Slide 1: Molecular Basis of Inheritance - Structure of mature mRNA

• mRNA (messenger RNA) is a crucial molecule involved in the process of gene expression.
• It carries the genetic information from DNA in the nucleus to the ribosomes in the cytoplasm.
• The structure of mature mRNA is adapted for efficient protein synthesis.

Slide 2: Components of mRNA

• mRNA is composed of three main components:
  • 5’ Untranslated Region (UTR): Contains regulatory sequences and the translation start codon.
  • Coding Region: Contains nucleotide triplets, called codons, which specify the amino acid sequence of the protein.
  • 3’ UTR: Contains sequences involved in the termination of translation and mRNA degradation.

Slide 3: Structure of mRNA

• The structure of mature mRNA can be divided into three parts:
  1. Cap Structure: A modified guanine nucleotide is added at the 5’ end, forming a 5’ cap. This cap protects the mRNA from degradation and assists in ribosome binding.
  2. Coding Region: Contains a series of codons that specify the sequence of amino acids in the protein.
  3. Poly-A Tail: A string of adenine nucleotides is added at the 3’ end, forming a poly-A tail. This tail provides stability to the mRNA and facilitates its export from the nucleus.

Slide 4: 5’ Untranslated Region (UTR)

• The 5’ UTR is found at the 5’ end of mature mRNA.
• It contains regulatory sequences involved in various processes, such as:
  • Initiation of translation
  • mRNA stability
  • Localization and transport of mRNA

Slide 5: Coding Region

• The coding region of mRNA is the portion that is translated into a protein.
• It is composed of a series of nucleotide triplets called codons.
• Each codon corresponds to a specific amino acid or a stop signal.
• For example, the codon AUG codes for the amino acid methionine, which is often the start codon for protein synthesis.

Slide 6: Reading Frame

• The reading frame of an mRNA determines how the codons are interpreted during translation.
• There are three possible reading frames in an mRNA molecule.
• The correct reading frame is established by the start codon and is maintained until a stop codon is reached.

Slide 7: Open Reading Frame (ORF)

• An open reading frame (ORF) is a coding region that contains a start codon followed by one or more codons and ends with a stop codon.
• The ORF represents a potential gene or protein-coding sequence.

Slide 8: 3’ Untranslated Region (UTR)

• The 3’ UTR is found at the 3’ end of mature mRNA.
• It contains sequences involved in mRNA stability, termination of translation, and the degradation of mRNA.
• It also plays a role in the post-transcriptional regulation of gene expression.

Slide 9: Cap-Dependent Translation Initiation

• Cap-dependent translation initiation is the most common mechanism of translation initiation in eukaryotes.
• The 5’ cap structure interacts with translation initiation factors and ribosomes to facilitate the binding of ribosomes to the mRNA.
• This process ensures efficient translation of the mRNA into a protein.

Slide 10: Poly-A Tail

• The poly-A tail is a string of adenine nucleotides added at the 3’ end of mature mRNA.
• It enhances the stability of the mRNA and protects it from degradation.
• The poly-A tail also plays a role in the export of mRNA from the nucleus and in the regulation of mRNA translation and decay.

11. Role of 5’ Untranslated Region (UTR)

• Contains regulatory sequences that help in the initiation of translation.
• Several upstream open reading frames (uORFs) present in the 5’ UTR can control the protein expression level.
• Example: The 5’ UTR of the ATF4 mRNA contains uORFs that regulate its translation in response to stress signals.

12. Role of Coding Region

• Contains codons that specify the sequence of amino acids in a protein.
• The genetic code is universal, with the same codons representing the same amino acids across species.
• Example: The codon sequence AUG specifies the amino acid methionine in all organisms.

13. Role of 3’ Untranslated Region (UTR)

• Contains sequences that influence mRNA stability and degradation.
• Binding sites for regulatory proteins and microRNAs are often found in the 3’ UTR.
• Example: The binding of microRNAs to the 3’ UTR of target mRNA leads to translational repression or mRNA degradation.

14. Translation Initiation Factors

• Proteins that assist in the binding of ribosomes to the mRNA and the initiation of translation.
• Examples: eIF4E, eIF4G, and eIF4A form a complex that interacts with the 5’ cap structure.
• eIF2 plays a key role in the recognition of the start codon and the recruitment of the small ribosomal subunit.

15. Ribosomes and Translation

• Ribosomes are large complexes of proteins and rRNA that carry out translation.
• Consist of a small and large subunit, which come together on the mRNA during translation initiation.
• The large subunit has the peptidyl transferase activity required for peptide bond formation between amino acids.

16. Start Codon

• The start codon serves as the initiation signal for translation.
• The most common start codon is AUG, which codes for methionine.
• Alternative start codons, such as GUG and UUG, can also be used in certain contexts.

17. Stop Codons

• Stop codons (UAA, UAG, and UGA) signal the termination of translation.
• They do not code for any amino acid and do not have tRNAs associated with them.
• Release factors recognize the stop codons and promote the release of the newly synthesized protein.

18. Reading Frame Shifts

• Reading frame shifts occur when there is a deletion or insertion of nucleotides in the coding region.
• This alters the sequence of codons and can lead to a completely different protein being synthesized.
• Example: Frameshift mutations can result in severe genetic diseases, such as Duchenne muscular dystrophy.

19. Alternative Splicing

• Alternative splicing is a mechanism that generates multiple mRNAs and proteins from a single gene.
• Different combinations of exons can be included or excluded during mRNA processing.
• Example: The Dscam gene in Drosophila undergoes extensive alternative splicing, resulting in over 38,000 different protein isoforms.

20. Regulation of mRNA Stability

• The stability of mRNA can be regulated by various factors, including RNA-binding proteins and miRNAs.
• Stabilizing elements in the 3’ UTR can prevent mRNA degradation.
• Example: AU-rich elements (AREs) in the 3’ UTR of many mRNAs determine their stability and turnover rate.

Slide 21: Regulation of mRNA Translation

• Translation of mRNAs can be regulated at various levels to control gene expression.
• Regulatory factors can influence the initiation, elongation, and termination of translation.
• Examples of regulation include:
  • Binding of regulatory proteins to specific RNA sequences
  • Interference of translation initiation by microRNAs
  • Alteration of ribosomal subunit availability or activity

Slide 22: Post-transcriptional Modifications

• mRNA molecules undergo post-transcriptional modifications before they are fully functional.
• Modifications include:
  • Addition of a 5’ cap and a 3’ poly-A tail
  • Splicing of introns
  • Editing of mRNA sequences by enzymes

Slide 23: Splicing of Introns

• Introns are non-coding regions within a gene that are transcribed into mRNA but are later removed.
• Splicing is the process by which introns are removed and exons are joined together.
• Splicing is catalyzed by the spliceosome, a complex of proteins and small nuclear RNAs (snRNAs).
• Alternative splicing can lead to the production of multiple protein isoforms from a single gene.

Slide 24: RNA Editing

• RNA editing is a post-transcriptional modification that changes the nucleotide sequence of an mRNA molecule.
• It is carried out by enzymes called RNA-editing enzymes.
• The most common form of RNA editing is the conversion of adenosine (A) to inosine (I) within mRNA molecules.
• RNA editing can affect the function and properties of encoded proteins.

Slide 25: Non-coding RNAs

• Non-coding RNAs (ncRNAs) are RNA molecules that do not code for proteins.
• They have various functions in the cell, including:
  • Regulating gene expression
  • Controlling mRNA stability and translation
  • Mediating RNA splicing and editing
• Examples of ncRNAs include microRNAs, long non-coding RNAs (lncRNAs), and small interfering RNAs (siRNAs).

Slide 26: MicroRNAs (miRNAs)

• MicroRNAs (miRNAs) are small ncRNAs that negatively regulate gene expression.
• They base-pair with target mRNAs, leading to mRNA degradation or translational repression.
• miRNAs play important roles in developmental processes, disease, and cellular homeostasis.
• Dysregulation of miRNA expression has been implicated in various diseases, including cancer.

Slide 27: Long Non-coding RNAs (lncRNAs)

• Long non-coding RNAs (lncRNAs) are RNA molecules that are longer than 200 nucleotides and do not code for proteins.
• They have diverse functions and can interact with DNA, RNA, and proteins.
• lncRNAs play roles in gene expression regulation, chromatin organization, and cellular processes.
• Dysregulation of lncRNAs has been associated with a wide range of diseases.

Slide 28: Small Interfering RNAs (siRNAs)

• Small interfering RNAs (siRNAs) are small double-stranded RNA molecules that regulate gene expression.
• They are involved in a process called RNA interference (RNAi).
• siRNAs guide the degradation of target mRNAs or inhibit their translation by binding to complementary sequences.
• RNAi is a powerful tool for gene silencing and has applications in research and therapy.

Slide 29: Riboswitches

• Riboswitches are RNA structures located in the untranslated regions of certain mRNAs.
• They can bind small molecules and regulate gene expression.
• Binding of the small molecule to the riboswitch induces a conformational change that affects mRNA stability or translation.
• Riboswitches are involved in the regulation of metabolic pathways in bacteria and some eukaryotes.

Slide 30: Inference of Protein Function from mRNA Structure

• The structure and sequence of mRNA can provide insights into the function of the encoded protein.
• Conserved sequence motifs in the coding region can indicate functional domains or regions.
• The presence of regulatory elements in the UTRs can suggest post-transcriptional regulation.
• Comparative genomics and computational analysis are used to infer protein function from mRNA structure and sequence data.