Molecular Genetics III: Gene Structure and Expression

60 flashcards covering gene structure, transcription, regulation, translation, Lac operon, and related clinical/translational concepts from the lecture notes.

What is the Central Dogma of molecular biology?

DNA → RNA → protein.

What is a gene?

A DNA sequence with a start and stop that specifies a polypeptide or functional RNA.

What does gene structure refer to?

Promoter, coding region, regulatory elements that control transcription and expression.

How do prokaryotic and eukaryotic gene organizations differ?

Prokaryotes use operons with polycistronic mRNA; eukaryotes have monocistronic mRNA with transcription and translation separated.

What is an operon?

A cluster of genes under a single promoter in prokaryotes.

What is polycistronic mRNA?

mRNA that encodes several proteins from an operon.

What is monocistronic mRNA?

mRNA that encodes a single protein.

Which RNA types are transcribed from DNA besides mRNA?

tRNA, rRNA, regulatory RNA, and hnRNA.

Which RNA polymerase transcribes mRNA in eukaryotes?

RNA polymerase II.

What does alpha-amanitin inhibit?

RNA polymerase II.

What is Actinomycin D and what does it do?

An intercalating agent that inhibits RNA polymerase in both prokaryotes and eukaryotes.

What is Rifampin's target?

Bacterial RNA polymerase.

Where does transcription start in prokaryotes?

At the promoter with -35 and -10 elements.

Where does transcription start in eukaryotes?

At a promoter often containing a TATA box around -25.

What recognizes prokaryotic promoters?

Sigma factor.

What recognizes eukaryotic promoters?

Transcription factors (TFs).

What are the two main transcription termination types in bacteria?

Rho-dependent and Rho-independent termination.

In what direction is transcription synthesized?

5' to 3'.

What are constitutive (housekeeping) genes?

Genes expressed under normal conditions without regulation.

What are regulated genes?

Genes whose expression is controlled by regulatory proteins (activators/repressors).

What are the two main types of regulatory proteins?

Activators and repressors.

What is the Lac operon an example of?

A classic model of prokaryotic gene regulation.

What elements comprise the Lac operon regulatory region?

CAP site, promoter, operator, lacZ, lacY, lacA.

What gene encodes the Lac repressor?

lacI.

What is the role of CAP-cAMP in lac operon regulation?

CAP-cAMP binds near the promoter to enhance transcription when glucose is low.

How does glucose level affect cAMP?

High glucose lowers cAMP; low glucose raises cAMP.

What happens to lac operon expression when glucose is low and lactose is present?

Lac genes are strongly expressed (induced).

What happens to lac operon expression when lactose is unavailable?

Lac genes are not expressed; repressor binds the operator.

What happens to lac operon expression when glucose is high and lactose is available?

Expression is very low or basal due to low cAMP.

What is the function of transcriptional enhancers and silencers?

Enhancers increase transcription; silencers decrease transcription via regulatory proteins.

What is promoter strength?

The affinity of a promoter for RNA polymerase and transcription factors; strong promoters drive high transcription.

What are post-transcriptional modifications?

5' capping, 3' polyadenylation, and exon splicing (plus snRNP involvement).

What is the 5' cap function?

Protection of the mRNA and aiding ribosome recognition for translation.

What is the 3' polyadenylation function?

Addition of a poly-A tail that stabilizes mRNA and aids export and translation.

What is exon splicing?

Removal of introns and joining of exons in pre-mRNA.

What is the role of snRNPs?

Components of the spliceosome that carry out splicing of pre-mRNA.

Which autoimmune diseases are associated with antibodies to snRNPs (e.g., U1 RNP)?

Systemic lupus erythematosus (SLE) and mixed connective tissue disease (MCTD).

Where does mature mRNA go after processing?

Cytoplasm.

What is the Shine-Dalgarno sequence?

A prokaryotic ribosome binding site that aligns the ribosome with the start codon via interaction with 16S rRNA.

What role does 16S rRNA play in translation initiation?

Part of the 30S subunit that base-pairs with the Shine-Dalgarno sequence to position the ribosome.

What are the ribosomal subunits in bacteria?

50S and 30S, forming the 70S ribosome.

What ribosomal subunits compose the eukaryotic ribosome?

40S and 60S, forming the 80S ribosome.

What is the start codon in translation?

AUG.

What amino acid does AUG code for at initiation?

Methionine (formylmethionine in bacteria for the initiating tRNA).

What initiator tRNA carries the initiating amino acid in bacteria?

tRNA^fMet (formylmethionine).

Which codons act as stop signals for translation?

UAA, UAG, UGA.

What are the A, P, and E sites on the ribosome?

A site: aminoacyl, P site: peptidyl, E site: exit.

What are the three stages of translation?

Initiation, elongation, termination.

What is the role of initiation factors in translation?

Assist in assembly of the initiation complex and start of translation.

What is the function of a tRNA anticodon?

Pairs with the mRNA codon to ensure correct amino acid incorporation.

Which antibiotics affect translation by acting on the 30S subunit to cause misreading?

Aminoglycosides (e.g., streptomycin, tobramycin, gentamicin).

Which antibiotics bind the 30S subunit to block tRNA binding?

Tetracyclines.

Which antibiotics bind the 50S subunit to prevent peptide bond formation?

Chloramphenicol (and macrolides are noted to affect peptide bond formation/translocation depending on source).

Which antibiotics bind the 50S subunit to inhibit translocation?

Macrolides (e.g., erythromycin, azithromycin).

Are transcription and translation coupled in prokaryotes?

Yes, they are typically coupled in prokaryotes.

Are transcription and translation coupled in eukaryotes?

No, they are separated in space and time.

What is the genetic code characterized by?

Degeneracy (multiple codons code for the same amino acid) and universality.

Which codon is the start codon and what amino acid does it typically code for?

AUG, coding for methionine.

Which codons code for phenylalanine?

UUU (and UUC) codes for phenylalanine.

What is the role of transcription factors in prokaryotes versus eukaryotes?

Prokaryotes use sigma factors; eukaryotes use transcription factors to recognize promoters.

What is the role of CAP in lac operon regulation?

CAP-cAMP binds near the promoter to enhance transcription when glucose is low.

What happens to the lac operon when lactose is present and glucose is low?

Strong expression due to induction and CAP activation.

What happens to the lac operon when lactose is absent or glucose is high?

Low or no expression due to repressor and low cAMP.

What is the role of the operator in the lac operon?

Repressor binding to the operator blocks RNA polymerase when lactose is absent.

What are enhancers and silencers?

Regulatory DNA elements that increase or decrease transcription via transcription factors.

What is the function of the 5' cap beyond protection?

Facilitates ribosome binding and initiation of translation.

What is exon splicing?

Joining of exons after intron removal to produce mature mRNA.

What is exon-intron structure of hnRNA?

hnRNA contains both exons and introns before processing.

What is the role of the spliceosome?

Catalyzes intron removal and exon ligation during splicing.

Which ribosomal RNA is part of the 30S subunit?

16S rRNA.

Which ribosomal RNA is part of the 50S subunit?

23S and 5S rRNA.

What is the difference between 70S and 80S ribosomes?

70S: prokaryotes; 80S: eukaryotes.

What is the role of the ribosome binding site in prokaryotes?

Shine-Dalgarno sequence aligns ribosome to start codon.

What is the role of 16S rRNA in initiating translation?

Base-pairs with Shine-Dalgarno to position the ribosome.

What is a mature mRNA?

Processed mRNA ready for export and translation in the cytoplasm.

What is the function of snRNPs in RNA processing?

Splice snRNPs are components of the spliceosome that remove introns.

Which autoimmune disease is associated with anti-snRNP antibodies?

Systemic lupus erythematosus (SLE) and mixed connective tissue disease (MCTD).

What is the role of 3' polyadenylation?

Signals mRNA stability and export; aids translation.

Where is the lac operon located in bacteria?

On the bacterial chromosome as a cluster of genes for lactose metabolism.

Which transcriptional polymerase transcribes rRNA in eukaryotes?

RNA polymerase I.

Which RNA polymerase transcribes tRNA in eukaryotes?

RNA polymerase III.

What is the consequence of high glucose on lac operon transcription?

Low cAMP leads to reduced CAP activation and reduced lac operon transcription.

What are RNAs that regulate gene expression but are not mRNA, tRNA, or rRNA called?

Regulatory RNAs.

What is the start signal for transcription in prokaryotes?

Promoter elements at -35 and -10 recognized by RNA polymerase/sigma.

What is the promoter element in many eukaryotes located around -25 called?

TATA box.

What is the significance of the -35 and -10 promoter elements?

They are recognition sites for bacterial RNA polymerase/sigma factor to start transcription.

What is the effect of antibiotics on translation?

They can inhibit initiation, elongation, or peptide bond formation, disrupting protein synthesis.

What is Shine-Dalgarno?

Ribosome binding site in prokaryotic mRNA that aligns ribosome with start codon.

What is the typical start amino acid in bacteria?

Formylmethionine (fMet) carried by initiator tRNA.

What distinguishes eukaryotic mRNA processing from prokaryotic?

Eukaryotes extensively cap, polyadenylate, and splice; translation is separate from transcription.

Which stage of translation involves reading the mRNA codons to add amino acids?

Elongation.

Which stage of translation ends with a stop codon?

Termination.

What is a Rho-dependent termination?

Termination requiring the Rho helicase to disengage RNA polymerase.

What is a Rho-independent termination?

Termination via a hairpin loop in RNA causing polymerase dissociation.

What happens to mRNA after transcription in bacteria?

It is translated simultaneously with transcription in many cases.