Chapter 13 notes

2066925-19050Chapter 13: Translation genes encode the information/production of proteins for building polypeptides which affects the phenotype mutations lead to defects in genotype affects phenotype Protien Synthesis proteins give a cell (1) structure and (2) function Structural Genes: Genes that encode polypeptides and are transcribed into messenger RNA (mRNA) Genetic Code: the nucleotide language of mRNA is translated into the amino acid language of proteins right3848100Genetic information in mRNA has three nucleotides known as codons Start codon: AUG Start codon: first codon that ribosome reads to start translating Stop Codons (nonsense codons): UAA, UAG, UGA There are 20 different amino acids to build a polypeptide (each codon is responsible for a particular amino acid) 2 nucleotides = 4^2 = 16 (not enough) 3 nucleotides = 4^3 = 64 codons Use more than one codon to specify amino acid Genetic Code is DEGENERATE: multiple ways to encode the same information as different codons mean the same amino acid For example: GGU, GGC, GGA and GGG all code for lysine right6334125In most instances, the third base is the degenerate base: WOBBLE BASE tRNA binds tightly to the first 2 base pairs – the third position is wobbly In the codon-anticodon recognition process, the first two positions pair strictly according to the A – U /G – C rule However, the third position can actually “wobble” or move a bit, tolerating certain types of mismatches and allowing multiple codons to be recognized by the same tRNA Prokaryote: 5’ AUG……UAA 3’ (coding region – translated) Eukaroyte: 5’ (Guanosine Cap) AUG….UAA (Poly A tail) 3’ (coding region – translated) 5057775-85725tRNA has the ability to recognize which amino acid goes with which codon Ribosome builds the polypeptide chain (has directionality 5’ 3’) 5’ NON-template 3’ 3’ Template strand5’ 5’ mRNA strand 3’ codons 3’ Anti Codon 5’ anti codons that specifies amino acid Amino Acids: 20 amino acids and each one contains a different side chain (R) Side chain determines how protein gets folded Types: (1) Nonpolar Amino Acids (Hydrophobic) They are often buried within the interior of a folded protein Some nonpolar amino acids can be found on the surface; however, they must be protected for a while (chaperone proteins) (2) Polar/Charged Amino Acids (Hydrophilic) Usually found on the surface of the protein Lysine & Arginine = positive/polar charged 27908251371600Polypeptide synthesis has a directionality that parallels the 5’ to 3’ orientation of mRNA (N-terminus C-terminus) During each cycle of elongation, a peptide bond is formed between the last amino acid in the polypeptide chain and the amino acid being added POLYPEPTIDE BOND::: 28575004210050Condensation reaction: Carboxyl group removes the charged O- and the Amino group loses 2 hydrogen’s to yield a water H3N+ Amino terminus (N-terminus) 5’ end of mRNA CO-2 Carboxyl Terminus (C-terminus) (new amino acids get added to the Carboxyl terminus) 3’end of mRNA 49911006438900Protiens : There are four levels of structures in proteins 1. Primary - amino acid sequence 2. Secondary – structures within a polypeptide formed by interactions between the atoms that make the peptide bond Alpha (?) Helices: carbonyl and amino group line up Beta (?) Helices Held together by HYDROGEN/PEPTIDE bonds Side chains influence whether goes into Alpha or Beta Sheet Ex) PROLINE will stop the formation of an alpha helix due to large side chains 3. Tertiary – 3D structure of the polypeptide (mixture of Beta and Alpha Helices) Hydrogen bonds – help stabilize Ionic bonds Disulfide bond/bridge Van Der Waals Interactions (every atom with have a neg/pos charge at any given time) 34099502209800Hydrophobic interactions – getting hydrophilic side chains in the middle of the protein (disrupts fever water molecules) -24765024098254. Quaternary – 2+ polypeptide interactions Homodimer 2 of the same polypeptides Heterodimers 2 different polypeptides Dimer 2 polypeptides Tridimer three polypeptides Tetradimer 4 polypeptides 37623756200775Sorting signals direct a protein to its correct location Each sorting signal is recognized by a specific cellular component, often a protein, that facilitates the sorting of the protein to its correct compartment (Must have a signal within sequence that allows them to be sent to the right place) Sorting is more complicated in eukaryotes than in bacteria since eukaryotes are compartmentalized into organelles Ex) a protein destined for the nucleus will be sent there directily from the cytoplasm via a signal 4029075-419100Recognition Between tRNA and mRN During mRNA-tRNA recognition, the anticodon in tRNA binds to a complementary codon in mRNA tRNA shape: 3’ end – amino acid attach All have clover-like shapes Intermolecular hydrogen bonds Modifications to make tRNA unique (pick up correct amino acid!) creates a different shape Charging of tRNAs The enzymes that attach amino acids to tRNAs are known as aminoacyl-tRNA synthetases There are 20 types, one for each amino acid 500 genes but only 48 different tRNA – duplication is present to increase levels of a particular protein Very low error rate Sequences throughout tRNA – better at recognizing where aminoacyl-tRNA synthetases should bind to Aminoacyl-tRNA synthetases catalyze a two-step reaction involving three different molecules Amino acid, tRNA and ATP (1) aminoacyl-tRNA synthetases recognizes only one amino acid (2) binds an ATP to amino acid and creates AMP – Amino Acid (3) Bring in tRNA – breaks bond between AMP – amino acid to attach 39243004095750 Bacteria Translation: Bacteria contain one type of ribosome found in their cytoplasm Synthesis and assembly of all ribosome components occurs in the cytoplasm During bacterial translation, the mRNA lies on the surface of the 30S subunit As a polypeptide is being synthesized, it exits through a hole within the 50S subunit Has a 30S and 50S subunit Ribosomes contain three discrete sites Peptidyl site (P site) – contains polypeptide chain Aminoacyl site (A site) – next amino acid enters the ribosome Exit site (E site) – exit/empty tRNA exits ribosome from E site *base pairing allows codons to attach to ribosome by hydrogen bonding 28956007000875Initiation in Bacteria The binding of mRNA to the 30S subunit is facilitated by a Shine-Dalgaro Sequence 9 base pair sequence – used to place the AUG in the P site of the prokaryotic ribosome Start codon – starts in p site to initiate translation Fmet – modified version use to initiate synthesis (does not get added to polypeptide chain) IF3 (initiation factor 3) Brings in IF2 Promotes the binding of the initiator tRNA fmet IF2 and IF3 get released and 50S subunit associates with the 30S subunit tRNA fmet is the only charged tRNA that enters through the P site – all others enter through the A site Elongation in Bacteria tRNA enters from the A site and polypeptide chain moves to the P site until the empty tRNA gets released at the E site 38576252124075Decoding Function of the Ribosome: 16S rRNA (a part of the 30S ribosomal subunit) plays a key role in codon-anticodon recognition It can detect an incorrect tRNA bound at the A site It will prevent elongation until the mispaired tRNA is released Translation Termination in Bacteria The final stage occurs when a stop codon is reached in the mRNA These codons are not recognized by tRNAs, but by proteins called release factors Release factors mimics the structure of the tRNA so that it can fit into the A site A stop codon causes release factor to base pair with the mRNA. This will detach the finished polypeptide from the last tRNA and allow it to dissociate from the ribosome. Translation stops. Bacteria have three release factors RF1, which recognizes UAA and UAG RF2, which recognizes UAA and UGA RF3, which does not recognize any of the three codons It binds GTP and helps facilitate the termination process Ex) Hit UAA codon and recognized by release factor Release factor binds and catalyzes release of peptide. Kicks out the tRNA present at the A site. Whole thing falls apart/dissociates mRNA & ribosomal subunits are used by diff ribosome Bacterial Translation Can Begin Before Transcription Is Completed Bacteria lack a nucleus Therefore, both transcription and translation occur in the cytoplasm As soon an mRNA strand is long enough, a ribosome will attach to its 5’ end COUPLING: translation begins before transcription ends A polyribosome or polysome is an mRNA transcript that has many bound ribosomes in the act of translation Translation in Eukaryotes: Eukaryotic cells have two types of ribosomes: One type is found in the cytoplasm (either free or bound to the ER) The other is found in organelles (mitochondria or chloroplasts) Transcription occurs in the nucleus and is released into the cytoplasm for translation Eukaryotic Ribsomes: Small (40S) and large (60S) ribosomes (assembled in nucleolus and then transported to the cytoplasm) Polyribosome: multiple ribosomes translating at the same time. Ribosome scans until AUG. Small ribosome sticks & sticks tRNA into P site. Initiation in Eukaryotes: Translation in eukaryotes is similar to that in prokaryotes 38100003057525Eukaryotes have G’Cap ------ PolyA tail (without cap/tail – translation can not occur) Major differences occur during translational initiation: the assembly of the initiation complex is similar to that in bacteria, but additional factors are required The initiator tRNA carries a methionine rather than a formylmethionine The start codon for eukaryotic translation is AUG (enters into the P site) It is usually the first AUG after the 5’ Cap 5’cap must be present or translation will not occur The 5’ cap attracts binding proteins of tRNA (methionine) Poly A tail – more poly A binding is increased levels of translation Some initiation factors associate with polyA binding proteins at the polyA tail Proteins at the polyA tail help to stimulate the binding of initiation factors PolyA tail is protected by proteins that are attracted to initiation factors that are attracted to the cap. More initiation factors lead to happier cap proteins which results in increased protein translated *Interaction between 5’ and 3’. Initiation factors that bind to the cap are from polyA binding protein happier cap proteins more efficient proteins. Overall Summary of Initiation: A number of initiation factors bind to the 5’ cap in mRNA These are joined by a complex consisting of the 40S subunit, tRNAmet, and other initiation factors The entire assembly moves along the mRNA scanning for the right start codon Once it finds this AUG, the 40S subunit binds to it The 60S subunit joins This forms the 80S initiation complex Termination in Eukaryotes: Eukaryotes only have one release factor eRF, which recognizes all three stop codons