Cell stuff-6

RNA Structure and Function

• RNA is a single-stranded molecule with a deeper and narrower major groove compared to DNA.
• The extra hydroxyl group on the ribose sugar of RNA contributes to its unique secondary structure compared to DNA.
• RNA's single-stranded nature allows it to adopt diverse three-dimensional structures, enabling a wide range of functions.

DNA to RNA Transcription

• DNA serves as a template for RNA synthesis, where the RNA sequence is complementary to the DNA template.

Gene Regulation

• Cells regulate the expression of genes by controlling the amount of mRNA transcribed for each gene.

Types of RNA

• mRNA (messenger RNA): Carries genetic code for proteins.
• rRNA (ribosomal RNA): Forms the core structure of ribosomes, essential for protein synthesis.
• tRNA (transfer RNA): Adapters between mRNA and amino acids during protein synthesis.
• snRNA (small nuclear RNA): Involved in various nuclear processes, including pre-mRNA splicing.

DNA Supercoiling

• Negative supercoiling: A deficit of helical turns, making the DNA more compact and easier to unwind for replication and transcription.
• Positive supercoiling: An excess of helical turns, making the DNA more tightly wound and more stable.

Transcription Factors: TBP and TFIIH

• TBP (TATA Binding Protein): Recognizes and binds to the TATA box, initiating transcription in eukaryotes.
• TFIIH (Transcription Factor II H): A multi-subunit protein complex that unwinds DNA (helicase activity) and phosphorylates the C-terminal domain (CTD) of RNA polymerase II (kinase activity).

5' Capping

• 5' capping: A protective group is attached to the 5' end of mRNA, crucial for translation initiation in eukaryotes.
• The process involves the addition of a nucleotide to the 5' end.
• The cap-binding complex (CBC) recognizes and interacts with the 5' cap.

RNA Splicing

• RNA splicing: Removal of introns from pre-mRNA to create a continuous sequence of exons carrying protein-coding information.
• Genes contain variable numbers of exons.
• Spliceosomes, complex ribonucleoprotein assemblies, perform splicing.

Transcription Elongation

• RNA polymerase is absolutely processive, meaning a single polymerase molecule synthesizes the entire RNA molecule.

Genetic Code

• Triplets: A set of three nucleotides (codon) codes for an amino acid.
• 64 triplets: 61 encode amino acids, and 3 serve as stop codons.
• Universality: The genetic code is nearly universal across all organisms.
• Redundancy: Several codons can code for the same amino acid.

Aminoacyl-tRNA Synthetases

• Aminoacyl-tRNA synthetases: Enzymes that attach the correct amino acid to the corresponding tRNA.
• They utilize energy from ATP to form a high-energy ester bond between the amino acid and tRNA.
• There are 20 aminoacyl-tRNA synthetases, one for each amino acid.

tRNA Structure and Function

• tRNA: Has a specific amino acid attachment site and a specific anticodon loop for recognizing mRNA codons.
• Clover leaf assembly: The distinctive three-dimensional structure of tRNA.

tRNA Selection by Aminoacyl-tRNA Synthetases

• Aminoacyl-tRNA synthetases identify the correct tRNA using multiple criteria:
  • Nucleotides in the anticodon region.
  • Nucleotides in other regions of the tRNA.
  • Structural features of the tRNA.

Inosine and Wobble Base Pairing

• Inosine: A modified nucleoside that can form two hydrogen bonds.
• Wobble base pairing: Reduced structural constraints between the third base of the codon and the first base of the anticodon allow for imperfect Watson-Crick base pairing.
• Chemical modifications: Around 10% of all bases in tRNA undergo chemical modifications.

tRNA Anticodon and mRNA Codon Pairing

• tRNA anticodon: The "second adaptor" that binds to a matching codon on mRNA.
• Coupled amino acids: The attached amino acid undergoes editing, where incorrect amino acids are hydrolyzed, ensuring accuracy.
• Inosine at the wobble position: Allows for base pairing between different codons and the same anticodon.

Ribosome Function

• Ribosomes: Catalyze peptide bond formation.
• Bacterial ribosomes: Synthesize approximately 20 amino acids per second.
• Eukaryotic ribosomes: Synthesize approximately 2 amino acids per second.
• Accuracy: One mistake for every 10,000 amino acids.

Ribosome Structure

• Prokaryotes (70S):
  • 50S large subunit: Consists of 34 proteins.
  • 30S small subunit: Consists of 21 proteins.
• Eukaryotes (80S):
  • 60S large subunit: Consists of 49 proteins.
  • 40S small subunit: Consists of 33 proteins.

Ribosome Components and Functions

• rRNA in the large subunit: Provides the catalytic site for peptide bond formation.
• Ribosomal proteins: Stabilize the ribosome's core structure, facilitate conformational changes, and aid in the correct folding of rRNA.

Ribosome Accuracy and Induced Fit

• Induced fit: The 16S rRNA folds tightly around the tRNA/EF-Tu (GTP) complex only when there is a correct base-pair match between the mRNA codon and tRNA anticodon. This tight fold triggers GTP hydrolysis by EF-Tu, driving the reaction forward.
• Kinetic proofreading: A time delay before peptide bond synthesis allows for the preferential removal of weakly bound tRNAs from the A site, enhancing accuracy.

Energy Requirements for Protein Synthesis

• Incorporating one amino acid into a protein requires 2 ATP for charging tRNA and 2 GTP for translation.

Polyribosomes

• Polyribosomes (polysomes): Multiple ribosomes translating the same mRNA molecule sequentially.

Selenocysteine

• Selenocysteine (Sec): A 21st amino acid, crucial for the function of certain enzymes.
• Specialized tRNA charged with serine: Converted to selenocysteine.

Topoisomerases

• Topoisomerases I and II: Relieve tension in DNA in prokaryotes.
• Gyrase (a type II topoisomerase): Relieves tension in DNA in eukaryotes.

RNA Splicing: Two Transesterification Reactions

• First transesterification: The intron, flanked by two exons, is cleaved from one exon.
• Second transesterification: The two exons are joined, forming a separate intron and a single exon.
• This process allows for alternative splicing, where different combinations of exons can be included in the final mRNA.

Polyadenylation

• Polyadenylation: A specific sequence is recognized by a protein, leading to cleavage of the RNA from RNA polymerase.
• PAP (Poly-A polymerase) enzyme: Adds a string of adenine nucleotides (poly-A tail) to the 3' end of mRNA.
• PABP (Poly-A binding proteins): Regulate the length of the poly-A tail.