Mastering the Central Dogma: DNA, RNA, Protein, and Repair Mechanisms

What is the central dogma of molecular biology?

The flow of genetic information from DNA to RNA to protein.

Where is DNA stored in a cell?

In the nucleus.

What is the role of RNA in the central dogma?

RNA acts as a messenger that carries the genetic information from DNA to the cytoplasm for protein synthesis.

What process converts DNA into RNA?

Transcription.

What is the template strand in transcription?

The strand of DNA that is read by RNA polymerase to synthesize RNA.

What is the informational strand of DNA?

The strand that has the same sequence as the RNA (with T's instead of U's) and contains the actual code information.

What experiment provided proof that RNA is synthesized in the nucleus?

The pulse-chase experiment.

What radioactive substance was used in the pulse-chase experiment to trace RNA?

Tritiated uridine.

What are the three key structural differences between RNA and DNA?

1. RNA has ribose sugar; DNA has deoxyribose. 2. RNA uses uracil instead of thymine. 3. RNA is usually single-stranded.

How does the hydroxyl group in RNA affect its structure?

It allows RNA to fold into complex shapes and act as a nucleophile.

What is a ribozyme?

An RNA molecule that can act as an enzyme.

What is the significance of uracil in RNA?

Uracil can pair with adenine and also form a stable pair with guanine, allowing for more complex RNA structures.

What type of secondary structures can RNA form?

Stem loops and hairpins.

What is transcription in bacteria?

The process of making RNA from a DNA template in prokaryotic cells.

What happens during the 'pulse' phase of the pulse-chase experiment?

Cells are exposed to a radioactive substance that incorporates into newly synthesized RNA.

What happens during the 'chase' phase of the pulse-chase experiment?

Cells are flooded with non-radioactive uridine, diluting the radioactive RNA.

What is the role of tRNA in protein synthesis?

tRNA carries amino acids to the ribosome and matches them to the corresponding codons in mRNA.

Why is RNA considered a multi-tool in the cell?

Because it serves informational, structural, and catalytic roles.

What is the significance of RNA being single-stranded?

It allows for more complex folding and the formation of secondary structures.

What is the function of the ribose sugar in RNA?

It contributes to RNA's ability to fold into complex structures and participate in chemical reactions.

What is the main function of RNA polymerase?

To synthesize RNA from a DNA template during transcription.

What is the difference between coding and non-coding strands of DNA?

The coding strand has the same sequence as the RNA, while the non-coding strand is the template for RNA synthesis.

How does RNA's ability to form complex structures benefit the cell?

It allows RNA to perform various functions, including catalysis and regulation of gene expression.

What is the role of the cytoplasm in protein synthesis?

It is where ribosomes translate mRNA into proteins.

What is the significance of the 2' hydroxyl group in RNA?

It allows RNA to have a more reactive and flexible structure compared to DNA.

What is the primary role of RNA polymerase in bacterial transcription?

To initiate transcription by binding to the correct starting place on the DNA.

What does 'cis-acting' refer to in the context of bacterial transcription?

It refers to signals on the same DNA molecule that are necessary for transcription initiation.

What is the transcriptional start site (TSS) in bacterial transcription?

The position on the DNA where transcription begins, designated as plus one.

How did researchers identify the core promoter in bacterial genes?

By using multiple sequence alignment to find conserved sequences upstream of the TSS.

What are the two conserved sequences identified in bacterial promoters?

One around the negative 35 position and another around the negative 10 position.

What is a holoenzyme in the context of RNA polymerase?

The complete active complex that includes the core enzyme and the sigma factor.

What is the function of the sigma factor in bacterial transcription?

To guide the RNA polymerase to the correct promoter sequence.

What happens to the sigma factor once transcription begins?

It usually detaches from the RNA polymerase after initiation.

What is the role of Rho protein in transcription termination?

It acts as a helicase that unwinds the RNA-DNA hybrid to terminate transcription.

What is the RUT site in bacterial transcription?

A specific cis-acting sequence on the RNA that Rho protein binds to for termination.

What is rho-independent termination?

A method of transcription termination that relies solely on the RNA sequence forming a hairpin structure.

How does the hairpin structure contribute to rho-independent termination?

It causes RNA polymerase to pause, leading to destabilization of the RNA-DNA complex.

What is the significance of the stretch of A's in rho-independent termination?

It pairs with U's in the RNA, which are weaker connections, facilitating the release of the RNA.

What complicates transcription in eukaryotes compared to bacteria?

The presence of a nuclear membrane requires additional transport and processing systems for RNA.

How many distinct RNA polymerases do eukaryotes have, and what is their purpose?

Three distinct RNA polymerases, each specialized for different types of RNA.

What is the role of RNA polymerase I in eukaryotic transcription?

It is primarily responsible for synthesizing ribosomal RNA (rRNA).

What is the importance of processing in eukaryotic transcription?

It involves modifications to RNA, such as splicing and capping, necessary for functional mRNA.

What is a transcription bubble?

The region of unwound DNA where RNA synthesis occurs during transcription.

What is the function of the transcriptional termination signal in bacteria?

To signal the end of transcription and facilitate the release of the newly synthesized RNA.

What is the difference between rho-dependent and rho-independent termination?

Rho-dependent requires the Rho protein, while rho-independent relies on RNA structure alone.

What happens during the pause of RNA polymerase in rho-independent termination?

The stress from the hairpin structure and weak base pairs lead to the release of RNA.

What is the role of ATP in rho-dependent termination?

It provides energy for the Rho protein to chase and unwind the RNA-DNA hybrid.

What is the significance of sigma factors in bacterial transcription regulation?

Different sigma factors allow bacteria to respond to various environmental stresses by activating specific genes.

What is the role of the core RNA polymerase during transcription?

It synthesizes the RNA strand by adding nucleotides complementary to the DNA template.

What does RNA polymerase I transcribe?

It transcribes the genes for the major ribosomal RNAs: 18S, 5.8S, and 28S RNAs.

Where does RNA polymerase I operate?

Exclusively in the nucleolus, a dense region within the nucleus.

What is the primary function of RNA polymerase II?

It transcribes all the genes that code for proteins, producing messenger RNAs (mRNAs) and most small non-coding RNAs.

What types of RNAs does RNA polymerase II produce?

mRNAs, microRNAs, and small nuclear RNAs (snRNAs) involved in splicing.

What is the role of RNA polymerase III?

It handles the transcription of short, essential non-coding RNAs, including transfer RNAs (tRNAs) and 5S ribosomal RNA.

What is a key difference between eukaryotic and bacterial transcription initiation?

Eukaryotes require a complex of general transcription factors (GTFs) for initiation, while bacteria use a sigma factor.

What are general transcription factors (GTFs)?

Proteins that assist RNA polymerase II in initiating transcription, labeled as TFII, TFIIG, TFID, etc.

What is the TATA box?

A core promoter element located around -30 that is recognized by the TATA binding protein (TBP) during transcription initiation.

How many human protein-coding genes have a clear TATA box?

Only about 25% of human protein-coding genes have a clear TATA box.

What initiates the transcription process in eukaryotes?

The process usually starts with the binding of the TATA binding protein (TBP) to the promoter.

What is the function of TFIIH in transcription?

TFIIH has helicase activity that unwinds DNA around the transcription start site (TSS), creating a transcription bubble.

What is the role of enhancers and silencers in gene regulation?

Enhancers boost transcription, while silencers reduce it, often acting from a distance by looping DNA to interact with GTFs.

What is the C-terminal domain (CTD) of RNA polymerase II?

A long, flexible tail made of repeats of a 7-amino acid sequence that coordinates RNA processing.

What does the phosphorylation pattern on the CTD indicate?

It acts as a code that determines which processing factors can bind and when during transcription.

What happens to the CTD when RNA polymerase II first binds the promoter?

The CTD is mostly unphosphorylated at this stage.

What is the first modification that occurs after transcription begins?

The addition of a 5' cap to the RNA.

What is the structure of the 5' cap?

A modified guanine nucleotide added backwards, linked by a 5' to 5' triphosphate linkage.

What are the functions of the 5' cap?

It protects RNA from degradation and is essential for mRNA export from the nucleus and initiation of translation.

What is splicing in RNA processing?

The removal of non-coding introns and joining of coding exons in the pre-mRNA.

When does splicing occur?

It often occurs co-transcriptionally, while RNA is still being synthesized.

What sequences are crucial for recognizing intron-exon boundaries?

The five-foot splice site (usually GU), the three-foot splice site (usually AG), and an internal branch point adenine (A) residue.

What is the spliceosome?

A large complex made of proteins and small nuclear RNAs (snRNAs) that performs splicing.

Which snRNAs are involved in the spliceosome?

U1, U2, U4, U5, and U6.

What role do snRNAs play in splicing?

The RNA components perform critical recognition and catalysis during splicing.

How does U1 snRNA contribute to splicing?

It base pairs with the conserved five-foot splice site sequence.

What happens during the first step of splicing?

The 2-foot hydroxyl group of the branch point adenine acts as a nucleophile, attacking the phosphate at the five-foot splice site.

What is formed during the first step of splicing?

A lariat intermediate, a loop structure held together by a unique 5' to 2' phosphodiester linkage.

What occurs in the second step of splicing?

The newly freed 3' OH group of the upstream exon attacks the phosphate at the three-foot splice site, joining the exons together.

What is the function of exon splicing enhancers (ESEs)?

They bind specific transacting helper proteins to flag exons for the spliceosome, ensuring accurate splicing.

What is cleavage and polyadenylation in mRNA processing?

The process that defines the end of mRNA, involving cutting the RNA and adding a poly A tail.

What sequences are recognized during cleavage and polyadenylation?

The AAUAAA polyadenylation signal (PAS) and a downstream GU-rich sequence.

What is the role of CPSF and CSTF in mRNA processing?

CPSF binds to the PAS, and CSTF binds to the GU-rich region, forming a complex that recruits endonuclease enzymes for cleavage.

What does poly A polymerase do?

It adds adenine nucleotides to the 3' end of the mRNA, forming a poly A tail.

What is the typical length of a poly A tail?

About 50 to 250 adenine nucleotides.

What are the functions of the poly A tail?

It provides stability, protects the 3' end from degradation, and is crucial for nuclear export and translation initiation.

How does RNA polymerase II stop transcription?

The uncapped 5' end of the trailing RNA is recognized by the exonuclease XRN2, which degrades the RNA until it catches up with RNA polymerase II, causing termination.

What is the significance of group 2 self-splicing introns?

They can perform splicing reactions independently, providing evidence that RNA itself can act as a catalyst.

What is alternative splicing?

The process by which different combinations of exons are joined to produce multiple protein isoforms from a single gene.

What is the role of transacting proteins in splicing?

They assist in the recognition of splice sites and enhance the accuracy of splicing.

What happens to the intron after splicing?

The intron lariat is released and subsequently degraded.

What is the role of the 2-foot hydroxyl group in splicing?

It acts as a nucleophile in the transesterification reactions during splicing.

What is the final product of mRNA processing?

A mature mRNA that is capped, spliced, polyadenylated, and ready for export to the cytoplasm.

What is the role of XRN2 in RNA degradation?

XRN2 recognizes uncapped RNA ends and rapidly degrades the remaining RNA strand.

What initiates the termination of transcription?

The collision between XRN2 and the RNA polymerase complex causes Pol 2 to dissociate from the DNA template.

What is the challenge after mRNA processing?

The challenge is translation, converting nucleotides into amino acids.

Who proposed the triplet code for amino acids?

George Gamow proposed that the genetic code is a triplet code based on the number of bases and amino acids.

What is the significance of the triplet code?

It allows for 64 possible combinations, which is sufficient to code for 20 amino acids.

What is a classic example of a genetic mutation affecting amino acids?

Sickle cell anemia, where one DNA base change causes one amino acid change in hemoglobin.

What did Crick and Brenner's experiments demonstrate?

They showed that insertions or deletions of bases can cause frame shifts, while inserting or deleting three bases restores the reading frame.

What is the wobble hypothesis?

The wobble hypothesis states that the third base of a codon can tolerate non-standard base pairing with the tRNA anticodon.

How does the wobble position affect tRNA usage?

It allows one tRNA to recognize multiple codons, reducing the total number of tRNAs needed.