RNA Processing and Intro to Translation

Exam 2 is next week, Wednesday through Friday (Mar. 12-14).
- Ensure timely CBTF reservation.
Friday, March 14 is the drop deadline.
Lectures:
- Monday: Concludes Exam 2 material.
- Wednesday (March 12): Exam 3 material.
- Friday the 14th: No class.
Practice Exam 2: Available with a board for questions.
Student hours:
- Today 4:00-5:30 in 124 Burrill Hall.
- Friday 9:30-11:00 via Zoom.

Introns exhibit significant length variation (tens to tens of thousands of bases).
Occurs post-transcriptionally but usually concurrently with transcription.
Completion is mandatory before mRNA export from the nucleus.
Splice point conservation: Sequences at intron ends are conserved, marking splice points. The remaining intron sequence may have regulatory functions.
Mechanism: Carried out by snRNPs (small nuclear RNA molecules and proteins). These precisely remove introns and join exon ends.

Consequences: Leads to non-functional proteins.
Thalassemias: Often results from inaccurate intron splicing affecting hemoglobin production.
Mutations:
- DNA mutations are carried over to RNA.
- Disrupt snRNP recognition of intron/exon junctions.
- Intron retention occurs.
False splice sites: snRNPs may utilize incorrect splice sites, leading to the removal of necessary exon sequences and defective protein synthesis.

Human genome: Contains approximately 21,000 genes, which is less than initially hypothesized.
Gene count: Not substantially more than simpler organisms like fruit flies and nematode worms.
Gene size consistency: Coding region size is generally similar across different organisms.
Gene assembly: Human genes utilize extensive combinatorial arrangements of coding regions through alternative splicing.

Exon usage: Not all exons in primary mRNA are necessarily included in the final transcript.
Outcome: Different mature mRNAs are produced, leading to different proteins.
Prevalence: Affects 50% to 90% of human genes.
- Transcript variability: A gene can produce from 2 to thousands of different transcripts.
- Human average: Approximately 3-4 different transcripts per gene.
Protein diversity: Accounts for the production of around 100,000 proteins from 21,000 genes via different combinations of exons.

RNA 5’-triphosphatase: Removes a phosphate $\text{P}_i$ .
Guanylyl transferase: Hydrolyzes GTP, attaching GMP to the 5’ end and releasing $\text{PP}_i$ .
Methyltransferase: Attaches a methyl group to the 5’ end.

Poly(A) tail: Added post-transcriptionally to the 3′ end by poly-A polymerase to enhance stability and translation efficiency.

Start signal: Facilitates recognition of the mRNA as the starting point for translation.
Stability: Offers protection against degradation by RNases, thereby enhancing mRNA stability.

Stability: Provides temporary stability by protecting against RNase degradation.
Translation efficiency: Aids in efficient protein production from a single mRNA molecule.

Includes:
- Capping at 5' end.
- Poly-A addition at 3' end.
- Excision and splicing.

Protein synthesis: mRNA converted into protein.
Genetic information: Nucleotide sequence (ACGU) contains protein synthesis instructions.
- Building blocks: Proteins are composed of amino acids.

Codon-amino acid relationship: No direct one-to-one relationship between a single nucleotide and an amino acid.

extensive

Limitations of one-to-one coding: If each nucleotide coded for one amino acid, only 4 amino acids could be specified, insufficient for the 20 required.
Two-nucleotide combinations:
- Possibilities: $4^2 = 16$ combinations.
- Insufficiency: Still not adequate to code for 20 amino acids.

Three-nucleotide combinations:
- Calculation: $4 \times 4 \times 4 = 4^3 = 64$
- Adequacy: Minimum number of nucleotides required to code for all 20 amino acids.

Artificial mRNA synthesis: Created a synthetic mRNA with 60 Uracils—5′-UUUUUUUUUUU…UUUU-3′ (poly-U).

In vitro translation: Fed the synthetic mRNA to a protein synthesis system.
- Result: Produced a polypeptide of 20 Phenylalanines, confirming that UUU codes for Phenylalanine and the code is triplet.

Further experiments:
- Revealed the specification of each of the 64 codons.
- 61 codons specify amino acids.
- 3 codons indicate the end of protein synthesis (stop codons).

Redundancy in the genetic code:
- Degeneracy: Most amino acids are coded by multiple codons.
- Unambiguous: Each codon specifies only one amino acid.
- Non-overlapping: Codons are read sequentially without overlap.