You are culturing bacteria on lactose-rich and glucose-free media. These bacteria regulate gene expression via the lac operon to ferment lactose into glucose and galactose for their metabolic needs. You add free glucose to the media. The addition of glucose reduces lactose fermentation secondary to which of the following changes?
Q22
A 55-year-old African American female presents to her breast surgeon for a six-month follow-up visit after undergoing a modified radical mastectomy for invasive ductal carcinoma of the left breast. She reports that she feels well and her pain has been well controlled with ibuprofen. However, she is frustrated that her incisional scar is much larger than she expected. She denies any pain or pruritus associated with the scar. Her past medical history is notable for systemic lupus erythematosus and multiple dermatofibromas on her lower extremities. She has had no other surgeries. She currently takes hydroxychloroquine. On examination, a raised hyperpigmented rubbery scar is noted at the inferior border of the left breast. It appears to have extended beyond the boundaries of the initial incision. Left arm range of motion is limited due to pain at the incisional site. Abnormal deposition of which of the following molecules is most likely responsible for the appearance of this patient’s scar?
Q23
A medical student is studying digestive enzymes at the brush border of the duodenum. He isolates and inactivates an enzyme in the brush border that has a high affinity for the pancreatic proenzyme trypsinogen. When the enzyme is inactivated, trypsinogen is no longer converted to its active form. Which of the following is the most likely underlying mechanism of this enzyme?
Q24
A 30-year-old African American woman develops a facial rash in a "butterfly" pattern over her face and complains of feeling tired and achy in her joints. In the course of a full rheumatologic workup you note that she has anti-snRNP antibodies. Which of the following do snRNPs affect?
Q25
A 82-year-old woman is brought to the emergency department from a retirement community after she was found down during the evening. On presentation, she complains that she experienced several hours of nausea, vomiting, crampy abdominal pain, and diarrhea prior to blacking out. She said that she cannot recall any factors that may have triggered her symptoms; however, she recalls that some of her friends with whom she eats also had similar symptoms earlier in the day and were brought to the hospital. They often go for walks and occasionally cook for themselves from a garden that they keep in the woods behind the facility. One of the residents on the team recalls seeing other patients from this facility earlier today, one of whom presented with kidney failure and scleral icterus prior to passing away. The enzyme most likely affected in this case has which of the following functions?
Q26
A 15-year-old boy presents with shortness of breath on exertion for the past 2 weeks. Although he does not have any other complaints, he is concerned about not gaining much weight despite a good appetite. His height is 188 cm (6 ft 2 in) and weight is 58 kg (124 lb). His blood pressure is 134/56 mm Hg and his pulse rate is 78/min. On cardiac auscultation, his apex beat is displaced laterally with a diastolic murmur lateral to the left sternal border. Slit-lamp examination shows an upward and outward displacement of both lenses. Synthesis of which of the following proteins is most likely defective in this patient?
Q27
A scientist wants to extract mRNA from a cell line of interest, amplify a specific mRNA, and insert it into a plasmid so that he can transfect it into a cell in order to over-express that protein. Which of the following proteins is required for the first step of amplification of this mRNA?
Q28
A 5-year-old boy is brought to the physician because of recurrent respiratory infections and difficulty walking for 2 months. Physical examination shows numerous telangiectasias on the nose, ears, and neck. There is overshoot on the finger-to-nose test. He has a narrow-based gait. Genetic analysis shows a nonsense mutation in the ataxia-telangiectasia gene (ATM gene). Sequencing of the encoded truncated protein shows that the C-terminal amino acid is not methionine but another amino acid. The last correctly incorporated amino acid is most likely encoded by which of the following tRNA anticodons?
Q29
A 25-year-old male is brought to the emergency department by his friends after a camping trip. He and his friends were in the woods camping when the patient started experiencing severe right upper quadrant abdominal pain after foraging and ingesting some wild mushrooms about 3 hours earlier. The patient is lethargic on exam and appears jaundiced. He has scleral icterus and is severely tender to palpation in the right upper quadrant. He has scattered petechiae on his extremities. Liver function tests are:
Serum:
Na+: 134 mEq/L
Cl-: 100 mEq/L
K+: 4.2 mEq/L
HCO3-: 24 mEq/L
Urea nitrogen: 50 mg/dL
Glucose: 100 mg/dL
Creatinine: 1.4 mg/dL
Alkaline phosphatase: 400 U/L
Aspartate aminotransferase (AST, GOT): 3278 U/L
Alanine aminotransferase (ALT, GPT): 3045 U/L
gamma-Glutamyltransferase (GGT): 100 U/L
The most likely cause of this patient’s clinical presentation acts by inhibiting which of the following molecules?
Q30
An investigator is studying the effects of zinc deprivation on cancer cell proliferation. It is hypothesized that because zinc is known to be a component of transcription factor motifs, zinc deprivation will result in slower tumor growth. To test this hypothesis, tumor cells are cultured on media containing low and high concentrations of zinc. During the experiment, a labeled oligonucleotide probe is used to identify the presence of a known transcription factor. The investigator most likely used which of the following laboratory techniques?
Transcription/translation US Medical PG Practice Questions and MCQs
Question 21: You are culturing bacteria on lactose-rich and glucose-free media. These bacteria regulate gene expression via the lac operon to ferment lactose into glucose and galactose for their metabolic needs. You add free glucose to the media. The addition of glucose reduces lactose fermentation secondary to which of the following changes?
A. Increased level of cAMP
B. Increased binding by the repressor to the operator
C. Decreased binding by the repressor to the operator
D. Decreased level of cAMP (Correct Answer)
E. Increased binding of CAP to DNA
Explanation: ***Decreased level of cAMP***
- The addition of **glucose** leads to a **decrease in intracellular cAMP levels**, which is a key component in catabolite repression.
- Reduced cAMP means less cAMP-CAP complex formation, thus **decreasing the positive regulation** of the *lac* operon.
*Increased level of cAMP*
- An **increased level of cAMP** would occur in the **absence of glucose**, which would then promote the formation of the **cAMP-CAP complex** necessary for *lac* operon activation.
- This would lead to **increased lactose fermentation**, which is the opposite of the scenario described.
*Increased binding by the repressor to the operator*
- The **repressor protein** binds to the operator in the **absence of lactose** to inhibit transcription.
- Lactose's presence (even with glucose) would lead to the conversion into **allolactose**, which binds to the repressor and *prevents* its binding to the operator.
*Decreased binding by the repressor to the operator*
- This scenario would happen in the **presence of lactose**, as **allolactose** would bind to the repressor and cause it to dissociate from the operator.
- While lactose is present in the initial setup, the question focuses on the *inhibitory effect of glucose*, which is independent of repressor binding related to lactose.
*Increased binding of CAP to DNA*
- **CAP (catabolite activator protein)** binding to DNA is *stimulated* by its association with **cAMP**.
- Since glucose leads to decreased cAMP, it would result in **decreased CAP binding to DNA**, thereby reducing *lac* operon transcription.
Question 22: A 55-year-old African American female presents to her breast surgeon for a six-month follow-up visit after undergoing a modified radical mastectomy for invasive ductal carcinoma of the left breast. She reports that she feels well and her pain has been well controlled with ibuprofen. However, she is frustrated that her incisional scar is much larger than she expected. She denies any pain or pruritus associated with the scar. Her past medical history is notable for systemic lupus erythematosus and multiple dermatofibromas on her lower extremities. She has had no other surgeries. She currently takes hydroxychloroquine. On examination, a raised hyperpigmented rubbery scar is noted at the inferior border of the left breast. It appears to have extended beyond the boundaries of the initial incision. Left arm range of motion is limited due to pain at the incisional site. Abnormal deposition of which of the following molecules is most likely responsible for the appearance of this patient’s scar?
A. Type III collagen
B. Proteoglycan
C. Elastin
D. Type I collagen (Correct Answer)
E. Type II collagen
Explanation: ***Correct: Type I collagen***
- Keloids are characterized by an **overgrowth of dense, disorganized type I collagen fibers** that extend beyond the original wound boundaries. The patient's scar is described as a **"raised, hyperpigmented, rubbery scar" that "extended beyond the boundaries of the initial incision,"** which is characteristic of a keloid.
- Patients with **African American ethnicity**, a history of **dermatofibromas** (which can predispose to keloid formation), and a lack of pain or pruritus are all consistent with a keloid.
- Type I collagen comprises **over 80% of the collagen in mature keloid tissue** and accounts for the characteristic firm, raised appearance.
*Incorrect: Type III collagen*
- **Type III collagen** is prominent during the **initial proliferative phase of wound healing** and is later replaced by type I collagen in mature scars.
- While present early in wound healing, its excessive deposition is not the primary feature of a **mature keloid** that extends beyond the wound margins.
- Normal scars have a type I to type III collagen ratio of approximately 4:1, while keloids have a much higher ratio.
*Incorrect: Proteoglycan*
- **Proteoglycans**, such as decorin and biglycan, are components of the extracellular matrix that play a role in collagen fibril assembly and tissue hydration.
- Although proteoglycans are found in keloids, their **abnormal deposition** is secondary to the extensive collagen formation and not the primary structural molecule responsible for the bulk and characteristic appearance of the scar.
*Incorrect: Elastin*
- **Elastin** provides **elasticity and recoil** to tissues, such as skin, blood vessels, and ligaments.
- Keloids are characterized by **fibrosis and rigidity**, not increased elasticity, and abnormal elastin deposition is not the hallmark of their pathogenesis.
*Incorrect: Type II collagen*
- **Type II collagen** is primarily found in **hyaline cartilage** and vitreous humor, providing resistance to intermittent pressure.
- It is **not a significant component of skin or scar tissue**, making its abnormal deposition irrelevant to the pathogenesis of cutaneous keloids.
Question 23: A medical student is studying digestive enzymes at the brush border of the duodenum. He isolates and inactivates an enzyme in the brush border that has a high affinity for the pancreatic proenzyme trypsinogen. When the enzyme is inactivated, trypsinogen is no longer converted to its active form. Which of the following is the most likely underlying mechanism of this enzyme?
A. Attachment of a carbohydrate to a side chain
B. Phosphorylation of an amino acid side chain
C. Carboxylation of a glutamate residue
D. Cleavage of a propeptide from an N-terminus (Correct Answer)
E. Conjugation of ubiquitin to lysine residue
Explanation: ***Cleavage of a propeptide from an N-terminus***
- The enzyme described is **enteropeptidase (also known as enterokinase)**, which is located in the **duodenal brush border**.
- Enteropeptidase's primary function is to activate **trypsinogen** by cleaving a small **N-terminal hexapeptide**, converting it into its active form, **trypsin**.
*Attachment of a carbohydrate to a side chain*
- This process is known as **glycosylation** and can affect protein folding, stability, and recognition, but it's not the primary mechanism by which brush border enzymes like enteropeptidase activate zymogens.
- While some enzymes are glycosylated, inactivation of this mechanism would not halt trypsinogen activation in this specific enzymatic pathway.
*Phosphorylation of an amino acid side chain*
- **Phosphorylation** is a common post-translational modification that regulates enzyme activity by adding a phosphate group, often to serine, threonine, or tyrosine residues.
- While important for many cellular signaling pathways and enzyme regulation, it is not the mechanism by which enteropeptidase activates trypsinogen.
*Carboxylation of a glutamate residue*
- **Carboxylation** typically involves the addition of a carboxyl group, notably important for blood clotting factors (e.g., vitamin K-dependent carboxylation).
- This modification is not involved in the activation of pancreatic proenzymes by brush border enzymes in the duodenum.
*Conjugation of ubiquitin to lysine residue*
- **Ubiquitination** is a process that tags proteins for degradation by the proteasome or can regulate protein function and localization.
- This is a mechanism for protein turnover and regulation, not for the activation of a proenzyme like trypsinogen.
Question 24: A 30-year-old African American woman develops a facial rash in a "butterfly" pattern over her face and complains of feeling tired and achy in her joints. In the course of a full rheumatologic workup you note that she has anti-snRNP antibodies. Which of the following do snRNPs affect?
A. Transcription of mRNA
B. Intron removal from the mRNA (Correct Answer)
C. Protection of mRNA from degradation
D. Polyadenylation of the 3' end of mRNA
E. Addition of the 5' 7-methylguanosine cap of mRNA
Explanation: ***Intron removal from the mRNA***
- **Small nuclear ribonucleoproteins (snRNPs)** are crucial components of the **spliceosome**, the molecular machinery responsible for removing non-coding introns from pre-mRNA.
- **snRNPs** recognize and bind to specific sequences within introns and at exon-intron junctions, guiding the splicing process to produce mature mRNA.
*Transcription of mRNA*
- **Transcription** is the process where DNA is copied into RNA, primarily catalyzed by **RNA polymerase**.
- While snRNPs are involved in post-transcriptional modification, they do not directly affect the initial synthesis of the mRNA transcript.
*Protection of mRNA from degradation*
- The **poly-A tail** and the **5' cap** play significant roles in protecting mRNA from degradation by exonucleases.
- While splicing is essential for producing a functional message, snRNPs themselves are not primarily involved in the degradation protection mechanism.
*Polyadenylation of the 3' end of mRNA*
- **Polyadenylation** involves the addition of a **poly-A tail** to the 3' end of the mRNA, which is mediated by poly-A polymerase.
- This process is distinct from splicing and occurs after the mature mRNA has been formed.
*Addition of the 5' 7-methylguanosine cap of mRNA*
- The **5' cap**, a 7-methylguanosine residue, is added to the 5' end of the mRNA during transcription and is crucial for ribosome binding and mRNA stability.
- This capping process occurs early in mRNA synthesis and is not directly mediated by snRNPs.
Question 25: A 82-year-old woman is brought to the emergency department from a retirement community after she was found down during the evening. On presentation, she complains that she experienced several hours of nausea, vomiting, crampy abdominal pain, and diarrhea prior to blacking out. She said that she cannot recall any factors that may have triggered her symptoms; however, she recalls that some of her friends with whom she eats also had similar symptoms earlier in the day and were brought to the hospital. They often go for walks and occasionally cook for themselves from a garden that they keep in the woods behind the facility. One of the residents on the team recalls seeing other patients from this facility earlier today, one of whom presented with kidney failure and scleral icterus prior to passing away. The enzyme most likely affected in this case has which of the following functions?
A. Synthesis of large ribosomal RNA
B. Synthesis of messenger RNA (Correct Answer)
C. Synthesis of small nucleolar RNA
D. Synthesis of 5S ribosomal RNA
E. Synthesis of transfer RNA
Explanation: ***Synthesis of messenger RNA***
- The clinical presentation (nausea, vomiting, crampy abdominal pain, diarrhea, hepatotoxicity with scleral icterus, acute kidney injury, and death), combined with the history of eating from a **garden in the woods**, is highly suggestive of **Amanita phalloides (death cap mushroom)** poisoning.
- The primary toxin is **alpha-amanitin**, which specifically and potently inhibits **RNA polymerase II**.
- **RNA polymerase II** is responsible for transcribing all **messenger RNA (mRNA)** in eukaryotic cells, which is essential for protein synthesis.
- Inhibition of mRNA synthesis leads to **inability to produce new proteins**, causing hepatocyte and renal tubular cell death, explaining the liver failure (jaundice, scleral icterus) and kidney failure seen in severe cases.
- This is the **classic biochemical mechanism** tested in alpha-amanitin poisoning questions.
*Synthesis of large ribosomal RNA*
- Large ribosomal RNAs (28S, 18S, 5.8S rRNA) are synthesized by **RNA polymerase I**, not RNA polymerase II.
- Alpha-amanitin has **minimal effect** on RNA polymerase I, even at high concentrations.
- This enzyme is not the primary target in mushroom poisoning.
*Synthesis of 5S ribosomal RNA*
- The 5S ribosomal RNA is synthesized by **RNA polymerase III**, not RNA polymerase II.
- RNA polymerase III is relatively **resistant** to alpha-amanitin compared to RNA polymerase II.
- While very high concentrations may affect it, this is not the primary mechanism of toxicity.
*Synthesis of transfer RNA*
- Transfer RNA (tRNA) is synthesized by **RNA polymerase III**, not RNA polymerase II.
- Like 5S rRNA, RNA polymerase III is much less sensitive to alpha-amanitin inhibition.
- This is not the primary target explaining the clinical toxicity.
*Synthesis of small nucleolar RNA*
- While **RNA polymerase II** does transcribe some small nucleolar RNAs (snoRNAs), this is **not its primary or most clinically relevant function**.
- Most snoRNAs are encoded within introns of host genes and processed from pre-mRNA transcripts.
- The critical toxicity of alpha-amanitin results from inhibition of **mRNA synthesis**, not snoRNA synthesis.
- In medical education and board examinations, RNA polymerase II inhibition by alpha-amanitin is tested in the context of **mRNA synthesis**.
Question 26: A 15-year-old boy presents with shortness of breath on exertion for the past 2 weeks. Although he does not have any other complaints, he is concerned about not gaining much weight despite a good appetite. His height is 188 cm (6 ft 2 in) and weight is 58 kg (124 lb). His blood pressure is 134/56 mm Hg and his pulse rate is 78/min. On cardiac auscultation, his apex beat is displaced laterally with a diastolic murmur lateral to the left sternal border. Slit-lamp examination shows an upward and outward displacement of both lenses. Synthesis of which of the following proteins is most likely defective in this patient?
A. Fibronectin
B. Elastin
C. Fibrillin (Correct Answer)
D. Reticular fibers
E. Laminin
Explanation: ***Fibrillin***
- The patient's presentation with **tall stature**, **arachnodactyly** (implied by tall, thin build), **ectopia lentis** (upward and outward lens displacement), and a **diastolic murmur** (suggesting aortic root dilation or dissection, or mitral valve prolapse) are classic features of **Marfan syndrome**.
- **Marfan syndrome** is caused by a defect in the gene encoding **fibrillin-1**, a glycoprotein essential for the formation of elastic fibers and connective tissue integrity.
*Fibronectin*
- **Fibronectin** is involved in cell adhesion, growth, migration, and differentiation, and plays a crucial role in wound healing and embryonic development.
- While essential for connective tissue, defects in fibronectin are not typically associated with the constellation of symptoms seen in Marfan syndrome.
*Elastin*
- **Elastin** works in conjunction with fibrillin to provide elasticity to tissues like the skin, lungs, and blood vessels.
- While Marfan syndrome affects elastic fibers, the primary defect is in fibrillin, which then impairs the proper formation and function of elastin-containing microfibrils.
*Reticular fibers*
- **Reticular fibers** are fine collagen fibers (primarily type III collagen) that form a delicate supporting network in various tissues and organs.
- Defects in reticular fibers are not characteristic of Marfan syndrome; Marfan syndrome is specifically linked to fibrillin defects.
*Laminin*
- **Laminins** are major proteins of the **basal lamina**, essential for cell adhesion and differentiation in epithelial and endothelial tissues.
- Genetic defects in laminin components are often associated with muscular dystrophies or epidermolysis bullosa, not the Marfanoid features presented.
Question 27: A scientist wants to extract mRNA from a cell line of interest, amplify a specific mRNA, and insert it into a plasmid so that he can transfect it into a cell in order to over-express that protein. Which of the following proteins is required for the first step of amplification of this mRNA?
A. Restriction digestion enzymes
B. RNA polymerase
C. Reverse transcriptase (Correct Answer)
D. Ligase
E. Taq DNA polymerase
Explanation: ***Reverse transcriptase***
- This enzyme is crucial for synthesizing a **complementary DNA (cDNA)** strand from an **mRNA template**, a process known as reverse transcription.
- The resulting cDNA can then be amplified using PCR, which is necessary for inserting the gene into a plasmid for overexpression.
*Restriction digestion enzymes*
- These enzymes are used to **cut DNA at specific recognition sequences**, creating sticky or blunt ends.
- Their role comes after amplification, when the cDNA needs to be inserted into a plasmid, requiring the plasmid and cDNA to be cut to facilitate ligation.
*RNA polymerase*
- This enzyme is responsible for synthesizing **RNA from a DNA template** during transcription.
- It is not involved in converting mRNA back into DNA, which is the required first step for amplifying mRNA.
*Ligase*
- DNA ligase is an enzyme that **joins DNA fragments** by forming phosphodiester bonds.
- It is used later in the process to insert the amplified cDNA into the plasmid backbone, after the DNA has been cut by restriction enzymes.
*Taq DNA polymerase*
- This enzyme is a **thermostable DNA polymerase** used in the polymerase chain reaction (PCR) to amplify DNA.
- While essential for the amplification step (after reverse transcription), it cannot directly use an mRNA template to synthesize DNA; it requires a DNA template.
Question 28: A 5-year-old boy is brought to the physician because of recurrent respiratory infections and difficulty walking for 2 months. Physical examination shows numerous telangiectasias on the nose, ears, and neck. There is overshoot on the finger-to-nose test. He has a narrow-based gait. Genetic analysis shows a nonsense mutation in the ataxia-telangiectasia gene (ATM gene). Sequencing of the encoded truncated protein shows that the C-terminal amino acid is not methionine but another amino acid. The last correctly incorporated amino acid is most likely encoded by which of the following tRNA anticodons?
A. 3'UAC5'
B. 3'ACC5' (Correct Answer)
C. 3'AUC5'
D. 3'ACU5'
E. 3'AUU5'
Explanation: ***3'ACC5'***
- A **nonsense mutation** creates a **premature stop codon**, resulting in a **truncated protein**. The question states the C-terminal amino acid is *not* methionine, meaning the **last correctly incorporated amino acid** before the stop codon must be something other than methionine.
- The anticodon **3'ACC5'** pairs with the mRNA codon **5'UGG3'**, which codes for **tryptophan**. This represents a legitimate amino acid that could be the last one incorporated before a premature stop codon, and since it's not methionine, it satisfies the question's constraint.
*3'UAC5'*
- This anticodon pairs with the mRNA codon **5'AUG3'**, which codes for **methionine** (typically the start codon).
- The question explicitly states the C-terminal amino acid is *not* methionine, directly ruling out this option as the last correctly incorporated amino acid.
*3'AUC5'*
- This anticodon would pair with the mRNA codon **5'UAG3'**, which is the **amber stop codon**.
- **Stop codons are not recognized by tRNAs** but by release factors. Therefore, no amino acid would be incorporated at this position, making this incompatible with "last correctly incorporated amino acid."
*3'ACU5'*
- This anticodon would pair with the mRNA codon **5'UGA3'**, which is the **opal stop codon**.
- Like UAG, stop codons are recognized by release factors, not tRNA anticodons. No amino acid incorporation occurs at stop codons.
*3'AUU5'*
- This anticodon would pair with the mRNA codon **5'UAA3'**, which is the **ochre stop codon**.
- This is another stop codon that terminates translation via release factors, not through tRNA-mediated amino acid incorporation.
Question 29: A 25-year-old male is brought to the emergency department by his friends after a camping trip. He and his friends were in the woods camping when the patient started experiencing severe right upper quadrant abdominal pain after foraging and ingesting some wild mushrooms about 3 hours earlier. The patient is lethargic on exam and appears jaundiced. He has scleral icterus and is severely tender to palpation in the right upper quadrant. He has scattered petechiae on his extremities. Liver function tests are:
Serum:
Na+: 134 mEq/L
Cl-: 100 mEq/L
K+: 4.2 mEq/L
HCO3-: 24 mEq/L
Urea nitrogen: 50 mg/dL
Glucose: 100 mg/dL
Creatinine: 1.4 mg/dL
Alkaline phosphatase: 400 U/L
Aspartate aminotransferase (AST, GOT): 3278 U/L
Alanine aminotransferase (ALT, GPT): 3045 U/L
gamma-Glutamyltransferase (GGT): 100 U/L
The most likely cause of this patient’s clinical presentation acts by inhibiting which of the following molecules?
A. RNA polymerase II (Correct Answer)
B. RNA polymerase III
C. Topoisomerase
D. RNA polymerase I
E. Prokaryote RNA polymerase
Explanation: ***RNA polymerase II***
- The clinical presentation with severe hepatotoxicity (jaundice, elevated AST/ALT, RUQ pain, petechiae, lethargy) following wild mushroom ingestion is highly suggestive of poisoning by **Amanita phalloides** (death cap mushroom).
- The primary toxin in *Amanita phalloides* is **alpha-amanitin**, which specifically inhibits **RNA polymerase II**, thereby halting mRNA synthesis and leading to cellular death, particularly in rapidly dividing cells and hepatocytes.
*RNA polymerase III*
- **RNA polymerase III** is responsible for synthesizing **tRNA** and **5S ribosomal RNA**.
- While essential for cell function, it is not the primary target of amanitin toxins, and its inhibition would not directly cause the severe hepatotoxicity observed.
*Topoisomerase*
- **Topoisomerases** are enzymes that regulate the supercoiling of **DNA** during replication, transcription, and repair.
- While critical for cell survival, they are not the target of the toxins found in *Amanita phalloides* mushrooms.
*RNA polymerase I*
- **RNA polymerase I** is responsible for synthesizing most **ribosomal RNA (rRNA)**.
- While also essential, it is less sensitive to **alpha-amanitin** than RNA polymerase II, requiring much higher concentrations for inhibition.
*Prokaryote RNA polymerase*
- **Prokaryote RNA polymerase** is fundamentally different in structure and function from eukaryotic RNA polymerases.
- **Alpha-amanitin** specifically targets eukaryotic RNA polymerases and has no significant inhibitory effect on prokaryotic RNA polymerase.
Question 30: An investigator is studying the effects of zinc deprivation on cancer cell proliferation. It is hypothesized that because zinc is known to be a component of transcription factor motifs, zinc deprivation will result in slower tumor growth. To test this hypothesis, tumor cells are cultured on media containing low and high concentrations of zinc. During the experiment, a labeled oligonucleotide probe is used to identify the presence of a known transcription factor. The investigator most likely used which of the following laboratory techniques?
A. ELISA
B. PCR
C. Western blot
D. Northern blot
E. Southwestern blot (Correct Answer)
Explanation: ***Southwestern blot***
- A **Southwestern blot** specifically identifies **DNA-binding proteins** (such as transcription factors) by detecting their ability to bind to specific **labeled DNA oligonucleotide probes**
- The technique involves: protein separation by gel electrophoresis → transfer to membrane → probing with **labeled double-stranded DNA oligonucleotide**
- This directly answers the question: using a labeled oligonucleotide probe to identify a transcription factor
*ELISA*
- **ELISA** detects and quantifies proteins using **antibody-antigen interactions**, not DNA-binding activity
- While it could detect the presence of a transcription factor protein, it cannot assess the protein's ability to bind to specific DNA sequences
- Does not utilize oligonucleotide probes for detection
*PCR*
- **PCR** amplifies specific **DNA sequences** but does not detect or characterize proteins
- This technique would amplify DNA, not identify DNA-binding proteins
- Not applicable for detecting transcription factor presence or function
*Western blot*
- **Western blot** detects specific proteins using **antibodies**, not oligonucleotide probes
- While it could confirm transcription factor protein presence, it cannot assess DNA-binding capability
- Uses antibody-based detection, not nucleotide probe-based detection
*Northern blot*
- **Northern blot** detects specific **RNA molecules**, not DNA-binding proteins
- Uses labeled DNA or RNA probes to detect RNA, not to detect proteins that bind DNA
- Wrong target molecule (RNA vs. proteins)
