Protein Synthesis & Function (finished)

• Protein primary structure: the amino acid sequence of a protein
• Protein secondary structure: initial folding a peptide chain that creates alpha-helices and beta-sheets
• Protein tertiary structure: 3D structure of a single polypeptide chain
• Protein quaternary structure: 3D structure of multiple polypeptide chains
• Motif: a sequence of amino acids or a sequence in DNA that appears multiple times through out the proteome or genome (respectively) usually associate with a particular function

  • Motifs can be formed as structural elements that are not necessarily tied a specific sequence
• Domain: region within a protein that can function independently of the total protein within which it is found
• Proteome: collective protein information found in an organism, tissue, cell, fluid or other definable compartment
• Genome: the collective genetic information found within an organism
• Translation is the decoding of mRNA that provides information about:

  • Instructions for building a polypeptide through codons
• mRNA codons are read 5' to 3' by transfer RNAs (tRNAs) that possess anti-codons
• Codons are features of mRNA only, but the "instructions" come from DNA
• Translation takes place inside the ribosomes
• Ribosomes are made up for the 40s (33 proteins) and 60s (46 proteins) multimeric subunits

  • 40s: 18s rRNA (transcribed by RNA pol I)
  • 60s: 28s, 5.8s (transcribed by RNA pol I; in nucleolus), 5s rRNAs (transcribed by RNA pol III; outside nucleolus)
• s in 40s and 60s subunits stands for Svedberg units

  • A sedimentation coefficient
  • The larger the number of s, the quicker it will settlement at a high speed
• rRNAs are the most abundant RNAs in every cell because for every mRNA there's a need for many rRNAs to make a ribosome
• Ribosomal RNA is not translated into protein
• mRNA is transcribed by Pol II
• Pol III typically only transcribes short RNAs
• Functions of rRNA in Ribosomes:

  • Structural: framework that holds ribosomes together
  • Subunit Coordination: aids proper alignment of subunits
  • Binding Sites for tRNA: positions the tRNA in ribosome
  • Conformational Changes: allows ribosome to move along mRNA
  • Catalytic: facilitates chemical rxns involved in peptide elongation
• rRNA Modifications: play a role in biogenesis and function of ribosome

  • Ribosome assembly
  • Ribosome stability
  • tRNA recognition
  • Codon-anticodon interactions
  • Peptide bond formation
• Examples of rRNA Modifications:

  • Methylation of 2-OH position on nucleotide ribose sugar
  • Isomerizations of uridine nucleotides to pseudouridine
  • Acetylation
• Ribosomal assembly will happen mainly in the nucleolus where rRNA are made

  • Other components are in the nucleoplasm and the cytoplasm
  • Assembly of the complex isn't all in the nucleolus because it would be too large to transport out
• Cisternae are membrane-bound structures that are found in the endoplasmic reticulum and help with the functioning of ribosomes
• 2 Types of Ribosomes:

  1. Membrane-bound: most abundant, on surface of RER
  2. Free form: in cytosol (not in nucleus or other organelles), synthesizes proteins in plasma
• Endoplasmic Reticulum's products are all meant to be secreted or sit on the cell surface - can be modified along the way
• mRNAs are targets to be processed and are easily identified because they're polyadenylated at their 3' end to make a polyA "tail"

  • A-tail is bound by polyA binding protein
• PolyA tail:

  • Stabilizes mRNA
  • Forms translation initiation complex
• Translation Initiation Complex:

  • mRNA activation complex
  • Pre-initiation complex (PIC)
• Pre-initiation complex (PIC) is made of:

  • Ribosomal 40S subunit
  • Multiple initiation factors
  • Initiator methionine-tRNA (P site)
• All translation in mammals start with a methionine amino acid
• tRNAs use anti-codons to read codons

  • Anti-codons and codons associate with one another through base pair complementarity
• tRNAs become charged when they're in the cytoplasm in become attached to a specific amino acid (through aminoacyl-tRNA synthetase)

  • Amino acids that attach to tRNAs are specific to the tRNA's anti-codon
• If the codon for methionine is AUG, what is the anti-codon sequence?


  UAC
• The redundancy in genetic code decreases the number of tRNAs required
• The third position in the codon is called a "wobble base" because it is not a regular base like the first two
• Inosine is in the first position of an anti-codon

  • Binds to all four bases
• Steps of Translation:

  1. Initiation: 60S subunit engages with translation initiation complex
  2. Elongation: "charged" anti-codons are matched with tRNAs which wil transfer amino acids onto a growing polypeptide chain
  3. Termination: at a stop codon (UAA, UAG, UGA), synthesis will end and product is released
• Multiple ribosomes can translate an mRNA at the same time
• Translation steps:

  1. Methionine codon (AUG) binds with Met-tRNA (P site)
  2. Aminoacyl-tRNA binds with aminoacyl-site (A site)
  3. Methionine is released from its tRNA
  4. Ribosome moves 5' to 3' along mRNA and discharges empty tRNA through E site
  5. Shifts peptide into P site and continues process until it reaches the stop codon
  6. Once at stop codon, hydrolysis of the ester bond will release the protein
• Rifamycin: prevents RNA synthesis