GENETICS - CLUTCH CH.11 TRANSLATION.

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2 CONCEPT: GENETIC CODE Nucleotides and amino acids are translated in a 1 to 1 method The triplet code states that three nucleotides codes for one amino acid - A codon is a term for the three nucleotides - The reading frame determines the nucleotide in which the codons should be read The triplet code is: - Nonoverlapping, meaning that the three nucleotides represent one single codon, not multiple codons - Degenerate, meaning that some amino acids are coded by more than one codon - Nearly universal as most organisms use the same code - Initiated by a start codon (AUG) and terminated by stop codons (UAA, UAG, UGA) The triplet code was discovered by many different The bacteriophage r11 locus studied by Brenner - Two phages, each infected and lysed a different strain of E.coli (B or K12) - Certain mutations prevented lysing - Brenner added proflavin, a chemical that causes a single nucleotide mutation - These proflavin treated bacteriophages would revert and resemble WT - This was due to the original mutation disturbing the reading frame, and proflavin correcting it Page 2

3 DNA mrna Polypeptide Wild-Type TGCTGCTGCTGCTGC ACGACGACGACGACG Thr Thr Thr Thr Thr Lyses Bacteria Mutation DNA mrna Polypeptide TGCGCTGCTGCTGCT ACGCGACGACGACGA Thr Arg Arg Arg Arg Doesn't Lyse Bacteria Proflavin DNA mrna Polypeptide TGCGCTGCCTGCTGC ACGCGACGGACGACG Thr Arg Arg Thr Thr Lyses Bacteria The ability to synthesize mrna allowed for the triplet code - Nirenberg and Matthaei created RNA homopolymers, that repeated only one nucleotide - Then, they allowed E. coli to create a protein using the RNA homopolymers as a template - Afterwards they used RNA heteropolymers, that repeated two or more nucleotides RNA Homopolymers UUUUUUUUUUUUUUUUUUUUUUUU Phe Phe Phe Phe Phe Phe Phe Phe Phe Phe Page 3

4 PRACTICE: 1. Which of the following characteristics does NOT describe the triplet codon code? a. Degenerate b. Nonoverlapping c. Nearly Universal d. Overlapping 2. Which of the following codons is a start codon? a. AUG b. UAA c. UAG d. UGA Page 4

5 3. Which of the following were used to discover the triplet code? a. DNA homopolymers b. RNA homopolymers c. Protein lysis d. DNA sequencing Page 5

6 CONCEPT: Transfer RNA Transfer RNA (trna) is responsible for translating a codon into an The structure of a trna has - An anticodon which is complementary to the codon - An amino acid attachment site - A structure like a clover leaf Aminoacyl-tRNA synthetases attach amino acids onto the trna - There are 20 aminoacyl trna synthetases, one for each amino acid - A charged trna has an amino acid attached to it trna structure. Yellow is the amino acid binding site, grey is the anticodon Page 6

7 PRACTICE: 1. Which of the following structures is not a part of a transfer RNA? a. Anticodon b. Amino acid attachment site c. Codon d. Clover leaf structure 2. Which of the following enzymes is responsible for attaching amino acids onto the trna? a. trna attachases b. Aminoacyl-tRNA synthetases c. Aminoacyl-tRNA attachases d. trna lysases Page 7

8 CONCEPT: RIBOSOME STRUCTURE The Ribosome is a RNA-protein complex responsible for translating mrna into The ribosome structure has: - One large and one small subunit - A composition of 2/3 rd RNA and 1/3 rd protein The ribosome is in the nucleolus The ribosome positions the trna onto the mrna - A (aminoacyl) site binds incoming charged trna molecules, and matches the anticodon with the codon - P (peptidyl) site is the location where the amino acid is attached to the growing peptide chain - E (exit) site is the location where the deacetylated trna is ready to be released - Decoding center assures only the proper trna is matched with the codon - Peptidyltansferase center is the region where the peptide bond is catalyzed Page 8

9 PRACTICE: 1. Which of the following is true regarding the ribosome structure? a. Ribosomes are made up of only proteins b. Ribosomes are made up of only RNA c. Ribosomes are made up of both protein and RNA d. Ribosomes are made up of neither protein nor RNA 2. Which of the following is not a ribosomal position used to add amino acids to a growing polypeptide chain? a. A site b. C site c. P site d. E site Page 9

10 3. Which of the following ribosomal sites is responsible for adding the amino acid to a growing polypeptide chain? a. A site b. C site c. P site d. E site 4. Ribosomal assembly occurs where in the cell? a. Golgi b. Cytoplasm c. Endoplasmic Reticulum d. Nucleolus Page 10

11 CONCEPT: TRANSLATION Translation is the process of turn mrna into protein, and occurs in three steps: initiation, elongation, and termination Prokaryotic translation initiation requires a specific - The shine-delgarno sequence is responsible for prokaryotic initiation - Proceeds the initiation codon, and helps position the initiator trna - Initiation factors (IF1,2,3) are required for correct initiation Eukaryotic translation initiation requires many proteins - mrna in the cytoplasm has many secondary structures, and is covered in proteins - Initiation factors (Eif4,A,B,G) associate with the 5 cap, remove proteins, and expose the mrna - The initiation complex scans the mrna looking for the AUG start codon - A kozak sequence is a consensus sequence around the start codon that increases translation efficiency An initiator trna initiates - For prokaryotes the trna is attached to N-formylmethionine - For eukaryotes the trna is attached to an initator methionine (trna met i) Page 11

12 Once the AUG start codon has been found, the ribosome is and elongation can begin Each of the ribosomal sites (A,P,E) are important during translation - Elongation factors (Ef-Tu, Ef-G) assist the ribosome and trna in protein synthesis - These are controlled through GTP hydrolysis 1. A charged trna binds to Ef-Tu-GTP, and enters into the A site 2. GTP is hydrolyzed and Ef-Tu is released 3. The trna moves to the P site, and the amino acid is attached to the growing polypeptide chain 4. EF-G binds in the P site 5. EF-G-GTP hydrolysis moves the trna from the P to the E site Termination is through stop codons and release factors Release factors are proteins that recognize stop codons - Stop codons include UGA, UAA, OR UAG When a ribosome encounters a stop codon, and release factors binds instead of a trna - The release factors hydrolyze GTP and this terminates translation Page 12

13 The wobble hypothesis states that the third nucleotide in a codon is less than the first two - Allows the anticodon of the trna to pair with more than one mrna sequence - Helps multiple codons code for the same amino acid Leu Leu trna G A G trna G A G mrna C U C mrna C U U Page 13

14 PRACTICE: 1. In prokaryotes, which of the following sequences is responsible for initiating translation? a. Kozak sequence b. Initiation sequence c. Shine-delgarno sequence d. Elongation sequence 2. True or False: The methionine used to initiate translation is the same methionine used during translation elongation. a. True b. False Page 14

15 3. Which of the following chemical reactions provides the ribosome with the energy required to complete translation? a. ATP hydrolysis b. GTP hydrolysis c. Protein lysis d. H2O hydrolysis 4. Which of the following represents the wobble hypothesis? a. CUC and CUA encode for different amino acids b. CUC and CUU encode for the same amino acid c. trna is specific for only one codon d. CUC and CUG encode for stop codons Page 15

16 GENETICS - CLUTCH CONCEPT: PROTEINS Proteins are composed of amino acid monomers, organized into polypeptide chains There are four levels of proteins - Primary structure is the amino acid sequence in a polypeptide chain - Secondary structure is the local structure found in a polypeptide chain - Includes alpha helices and beta sheets - Tertiary structure is the 3D structure of the entire polypeptide chain - Quaternary structure is the 3D structure of multiple polypeptide chains in a protein Each protein has an amino end (NH2) and a carboxyl end (COOH) Page 16

17 Amino acid R groups provide proteins with certain properties - R groups can be: nonpolar, polar, positively charged, negatively charged Proteins are into two types - Globular proteins are compact proteins - Fibrous proteins are linear proteins Proteins have domains which are structural regions that have specific functions Chaperone proteins are responsible for helping proteins fold correctly Page 17

18 PRACTICE: 1. Which of the following protein structures describes a 3D structure of one polypeptide chain? a. Primary structure b. Secondary structure c. Tertiary structure d. Quaternary structure 2. Which of the following describes the amino acid sequence of a polypeptide chain? a. Primary structure b. Secondary structure c. Tertiary structure d. Quaternary structure Page 18

19 3. Which of the following describes the 3D structure of multiple polypeptide chains in a single protein? a. Primary structure b. Secondary structure c. Tertiary structure d. Quaternary structure 4. Which of the following describes the local structures formed in a single polypeptide chain? a. Primary structure b. Secondary structure c. Tertiary structure d. Quaternary structure Page 19