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Biochemistry

This chapter explores the central dogma of molecular biology, focusing on gene expression and protein synthesis. Topics include transcription, translation, the genetic code, and gene regulation.

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Biochemistry

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  1. Biochemistry Chapter 26 Gene Expression and Protein Synthesis

  2. Problem Sets • PS #1 • Sections 26.1 – 26.5 • # 6, 7, 8, 9, 10, 11, 13, 16, 18, 23, 24, 27, 28, 29, 30, 31 • Ps #2 • Sections 26.6 – 26.9 • # 33, 34, 35, 36, 38, 39, 40, 41, 43, 44, 45, 46, 48, 67

  3. 26.1 The Central Dogma of Molecular Biology The information contained in DNA molecules is transferred to RNA molecules and then from RNA molecules the information is expressed in the structure of proteins Gene expression – the activation of a gene to produce a protein

  4. 26.2 Transcription Binding proteins attach to DNA near transcription site and relax higher-order structure Helicase unwinds the double helix Template Strand (antisense strand) – DNA strand that serves as the template for RNA synthesis; complementary to RNA Coding Strand (sense strand) – complementary DNA strand; not used as template; has same sequence as RNA

  5. 26.2 Transcription • RNA Polymerases catalyze transcription • RNA pol I – catalyzes formation of rRNA • RNA pol II – catalyzes formation of mRNA • RNA pol III – catalyzes formation of tRNA, ribosomal units, and small regulatory RNAs • Eukaryotic genes have two parts • Structural gene – gets transcribed • Regulatory portion – controls the transcription • Elongation • RNA polymerase links ribose to phosphate

  6. 26.2 Regulatory Sequences • Promoter • Beginning of gene • Contains initiation signal and consensus sequence • Consensus Sequence • “TATA box” – TATAAT sequence • Approximately 26 bases upstream of gene • Binding site for transcription proteins • Initiation Signal • “Start here” sequence unique to each gene

  7. 26.2 Regulatory Sequences • Termination Sequence • Signal to stop transcription • End of RNA pol II is phosphorylated, which allows it to perform elongation • Termination sequence dephosphorylates RNA pol II, ending elongation • Post-transcription processes • 5’ end capped with methylated guanine • Poly-A tail added to 3’ end (100-200 adenosines) • Introns are spliced out

  8. 26.2 Transcription

  9. 26.3 Translation • Ribosome dissociates into 2 parts • mRNA sandwiched betweenand stretched out • Codons – base triplets • tRNAs attach to amino acids byaminoacyl-tRNA-synthetases • Anticodon loop lines up withmRNA codon to bring proper amino acid

  10. 26.4 The Genetic Code • Sequences of three nucleotides (codons) act as codes for the 20 amino acids • Code is virtually universal for all known life • 64 triplet combinations, but only 20 aa’s • Some aa’s have several codons • Stop sequences: UAA, UAG, UGA • Initiation sequence: AUG • Codes for methionine (often trimmed from protein)

  11. 26.5 Protein Synthesis

  12. 26.5 Protein Synthesis – Activation Each amino acid is activated by reaction with ATP Activated amino acid attached to proper tRNA by a synthetase: Connection must be right every time!

  13. 26.5 Protein Synthesis – Initiation • Formation of the pre-initiation complex • tRNAfMet (carries formylated methionine) attached to smaller part of ribosome (30S) with GTP • Migration to mRNA • pre-initiation complex binds to mRNA • Shine-Delgarno sequence of mRNA lines up with complement on 30S ribosomal unit • UAC anticodon of tRNAfMet lines up with start codon (AUG) • Forming the full ribosomal complex • Larger (50S) ribosome segment attaches • P site – binding site for growing peptide chain • A site – accepts incoming tRNA with the next amino acid

  14. Formation of the pre-initiation complex Migration to mRNA Forming the full ribosomal complex

  15. 26.5 Protein Synthesis – Elongation • Binding to the A site • Aminoacyl-tRNA with the right anticodon sequence fits into the A site (catalyzed by elongation factors) • Forming the first peptide bond • Peptidyl transferase forms a peptide bond between the new amino acid and fMet; empty tRNA remains • Translocation • Ribosome moves down one codon; peptide is translocated from A site to P site; empty tRNA moves to E site • Forming the second peptide bond • Next aminoacyl-tRNA binds to A site and process repeats

  16. 26.5 3D Model of a Ribosome 50S ribosome tRNA (P site) tRNA (A site) Elongation factor mRNA 30S ribosome

  17. 26.5 Protein Synthesis – Elongation Electrons in amino group make a “nucleophilic” attack on carbonyl group Catalyzed by the rRNA molecule Ribozyme – RNA molecule acting as an enzyme

  18. 26.5 Protein Synthesis – Termination • After final translocation, ribosome reads a stop codon (UAA, UGA, or UAG) • Release factors cleave the peptide chain from the last tRNA • tRNA released from the P site • mRNA released from ribosome

  19. Ribosome encounters stop codon on mRNA Release factors and GTP bind to A site Peptide is hydrolyzed from tRNA Complex dissociates

  20. 26.6 Gene Regulation • Process by which genes are turned on and off as needed • Control sites lie upstream of the structural gene • Since RNA is transcribed 5’  3’, DNA is read 3’  5’ and control structures are at the 3’ end • Control mechanisms • Can occur at the transcriptional level, post-transcriptional level, or translational level

  21. 26.6 Gene Regulation – Transcriptional Level • Promoters • Located adjacent to transcription site • Consist of initiator and conserved sequence like a TATA box (TATAAT) or GC box (GGGCGG) • RNA Pol II does not bind well to DNA; requires binding proteins called General Transcription Factors (GTF) to position RNA Pol II • 6 GTFs (named TFIIA through TFIIF) bind to DNA and RNA Pol II to form initiation complex • Transcription starts when Pol II is phosphorylated (open complex)

  22. 26.6 Gene Regulation – Transcriptional Level • Enhancers • May lie thousands of nucleotides away from transcription site • Brought near promoter by formation of a loop • Transcription factor binds to enhancer and forms a bridge to the TFIID at the transcription site Silencers – opposite of enhancers

  23. 26.6 Gene Regulation – Transcriptional Level • Response elements • Type of enhancer that is activated by its transcription factor in response to an outside stimulus • Eg, receptor with a bound steroid hormone can interact with a response element, starting transcription • Signal can originate outside of the cell • Eg, the G-protein cAMP cascade can trigger the phosphorylation of transcription factors

  24. 26.6 Gene Regulation – Transcriptional Level How do transcription factors find the right gene control sequences? Metal-binding fingers – secondary protein structures formed by metal ion coordination with certain amino acid residues Zinc fingers fit into major grooves and allow protein to find and bind to active sites

  25. 26.6 Gene Regulation – Post-Transcriptional Level A single gene can produce several different proteins by Alternate Splicing Allows ~30,000 human genes to produce over 90,000 different proteins

  26. 26.6 Gene Regulation – Translational Level • Mainly “quality control” mechanisms • tRNA specificity for its unique amino acid • Aminoacyl-tRNA synthetases (AARS) have “sieving portions” that exclude all but the proper amino acid • Recognition of the stop codon • Post-translational controls • Removal of methionine from n-terminus • Chaperoning (proteins make peptide fold properly) • Degradation of misfolded proteins (proteasomes)

  27. 26.7 Mutations • Mutation • Error in copying a sequence of bases • Can occur in replication (1 in 10 billion) • Consequences • Harmless (codes for same or similar amino acid) • Genetic disease (significantly alters protein) • Beneficial (very rare in nature) • Causes • Ionizing radiation, mutagens, carcinogens

  28. 26.8 Recombinant DNA Use restriction endonuclease to cleave bacterial plasmid (circular DNA) at desired location Use same restriction endonuclease to cut desired human gene from chromosome Mix two solutions in the presence of DNA ligase; Sticky ends will splice together

  29. 26.9 Gene Therapy • Technique using viruses to insert genes for a missing protein in somatic cells • Ex vivo delivery • Somatic cells removed, infected, and reinserted • Maloney murine leukemia virus (MMLV) often used • In vivo delivery • Virus is used to directly infect patient’s tissues • Adenovirus is commonly used • It’s illegal to tamper with reproductive cells

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