bio 99 mt4

What is a codon?

A trinucleotide (triplet) sequence on mRNA that codes for a specific amino acid. [cite: 6]

What amino acid do the codons AAG, CAU, and UGG code for?

AAG codes for Lysine (Lys); CAU codes for Histidine (His); UGG codes for Tryptophan (Trp). [cite: 4, 7]

What is the adapter molecule that reads mRNA sequences and translates them into an amino acid sequence?

tRNA (Transfer RNA), which possesses both an anticodon arm and an amino acid arm. [cite: 8]

If an mRNA codon sequence is 5'-GCA-3', what is its corresponding tRNA anticodon?

3'-CGU-5' (or 5'-UGC-3'). [cite: 9, 10]

What does it mean that the genetic code is "degenerate"?

Multiple different codons can encode for the same amino acid (64 possible codons exist but only 20 amino acids). [cite: 10, 11]

What are the standard universal Start and Stop codons?

Start: AUG (Methionine). Stop: UAA, UAG, and UGA. [cite: 13]

How many potential reading frames exist for a single-stranded mRNA versus a double-stranded DNA molecule?

mRNA has 3 potential reading frames; double-stranded DNA has 6 potential reading frames (3 per anti-parallel strand). [cite: 14, 18]

What constitutes an Open Reading Frame (ORF)?

A continuous nucleotide sequence that contains a start-to-stop coding sequence without frame disruptions. [cite: 16, 35, 36]

What is the core premise of Crick's Wobble Hypothesis?

The pairing between the third base of a codon and the first base of an anticodon allows a single tRNA to recognize multiple codons. [cite: 20, 24]

According to the U-G Wobble Rule, what bases can an anticodon ending in U or G recognize?

Anticodon U recognizes codon A and G; Anticodon G recognizes codon C and U. [cite: 20, 22]

According to the Inosine (I) Wobble Rule, what bases can an anticodon containing Inosine pair with?

Inosine can base pair with Cytosine (C), Uracil (U), or Adenine (A). [cite: 27, 28]

Why is the codon 5'-GUG-3' NOT recognized by the tRNA anticodon 3'-CAI-5'?

Because the third base of the codon is G, and Inosine (I) can only pair with C, U, or A. [cite: 29, 33]

What structural modification occurs during tRNA processing in eukaryotes but NOT in prokaryotes?

The removal of introns (prokaryotic tRNAs do not contain introns). [cite: 62, 64, 65]

To which chemical group do amino acids covalently bind on a tRNA molecule?

The 3' (or 2') hydroxyl (-OH) group at the CCA terminal end of the tRNA. [cite: 51, 76, 77]

What are "identity molecules" on a tRNA?

Specific nucleotides scattered throughout a tRNA that are uniquely recognized by its corresponding aminoacyl-tRNA synthetase. [cite: 52, 54, 80]

What are the two discrete steps of tRNA activation by aminoacyl-tRNA synthetases?

Step 1: Amino acid + ATP -> aminoacyl-AMP + PPi. Step 2: Aminoacyl-AMP + tRNA -> aminoacyl-tRNA + AMP. [cite: 89]

How do Class 1 and Class 2 aminoacyl-tRNA synthetases utilize proofreading sites to maintain fidelity?

They utilize an acylation site to attach the amino acid. The proofreading site specifically excludes the correct amino acid by size, but captures and hydrolyzes incorrect amino acids. [cite: 58, 60]

What is the bacterial initiator tRNA, and how is it chemically modified?

tRNAfMet; a transformylase adds a formyl group to the N-terminus of the methionine, preventing internal peptide bonding. [cite: 61, 94]

What is the eukaryotic initiator tRNA, and is its amino acid modified?

tRNAiMet; the attached methionine remains unmodified. [cite: 61, 95]

What did Harry Noller's ribosomal experiment using puromycin prove about peptide bond formation?

It proved that rRNA (not ribosomal proteins) is the primary catalytic component necessary for peptide bond formation. [cite: 100, 102]

What does the chemical compound Kethoxal do to ribosomes?

It selectively damages guanine residues in RNA, which drastically decreases ribosomal translation activity over time. [cite: 103]

What are the three tRNA binding sites on a ribosome, and what are their functions?

A site (Acceptor): new tRNAs enter; P site (Peptidyl): holds growing polypeptide chain; E site (Exit): expels uncharged tRNAs. [cite: 104]

What is the purpose of the Shine-Dalgarno sequence in bacterial translation initiation?

It is a consensus sequence on mRNA that base pairs with the 16S rRNA of the 30S small subunit to align the start codon at the P site. [cite: 107, 109]

What are the distinct functions of bacterial initiation factors IF-1, IF-2, and IF-3?

IF-1 blocks the A site; IF-2 (bound to GTP) escorts the initiator tRNAfMet; IF-3 prevents the 50S large subunit from prematurely binding. [cite: 108, 109, 110]

What triggers the release of bacterial initiation factors and allows the 50S large subunit to bind?

The hydrolysis of GTP to GDP on IF-2. [cite: 111]

How does eukaryotic translation initiation step 1 differ fundamentally from bacterial step 1?

In eukaryotes, eIF1A blocks the A site and eIF3 blocks the large subunit, but mRNA recruitment does NOT happen during this initial step. [cite: 113]

What comprises the eukaryotic eIF4F complex, and what is its collective function?

eIF4E (binds 5' cap), eIF4A (ATPase/RNA helicase), and eIF4G (adapter linking to eIF3). It escorts mRNA to the small subunit. [cite: 115]

How do eukaryotic ribosomes locate the start codon during translation initiation?

The pre-initiation complex binds at the 5' cap and travels along the mRNA ("scanning") until it hits the first AUG within a Kozak sequence. [cite: 115, 116]

How many high-energy phosphate molecules are consumed during eukaryotic initiation complex assembly?

Three total: 1 ATP is consumed during mRNA scanning/loading, and 2 GTPs are hydrolyzed to drive the release of initiation factors. [cite: 115, 117]

What is an Internal Ribosomal Entry Site (IRES)?

An mRNA sequence in eukaryotes that directly binds eIF4F to allow cap-independent translation initiation away from the 5' cap. [cite: 119]

What elongation factor is directly responsible for translocating the ribosome one codon forward?

EF-G via GTP hydrolysis. [cite: 124]

Why does the antibiotic puromycin prematurely terminate translation?

It mimics the 3' end of an aminoacyl-tRNA, enters the A site, and accepts the growing polypeptide chain, preventing further elongation. [cite: 101, 125]