Protein synthesis is a fundamental cellular process that plays a critical role in the growth, development, and maintenance of all living organisms. Understanding the intricacies of protein synthesis is key to unraveling the mechanisms behind cellular functions and unlocking the secrets of life itself.
The process of protein synthesis involves two main steps: transcription and translation. During transcription, the DNA sequence in a gene is transcribed into a complementary messenger RNA (mRNA) molecule. This mRNA molecule carries the genetic information from the nucleus to the cytoplasm, where translation takes place.
In translation, the mRNA molecule serves as a template for the assembly of amino acids into a polypeptide chain. Amino acids, the building blocks of proteins, are brought to the ribosomes, the cellular machinery responsible for protein synthesis, by transfer RNA (tRNA) molecules. Each tRNA molecule carries a specific amino acid and has an anticodon that matches the codon on the mRNA. This allows the tRNA to deliver the correct amino acid in the sequence dictated by the mRNA.
As the ribosome moves along the mRNA molecule, reading the codons and bringing in the corresponding amino acids, a growing polypeptide chain is formed. This chain undergoes various modifications, such as folding, cleavage, and post-translational modifications, to attain its functional conformation.
Protein synthesis is a tightly regulated process, with multiple checkpoints and control mechanisms to ensure accuracy and fidelity. Errors in protein synthesis can lead to malfunctioning proteins or even disease.
Multiple Choice Questions
Following are the characteristics of the genetic code, Except:
a) Specificity
b) Universal
c) Redundant
d) Overlapping
2) Aminoacyl t-RNA synthetase catalyzes the addition of amino acids to the growing polypeptide chain and it requires four high-energy phosphates.
They are:
a) 4 ATP
b) 4 GTP
c) 2 ATP, 2 GTP
d) 1 ATP, 3 GTP
3) The ribosome has three binding sites (A, P, E) for tRNA molecules.
Which of the following is NOT the correct statement regarding these sites?
a) The A site binds to an incoming aminoacyl-tRNA
b) The P site codon is occupied by peptidyl-tRNA (an amino acid containing tRNA)
c) The E site is occupied by empty t-RNA as it is exiting the ribosome
d) None of the Above
4) Shine Dalgarno sequence is located six to ten bases upstream of the initiation codon of mRNA.
It consists of:
a) Purine-rich nucleotide sequence
b) Pyrimidine-rich nucleotide sequence
c) Uracil-containing nucleotide sequence
d) None of the above
5) Which of the following is the initiation codon?
a) UGA
b) AUG
c) CUA
d) GAA
6) In prokaryotes, the initiation factors (IF-1, IF-2, and IF-3) are involved in the initiation of protein synthesis.
Which of the following factors facilitates the initiation codon?
a) IF-1
b) IF-2
c) IF-3
d) All of the above
7) Fill in the blanks:-
EF-Tu and EF-Ts bind to appropriate tRNA to the codon in the empty sites.
These factors are involved in the............................ of translation.
a) Initiation
b) Elongation
c) Termination
d) Trimming
8) Chloramphenicol is a class of antibiotics that inhibit protein synthesis by inhibiting.......................................
a) Aminoacyl transferase
b) Peptidyl transferase
c) Initiation factor 1
d) Elongation factor
9) Fill in the blanks:-
Puromycin, a structural analog of tRNA, is a class of antibiotics that inhibit protein synthesis by..............................
a) inhibiting amino acyltransferase
b) inhibiting peptidyl transferase
c) early termination of the peptide chain
d) None of the above
10) Tetracyclin is a class of antibiotics that inhibit protein synthesis by blocking
a) binding of initiation factors
b) binding of elongation factors to tRNA
c) binding of aminoacyl tRNA to the mRNA-ribosome complex
d) None of the above
11) Which one of the following is Not true about genetic code?
a) It is degenerate
b) It is unambiguous
c) It is nearly universal
d) It is overlapping
12) Which of the following is not the component of ribosomal RNA present in prokaryotes?
a) 23S rRNA
b) 18S rRNA
c) 16S rRNA
d) 5S rRNA
13) Which of the following is not the component of ribosomal RNA present in eukaryotes?
a) 28S rRNA
b) 18S rRNA
c) 16S rRNA
d) 5S rRNA
14) Which of the following is the site for attachment of amino acid in tRNA molecule?
a) 5' end
b) 3' end
c) anti-codon loop
d) None of the above
15) Lactose Operon is a set of lactose metabolizing genes that is co-coordinately expressed and regulated. The following is not the gene of lactose operon:
a) LacX
b) LacZ
c) LacY
d) LacA
16) Which of the following is not the positive regulator of Lac operon
a) Allolactose
b) Glucose
c) Lactose
d) cAMP
17) Which of the following is the FALSE statement of the Lactose operon?
a) Lac Operon is activated when glucose is absent
b) Lac Operon is activated when lactose is present
c) Lac Operon is activated when glucose is absent and lactose is present
d) Lac Operon is activated when glucose is present and lactose is absent
18) Which of the following gene encodes for the repressor protein of lac operon?
a) LacI
b) LacZ
c) LacY
d) LacA
19) LacZ encodes for a protein.............................
a) permease
b) beta-galactosidase
c) transacetylase
d) repressor protein
20) Adenylyl cyclase is an enzyme that is active in the absence of................................
a) Allolactose
b) Glucose
c) Lactose
d) cAMP
21) Peptidyl transferase enzyme is present in:
a) Messenger RNA
b) Transfer RNA
c) Ribosomal RNA
d) Small Nuclear RNA
21) The following are the post-translational modifications that may be required for trafficking or the function of the proteins, Except:
a) Hydroxylation
b) Glycosylation
c) Oxygenation
d) Phosphorylation
Multiple Choice Answers
1)- d) Overlapping
Four key characteristics of the genetic code:
Universality: The genetic code is nearly universal, meaning that the same set of codons is used to encode the same amino acids across a wide range of organisms. For example, the codon "AUG" typically codes for the amino acid methionine in most organisms. This universality allows scientists to study and compare genetic information across different species.
Redundancy (Degeneracy): The genetic code exhibits redundancy or degeneracy, which means that multiple codons can code for the same amino acid. For instance, the amino acid leucine can be specified by six different codons: "UUA," "UUG," "CUU," "CUC," "CUA," and "CUG." This redundancy provides some flexibility and robustness to the genetic code, as mutations in the DNA sequence may not always result in changes to the encoded amino acid.
Start and Stop Codons: The genetic code contains specific start and stop codons that mark the beginning and end of protein synthesis. The start codon, "AUG," usually codes for methionine and serves as the initiation signal for protein synthesis. The stop codons, "UAA," "UAG," and "UGA," do not code for any amino acid but instead signal the termination of protein synthesis.
Non-overlapping: The genetic code is non-overlapping, meaning that each codon is read as a distinct unit without overlapping with the neighboring codons. Consequently, each nucleotide in the DNA sequence is part of only one codon and contributes to the specification of a single amino acid in the resulting protein.
2)- c) 2 ATP, 2 GTP
3)- d) None of the Above
A site (Aminoacyl site): The A site is the location within the ribosome where the incoming aminoacyl-tRNA molecule binds. It is called the "aminoacyl site" because it accommodates the aminoacyl-tRNA complex that carries the next amino acid to be added to the growing polypeptide chain. The codon of the mRNA being read by the ribosome is matched with the anticodon of the incoming aminoacyl-tRNA molecule in the A site. If the codon-anticodon pairing is correct, the amino acid is transferred from the tRNA in the A site to the growing polypeptide chain in the P site.
P site (Peptidyl site):
The P site is the location within the ribosome where the growing polypeptide chain is held. It is called the "peptidyl site" because it accommodates the peptidyl-tRNA complex, which carries the nascent polypeptide chain. The peptidyl-tRNA molecule is positioned in the P site with its attached amino acid adjacent to the previously synthesized amino acid in the chain. The peptidyl transferase activity of the ribosome catalyzes the formation of peptide bonds between the amino acids, resulting in the elongation of the polypeptide chain.
E site (Exit site): The E site is the location within the ribosome where the tRNA molecule, after donating its amino acid to the growing polypeptide chain, exits the ribosome. It is called the "exit site" because it is where the now uncharged tRNA is ejected from the ribosome. After peptide bond formation in the P site, the spent tRNA moves to the E site before being released from the ribosome. The E site then becomes available to accommodate a new aminoacyl-tRNA molecule in the next round of elongation.
4)- a) Purine-rich nucleotide sequence
The Shine-Dalgarno sequence consists of a short stretch of nucleotides with a consensus sequence in bacterial mRNA. The consensus sequence is typically characterized by a purine-rich region, particularly containing the sequence 5'-AGGAGG-3'.The Shine-Dalgarno sequence is typically located on the mRNA molecule, a few nucleotides upstream (5' direction) of the start codon (usually AUG) that initiates protein synthesis.
5)- b) AUG
The AUG codon is the most common initiation codon and is typically recognized as the start codon in eukaryotes and archaea. In eukaryotes, the AUG codon specifies the amino acid methionine. 6)- b) IF-2
IF-1 (Initiation Factor 1) is a protein involved in the initiation phase of protein synthesis in bacteria. It is one of the initiation factors that play a role in the assembly of the ribosome and the positioning of the mRNA and initiator tRNA during translation initiation.
7)- b) Elongation
EF-Tu (Elongation Factor Tu) and EF-Ts (Elongation Factor Ts) are essential proteins involved in the elongation phase of protein synthesis in bacteria. They play critical roles in the delivery of aminoacyl-tRNA to the ribosome and the accuracy of codon-anticodon recognition.
8)-c) Peptidyl Transferase
Chloramphenicol inhibits bacterial protein synthesis by binding to the bacterial ribosome. It specifically binds to the 50S subunit of the ribosome and prevents the formation of peptide bonds between amino acids during translation. This inhibition blocks the synthesis of bacterial proteins, leading to bacterial growth inhibition.
9)-c) early termination of the peptide chain
Puromycin acts by mimicking the 3' end of aminoacyl-tRNA and is incorporated into the growing polypeptide chain during translation. Once incorporated, it causes premature termination of protein synthesis by acting as a chain-terminating agent. This termination occurs because puromycin lacks the necessary components to form peptide bonds with subsequent amino acids.
10)-c) binding of aminoacyl tRNA to the mRNA-ribosome complex
Tetracycline inhibits bacterial protein synthesis by binding to the bacterial ribosome and interfering with the attachment of aminoacyl-tRNA to the ribosomal A site. It specifically binds to the 30S subunit of the ribosome and blocks the entry of aminoacyl-tRNA, thereby preventing the elongation of the growing peptide chain.
11)-d) It is overlapping
12)-b) 18S rRNA
In prokaryotes, the ribosomal RNA (rRNA) consists of three main components: 16S rRNA, 23S rRNA, and 5S rRNA. These components are essential for the structure and function of the ribosome, which is responsible for protein synthesis.
16S rRNA: The 16S rRNA is a small subunit of the prokaryotic ribosome. It plays a crucial role in the initiation of protein synthesis and provides the binding site for mRNA and the anticodon region of tRNA. It is involved in decoding the genetic information on the mRNA and helps in the accurate recognition of the start codon during translation initiation.
23S rRNA: The 23S rRNA is a large subunit of the prokaryotic ribosome. It has several important functions, including catalyzing the formation of peptide bonds between amino acids during translation. The 23S rRNA has peptidyl transferase activity, which is responsible for the enzymatic reaction that joins amino acids together to form a polypeptide chain. It also provides a framework for the ribosome's overall structure and stability.
5S rRNA: The 5S rRNA is another component of the prokaryotic ribosome, found in the large subunit. It contributes to the overall structure and stability of the ribosome and helps in the binding of various protein factors involved in ribosome assembly and function.
13)-c) 16S rRNA
In eukaryotes, the ribosomal RNA (rRNA) consists of four main components: 18S rRNA, 5.8S rRNA, 28S rRNA, and 5S rRNA. These rRNA molecules are crucial for the structure and function of the eukaryotic ribosome, which is responsible for protein synthesis.
18S rRNA: The 18S rRNA is a small subunit of the eukaryotic ribosome. It plays a key role in the decoding of genetic information and provides the binding site for mRNA and the anticodon region of tRNA during translation. It helps in the accurate recognition of the start codon and is involved in the initiation of protein synthesis.
5.8S rRNA: The 5.8S rRNA is a component found in the internal transcribed spacer (ITS) region of the eukaryotic ribosomal RNA. It is located between the 18S and 28S rRNA molecules. The exact function of the 5.8S rRNA is not fully understood, but it is believed to contribute to the overall structure and stability of the ribosome.
28S rRNA: The 28S rRNA is a large subunit of the eukaryotic ribosome. It is involved in the catalysis of peptide bond formation during translation. The 28S rRNA has peptidyl transferase activity, similar to the 23S rRNA in prokaryotes, and is responsible for the enzymatic reaction that joins amino acids together to form a polypeptide chain. It provides the framework for the ribosome's overall structure and stability.
5S rRNA: The 5S rRNA is another component of the eukaryotic ribosome, found in the large subunit. It contributes to the overall structure and stability of the ribosome, similar to its role in prokaryotes. The 5S rRNA also helps in the binding of various protein factors involved in ribosome assembly and function.
14)-b) 3' end
The site for the attachment of an amino acid in a transfer RNA (tRNA) molecule is known as the "acceptor stem" or "aminoacyl site." This site is located at the 3' end of the tRNA molecule. The acceptor stem consists of a specific sequence of nucleotides that are complementary to the corresponding amino acid.
15)-a) LacX
Three structural genes in the lac operon are:
lacZ: This gene encodes the enzyme β-galactosidase, which is responsible for the hydrolysis of lactose into glucose and galactose. It also converts lactose into allolactose, an inducer molecule that plays a role in the regulation of the operon.
lacY: This gene encodes the lactose permease, a membrane protein that facilitates the transport of lactose into the bacterial cell.
lacA: This gene encodes the enzyme transacetylase, which is involved in the metabolism of certain galactosides but its precise function is not fully understood.
16)-b) Glucose
The lac operon is subject to both positive and negative regulation, and the presence of glucose leads to a phenomenon known as catabolite repression, which inhibits the expression of the lac operon.
17)-d) Lac Operon is activated when glucose is present and lactose is absent.
18)-a) LacI
The lac I gene is a regulatory gene in the lac operon system found in Escherichia coli (E. coli) and related bacteria. It encodes the lac repressor protein, which is a key regulator of the lac operon. The lac repressor acts as a negative regulator by binding to the operator sequence of the lac operon and inhibiting the transcription of the structural genes lacZ, lacY, and lacA.
19)-b) beta-galactosidase
The lacZ gene codes for β-galactosidase, an enzyme that catalyzes the hydrolysis of lactose into its component sugars, glucose and galactose.
20)-b) Glucose
When glucose levels are low, the concentration of cAMP increases in the cell. The increased levels of cAMP bind to the CRP protein, resulting in a conformational change that allows CRP to bind to the CRE. This binding of cAMP-CRP to the CRE helps activate the transcription of the lac operon, especially when glucose levels are low and lactose is present.
21)-c) Ribosomal RNA
The peptidyl transferase enzyme is present in the ribosome. More specifically, it is a catalytic activity associated with the large subunit of the ribosome, both in prokaryotes (70S ribosome) and eukaryotes (80S ribosome). The peptidyl transferase activity is responsible for the formation of peptide bonds between amino acids during protein synthesis.
22-c) Oxygenation
Examples of post-translational modifications involved in protein trafficking:
Phosphorylation: Phosphorylation is a common PTM that involves the addition of a phosphate group to specific amino acid residues, typically serine, threonine, or tyrosine. Phosphorylation can regulate protein-protein interactions, alter protein conformation, and promote binding to trafficking machinery or sorting signals, thereby influencing protein trafficking.
Glycosylation: Glycosylation involves the addition of sugar molecules to specific amino acid residues. It can occur in the endoplasmic reticulum (ER) and Golgi apparatus and plays a crucial role in the sorting and trafficking of proteins. Glycosylation can serve as a signal for protein transport and localization to specific organelles or cell surface.
Ubiquitination: Ubiquitination is the attachment of small protein tags called ubiquitin to lysine residues of target proteins. It can serve as a sorting signal for proteins to be targeted for degradation or trafficking to specific cellular compartments. Ubiquitination is involved in various intracellular trafficking processes, including endocytosis, lysosomal targeting, and sorting in the trans-Golgi network.
Acetylation: Acetylation involves the addition of an acetyl group to lysine residues. It can affect protein-protein interactions, stability, and subcellular localization. Acetylation has been implicated in the regulation of protein trafficking pathways, including nuclear-cytoplasmic transport and vesicular trafficking.
Palmitoylation: Palmitoylation is the attachment of a fatty acid, such as palmitate, to cysteine residues of proteins. This modification can regulate membrane association and trafficking of proteins by promoting their localization to lipid rafts or specific membrane compartments.
Methylation: Methylation involves the addition of a methyl group to specific amino acids, such as lysine or arginine. Protein methylation can influence protein-protein interactions, binding to trafficking machinery, and subcellular localization.
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