Genetics Exam 4: Chapter 9

What is a protein?

A polymer of amino acids joined by peptide bonds; a functional protein can contain one or more polypeptide chains.

What groups are connected by a peptide bond?

The carboxyl group of one amino acid and the amino group of another.

What are the two ends of a polypeptide?

The N-terminus (amino end) and C-terminus (carboxyl end).

In which direction is a polypeptide synthesized?

From N-terminus to C-terminus; new amino acids are added to the C-terminus.

What is primary protein structure?

The linear sequence of amino acids in a polypeptide.

What is secondary protein structure?

Local folding of the polypeptide backbone into structures such as alpha helices and beta sheets.

What stabilizes alpha helices and beta sheets?

Hydrogen bonds between groups in the polypeptide backbone.

What is tertiary protein structure?

The overall three-dimensional shape of a single polypeptide.

What is quaternary protein structure?

The assembly of two or more polypeptide chains into a protein.

How does a gene’s nucleotide sequence relate to its protein?

The sequence of nucleotides determines the sequence of amino acids through the genetic code.

What is a codon?

A sequence of three mRNA nucleotides that specifies an amino acid or a stop signal.

What does it mean that the genetic code is degenerate?

Multiple codons can specify the same amino acid.

Does a single codon normally specify several different amino acids?

No. In the standard genetic code, each codon specifies one particular amino acid or a stop signal.

What does nonoverlapping mean?

Each nucleotide belongs to only one codon within a reading frame; consecutive codons do not share nucleotides.

How many nucleotides are in one codon, and how many codons does each nucleotide belong to within a reading frame?

Three nucleotides per codon; each nucleotide belongs to one codon.

What does it mean that the genetic code is continuous?

Codons are read consecutively without gaps from the start codon to the stop codon.

What is a reading frame?

The way a nucleotide sequence is divided into consecutive groups of three.

How many possible reading frames are there on one mRNA strand?

Three, depending on which nucleotide begins the grouping.

In which direction does the ribosome read mRNA?

5′ to 3′.

What is the usual start codon, and what amino acid does it specify?

AUG; methionine. In bacterial initiation, the first amino acid is formylmethionine.

What are the three stop codons?

UAA, UAG, and UGA.

Do stop codons specify amino acids during normal translation?

No. They signal termination.

How many codons exist in the standard genetic code?

64: 61 specify amino acids and 3 are stop codons.

Why can degeneracy reduce the effect of a nucleotide substitution?

A changed codon may still specify the same amino acid.

Does every nucleotide substitution change the amino acid?

No. Some substitutions produce a different codon for the same amino acid.

In AUG | GCU | AAA, how many codons are directly changed by replacing one nucleotide in GCU?

One codon, because the code is nonoverlapping.

What amino acid did synthetic poly-U RNA produce in experiments deciphering the genetic code?

Phenylalanine, showing that UUU specifies phenylalanine.

What amino acid did synthetic poly-C RNA produce?

Proline, showing that CCC specifies proline.

Why can a repeating GUU RNA sequence produce different amino acid sequences?

Different reading frames yield GUU, UUG, or UGU codons, specifying valine, leucine, or cysteine.

How do you read a standard mRNA codon table?

Read the codon 5′ to 3′, using its first, second, and third bases to locate the amino acid or stop signal.

What is the role of tRNA in translation?

It acts as an adaptor, pairing with an mRNA codon and delivering an amino acid.

What is an anticodon?

A three-nucleotide sequence in tRNA that pairs with an mRNA codon.

How do the codon and anticodon align?

They pair complementarily and antiparallel to one another.

What anticodon pairs with the codon 5′–AUG–3′?

3′–UAC–5′, equivalent to 5′–CAU–3′.

What anticodon pairs with the codon 5′–GCU–3′ using standard complementary pairing?

3′–CGA–5′, equivalent to 5′–AGC–3′.

Where does an amino acid attach to a tRNA?

At the terminal adenosine of the 3′-CCA end.

What is the approximate length of a tRNA?

About 75–90 nucleotides; the slides describe approximately 75.

What are the secondary and tertiary shapes of tRNA?

A cloverleaf secondary structure and an L-shaped three-dimensional structure.

How can a single-stranded tRNA contain double-helical stems?

Complementary regions within the same RNA molecule base-pair with one another.

What are examples of modified bases found in tRNA?

Dihydrouridine, pseudouridine, and inosine.

When are modified tRNA bases produced?

After transcription, enzymes modify some of the original RNA nucleotides.

What enzyme attaches an amino acid to its matching tRNA?

Aminoacyl-tRNA synthetase.

What does charging a tRNA mean?

Attaching the appropriate amino acid to the tRNA.

What is a charged tRNA also called?

An aminoacyl-tRNA.

Why is aminoacyl-tRNA synthetase accuracy important?

The ribosome checks codon–anticodon pairing, so correct amino acid attachment is essential for inserting the correct amino acid.

How do aminoacyl-tRNA synthetases reduce charging errors?

They recognize the correct amino acid and tRNA and use proofreading or editing mechanisms.

What is wobble pairing?

Flexible base pairing that allows one tRNA to recognize more than one codon.

Which codon position is the wobble position?

The third nucleotide, at the codon’s 3′ end.

Which anticodon position participates in wobble pairing?

The first nucleotide, at the anticodon’s 5′ end.

At the wobble position, which codon bases can an anticodon G recognize?

C or U.

At the wobble position, which codon bases can an anticodon U recognize?

A or G.

At the wobble position, which codon bases can anticodon inosine recognize?

A, C, or U.

At the wobble position, which codon base does an anticodon A recognize?

U.

At the wobble position, which codon base does an anticodon C recognize?

G.

What two types of molecules make up ribosomes?

Ribosomal RNA (rRNA) and proteins.

What are the bacterial ribosomal subunits and complete ribosome?

30S small subunit and 50S large subunit; together they form a 70S ribosome.

What are the eukaryotic cytoplasmic ribosomal subunits and complete ribosome?

40S small subunit and 60S large subunit; together they form an 80S ribosome.

What do S values measure, and why do they not add arithmetically?

They measure sedimentation behavior, which depends on size, shape, and density; they are not simple mass measurements.

Which rRNA is in the bacterial small subunit?

16S rRNA.

Which rRNAs are in the bacterial large subunit?

23S and 5S rRNAs.

Which rRNA is in the eukaryotic small subunit?

18S rRNA.

Which rRNAs are in the eukaryotic large subunit?

28S, 5.8S, and 5S rRNAs.

What is the main decoding role of the small ribosomal subunit?

It helps ensure correct pairing between the mRNA codon and tRNA anticodon.

What is the main catalytic role of the large ribosomal subunit?

It catalyzes peptide bond formation at the peptidyl transferase center.

What directly catalyzes peptide bond formation: rRNA or ribosomal protein?

rRNA in the large subunit.

What is the A site?

The aminoacyl site, which receives incoming charged tRNAs during elongation.

What is the P site?

The peptidyl site, which holds the tRNA carrying the chain before peptide bond formation and after translocation.

What is the E site?

The exit site, where an empty tRNA passes before leaving the ribosome.

In what order does a typical elongating tRNA move through the ribosome?

A → P → E.

Which site does the initiator tRNA enter?

The P site directly.

What are the three stages of translation?

Initiation, elongation, and termination.

What is assembled during translation initiation?

The mRNA, initiator tRNA, and small and large ribosomal subunits, with help from initiation factors.

What is the Shine–Dalgarno sequence?

A bacterial mRNA sequence upstream of the start codon that helps position the ribosome.

What pairs with the Shine–Dalgarno sequence?

A complementary region of 16S rRNA in the bacterial small subunit.

How does eukaryotic translation initiation usually locate the start codon?

The small subunit is recruited near the 5′ cap and scans for AUG in an appropriate sequence context.

What is the Kozak sequence?

A sequence context surrounding the start AUG that helps eukaryotic ribosomes recognize it.

What amino acid does the bacterial initiator tRNA carry?

Formylmethionine (fMet).

What amino acid does the eukaryotic initiator tRNA carry?

Methionine (Met).

What are roles of initiation factors?

They help assemble the initiation complex, position the initiator tRNA, and prevent premature large-subunit joining.

What additional initiation functions occur in eukaryotes?

Initiation factors help with mRNA recruitment, scanning, and interactions that bring the mRNA’s ends together.

Which ribosomal site is available for the next charged tRNA after initiation?

The A site; the initiator tRNA occupies the P site.

What are the three repeating events of elongation?

Charged tRNA delivery, peptide bond formation, and translocation.

What does bacterial EF-Tu do?

It delivers a charged tRNA to the A site.

What is the eukaryotic equivalent of EF-Tu?

eEF1α.

During peptide bond formation, where does the growing chain transfer?

From the P-site tRNA to the amino acid attached to the A-site tRNA.

Immediately after peptide bond formation, before translocation, which tRNA carries the chain?

The A-site tRNA.

Immediately after peptide bond formation, what has happened to the P-site tRNA?

It has lost its chain and is empty.

What does bacterial EF-G do?

It promotes translocation of the ribosome along the mRNA.

What is the eukaryotic equivalent of EF-G?

eEF2.

How far does the ribosome advance during each translocation step?

One codon, or three nucleotides, toward the mRNA’s 3′ end.

During translocation, where does the tRNA carrying the chain move?

From the A site to the P site.

During translocation, where does the empty P-site tRNA move?

To the E site, from which it exits.

Immediately after translocation, which site holds the tRNA carrying the chain?

The P site.

How do chain transfer and tRNA movement differ during elongation?

The chain transfers P → A during peptide bond formation; the tRNA carrying it then moves A → P during translocation.

What triggers normal translation termination?

A stop codon enters the A site.

What recognizes a stop codon during normal termination?

A protein release factor, rather than a tRNA.

What does a release factor cause?

Hydrolysis of the bond attaching the completed polypeptide to the P-site tRNA, releasing the protein.

What happens to the ribosome after termination?

It is disassembled and recycled so its components can be used again.

What is a nonsense mutation?

A mutation that converts an amino acid codon into a premature stop codon.

What is the usual effect of a nonsense mutation on a protein?

Translation ends early, producing a shortened protein.