Q&A: Gene Expression and Regulation

Flashcards covering transcription, RNA structure and types, translation, the genetic code, post-translational modifications, and gene expression regulation.

Where do transcription and translation occur in eukaryotic cells according to the Central Dogma?

Transcription occurs in the nucleus (converting DNA to mRNA), while translation occurs in the cytoplasm on the rough endoplasmic reticulum (RER) (converting mRNA to protein).

Which nitrogenous base replaces thymine ($\text{T}$) in RNA molecules?

Uracil ($\text{U}$) replaces thymine.

Why is RNA highly susceptible to hydrolysis and chemically unstable compared to DNA?

Because its sugar component is ribose, which contains a reactive $2'\text{-OH}$ hydroxyl group.

How do DNA and RNA compare in terms of standard secondary structure and chemical stability?

DNA is usually double-stranded with a double helix structure and is stable, whereas RNA is usually single-stranded with many secondary structure types and is easily degraded.

What proportion of total cellular RNA is ribosomal RNA ($\text{rRNA}$), and what is its primary catalytic role?

$\text{rRNA}$ constitutes $80\%$ of total RNA and acts as the catalytic subunit of ribosomes (peptidyl-transferase).

What are the structural features of transfer RNA ($\text{tRNA}$)?

It is a small ($80$ nucleotides) cloverleaf structure containing an anticodon loop and an acceptor stem with the sequence $5'\text{-CCA-}3'$.

What structural elements compose a mature eukaryotic messenger RNA ($\text{mRNA}$) molecule?

A $5'$ cap ($7\text{-methylguanosine}$), a coding sequence for protein synthesis, and a $3'$ poly(A) tail of $20\text{--}250$ adenine nucleotides.

What is the primary function of microRNA ($\text{miRNA}$) in eukaryotic cells?

It inhibits the translation of messenger RNA ($\text{mRNA}$).

What class of RNA triggers the degradation of other RNA molecules?

Small interfering RNA ($\text{siRNA}$).

Which RNA polymerase synthesizes messenger RNA ($\text{mRNA}$), and how does the size of its products compare to other RNA polymerases?

RNA polymerase II, which synthesizes the largest RNA products.

Which RNA polymerases synthesize ribosomal RNA ($\text{rRNA}$) and transfer RNA ($\text{tRNA}$), respectively?

RNA polymerase I synthesizes $\text{rRNA}$ (most abundant), and RNA polymerase III synthesizes $\text{tRNA}$ (smallest).

What are three defining characteristics of transcription catalyzed by RNA polymerases?

It requires no primer, synthesizes in the $5' \rightarrow 3'$ direction, and has no proofreading activity.

How are the template strand and non-template strand of DNA defined during transcription?

The template strand is the antisense (noncoding) strand that is transcribed, while the non-template strand is the sense (coding) strand.

Which sequence elements are located in the core (basal) promoter, and what function do they serve?

The TATA-box and Inr (Initiator) sequences, which are required for binding general transcription factors ($\text{GTFs}$).

Which regulatory sequences are present in the proximal promoter region, and what binds to them?

CAAT and GC boxes, which serve as binding sites for specific transcription factors ($\text{STFs}$).

What components form the transcription pre-initiation complex at the gene promoter?

Six general transcription factors ($\text{GTFs}$) and RNA polymerase II assembled near the transcription start site ($\text{TSS}$).

How does the toxin amanitin from poisonous mushrooms affect transcription?

It strongly inhibits RNA polymerase progression.

What sequence acts as the termination and polyadenylation signal during eukaryotic transcription?

$\text{AAUAAA}$.

Which enzyme synthesizes the poly(A) tail on pre-mRNA, and what energy source does it utilize?

Polyadenylate-polymerase, using $ATP$ to add adenine residues.

What is the function of the $5'$ 7-methylguanosine cap added to pre-mRNA?

It serves a protective role by being resistant to most nucleases.

What consensus nucleotides mark the intron boundaries at the $5'$ and $3'$ splice sites during RNA splicing?

The $5'$ splice site of the intron starts with $\text{GU}$, and the $3'$ splice site junction ends with $\text{AG}$ ($\text{AG/GU}$ consensus).

How many total codons comprise the standard genetic code, and how many code for amino acids?

There are $64$ total codons:

• $61$ sense codons that code for amino acids

• $1$ start codon ($\text{AUG}$)

• $3$ stop codons ($\text{UGA, UAA, UAG}$).

What sequence is the start codon in mRNA, and what amino acid does it encode?

$\text{AUG}$, which codes for Methionine ($\text{Met}$ ).

What does degeneracy (redundancy) of the genetic code refer to?

It means that some amino acids are encoded by more than one codon.

(for instance, $6$ different codons code for Arginine).

What does the unambiguous property of the genetic code signify?

It means that each specific codon codes for only one amino acid.

What are the three tRNA binding sites in a ribosome?

The A site (aminoacyl-tRNA), P site (peptidyl-tRNA), and E site (exit).

What enzyme catalyzes the attachment of amino acids to their specific tRNAs?

Aminoacyl-tRNA synthetase.

Where is the amino acid attached to the tRNA molecule during charging?

A bond is formed between the carboxyl group of the aminoacyl-AMP and the $3'\text{-OH}$ group of the Adenine residue in the $5'\text{-CCA-}3'$ acceptor stem.

What is the Wobble hypothesis?

The principle that non-traditional base-pairing can occur at the $3'$ position of the codon (pairing with the $1\text{st}$ position, or $5'$ end, of the tRNA anticodon), allowing one tRNA to recognize multiple codons.

Which eukaryotic ribosomal subunits assemble to form the functional ribosome during translation initiation?

The small $40\text{S}$ subunit and the large $60\text{S}$ subunit assemble to form the complete $80\text{S}$ ribosome.

To which site on the ribosome does the initial Met-tRNA complex bind during translation initiation?

It is directed to the P (peptidyl) site.

Which activity catalyzes peptide bond formation between amino acids during translation elongation?

Peptidyl transferase activity (catalyzed by the rRNA component of the large subunit).

Which elongation factors and energy molecules facilitate tRNA binding to the A site and ribosome translocation?

$\text{eEF1A}\cdot\text{GTP}$ facilitates aminoacyl-tRNA delivery to the A site, and $\text{eEF2}\cdot\text{GTP}$ drives translocation.

How is translation terminated when a stop codon reaches the A site of the ribosome?

Release factors ($\text{RF}$ ) bind to the stop codon at the A site, causing the newly synthesized polypeptide to be cleaved and released from the tRNA in the P site.

What is a polysome (polyribosome) and what purpose does it serve?

A structure comprising multiple ribosomes simultaneously translating a single mRNA molecule, increasing the rate of protein synthesis.

On which amino acid side chains does protein phosphorylation commonly occur?

On the hydroxyl ($\text{-OH}$ ) groups of Serine, Threonine, and Tyrosine.

How are proteins designated for rapid degradation by cellular proteases?

They are marked for destruction by ubiquitin attachment.

What is an example of gene regulation at the DNA level via gene amplification?

Generating $100\text{--}1000$ copies of a gene, such as the gene amplification that causes drug resistance to methotrexate.

How does RNA editing alter Apolipoprotein B ($\text{ApoB}$) expression in the intestine compared to the liver?

In the intestine, RNA editing changes a $\text{CAA}$ codon to a $\text{UAA}$ stop codon, yielding truncated ApoB-48 ($2152$ amino acids) instead of full-length ApoB-100 ($4563$ amino acids) produced in the liver.

How do microRNAs ($\text{miRNA}$) and small interfering RNAs ($\text{siRNA}$) regulate gene expression post-transcriptionally?

They bind to the $3'\text{-UTR}$ of target mRNA to inhibit translation or trigger mRNA cleavage and degradation.