OIA1003 NUCLEIC ACIDS II

Transcription

The process of synthesizing RNA from a DNA template.

Central Dogma of Molecular Biology

DNA → RNA → Protein, illustrating genetic information flow.

RNA Polymerase

The enzyme responsible for RNA synthesis from a DNA template.

Messenger RNA (mRNA)

Carries genetic instructions from DNA to ribosomes for protein synthesis.

Ribosomal RNA (rRNA)

Forms the structural and functional components of ribosomes.

Transfer RNA (tRNA)

Delivers amino acids to the ribosome during translation.

Small Nuclear RNA (snRNA)

Involved in RNA splicing.

MicroRNA (miRNA)

Regulates gene expression via RNA interference (RNAi).

Template Strand

The DNA strand used by RNA polymerase for RNA synthesis.

Coding (Sense) Strand

The non-template DNA strand, which has the same sequence as mRNA (except T → U substitution).

Promoter Region

A specific DNA sequence where RNA polymerase binds to initiate transcription.

Consensus Sequences

Conserved promoter regions:

Prokaryotes: -35 sequence (TTGACA) & Pribnow box (-10, TATAAT).

Eukaryotes: TATA box (-25), CAAT box (-75), GC box.

Prokaryotic RNA Polymerase

A single RNA polymerase transcribes all RNA types.

Holoenzyme = Core enzyme + Sigma factor.

Eukaryotic RNA Polymerases

RNA Pol I: rRNA synthesis (28S, 18S, 5.8S).

RNA Pol II: mRNA, snRNA, miRNA synthesis.

RNA Pol III: 5S rRNA and all tRNA synthesis.

Sigma Factor (σ)

Prokaryotic transcription initiation factor, helps RNA polymerase bind to the promoter.

Initiation

RNA polymerase binds to promoter, forms a transcription bubble, and starts RNA synthesis.

Elongation

RNA polymerase adds ribonucleotides (NTPs) in the 5’ → 3’ direction.

Termination

RNA synthesis stops when RNA polymerase reaches a termination signal.

Rho-Independent Termination

RNA forms a GC-rich hairpin loop followed by a UUU sequence, causing RNA polymerase to dissociate.

Rho-Dependent Termination

The Rho protein (ATP-dependent helicase) binds RNA, moves toward RNA polymerase, and separates the RNA-DNA hybrid.

5’ Capping

Addition of 7-methylguanosine (m7G) to the 5’ end of mRNA for stability and ribosome recognition.

3’ Polyadenylation (Poly-A Tail)

Poly(A) polymerase adds 100-200 adenine residues at the 3’ end to protect mRNA from degradation.

RNA Splicing

Introns (non-coding) are removed and exons (coding) are joined by spliceosomes (snRNPs).

Alternative Splicing

Allows a single gene to encode multiple proteins.

RNA Editing

Modification of mRNA bases (e.g., A → I by adenosine deaminase).

Nuclear Export

Mature mRNA is exported from the nucleus to the cytoplasm for translation.

mRNA Stability

Poly-A tail and 5’ cap prevent degradation.

Prokaryotes

Transcription occurs in the cytoplasm.

No introns, no mRNA modifications.

Polycistronic mRNA (multiple genes in one mRNA).

Eukaryotes

Transcription occurs in the nucleus.

Introns must be spliced out.

Monocistronic mRNA (one gene per mRNA).

Rifampin (Rifampicin)

Inhibits bacterial RNA polymerase, used for tuberculosis treatment.

Actinomycin D (Dactinomycin)

Intercalates DNA, blocking transcription

α-Amanitin (Toxin from Death Cap Mushroom)

Inhibits eukaryotic RNA polymerase II, causing severe hepatotoxicity.

Cordycepin (3'-Deoxyadenosine)

Terminates RNA chain elongation.

RNA Virus Mutations

RNA viruses mutate more frequently than DNA viruses due to lack of proofreading

Examples of RNA Viruses

Ebola, Rabies, Hepatitis C, Polio, Measles, SARS-CoV-2.

Ribozymes

RNA molecules with enzymatic activity, e.g., self-splicing introns.

Long Non-Coding RNAs (lncRNAs)

Regulate gene expression without coding for proteins.

siRNA & miRNA (RNA Interference - RNAi)

siRNA (small interfering RNA): Targets mRNA for degradation.

miRNA (microRNA): Suppresses gene expression post-transcriptionally.