Ch 27- Protein Synthesis

What is the genetic code composed of?

The genetic code is composed of 64 codons, 61 of which encode amino acids and 3 induce termination of protein synthesis.

What are the characteristics of the universal genetic code?

The universal genetic code is degenerate, unambiguous, nonoverlapping, and punctuation-free.

How do transfer RNAs (tRNAs) function in protein synthesis?

tRNAs decode the genetic code of messenger RNAs (mRNAs) by carrying specific amino acids to the ribosome.

What are the three main steps of protein synthesis?

The three main steps of protein synthesis are initiation, elongation, and termination.

What is the role of aminoacyl-tRNA synthetases in translation?

Aminoacyl-tRNA synthetases covalently attach amino acids to their corresponding tRNAs, ensuring correct amino acid incorporation during protein synthesis.

What is the direction of mRNA translation during protein synthesis?

mRNA is translated from the 5'-end to the 3'-end.

What are the binding sites of ribosomes for tRNA?

Ribosomes have three binding sites for tRNA: A (aminoacyl), P (peptidyl), and E (exit) sites.

Where are ribosomes primarily found in eukaryotic cells?

Ribosomes are mainly found free in the cytosol or associated with the rough endoplasmic reticulum (RER).

What is required for the energy-intensive process of protein synthesis?

The cleavage of 4 high-energy bonds is required for each amino acid added, including ATP and GTP.

What is the significance of the CCA sequence at the 3'-end of tRNA?

The CCA sequence at the 3'-end of tRNA is where the amino acid is covalently attached.

What is the proteome?

The proteome is the complete set of proteins expressed in a cell.

What happens to nascent proteins before they become functional?

Nascent proteins need to be processed, which may include folding facilitated by chaperones.

What is the process of translation in relation to gene expression?

Translation is the second step of gene expression, following transcription.

How does the genetic code ensure specificity?

The genetic code ensures specificity by using a unique three-letter codon for each amino acid.

What is meant by the term 'degeneracy' in the genetic code?

Degeneracy refers to the fact that a single amino acid may be encoded by more than one codon.

What are co- and posttranslational modifications?

Co- and posttranslational modifications are processes that modify proteins after synthesis, affecting their function and activity.

What is the role of protein factors in translation?

Protein factors catalyze reactions and stabilize the synthetic machinery during translation.

What is the significance of the ribosomes in mitochondria?

Mitochondria contain their own ribosomes (55S) and circular DNA, allowing them to synthesize some of their own proteins.

What is the impact of alterations in the mRNA sequence?

Alterations in the mRNA sequence may result in disease or death.

What is the function of GTP in protein synthesis?

GTP is used for binding aminoacyl-tRNA to the A site and for translocation during protein synthesis.

What is the relationship between ribosomes and the endoplasmic reticulum?

RER-associated ribosomes synthesize proteins for export, membrane incorporation, or lysosomal import.

What are the roles of chaperones in protein folding?

Chaperones facilitate protein folding and prevent misfolding, which can lead to aggregation or degradation.

What is the significance of the initiation codon and termination codons in protein synthesis?

The initiation codon AUG starts translation, while termination codons UAA, UAG, and UGA signal the end of protein synthesis.

What is the process of amino acid charging on tRNA?

Amino acid charging involves forming an AMP-amino acid-enzyme complex, transferring the activated amino acid to tRNA, and releasing AMP and the enzyme.

What is the error rate for amino acid charging events on tRNA?

The error rate is less than 1 mischarging event out of 10,000 amino acid charging events.

What is one codon for phenylalanine and its corresponding tRNA anticodon?

One codon for phenylalanine is UUU, and its corresponding tRNA anticodon is AAA.

What is the structure of the anticodon region on tRNA?

The anticodon region typically consists of a sequence of seven nucleotides: variable (N), modified purine (Pu*), X, Y, Z (e.g., AAA), and two pyrimidines (Py) in the 3' to 5' direction.

What genetic condition is caused by tandem triplet repeats in mRNA?

Huntington disease and other triplet expansion diseases are caused by tandem triplet repeats.

What are frameshift mutations and their effects?

Frameshift mutations result from the addition or deletion of a base, altering the reading frame of mRNA and potentially changing the resulting protein.

How does prokaryotic mRNA differ from eukaryotic mRNA in terms of coding regions?

Prokaryotic mRNA has multiple coding regions, each with its own initiation and termination codons, while eukaryotic mRNA has only one coding region.

What are the ribosomal structures involved in protein synthesis in prokaryotes and eukaryotes?

Prokaryotic ribosomes are 70S (30S + 50S) and eukaryotic ribosomes are 80S (40S + 60S), with structural differences.

What occurs during the initiation of protein synthesis in eukaryotes?

The 3' end of mRNA associates with the 5' end during translation initiation, and the anticodon for methionyl-tRNA binds to the AUG codon.

What is the role of initiator tRNA (tRNAi) in protein synthesis?

tRNAi recognizes the AUG initiation codon and is facilitated by IF-2-GTP in prokaryotes and eIF-2-GTP in eukaryotes.

How does the tRNAi differ between prokaryotes and eukaryotes?

In prokaryotes, tRNAi carries N-formylmethionine (fMet), while in eukaryotes, it carries methionine (Met).

What happens to the N-terminal methionine during translation?

The N-terminal methionine is usually removed before translation is completed.

What is the role of GTP in the initiation of protein synthesis?

GTP hydrolyzes to GDP during the initiation process, and eIF-2 can be reactivated by eIF-2B.

What components are assembled during the initiation of protein synthesis?

The components include 2 ribosomal subunits, mRNA, the first aminoacyl-tRNA, GTP, and initiation factors (IFs).

What is the Shine-Dalgarno sequence and its function?

The Shine-Dalgarno sequence is a purine-rich sequence located upstream of the AUG codon in E. coli, helping the ribosome recognize the initiation site.

What is gene silencing?

Gene silencing is the process of inhibiting gene expression, often through mechanisms that alter nucleotide sequences.

What are the consequences of altering a nucleotide sequence?

Altering a nucleotide sequence can lead to mutations, including frameshift mutations and gene silencing.

What is the significance of the ribosome in protein synthesis?

Ribosomes, composed of rRNA and protein, are essential for translating mRNA into proteins in both prokaryotic and eukaryotic organisms.

What is the role of initiation factors in protein synthesis?

Initiation factors (IFs) assist in the assembly of the translation machinery and the recognition of the initiation codon.

What forms base pairs to position the 30S subunit on mRNA?

The 5'-end of the mRNA and the 3'-end of the 16S rRNA.

What is the role of the 5'-Cap in mRNA translation?

The 40S ribosomal subunit binds close to the cap structure at the 5'-end and moves along the mRNA until it encounters AUG, requiring ATP.

What is cap-independent initiation in translation?

It occurs when the 40S subunit binds close to AUG without the need for the 5'-Cap.

What catalyzes peptide bond formation during protein synthesis?

Peptidyltransferase, an activity intrinsic to rRNA (ribozyme) of the large subunit.

What are the roles of EF1 and EF2 in elongation?

EF1 and EF2 are elongation factors; prokaryotic translocation requires EF-G-GTP, while eukaryotes use EF-2-GTP.

What are the three sites on the ribosome involved in protein synthesis?

The P site (peptidyl-tRNA), A site (aminoacyl-tRNA), and E site (exit site).

What does the Wobble hypothesis explain?

It describes nontraditional base-pairing between the first nucleotide of the anticodon and the last nucleotide of the codon.

What are the steps of bacterial protein biosynthesis?

1. Peptide anchored to P site; 2. Charged tRNA binds to A site; 3. Transpeptidation forms peptide bond; 4. Non-charged tRNA released from P site; 5. Translocation from A site to P site; 6. Uncharged tRNA exits from E site.

What happens during the termination of protein synthesis?

Termination occurs when a termination codon moves to the A site, and releasing factors bind to the stop codon.

What are the roles of release factors RF-1 and RF-2 in E. coli?

RF-1 recognizes UAA and UAG; RF-2 recognizes UGA and UAA, leading to hydrolysis of the bond linking the peptide to tRNA.

How do eukaryotes differ in termination codon recognition?

Eukaryotes have a single eRF that recognizes all termination codons.

What is the function of endoproteases in protein modification?

They trim proteins to generate functional forms.

What are the effects of covalent attachments on proteins?

They can affect protein function, such as phosphorylation, hydroxylation, and glycosylation.

What is ubiquitination and its role in protein degradation?

Ubiquitination marks defective or rapidly turning over proteins for destruction by the proteasome in an ATP-dependent manner.

What is a polysome?

A cluster of ribosomes translating a single mRNA strand.

What is the significance of the nascent polypeptide chain orientation?

It is oriented from the N-terminal to the C-terminal.

What is the role of water in the termination process of protein synthesis?

Water is involved in the hydrolysis of the peptidyl-tRNA complex.

What are the components released at the end of protein synthesis termination?

mRNA, newly synthesized protein, free tRNA, 40S and 60S subunits, RF1, GDP-bound RF3, and inorganic Pi.

What is the role of protein kinases and phosphatases in protein function?

Protein kinases catalyze phosphorylation, while phosphatases dephosphorylate proteins.

Where does hydroxylation occur in protein modification?

In the rough endoplasmic reticulum (RER).

What is glycosylation?

The process of adding sugar moieties to proteins to produce glycoproteins.

What is the importance of translation regulation?

It controls the rate and timing of protein synthesis in response to cellular needs.