1. Transcription 
    DNA -> mRNA
    • Occurs in the nucleus (in eukaryotes)
    • Makes a single stranded copy of mRNA that can leave the nucleus
  2. 3 steps of transcription
    • Initiation
    • Elongation
    • Termination
  3. Initiation in transcription
    Transcriptions factors and RNA polymerase bind to the promoter of the gene (which genes are transcribed is tightly controlled)
  4. Elongation in transcription
    • DNA is unwound and RNA polymerase creates a strand of mRNA which is complementary to the template strand of DNA
    • RNA polymerase synthesizes the mRNA in the 5' to 3' direction
    • Occurs at a rate of ~20 bases per second
  5. Termination in transcription
    Transcription proceeds until the polymerase reaches the terminator sequence which causes the enzyme to dissociate from the DNA
  6. Initiation in bacteria
    • RNA polymerase + sigma (holoenzyme) can recognize and bind to promoter
    • -Different sigma proteins bind promoters with different DNA sequences
  7. RNA polymerase in elongation
    • Unwinds the helix and exposes 10-20 nucleotides at a time
    • Synthesizes mRNA from 5'->3'
    • --Does not need primer
    • Rate= 50 nucleotides per second
  8. Termination in bacteria
    • Transcription proceeds through a termination sequence
    • RNA forms hairpin
    • RNA polymerase releases transcript
  9. Differences in eukaryotic transcription
    • 3 main polymerases (each produces a certain type of RNA)
    • Promoters more divers (TATA box)
    • Basal transcription factors (not sigma) help RNA polymerase to recognize the promoter
    • Termination [poly(A) signal- signals the end of transcription]
    • Transcription and translation separated
  10. DNA template strand    5'_________3'
    Complementary strand 3'_________5'
    In the transcription, where would the promoter be located?

    • C) to the right of the template strand
    • RNA is synthesized 5->3, so it gets read from the other way
    • Reads from 3'->5', so new bases will be added 5'->3'
  11. The initial transcript in RNA processing in Eukaryotes
  12. Pre-mRNA
    • Must be modified in the nucleus before it can be transported to the cytoplasm for translation
    • -5' cap= modified guanine added to 5' end
    • -3' poly-A tail= enzyme adds 50-250 adenines to 3' end
  13. Important functions of pre-mRNA
    • Facilitate export from nucleus
    • Protect from degradation in cytoplasm
    • Help ribosomes attach to the 5' end for translation
  14. Introns
    • Long stretches of noncoding DNA in most eukaryotic genes
    • Between exons
  15. Exons
    Coding segments in most eukaryotic genes
  16. What must happen to introns in RNA splicing
    The intervening sequences (introns) are transcribed, but must be removed before translation
  17. Spliceosome
    • snRNAs + proteins= snRNPs (small nuclear ribonucleoproteins)
    • -recognize specific sequences at the end of introns
    • Cuts out introns and joins the exons back together
  18. 5' UTR EI I1 E2 I2 E3 I3 E4 UTR 3'
    Which components of the previous molecule will also be found in mRNA in the cytosol? 

    B) 5' UTR E1 E2 E3 E4 UTR 3'
  19. Alternative RNA splicing...

    B) can allow the production of proteins of different sizes and functions from a single mRNA
  20. Why do we have introns?
    • Some introns contain sequences which play a role in regulating gene expression
    • Allows a single gene to code for more than one polypeptide
    • They let you take out or keep exons
  21. Alternative RNA splicing
    • Some exons can be left out of final transcript
    • This allows humans to make 75,000-100,000 proteins with only ~20,000 genes
  22. Translation 
    mRNA -> protein
    • Occurs in the cytoplasm
    • mRNA is "read" 3 bases at a time (codon) to build a polypeptide
  23. Key players of translation
    • tRNAs
    • Ribosomes
  24. The codon for serine is UCG. The coding (non-template) strand of the DNA that encoded is ___ and the anticodon of the tRNA that recognizes it is ___.

    Image Upload 1
    B) TCG, AGC
  25. Transfer RNA (tRNA)
    • Translates messages from nucleic acids to amino acids
    • Transcribed from DNA template and folds to form 3D structure
    • Contains an anticodon
    • Carries a specific amino acid
  26. Anticodon
    Triplet which is complementary to codon on mRNA
  27. During eukaryotic translation, which of the following is NOT used?

    D) RNA polymerase
  28. Aminoacyl-tRNA synthetases
    • Enzymes which attach the amino acid to the tRNA
    • Active site can only fit specific combinations of tRNA and amino acids (ensures anticodon brings in correct amino acid)
    • tRNA with amino acid attached is "charged"
    • Only ~40 tRNAs (not the 61 you would expect... 1 for each possible codon)
    • --Flexible base pairing in 3rd position = wobble
  29. How many different aminoacyl-tRNA synthetases are there?
    20 different synthetases (1 for each amino acid)
  30. A mutant bacterial cell has a defective aminacyl-tRNA synthetase that attaches a lysine to tRNAs with the anticodon AAA instead of the normal phenylalane. The consequence for the cell will be that...

    B) Proteins in the cell will include lysine instead of phenylalanine at amino acid positions specified by the codon UUU
  31. Ribosome
    onsist of a small and large subunit composed of protein and ribosomal RNA (rRNA)
  32. Why are prokaryotic and eukaryotic ribosomes differences important in medicine?
    • Some antibiotic inactivate bacterial ribosomes without harming our own
    • Otherwise, the two ribosomes are very similar
  33. What catalyzes the formation of peptide bonds?
    rRNA not the protein
  34. 3 steps of translation
    • Initiation
    • Elongation
    • Termination
  35. Initiation in translation
    • Small unit of the ribosome, which the initiator tRNA (methione) already attached, binds to leader sequence of mRNA and scans for AUG
    • Large subunit binds and completes translation initiation complex
  36. Elongation in translation
    Ribosome moves along mRNA adding amino acids to the growing polypeptide chain
  37. Termination in translation
    Ribosome hits a stop codon and the subunits separate the polypeptide is released
  38. Initiation process in translation
    • rRNA in small subunit binds to complementary sequence on mRNA (ribosomal binding site) 
    • --helped by initiation factors
    • Initiator tRNA binds to start codon
    • Large subunit attaches to form translation initiation complex
  39. Elongation process in translation
    • Amino acids are added one by one to growing polypeptide chain
    • -Requires proteins= elongation factors
    • -Requires energy
  40. 3 ribosome sites in elongation
    • E- empty tRNA exits
    • P- tRNA with growing polypeptide
    • A- incoming (active) tRNA
  41. Termination process in translation
    • Elongation continues until a stop codon is reached
    • A release factor (protein shaped like a tRNA) binds to the stop codon in the A site
    • -causes the polypeptide to be released
    • The translation assembly breaks apart
  42. Polyribosomes
    • Typically a single mRNA is simultaneously translated by multiple ribosomes (polyribosomes)
    • 1 ribosome can make an average polypeptide in less than a minute
  43. Post-translational modification
    • Polypeptide must undergo correct secondary and tertiary folding 
    • -may require assistance of molecular chaperons
  44. Chemical post-translational modifications
    • Attachment of sugars, lipids, phosphate groups
    • Cleavage of polypeptide chain (i.e insulin)
    • Interaction of multiple subunits (quaternary structure)
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