iClcker points have been uploaded to Blackboard. Columns are titled: “Session 1 - 1/27/20” Translation and Protein Structure Molecular structure of proteins Polymers of amino acids 20 amino acids Exact order of amino acids determines the proteins structure and function Amino Acids Structures of the 20 Amino Acids Structures of the 20 Amino Acids Amino Acids in a Protein are Connected by Peptide Bonds The carboxyl group of one amino acid reacts with the amino group of the next releasing a molecule of water Ends of a protein are chemically distinct Amino end Carboxyl end Proteins = POLYPEPTIDES The formation of a peptide bond involves a reaction called ______. A. dehydration synthesis B. ester synthesis C. hydrolysis D. precipitation synthesis Which of the carbons in this peptide is involved in a peptide bond? A. 1 B. 2 C. 3 D. 4 Protein Structure Proteins have 3 dimensional structures Determined by the amino acid sequence Scientists have defined 4 levels of protein structure Primary structure Secondary structure Tertiary structure Quaternary structure Primary Protein Structure The sequence of amino acids Represented by a series of 3-letter or one-letter abbreviations Secondary Protein structures Result from hydrogen bonding in the peptide backbone 2 types of secondary structure: alpha helix (a helix) beta sheet (b sheet) The a-helix Polypeptide backbone twists into a righthanded coil The b-sheet Hydrogen bonds between neighboring strands The polypeptide folds back and forth on itself forming a pleated sheet Tertiary Protein Structure The three-dimensional conformation of a protein Defined by the interactions between the amino acid R groups Spatial distribution of hydrophobic and hydrophilic amino acids DETERMINES FUNCTION Structure of a bacterial protein Quaternary Protein Structure Some proteins are composed of 2 or more polypeptide chains Individual polypeptides are called subunits Can be identical or different Which of the following actions would affect the secondary, but not primary, structure of a protein? A. Change the sequence of amino acids B. Break the ionic bonds between amino acids C. Break the hydrogen bonds between amino acids D. Disrupt the interactions between two different polypeptide chains The individual polypeptide chains in a multi-subunit protein each have their own primary, secondary and tertiary structure. A. True B. False Which type of protein structure is determined by the sequence of amino acids? A. Primary B. Secondary C. Tertiary D. Quaternary E. Just secondary and tertiary F. All of the above Chaperones help some proteins fold properly Most proteins (~75%) fold within milliseconds of being synthesized Chaperones help proteins that fold more slowly Prevent the protein from folding incorrectly What happens when a protein unfolds? Proteins are only functional when they are in the proper conformation Conformation = folded 3D structure (active) Denatured = unfolded (inactive) What affects protein structure? Temperature pH Chemicals Enzymes Translation: how proteins are synthesized THE SEQUENCE OF AMINO ACIDS (1° STRUCTURE) DETERMINES HOW THE MOLECULE FOLDS INTO ITS 3-D CONFORMATION How is the sequence of amino acids specified? Specified by the sequence of nucleotides in the DNA This information has to be decoded Central dogma of molecular biology Step 1: TRANSCRIPTION Step 2: TRANSLATION What components are needed for translation? Ribosomes Complexes of RNA and protein Site of translation mRNA Transfer RNAs(tRNAs) Aminoacyl tRNA synthetases The Ribosome Bind the mRNA and are the site of translation Each consists of a small subunit and a large subunit Large subunit: Has 3 tRNA binding sites Major function: setting up the correct reading frame mRNA is read in successive, nonoverlapping groups of 3 nucleotides called codons READ THIS SENTENCE: THEBIGBOYSAWTHEBADMANRUN Each group of 3 letters/nucleotides represents a codon Codons Each acid codon in mRNA codes for an amino In the sentence above it is clear that the sentence begins with THE What if you did not know the sentence began with THE and were given the following? ZWTHEBIGBOYSAWTHEBADMANRUN POSSIBLE READING FRAMES: ZWT Z WTH EBI GBO YSA WTH EBA DMA NRU N ZW HEB IGB OYS AWT HEB ADM ANR UN THE BIG BOY SAW THE BAD MAN RUN An mRNA can only be translated into the correct protein if it is translated in the correct reading frame Transfer RNA (tRNA) Do the actual translation Small RNA molecules of 70-90 nucleotides Anticodon – base pairs with the mRNA codon Amino acid attachment site (3’ end) Aminoacyl tRNA synthetases Connect amino acids to specific tRNA molecules The Role of Base Pairing The Genetic Code The 20 amino acids ae coded for by 61 codons Many amino acids are specified by more than one codon (redundant) Codon AUG codes for methionine (M) Called the initiation or start codon Position of this codon determines the reading frame Deciphering the genetic code Made mRNAs of know sequence and added these to a solution containing the components needed for translation Let translation take place and then analyzed the resulting polypeptide The Genetic Code Finding codons in the genetic code table: Codon CGG 1. Identify the row corresponding to the 1st nucleotide 2. Identify the column corresponding to the 2nd nucleotide 3. Find the row corresponding to the 3rd nucleotide Translation 3 steps: Initiation: AUG codon is recognized and reading frame is established Elongation: amino acids are added one by one to the growing polypeptide Termination: addition of amino acids stops and the polypeptide is released Translation: initiation Initiation factors bind to the 5’ cap on the mRNA Recruit the small ribosomal subunit and the tRNAMet Scan the mRNA for first AUG codon Translation: initiation Large ribosomal subunit joins the complex when the AUG is reached Next tRNA joins the ribosome at the “A” site Translation: initiation Formation of a peptide bond between Met and the next amino acid Translation: elongation The ribosome shifts one codon to the right Uncharged tRNAmet moves to the E site Peptide bearing tRNA moves to the P site Next charged tRNA enters at the A site Translation: elongation Polypeptide transfers to the A site amino acid Ribosome shifts one codon to the right Process continues until one of the stop codons UAG, UAA or UGA is reached Translation: Termination Stop codons do not code for an amino acid When the stop codon is reached, a protein called a release factor binds to the A site The newly synthesized polypeptide is released Small and large ribosomal subunits separate from the mRNA and each other Translation initiation in prokaryotes In prokaryotes: Initiation complex forms at a mRNA sequence called a Shine-Dalgarno sequence AUG codon is a specific number of nucleotides downstream of this sequence Polycistronic mRNAs What amino acid sequence is specific by this mRNA sequence? 5’-CCAUGCCCGGA-3’ A. PRO-CYS-PRO B. MET-PRO-GLY During translation, the ____ site within the ribosome holds the growing amino acid chain while the ____ site holds the next amino acid to be added to the chain. A. A,P B. E,A C. E,P D. P,A True or False: When amino acids are brought in by tRNA, they are joined together by hydrolysis reactions to form the growing protein. A. True B. False http://www.macmillanhighered.com/launchpad/morris2e/9880399#/launchpad/item/MODULE_bsi__C39E8337__576A__4FD1__8AF1__EE081D2D421C/morris2e_vsmap_gene_update?mode=Preview&getChildrenGrades=False&includeDiscussion=False&readOnly=False&toc=syllabusfilter&renderIn=fne
