BIOL-L211Exam # 4 Study Guide Lectures: 29 - 35Lecture 29 (November 12)Introduction to Genetic CodeHow many bases are in a codon, and what does it code for?3; A codon codes for one specific amino acidWhat is the three base pair code for a start codon, and for which amino acid does it code?AUG; it codes for methionineHow many naturally occurring amino acids are there and what are their defining characteristics?20; each amino acid has an amino group (hence "amino"), a carboxylic acid group (hence "acid),a hydrogen atom, and a side chain ("R" group = carbon containing chain which may or may not contain heteroatoms)How are codons arranged in an open reading frame, and what does an open reading frame codefor?Codons are arranged side by side, but not overlapping in an open reading frame, which codes for one specific protein.How were the original experiments to decipher genetic code performed?Transcripts were made with exclusively U's, A's, and C's; All U's produced PhenylalanineThen, transcripts were made with alternating nucleotidesCAC produced HistidineACA produced ThreonineWhat is transfer RNA (tRNA), and what does it code for?Transfer RNA does not code for anything. Instead, it recognizes codons by base pairing with them at its anti-codon in order to ensure the addition of the proper amino acid in response to the codon.What is the purpose of Pol III?Pol III synthesizes tRNA.Describe the structure of tRNA, and define the main components.tRNA has a cloverleaf structure with an anticodon segment (which binds a specific codon), an acceptor arm, In what direction is a codon read?The codon is read 5' to 3'Why is the genetic code degenerate?The genetic code is degenerate because there are only 20 amino acids, but there are 64 possiblecodon arrangements, meaning that some amino acids can be coded by multiple codons.What is the Wobble Effect?The phenomenon by which one codon can bind with more than one anticodon in certain situationsWhich nucleotide on the anticodon is capable of base pairing with more than one type of base?3'Which nucleotide of the codon is capable of pairing with more than one type of base in its respective position on the anticodon?5'What are the mixed-pair possibilities (for the Wobble Effect)?The Anticodon G can pair with U or CThe Anticodon U can pair with A or GThe Anticodon I can pair with A, U, or C (where I is inosine- unique to tRNAs)Explain the difference between silent, missense, nonsense, and frameshift mutations.Silent mutations are changes to a base pair in a codon that has no effect on the identity of the amino acid for which it codes. Missense mutations are changes to a base pair in a codon that alters the identity of the amino acid for which it codes. Nonsense mutations are changes to a base pair in a codon that changes its identity to that of a premature stop codon. Frameshift mutations are the addition or subtraction of base pairs in a quantity that is not a multiple of three, thus changing the identity of the protein for which an ORF codes.Lecture 30 (November 14)Introduction to TranslationWhat is Google's marketing strategy regarding genomic data?Google is creating a database to store genomic data. People will be able to pay to store data andpay to access/compare/analyze existing data.What are some of other groups competing with Google in this initiative?Microsoft, IBMWhat organelles are responsible for translation? Describe their composition.Ribosomes; Ribosomes are composed of a large and small subunit and contain A, P, and E sites (peptidyl transferase center- in large subunit) for translation; they are composed of rRNA (ribosomal RNA) and proteinsProvide a simplified version of the translation process.Initiator tRNA is recruited and interacts with AUG. The large subunit then binds. The second codon is aligned. The second tRNA comes. The peptide bond is formed and the ribosome movesover to the next codon. Initiator tRNA is transferred to the E site, where it is ejectedWhat are the main differences between translation in prokaryotes and translation in eukaryotes?Translation in prokaryotes occurs in the same location as translation. Additionally, translation initiation in prokaryotes is less complicated than translation initiation in eukaryotes, and involves different transcription initiation factors.What is polycistronic mRNA, where is it found, and under what circumstances does it occur?Polycistronic mRNA is found in prokaryotes and has multiple ORFs. It is found when genes are organized in an operon.What is monocistronic mRNA and where is it found?Monocistronic mRNA has only one ORF and is found in eukaryotes.What makes aminoacyl-tRNA synthetases unique?Aminoacyl-tRNA synthetases charges tRNAs.What makes a tRNA "charged" or "uncharged"?A charged tRNA has an amino acid bound to the acceptor stem; uncharged tRNA has no amino acidWhat are the building blocks (substance) of a ribosome?Ribosomal RNA and ProteinsWhat does the large subunit of the ribosome do, and how does its centrifugation velocity differ between prokaryotes and eukaryotes?The large subunit holds the peptidyl transferase center (A, P, and E sites); this center is responsible for forming the bonds between amino acids to form protiens60S in eukaryotes; 50S in prokaryotesWhat is a "Svedberg unit"?A unit to measure centrifugation velocityWhat does the small subunit of the ribosome do, and how does its centrifugation velocity differ between prokaryotes and eukaryotes?The small subunit is the first to bind mRNA, and is the location where mRNA is read by tRNAs40S in eukaryotes; 30S in prokaryotesName a relevant target of antibiotics in bacteria.The RibosomeWhat does the P site do?P site recruits initiator tRNAWhat does the A site do?The A site sets the alignment of the second codonWhat takes place at the E site?Ejection (of uncharged tRNA)Lecture 31 (November 17)Translation IWhat is the ribosomal binding site, where is it located, and what is its sequence in prokaryotes?The Ribosomal Binding Site (RBS) is a consensus sequence 3-9 base pairs upstream of the start codon; it is recognized and bound by ribosomes; 5'-AGGAGG-3'Which component of mRNA is the most important for the recruitment of the ribosome?5' capWhere are Kozak sequences found, and what do they do?Kozak sequences are found in eukaryotes and they increase the efficiency of translationWhere must the start codon always be placed for translation to begin?P siteWhat is the advantage of the polysome?Prevents mRNA from degrading as