Chapter 15: Translation of mRNA

Translation

produces a polypeptide using mRNA information

in prokaryote, translation occurs in

cytoplasm

in eukaryote, translation occurs in

cytoplasm

Transcription

produces an RNA copy of a gene

in prokaryotes, transcription occurs in

cytoplasm

in eukaryotes, transcription occurs in

nucleus

How can you determine the amino acid sequence of a polypeptide from DNA or mRNA sequences?

The coding strand DNA sequence matches the mRNA sequence (T is replaced with U). The template strand is complementary to the mRNA. The mRNA sequence translates directly into codons.

What is the genetic code and what is a codon?

The genetic code is the set of rules for translating information in DNA or mRNA into proteins; it is universal and redundant. A codon is a sequence of 3 nucleotides in mRNA that corresponds to a specific amino acid or stop signal.

What is the 'one gene-one enzyme' hypothesis?

a single gene controls the synthesis of a single enzyme, as demonstrated by Beadle and Tatum's experiments with neurospora mutants.

How did Beadle and Tatum experimentally verify the one-gene-one enzyme hypothesis?

They studied methionine biosynthesis in neurospora mutants, finding that each mutant was missing one specific enzyme in the pathway, linking each gene mutation to the loss of one enzyme.

What were the contributions of Nirenberg and Matthaei's cell-free translation experiments?

They added random mRNA to a translation system and found a correlation between the amount of radioactive amino acid incorporated into total protein and the predicted codons formed.

What novel method did Khorana use to synthesize RNA for translation experiments?

Khorana created short RNAs with known sequences, linked them into long copolymers, and used them in a cell-free translation system to find correlations with radioactive amino acid incorporation.

What did Nirenberg and Leder discover about RNA triplets?

They found that RNA triplets could stimulate ribosomes to bind to tRNA, with different triplets causing binding of different tRNAs and their associated amino acids.

How do you calculate the probabilities of specific codons in synthetic RNA?

P(codon) = P(1st base) × P(2nd base) × P(3rd base).

How can you match codon sequences to amino acids?

By using a table of the genetic code.

What is the start codon and its role in translation?

AUG, which codes for Methionine (Met) and begins the polypeptide sequence.

What are the stop codons and their role in translation?

UAA, UAG, and UGA, which signal the end of the translation process.

What is meant by 'wobble base' in the genetic code?

the flexibility in the base pairing at the third position of a codon, allowing for some variation in codon-anticodon pairing.

What does it mean that the genetic code is degenerate?

multiple synonymous codons can specify the same amino acid.

What is the third base in the codon-anticodon recognition process sometimes referred to as?

The wobble base

What pairing rule applies to the first two positions of the codon-anticodon recognition?

The AU/GC rule.

What are isoacceptor tRNAs?

tRNAs that have different anticodon sequences but can recognize the same codon.

What are the conserved features of tRNAs?

Three stem loops (D-loop, anticodon arm, TΨC arm), variable regions, 3' acceptor region, and modified nucleotides.

What is the role of the D-loop in tRNA?

It is involved in correct folding and recognition by aminoacyl-tRNA.

What is the function of the anticodon arm in tRNA?

It is involved in ribosome binding.

What is the significance of the 3' acceptor stem in tRNA?

It has a conserved CCA sequence at the 3' end where the amino acid is covalently attached by aminoacyl-tRNA synthetase.

What are some examples of modified nucleotides found in tRNA?

Inosine (I), methylinosine (ml), dihydrouridine (UH2), dimethylguanosine (m2G), ribothymidine (T), pseudouridine (P).

How does the anticodon sequence in tRNAs determine the polypeptide sequence from mRNA?

The anticodon in tRNA binds to a complementary codon in mRNA, and the tRNA carries the corresponding amino acid.

What are the steps involved in charging a tRNA?

Amino acid and ATP bind to aminoacyl-tRNA synthetase, PPi is released, a specific tRNA binds, the amino acid covalently bonds to tRNA, AMP is released, and the charged tRNA is released.

What are the three sites in the ribosome and their roles in translation?

A site, P site, E site

role of A site

where new tRNA charged with an amino acid resides

role of P site

where the tRNA attached to the polypeptide resides

role of E site

where the uncharged tRNA exits the ribosome

What is the first step in translation initiation in bacteria?

The mRNA, initiator tRNA, and ribosomal subunits associate to form an initiation complex.

What role do initiation factors IF1, IF2, and IF3 play in bacterial translation initiation?

assist in the formation of the initiation complex and the recognition of the start codon.

What is the Shine-Dalgarno sequence?

consensus sequence that helps position the mRNA on the ribosome during bacterial translation initiation.

How does the initiation of translation differ between prokaryotes and eukaryotes?

Eukaryotes use Kozak's rules for mRNA positioning, have different initiation factors (eIF), and the initiator tRNA carries methionine instead of formylmethionine.

What is the role of the 5' cap in eukaryotic translation initiation?

It is recognized by an initiation factor complex that helps bind the mRNA to the small ribosomal subunit.

What is the start codon in both prokaryotic and eukaryotic translation?

AUG.

What happens to IF1 and IF3 during bacterial translation initiation?

They are released after the large subunit binds to form the initiation complex.

What is the significance of the variable regions in tRNA?

They vary in length among different tRNAs and can affect recognition by specific enzymes.

What type of bond forms between the amino acid and tRNA during charging?

An ester bond

What is the function of modified nucleotides in tRNA?

They enhance structural stability, improve accuracy of codon recognition, and aid in folding and function.

What initiates the formation of the 80S initiation complex during translation?

The binding of the 40S small subunit to the start codon AUG, determined by Kozak's rules, followed by the joining of the 60S large subunit.

What are the two roles of 16S rRNA during translation?

detect incorrect tRNA at the A site + prevent elongation until the incorrect tRNA is released.

How does the 23S rRNA function as a ribozyme during translation?

it acts as peptidyl transferase, making a bond between the growing polypeptide and the new amino acid.

What are the steps involved in bacterial elongation during translation?

1. A charged tRNA binds to the A site with the help of EF-Tu and GTP hydrolysis. 2. Peptidyl transferase forms a bond between the growing polypeptide and the new amino acid. 3. The polypeptide is transferred to the A site. 4. The ribosome translocates one codon to the right, promoted by EF-G hydrolyzing GTP. 5. An uncharged tRNA is released from the E site. Repeat until a stop codon is reached.

What is the role of release factors in bacterial termination?

Release factors are proteins that recognize stop codons, mimicking tRNAs to bind to the ribosome A site, facilitating termination. Bacteria have three release factors: RF1 (UAA, UAG), RF2 (UAA, UGA), and RF3 (binds GTP to assist in termination).

How do prokaryotic and eukaryotic translation differ?

Prokaryotic translation occurs in the cytoplasm and can begin before transcription finishes, while eukaryotic translation occurs in the cytoplasm after mRNA processing and involves more complex initiation and elongation factors.

What is the directionality of an amino acid sequence?

The 5' end corresponds to the N-terminal (amino-terminal end near methionine), and the 3' end corresponds to the C-terminal (carboxyl-terminal end near cysteine).

How does the directionality of a polypeptide sequence correspond to mRNA?

As mRNA is read in the 5′ → 3′ direction, the polypeptide is synthesized from the N-terminus to the C-terminus, ensuring accurate translation of genetic information.

primary structure

amino acid sequence

secondary structure

alpha helices and beta sheets stabilized by hydrogen bonds

tertiary structure

3D conformation of a single polypeptide, determined by various interactions

quaternary structure

the association of multiple polypeptides to form a functional protein.

How does the R group of an amino acid influence its location in a folded protein?

Nonpolar (hydrophobic) amino acids are typically found in the interior of a folded protein, while polar and charged (hydrophilic) amino acids are more likely to be on the protein's surface.

What role do chaperones play in protein folding?

assist in the proper folding of polypeptides into their functional 3D structures.

What is the significance of the AUG start codon in translation?

signals the beginning of translation and codes for the amino acid methionine.

What is the function of EF-Tu during bacterial translation?

helps charged tRNA bind to the A site and hydrolyzes GTP to facilitate this process.

What is the function of EF-G during bacterial translation?

promotes the translocation of the ribosome by hydrolyzing GTP after the polypeptide is transferred to the A site.

How do release factors mimic tRNAs?

they have a 3D structure that resembles tRNAs, allowing them to bind to the ribosome A site at stop codons.

What happens to uncharged tRNA during translation?

it is released from the E site of the ribosome after the polypeptide is transferred to the A site.

What are the two main types of secondary structures in proteins?

alpha helices and beta sheets.

What interactions determine the tertiary structure of a protein?

hydrophobic and ionic interactions, hydrogen bonds, and Van der Waals interactions.

What is the final conformation of proteins composed of a single polypeptide?

tertiary structure.

What is quaternary structure in proteins?

when two or more polypeptides associate to create a functional protein.

What is the role of peptidyl transferase in translation?

it catalyzes the formation of peptide bonds between the growing polypeptide and incoming amino acids.