Chapter 12 – Gene Expression at the Molecular Level

A comprehensive set of question-and-answer flashcards covering key points from Chapter 12 on gene expression, including historical experiments, transcription, RNA processing, the genetic code, translation machinery, and the stages of translation.

At which two levels can gene function be studied?

The molecular function of the protein product and the organism’s trait that the gene confers.

How are the molecular and organismal levels of gene function connected?

The molecular function of a protein affects cell structure and activity, which in turn determines an organism’s traits.

What did Archbold Garrod’s study of inborn errors of metabolism lead him to propose?

That certain diseases are caused by a missing or defective enzyme due to a gene mutation.

Which metabolic disease did Garrod use as an example of a missing-enzyme disorder?

Alkaptonuria, caused by failure to convert homogentisic acid because of a defective enzyme.

What principle did Beadle and Tatum’s Neurospora crassa experiments establish?

The one gene–one enzyme (later refined to one gene–one polypeptide) hypothesis.

Why was the original hypothesis updated to "one gene, one polypeptide"?

Because not all proteins are enzymes and many proteins consist of multiple polypeptide chains encoded by separate genes.

State the Central Dogma of gene expression.

DNA is transcribed into RNA, and RNA is translated into polypeptide.

Define transcription.

The process of making an RNA copy of a gene’s DNA sequence.

Define translation.

The synthesis of a polypeptide using an mRNA template on a ribosome.

Which additional step occurs in eukaryotic gene expression but not in bacteria?

RNA processing—pre-mRNA is modified (capping, splicing, poly-A tail) to form mature mRNA.

Where do transcription and translation occur in bacteria?

Both processes take place in the cytoplasm because bacteria lack a nucleus.

Where do transcription, RNA processing, and translation occur in eukaryotes?

Transcription and RNA processing occur in the nucleus; translation occurs in the cytosol.

List the four key regions of a typical gene.

Regulatory sequence, promoter, transcribed region, and terminator.

Name the three stages of transcription.

Initiation, elongation, and termination.

During bacterial transcription initiation, which factor helps RNA polymerase recognize the promoter?

Sigma factor.

In which direction is RNA synthesized?

5′ → 3′ direction.

Which RNA polymerase transcribes mRNA in eukaryotes?

RNA polymerase II.

What is the role of general transcription factors in eukaryotes?

They assemble with RNA polymerase II at the promoter to form the pre-initiation complex needed for transcription to begin.

What are introns and exons?

Introns are non-coding sequences removed from pre-mRNA; exons are coding sequences that remain in mature mRNA.

What does the spliceosome consist of, and what is its function?

It is made of snRNPs (snurps) and removes introns precisely from pre-mRNA.

What is added to the 5′ end of eukaryotic mRNA during processing?

A 7-methylguanosine cap.

What modification is added to the 3′ end of eukaryotic mRNA?

A poly-A tail of 100–200 adenine nucleotides.

Why is the genetic code described as degenerate?

Because more than one codon can specify the same amino acid, providing tolerance to some mutations.

Define codon and anticodon.

Codon: a three-nucleotide sequence in mRNA specifying an amino acid or stop signal; Anticodon: the complementary three-nucleotide sequence in tRNA that pairs with a codon.

What amino acid is carried by a tRNA with anticodon 3′-CAG-5′?

Valine (it pairs with mRNA codon 5′-GUC-3′).

What establishes the reading frame during translation?

The start codon read by the ribosome.

What are the three stop codons?

UAA, UAG, and UGA.

Name the three sites on a ribosome involved in translation.

A site (Aminoacyl), P site (Peptidyl), and E site (Exit).

Contrast prokaryotic and eukaryotic ribosome sizes.

Prokaryotic ribosomes are 70S (50S large + 30S small), whereas eukaryotic cytosolic ribosomes are 80S (60S large + 40S small).

Why can antibiotics target bacterial translation without harming eukaryotic cells?

Because bacterial ribosomes differ structurally from eukaryotic ribosomes, allowing selective inhibition.

Describe the cloverleaf structure of tRNA.

The structure folds with an anticodon loop and an acceptor stem that binds a specific amino acid.

What enzyme attaches an amino acid to its correct tRNA?

Aminoacyl-tRNA synthetase.

What is a charged tRNA?

A molecule that is covalently linked to its designated amino acid.

List the three overall stages of translation.

Initiation, elongation, and termination.

What molecules are required to start bacterial translation?

mRNA with ribosomal-binding site, the small ribosomal subunit, initiator tRNA carrying fMet (formyl-methionine), and the large ribosomal subunit.

During elongation, what provides energy to position a new aminoacyl-tRNA in the A site?

GTP hydrolysis.

What catalyzes peptide bond formation during translation?

The ribosomal RNA (23S rRNA in bacteria) acting as a ribozyme.

What happens during translocation in elongation?

The ribosome moves one codon toward the 3′ end of mRNA, shifting tRNAs: A→P, P→E, and releasing the uncharged tRNA from the E site.

How is translation terminated?

When a stop codon enters the A site, a release factor binds, prompting hydrolysis of the polypeptide from the tRNA and disassembly of the ribosome-mRNA complex.

What is the function of initiation, elongation, and release (termination) factors?

Initiation factors assemble the ribosome-mRNA-tRNA complex; elongation factors assist tRNA entry and translocation; release factors recognize stop codons and promote termination.

What is the ribosomal binding site on bacterial mRNA called?

The Shine-Dalgarno sequence.

How is mRNA export from the nucleus linked to its 5′ cap?

The cap is recognized by nuclear export proteins that guide mature mRNA through nuclear pores to the cytosol.

Explain why adding or deleting one or two bases (but not multiples of three) in a coding sequence causes a frameshift mutation.

Because it alters the grouping of three-base codons downstream of the mutation, changing every subsequent amino acid.

Which ribosomal rRNA gene is commonly used in phylogenetic studies of bacteria?

The 16S rRNA gene of the small (30S) ribosomal subunit.

What does "S" stand for in ribosome sedimentation coefficients (e.g., 70S)?

Svedberg unit, a measure of how fast a particle sediments during centrifugation.

Give an example of an antibiotic that inhibits bacterial translation and its target.

Tetracycline—binds to the A site of the 30S subunit, preventing aminoacyl-tRNA entry.

Why can multiple ribosomes translate a single mRNA simultaneously in bacteria?

Because transcription and translation are coupled in the cytoplasm, allowing ribosomes to bind mRNA while it is still being synthesized.

What is the role of the promoter in transcription initiation?

It serves as the binding site for RNA polymerase and associated factors to begin transcription.

Why is RNA made with uracil instead of thymine?

It is energetically less costly to synthesize and functions equivalently in base-pairing during RNA processes.

Identify two RNA types besides mRNA produced by transcription that function without being translated.

tRNA and rRNA (also snRNA, miRNA, etc.).

Which RNA processing event helps stabilize eukaryotic mRNA in the cytosol?

Addition of the poly-A tail.

Name the consensus start codon and its encoded amino acid in eukaryotic translation.

AUG codon; it encodes methionine.