substrates: Ribonucleoside triphosphates (ATP, GTP, CTP, UTP).
○ Directionality: Synthesizes RNA in the 5’ to 3’ direction, reading the DNA
template in the 3’ to 5’ direction.
○ Energy Source: The energy comes from the hydrolysis of ribonucleoside
triphosphates (NTPs).
● DNA polymerase:
○ Template: Uses a single strand of DNA as a template to synthesize a
complementary strand of DNA.
○ Substrates: Deoxyribonucleoside triphosphates (dATP, dGTP, dCTP, dTTP).
○ D irectionality: Synthesizes DNA in the 5’ to 3’ direction, reading the
template strand in the 3’ to 5’ direction.
○ Energy Source: The energy comes from the hydrolysis of
deoxyribonucleoside triphosphates (dNTPs).
4 . Explain how a bacterial RNA polymerase recognizes where transcription will begin,
which DNA strand to transcribe, and when to stop.
● R
ecognition of the transcription start: The bacterial RNA polymerase recognizes a
specific sequence of bases known as thepromoter(e.g., -10 and -35 regions inE.
coli) upstream of the gene. The sigma factor of the RNA polymerase binds to the
promoter region, enabling the polymerase to start transcription.
● W
hich DNA strand to transcribe: RNA polymerase reads thenon-coding
(antisense)strand of DNA to synthesize mRNA, creating a complementary strand.
● T
ermination of transcription: Transcription ends when RNA polymerase encounters
aterminatorsequence, which can either form ahairpin loop(in the case of
rho-independent termination) or be recognized by therho protein(in rho-dependent
termination).
5. Contrast transcription initiation in prokaryotes and eukaryotes.
● Prokaryotes:
○ Transcription is initiated when the RNA polymerase binds directly to the
promoter region on DNA with the help of the sigma factor.
○ There is no separation between transcription and translation; both processes
can occur simultaneously.
● Eukaryotes:
○ Transcription requires additionaltranscription factorsthat help recruit RNA
polymerase to the promoter.
○ TheTATA boxis a common element in eukaryotic promoters.
○ Eukaryotic transcription occurs in the nucleus, and RNA must undergo
processing (e.g., splicing, 5' capping, polyadenylation) before being exported
to the cytoplasm for translation.
6. Compare the features of a eukaryotic gene with its mature mRNA transcript.
● Eukaryotic gene:
○ Containsexons(coding regions) andintrons(non-coding regions).
○ The gene is transcribed into a precursor mRNA (pre-mRNA) that includes
both exons and introns.
● Mature mRNA:
○ Introns aresplicedout during processing.
○ A5' capis added to the mRNA, which helps with stability and translation
initiation.
○ Apoly-A tailis added at the 3' end for stability and regulation of mRNA
degradation.
7. Predict the outcome of a defect in mRNA processing in a eukaryotic cell.
A defect in mRNA processing could lead to:
● I mproper splicing: Introns may not be removed, leading to a non-functional protein
or one with incorrect sequence.
● No 5' cap or poly-A tail: The mRNA may be unstable, leading to degradation or
failure to be translated.
● Incomplete or incorrect export to the cytoplasm: The mRNA may not be properly
exported from the nucleus, preventing translation.
These defects could lead to diseases or dysfunction in the cell.
8. Explain the key features of the genetic code and the wobble base pairing.
● Key features of the genetic code:
○ It isuniversal(with few exceptions), meaning it is the same across almost all
organisms.
○ It isdegenerate, meaning multiple codons can code for the same amino acid.
○ It isnon-overlappingandcontinuous.
● Wobble base pairing:
○ Refers to the flexibility in the third base of the codon-anticodon pair.
○ The third position in the codon allows somenon-standard pairings(e.g.,
inosine in the anticodon can pair with A, U, or C in the codon).
9 . Use the genetic code table to determine the amino acid sequence encoded by a defined
mRNA sequence.
Given mRNA sequence:5’–AUGUACGGAU–3’
● UG: Methionine (start codon)
A
● UAC: Tyrosine
● GGA: Glycine
● GAU: Aspartic acid
Thus, the amino acid sequence would be:Methionine-Tyrosine-Glycine-Aspartic acid.
10. Describe the structure and function of tRNA molecules and ribosomes.
● tRNA (transfer RNA):
○ tRNA molecules have acloverleaf structure, with three loops. One of the
loops contains theanticodon, which pairs with the mRNA codon during
translation.
○ The3’ endcarries the amino acid corresponding to the mRNA codon.
● Ribosomes:
○ Ribosomes are composed ofrRNAandproteinsand consist of alarge
subunitand asmall subunit.
○ The ribosome is the site ofprotein synthesis, where mRNA is translated into
an amino acid sequence by matching codons with tRNA anticodons.
1 1. Explain the steps by which a polypeptide is synthesized and released from the
ribosome.
● I nitiation: The ribosome assembles on the mRNA at the start codon (AUG). The first
tRNA (carrying methionine) binds to the start codon.
● Elongation: The ribosome moves along the mRNA, reading the codons and bringing
in the corresponding tRNAs with their attached amino acids. The amino acids are
joined bypeptide bondsto form a polypeptide.
● Termination: When a stop codon is encountered, a release factor binds to the
ribosome, causing the polypeptide to be released.
12. Contrast translation initiation in prokaryotes and eukaryotes.
● Prokaryotes:
○ Translation begins at theShine-Dalgarno sequenceon the mRNA, which is
recognized by the ribosome. The ribosome then binds to the mRNA and
initiates translation at the start codon.
● Eukaryotes:
○ Translation begins at the5' capof the mRNA. The small ribosomal subunit
binds to the cap, scans for the start codon (AUG), and then translation begins.
1 3. Describe each step experienced by a tRNA, starting with an uncharged tRNA in the
cytosol and ending with the release of the uncharged tRNA from a ribosome.
1. C harging: The uncharged tRNA in the cytosol ischargedwith an amino acid by
aminoacyl-tRNA synthetase.
2. Binding to ribosome: The charged tRNA binds to theA siteof the ribosome during
translation.
3. Peptide bond formation: The amino acid is added to the growing polypeptide chain.
4. Translocation: The ribosome moves along the mRNA, shifting the tRNA to theP
site.
5. Release: Once the tRNA has donated its amino acid, it is released from the ribosome
at theE site, becoming uncharged again.
1 4. Predict the consequences of an aminoacyl-tRNA synthetase attaching the wrong
amino acid to a tRNA, a mutation in the anti-codon sequence, and single-base mutations
in mRNA.
● Wrong amino acid attached to tRNA: This would result in the
incorporation of the wrong amino acid into the protein, potentially causing a nonfunctional or
misfolded protein.
● M utation in the anticodon sequence: A mutation could cause the tRNA to misread
the codons, leading to incorrect amino acid incorporation.
● Single-base mutation in mRNA: This could lead to asilent mutation(no change in
the protein), amissense mutation(a different amino acid), or anonsense mutation
(a premature stop codon), depending on the position of the mutation.
15. Explain the biological significance of polysomes.
Polysomes are clusters of ribosomes that translate a single mRNA molecule simultaneously.
his allows forefficient protein synthesis, as multiple copies of the same protein can be
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produced at once.
1 6. Illustrate in a diagram the transcription and the simultaneous translation of a
prokaryotic gene.
prokaryotic gene can have transcription and translation happening simultaneously because
A
both processes occur in thecytoplasm. As RNA polymerase transcribes the gene, ribosomes
begin translating the mRNA as it is synthesized, leading to a coordinated process.
1 7. Outline the steps by which a newly synthesized protein is moved into the nucleus,
transported into the mitochondrial matrix, inserted into the membrane, or exported
(secreted) outside the cell.
● N ucleus: Proteins destined for the nucleus typically have anuclear localization
signal(NLS) that allows them to be imported through thenuclear pore complex.
● Mitochondrial matrix: Proteins have amitochondrial targeting signaland are
transported into the matrix through translocators in the mitochondrial membrane.
● Membrane insertion: Proteins that will be inserted into membranes have asignal
sequenceand are inserted into the membrane of therough ER, and then transported
to the membrane.
● Secretion: Secretory proteins have asignal peptidethat directs them to therough
ER, where they are processed and transported via vesicles to theGolgi apparatus,
then to the plasma membrane for secretion.
1 8. Justify the claim that posttranslational modification and destination of a protein are
ultimately directed by the DNA sequence of the gene encoding the protein.
heDNA sequenceof a gene encodes the primary structure (amino acid sequence) of a
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protein. The sequence of amino acids dictates how the protein folds and interacts with other
molecules, which influences itsposttranslational modifications(e.g., phosphorylation,
glycosylation). Additionally, specific sequences in the protein (e.g., NLS, targeting signals)
determine itscellular destination(e.g., nucleus, mitochondria). Thus, theDNA sequenceis
the blueprint for both the protein's function and its final location within or outside the cell.
