Wednesday Notes: Chapter 15 and 18
Wednesday Notes: Chapter 15 and 18 30156
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This 5 page Class Notes was uploaded by Hannah Kennedy on Sunday August 7, 2016. The Class Notes belongs to 30156 at Kent State University taught by Dr. Helen Piontkivska in Spring 2016. Since its upload, it has received 9 views. For similar materials see ELEMENTS OF GENETICS in Biological Sciences at Kent State University.
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Date Created: 08/07/16
Lecture 7—8/3/16 Lecture Notes Ch. 15 and Ch. 18 Ch. 15: translation of mRNA 1. Key concepts a. mRNA encodes proteins i. structural genes = genes that encode an AA sequence ii. mRNA = the RNA transcribed from structural genes b. alternative splicing c. translation decodes mRNA into AA sequences i. degenerate = characteristic of the genetic code because the number of possible codons exceeds 20 AA rd rd ii. wobble base = the 3 base is referred to as this because it is the 3 base in the codon is the base that varies 1. the complementary base in the tRNA can wobble during the recognition of the 3 base of the codon d. protein function and its 3D structure 2. Genetic code in mRNA is used to make a polypeptide a. sense codons = the sequence of 3 bases in most codons that specifies a particular AA b. start codon = AUG codes for Met; the first codon that begins a polypeptide sequence i. reading frame = defined by the start codon; a sequence of codons determined by reading bases in groups of 3 beginning with the start codon 1. frameshift mutation = mutation in which a single-nucleotide insertion would alter the reading frame beyond the point of insertion and destroy proper protein function thereafter c. stop codons = non-sense codons = termination codons = UAA, UAG, UGA; used to end the process of translation d. codons in mRNA are recognized by the anticodons in tRNA 3. Proteins carry out diverse functions a. one-gene/one-enzyme hypothesis = the hypothesis that states that a single gene controls the synthesis of a single enzyme 4. Overview of polypeptide a. Peptide bond = formed as a polypeptide is made between the carboxyl group in the last AA of the polypeptide and the amino group in the AA being added i. Occurs via a condensation reaction b. N-terminus = the end at which the first AA is located at; amino group found here c. C-terminus = the end at which the last AA is located; carboxyl group found here d. R-group = side chain = each AA contains this with particular chemical properties i. Directionality of AA goes from the N-terminus to the C-terminus and corresponds to the 5’ to 3’ orientation of codon in mRNA 5. Amino acid structure a. Major properties i. Size ii. Charge iii. Hydrophilic/hydrophobic—play important role in dictating the shape 1. Hydrophobic AA are buried within the interior of a folded protein 2. Hydrophilic AA are more likely to be on the surface of a protein where they can favorably interact with water b. Amino acid sequence—proper folding is important for proper function (proteins fold in the most optimal formation) i. Primary—linear 1. Occur following gene transcription and mRNA translation— polypeptide linear chain with a defined AA sequence 2. Not yet a functional unit a. To become a functional unit, the polypeptide chain must fold to a 3-D structure which happens while the polypeptide is still being translated i. Thermodynamically favorable process (i.e. it is spontaneous) ii. Secondary—a regular, repeating shape; stabilized by the formation of H bonds between atoms in the polypeptide backbone 1. Alpha helix 2. Beta sheet (alpha or beta) a. Parallel b. Antiparallel iii. Tertiary—3D structure of proteins that arise from secondary structures folding into each other iv. Quaternary—made of 2 or more polypeptides that associate with each other to make a functional protein (e.g. hemoglobin) 6. Translation a. Ribosomes = the macromolecular arena where translation occurs (contains a large and small subunit that act as adaptors to bring the AA close enough so that a covalent bond can form between them) i. Subunits are made of rRNA and proteins ii. rRNA = ribosomal RNA = constitutes the mass of the ribosome iii. 3 sites on the ribosome 1. A site = site that you go to when you want to add an AA to a growing peptide chain 2. P site = site you go to after the A site where the AA is linked to the peptide chain 3. E site = site where the spent tRNA is moved by the large ribosomal subunit iv. Prokaryotic subunits are smaller and simpler Phe b. tRNA—named according to the AA they carry (e.g. tRNA ) i. codons in mRNA are recognized by the anticodons in tRNA 1. anticodons = 3-nucleotide sequences that are complementary to codons in mRNA a. codon/anticodon binding o ccurs in an antiparallel manner ii. tRNA molecules carry the AA that correspond to the codons in the mRNA so the order of codons in mRNA dictates the order of AA within iii. adaptor hypothesis = hypothesis by Crick that states that the position of an AA within a polypeptide is determined by the binding between the mRNA and an adaptor molecule (tRNA) carrying a specific AA iv. tRNA has 2 main functions 1. it recognizes a 3-base codon sequence in mRNA 2. it carries an AA specific for that codon v. common structural features 1. cloverleaf pattern a. 3 stem loops b. few locations with additional nucleotides not found in all tRNA molecules c. acceptor stem with a 3’ ss region vi. to function correctly it must have the correct AA attached to its 3’ end 1. aminoacyl tRNA-synthetase = enzymes that catalyze the attachment of AA to tRNA molecules (20 exist in the body: 1 for each AA) (rxn involves 3 molecules) a. AA b. tRNA molecule c. ATP i. Rxn process: synthetase recognizes AA and ATP. ATP is hydrolyzed resulting in the attachment of AMP to the AA and the release of pyrophosphate. Correct tRNA binds to the synthetase. AA becomes covalently attached to 3’ end of the tRNA molecule at acceptor stem. AMP is released. Charged tRNA = aminoacyl tRNA = results dur to the realease from aminoacyl tRNA synthetase vii. Wobble rules 1. Wobble rules = state that the first 2 positions of the codon pair strictly to the AU/GC rule but the third position can tolerate certain types of mismatches therefore the base at the 3 position doesn’t have to H bond as precisely with the corresponding base in the anticodon; enables a single tRNA to recognize more than one codon a. Isoacceptor tRNAs = when 2 or more tRNAs that differ at the wobble base are able to recognize the same codon c. 3 general stages to translation i. initiation 1. ribosomal subunits, mRNA, and the first tRNA assemble to form a complex. Ribosome slides along mRNA moving over the codons 2. initiator tRNA = specific tRNA that recognizes the start codon in the mRNA ii. elongation 1. Ribosome slides along mRNA moving over the codons a. As ribosome moves the tRNA molecules bind to mRNA in the ribosome and bring them the right AA 2. tRNAs bring the first AA to the A site and a series of peptidyl transferase reactions create a polypeptide a. at each step, the polypeptide is transferred from the A site to the P site and are released from the E site iii. Termination 1. Occurs when a stop codon is reached. Disassembly occurs and the newly made polypeptide is released 2. Release factor binds to a stop codon in the A site which promotes the cleavage of the polypeptide from the tRNA and the subsequent disassembly of the tRNA. mRNA, and ribosomal subunits Ch. 18: Gene Mutation and DNA repair 1. Key concepts a. Mutations b. DNA repair c. Transposable elements 2. Evolutionary roles of mutations a. Without mutations everything would be the same and we wouldn’t adapt therefore it provides diversity (e.g. gene families) 3. Types of mutations are classified by locations a. Somatic mutation b. Germ-line mutation i. Important for evolution: major phenotypic consequences, heritable therefore the offspring may disappear from population or thrive depending on fitness 4. Spontaneous mutation rates vary between species—due to efficiency of repair system a. Different organisms have different tolerances 5. Mutations as an evolutionary force a. Important but weak force 6. Categories of phenotypic change due to mutations a. Ex: in sickle-cell hemoglobin, a glutamine is replaced with a valine. What change likely occurred at that codon? i. Can look at genetic code and state which place the code changed at b. Ex: a rare dominant mutation expressed at birth was studied in humans. Records showed that 6 cases were discovered in 40,000 live births. Family histories revealed that in 2 cases, the mutation was already present in 1 of the parents. Calculate the spontaneous mutation rate for this mutation. What are some underlying assumptions that may affect our conclusions? i. Remember assumptions they are key ii. Variable expressivity iii. Genotypes accelerated when we were able to air travel c. What kinds of changes can we expect to arise from mutations? i. Hair color, eye color, ecological changes (where do you like to live), behavioral changes (who do you like to associate with), biochemical (what kinds of temperatures are you comfortable at?) etc. 7. Types of mutations a. Point mutations = nucleotide substitutions i. SNP = single nucleotide polymorphism ii. 3 classifications of point mutations 1. Substitution—replacing one letter with another a. AA substitution?: will see some consequences, however, if we replace a hydrophobic AA with another hydrophobic AA, we won’t see a big change if at all b. Depends on how critical the protein is 2. Deletion—omitting a nucleotide from the sequence, creating a frameshift a. Need to know the ancestors of the sequences (if it was longer then it’s a deletion, if shorter than its an insertion) 3. Insertion—adding 1 more nucleotide, creating a frameshift b. Spontaneous mutations c. Induced mutations i. Due to X-rays and gamma-rays 1. Displace nucleotides and result in gaps a. Most often they will be repaired, however, if not then mutations arise ii. Indirect actions 1. Photon interacting with electron, electron interact with water molecules in the cell, polarity causes more charged ion such as hydrogens, dose increases exponentially iii. Classic paradigm of radiation injury d. Chromosomal mutations i. Polyploidy ii. Aneuploidy iii. Inversion iv. Duplication v. Deletion vi. Simple translocation vii. Reciprocal translocation 8. How can we determine whether a certain chemical is mutagenic a. Take deficient mutants (can’t grow by themselves they need help), add mixture to filter paper disk, spread bacteria on agar medium without histidine, place disk on surface of medium, incubate, if there is a large accumulation of product then its mutagenic 9. Transposable elements a. Can disable a gene, can disrupt translation of a gene, can insert into an intron and have no influence b. Influence of transposons depend on the specific transposon
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