Protein Synthesis: tRNA Charging and Ribosome Structure

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Questions and Answers

What direction do new DNA strands grow during synthesis?

Only in a circular direction

3’ to 5’ direction

In both 5’ to 3’ and 3’ to 5’ directions

5’ to 3’ direction (correct)

What is the primary role of DNA ligase during DNA replication?

Catalyze the final phosphodiester linkage between fragments (correct)

Unwind the DNA helix

Add nucleotides to the leading strand

Replace RNA primers with DNA

Which strand is synthesized continuously during DNA replication?

Both strands are synthesized non-continuously

Lagging strand

Both leading and lagging strands

Leading strand (correct)

What defines a spontaneous mutation?

It occurs due to internal chemical reactions without outside influence. Signup and view all the answers

What is the role of Topoisomerase IV in prokaryotic replication?

Decatenate newly replicated DNA from old DNA Signup and view all the answers

What do induced mutations result from?

Agents from outside the cell, such as mutagens Signup and view all the answers

What occurs if a base alteration is not repaired before DNA replication?

A spontaneous mutation may result Signup and view all the answers

What is a characteristic of the lagging strand during DNA replication?

It is created in Okazaki fragments Signup and view all the answers

What is the role of introns in eukaryotic gene expression?

They are noncoding regions transcribed but removed before translation. Signup and view all the answers

What defines the reading frame during translation?

The start codon in the mRNA sequence. Signup and view all the answers

What is a silent mutation?

A substitution that does not alter the amino acid sequence. Signup and view all the answers

How does a deletion of one nucleotide affect protein synthesis compared to a deletion of three nucleotides?

It usually causes a reading frame shift, altering the entire protein. Signup and view all the answers

What best describes the genetic code?

Redundant but not ambiguous. Signup and view all the answers

What type of mutation results in a shortened protein due to a stop codon?

Nonsense mutation. Signup and view all the answers

Which mutation is primarily responsible for changing one amino acid to another in a protein?

Missense mutation. Signup and view all the answers

What happens if a deletion of three nucleotides occurs in the DNA sequence?

It removes one complete codon from the sequence. Signup and view all the answers

What type of mutation changes a stop codon to a sense codon, resulting in the addition of extra amino acids?

Loss-of-stop mutation Signup and view all the answers

What is the effect of a frameshift mutation during protein synthesis?

It alters the mRNA reading frame. Signup and view all the answers

Which type of RNA carries amino acids to the ribosome for protein assembly?

tRNA Signup and view all the answers

What is the primary role of rRNA in the cell?

To catalyze peptide bond formation Signup and view all the answers

What happens to proteins produced due to frameshift mutations?

They may contain extra or missing amino acids. Signup and view all the answers

How does tRNA translate mRNA codons into amino acids?

Through base pairing of anticodons Signup and view all the answers

Which mutation leads to a complete change in the protein structure due to changes in the reading frame?

Frameshift mutation Signup and view all the answers

Which option correctly identifies the role of mRNA?

To serve as a copy of a gene for translation. Signup and view all the answers

What is the role of the promoter in transcription initiation?

It serves as the binding site for RNA polymerase. Signup and view all the answers

Which component prevents transcription when lactose is absent?

Repressor protein Signup and view all the answers

How does lactose affect the activity of the repressor protein?

Lactose binds to the repressor and changes its shape. Signup and view all the answers

What is an operon?

A cluster of genes that operate with a shared promoter. Signup and view all the answers

What is the primary function of transcription factors in gene expression?

To either promote or inhibit transcription. Signup and view all the answers

What happens when lactose is present and binds to the repressor?

The repressor changes shape and releases from the operator. Signup and view all the answers

In the context of operons, what does the term 'negative regulation' refer to?

The prevention of gene transcription by repressor proteins. Signup and view all the answers

What initiates the binding of RNA polymerase to the promoter?

The removal of the repressor protein. Signup and view all the answers

What is the role of Aminoacyl tRNA synthetase in the translation process?

To bind specific amino acids to their corresponding tRNA. Signup and view all the answers

Which site of the ribosome is where the charged tRNA first binds during translation?

A site Signup and view all the answers

During translation elongation, what happens to the tRNA that was previously in the P site?

It translocates to the E site. Signup and view all the answers

Which of the following accurately describes the initiation phase of translation?

The initiation complex is formed with a charged tRNA and small ribosomal subunit. Signup and view all the answers

Which step in translation elongation requires energy?

Entering of charged tRNA into the A site. Signup and view all the answers

What is the first amino acid incorporated during translation?

Methionine Signup and view all the answers

Which of the following best describes a characteristic of the ribosomal large subunit?

It catalyzes peptide bond formation. Signup and view all the answers

How does the ribosome recognize the start codon in prokaryotes?

By using a sequence called the Shine-Dalgarno. Signup and view all the answers

Study Notes

Aminoacyl tRNA Synthetase

An enzyme that charges tRNA
Each tRNA synthetase only binds to one specific tRNA and amino acid
The amino acid fits perfectly in a space on the enzyme, and the tRNA also fits in a specific spot

Charging tRNA

tRNA must be "charged" with an attached amino acid to participate in protein synthesis
tRNA charging requires energy

Ribosome Structure

A large subunit with three binding sites:
- A (aminoacyl tRNA) site: binds the anticodon of charged tRNA
- P (peptidyl tRNA) site: where the tRNA with the growing polypeptide chain resides
- E (exit) site: where the uncharged tRNA exits

Translation

Three steps:
- Initiation: the small ribosomal subunit binds to mRNA and the initiator charged tRNA, forming an initiation complex
- Elongation: new amino acids are added to the growing polypeptide chain
- Termination: the process stops when a stop codon is reached

Initiation

The small ribosomal subunit binds to mRNA and the initiator charged tRNA
In prokaryotes, the small subunit binds to the Shine-Dalgarno sequence on mRNA
In eukaryotes, the small subunit binds to the 5' cap
The start codon is AUG
The first amino acid is always methionine, which can be removed after translation

Elongation

A new charged tRNA enters the A site, requiring energy
The large subunit catalyzes the transfer of the growing polypeptide chain from the P site to the A site, which does not require energy
The uncharged tRNA moves to the E site, and the tRNA with the growing chain moves to the P site, requiring energy

Termination

The ribosome encounters a stop codon
A release factor binds to the stop codon and triggers the release of the polypeptide chain
The ribosome dissociates from the mRNA

DNA Replication

DNA is replicated semi-conservatively, each new strand contains one old strand and one new strand
Replication occurs at a replication fork, where the DNA strands are separated
The leading strand is synthesized continuously, in the same direction as the unwinding of the DNA
The lagging strand is synthesized discontinuously, in the opposite direction from the unwinding of the DNA, forming Okazaki fragments

Okazaki Fragments

Short DNA fragments that are synthesized on the lagging strand
Named after Reiji Okazaki

Replacing Primer Fragments

DNA polymerase III adds nucleotides to the 3' end of the new primer, until reaching the primer of the previous fragment
DNA polymerase I then replaces the primer with DNA
DNA ligase then joins the newly synthesized DNA fragments

Replication Termination

In prokaryotes, Topoisomerase IV decatenates the newly replicated DNA from the old DNA

Mutations

Heritable changes in DNA sequences
Can have beneficial, harmful, or neutral effects on the protein

Spontaneous Mutations

Occur without outside influence
Can be caused by internal chemical reactions that alter bases
Example: deamination of cytosine to uracil

Induced Mutations

Caused by external mutagens
Example: radiation

Transcription Initiation

Occurs at specific DNA sequences called promoters
RNA polymerase binds to the promoter and starts transcription, creating an RNA copy of the DNA

Prokaryotic Gene Expression

Prokaryotic genes are often organized into operons
Operon: a gene cluster with a single promoter, including:
- A promoter
- Two or more structural genes
- An operator

Transcription Factors

Regulatory proteins that bind to the operator and affect transcription
Activators increase transcription
Repressors decrease transcription

Lac Operon

Inducible system that is only turned on when lactose is present
When lactose is absent, the repressor binds to the operator and prevents transcription
When lactose is present, lactose binds to the repressor, changing its shape and preventing it from binding to the operator
This allows RNA polymerase to bind to the promoter and transcribe the lac operon genes

RNA Processing

In eukaryotes, pre-mRNA is processed before it is translated
Introns (noncoding regions) are removed
Exons (coding regions) are spliced together

Central Dogma of Molecular Biology

Describes the flow of genetic information in a cell
DNA is transcribed to RNA
RNA is translated to protein

Codons and Translation

Three nucleotides (a codon) code for a specific amino acid
The start codon defines the reading frame
Shifts in the reading frame will change the codons and amino acids specified

Types of Mutations

Silent mutation: a base substitution that results in a codon for the same amino acid
Missense mutation: a base substitution that results in a codon for a different amino acid
Nonsense mutation: a base substitution that results in a stop codon
Frameshift mutation: an insertion or deletion of a base pair that alters the reading frame
Loss-of-stop mutation: a base substitution that changes a stop codon to a sense codon

Different Types of RNA

mRNA (messenger RNA): carries genetic information from DNA to ribosomes
tRNA (transfer RNA): carries amino acids to the ribosome
rRNA (ribosomal RNA): forms part of the ribosome structure

tRNA Structure

tRNA has a cloverleaf structure
One end has an anticodon that can base pair with a specific mRNA codon
The other end binds to an amino acid

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Description

Explore the critical processes involved in protein synthesis, focusing on aminoacyl tRNA synthetase and the ribosome structure. Understand how tRNA is charged with amino acids and the role of various binding sites in the ribosome during translation. This quiz covers the initiation, elongation, and termination phases of protein synthesis.