#3 BIOL 523: Gene Expression and Regulation - Flashcards

Flashcards testing core concepts of gene expression, transcription, RNA processing, genetic code, translation, and transcriptional regulation based on lecture material.

What is the definition of a gene as presented in the lecture notes?

A section of DNA that contains instructions for making one protein or functional RNA (like tRNA).

In which direction is RNA synthesized during transcription, and in which direction does RNA polymerase travel along the template strand?

RNA is synthesized in the $5' \rightarrow 3'$ direction, while RNA polymerase moves down the template DNA strand in the $3' \rightarrow 5'$ direction.

What do positive and negative numbers designate when mapping nucleotides relative to the transcription start site (+1)?

Positive numbers ($+$-sign) denote downstream nucleotides in the direction of transcription, while negative numbers ($-$$-sign) denote upstream nucleotides in the opposite direction.

What is the size of the transcription bubble formed in the active site of RNA polymerase?

The transcription bubble is a $12\text{--}14$ base-pair region of melted DNA.

What are three key properties that distinguish RNA polymerases from DNA polymerases involved in replication?

RNA polymerases catalyze the linkage of ribonucleotides (rNTPs) instead of deoxyribonucleotides (dNTPs), can initiate RNA chain synthesis without a primer, and are processive (completing an entire transcript without dissociating).

What is the approximate error rate of RNA polymerases during transcription?

RNA polymerases make approximately one mistake for every $10^4$ nucleotides copied into RNA.

What structure is added to the 5' end of eukaryotic pre-mRNAs, and what are its main functions?

A $5'$ methylated cap ($\text{m}^7\text{Gppp}$ cap) attached via a $5' \rightarrow 5'$ linkage is added to protect mRNA from degradation, assist in cytoplasmic export, and bind a protein factor needed for translation initiation.

How is the 3' end of eukaryotic pre-mRNA processed, and which enzyme performs this addition?

The $3'$ end is cleaved by an endonuclease and polyadenylated with a tail of $100\text{--}250$ adenine bases added by poly(A) polymerase without requiring a DNA template.

How does alternative RNA splicing generate functional diversity in eukaryotic cells?

Alternative splicing allows distinct protein isoforms to be expressed from a single eukaryotic gene in different cell types by selectively including or excluding specific exons.

What proportion of total cellular RNA is composed of mRNA versus rRNA in a typical mammalian cell?

mRNA composes only $3\text{--}5\text{\%}$ of total cellular RNA, whereas the majority of cellular RNA is rRNA.

According to Table 6-1, what is the biological function of microRNAs (miRNAs)?

MicroRNAs (miRNAs) regulate gene expression by blocking translation of specific mRNAs and causing their degradation.

Out of the 64 genetic code triplets, how many specify amino acids and how many serve as stop codons?

$61$ codons specify amino acids, and $3$ serve as stop codons (UAA, UAG, and UGA).

What is the difference between a missense (nonsynonymous) mutation and a silent (synonymous) mutation?

A missense mutation changes a codon to encode a different amino acid, whereas a silent mutation alters a codon without changing the encoded amino acid.

What conserved sequence exists at the 3' terminus of all mature tRNA molecules?

The trinucleotide sequence $5'\text{-CCA-}3'$, where an amino acid is attached to the $2'$ or $3'$ hydroxyl group of the terminal adenosine.

What is the Wobble hypothesis in translation?

The Wobble hypothesis describes the relaxed base-pairing rules between the third base ($3'$ end) of an mRNA codon and the first base ($5'$ end) of a tRNA anticodon, allowing one tRNA to recognize multiple codons.

How do aminoacyl-tRNA synthetases ensure high accuracy when charging tRNAs with their cognate amino acids?

They recognize specific sequences (primarily in the anticodon loop) and feature a second active site with proofreading/hydrolytic editing activity that removes mischarged amino acids.

What are the sedimentation coefficients and subunit compositions of bacterial and eukaryotic ribosomes?

Bacterial ribosomes are $70\text{S}$ (composed of a $50\text{S}$ large subunit and a $30\text{S}$ small subunit), while eukaryotic ribosomes are $80\text{S}$ (composed of a $60\text{S}$ large subunit and a $40\text{S}$ small subunit).

What are the roles of the A, P, and E ribosomal tRNA-binding sites?

The A (aminoacyl) site receives incoming aminoacyl-tRNAs, the P (peptidyl) site carries the tRNA holding the growing peptide chain, and the E (exit) site holds uncharged tRNAs before release.

Which specific tRNA initiates eukaryotic translation, and how does it differ from standard methionine tRNA?

Initiator tRNA ($\text{tRNA}_{\text{i}}^{\text{Met}}$) initiates translation; it possesses a distinct nucleotide sequence that allows eukaryotic initiation factors to recognize and position it directly into the ribosomal P site.

Which components assemble to form the eukaryotic 43S preinitiation complex?

The $40\text{S}$ small subunit bound to eIFs (eIF1, eIF1A, eIF3), eIF5, and the ternary complex (eIF2 bound to GTP and Met-$\text{tRNA}_{\text{i}}^{\text{Met}}$).

What sequence context surrounding the initiation codon facilitates start-site selection in eukaryotes?

The Kozak sequence, $(5')\text{ACCAUGG}(3')$.

Which translation initiation complex circularizes eukaryotic mRNA, and which proteins mediate these interactions?

The eIF4 complex circularizes mRNA: eIF4E binds the $5'$ cap, and eIF4G binds the cytoplasmic poly(A)-binding protein (PABPC) on the poly(A) tail.

Which elongation factor drives ribosomal translocation along the mRNA strand?

EF2-GTP, which hydrolyzes its bound GTP to induce a conformational change that translocates the ribosome by one codon.

Which release factors promote peptide chain termination upon encountering a stop codon?

eRF1 together with eRF3-GTP recognize stop codons in the A site and trigger cleavage of the peptidyl-tRNA bond at the P site.

Which bacterial antibiotic specifically blocks the peptidyl transferase reaction on ribosomes?

Chloramphenicol.

What percentage of control over protein concentration in cells is attributed to the rate of transcription?

$73\text{\%}$ of the variation in protein expression levels is controlled by the rate of transcription.

Which RNA species are transcribed by eukaryotic RNA Polymerase I, II, and III?

Pol I transcribes pre-rRNA ($28\text{S}$, $18\text{S}$, $5.8\text{S}$); Pol II transcribes mRNA, snRNAs, siRNAs, and miRNAs; Pol III transcribes tRNAs, $5\text{S}$ rRNA, snRNA U6, and $7\text{S}$ RNA.

What structural domain on RNA Polymerase II undergoes repeated phosphorylation during initiation and elongation?

The Carboxy-Terminal Domain (CTD) of the RPB1 subunit.

What are CpG islands, and why do they often serve as transcription promoters?

CpG islands are unmethylated CG-rich genomic regions (found at $∼ 70\text{\%}$ of protein-coding promoters) that bind histone octamers weakly, creating linker DNA zones accessible to transcription factors.

Which general transcription factor subunit directly binds to the TATA box element?

TBP (TATA box-binding protein), a subunit of general transcription factor TFIID.

What two key enzymatic roles are performed by TFIIH during transcription initiation?

TFIIH acts as a helicase (via its XPB subunit) to unwind DNA at the start site forming an open complex, and as a kinase module to phosphorylate the Pol II CTD.

What factors induce promoter-proximal pausing of RNA Polymerase II, and how is pausing overcome?

Promoter-proximal pausing ($< 100$ nt downstream) is induced by NELF and DSIF; elongation resumes when P-TEFb (cyclin T-CDK9) phosphorylates DSIF, NELF, and Serine 2 of the Pol II CTD.

What are promoter-proximal elements and enhancers?

Promoter-proximal elements are regulatory DNA sequences located within $∼ 200\text{ bp}$ of a start site, whereas enhancers are long-distance control elements located thousands of base pairs away.

How do DNA-binding domains of transcription factors specifically recognize target DNA sequences?

Through noncovalent interactions between amino acid side chains in an $\alpha$-helix of the domain and nitrogenous bases displayed along the major groove of DNA.

What are five common structural classes of DNA-binding domains in eukaryotic transcription factors?

Helix-turn-helix, Homeodomain, Zinc-finger, Leucine-zipper, and Basic Helix-loop-helix (bHLH) structures.

What is the function of the Mediator complex in eukaryotic transcriptional regulation?

Mediator is a large multiprotein complex that serves as a molecular bridge between DNA-bound transcription activators and RNA Polymerase II, directing Preinitiation Complex (PIC) assembly.

What six general mechanisms can eukaryotic repressor proteins use to repress gene transcription?

Competitive DNA binding, masking the activation surface, direct interaction with general transcription factors, recruitment of chromatin remodeling complexes, recruitment of histone deacetylases (HDACs), and recruitment of histone methyltransferases (HMTs).

what does this Codon go with?: AAA

LYSine amino acid encoded by mRNA

what does this Codon go with? : AUG

The start codon in mRNA that codes for the amino acid METhionine.

what does this Codon go with?": GCU

ALAnine amino acid encoded by mRNA

what does this Codon go with?: UGA

A STOP codon in mRNA that signals termination of translation.

what are the big 3 RNAs?

The three main types of RNA are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA), each playing a crucial role in the process of protein synthesis.