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Class Notes (Friday 10/7/16)

by: Tiffany Norris

Class Notes (Friday 10/7/16) Biol 201

Marketplace > Loyola Marymount University > Biology > Biol 201 > Class Notes Friday 10 7 16
Tiffany Norris
Loyola Marymount University

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Class notes based on Friday Oct 7th lecture.
Cell Function
Yiwen Fang
Class Notes
Biology, RNA, transcription, translation, protein, degradation
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This 4 page Class Notes was uploaded by Tiffany Norris on Friday October 7, 2016. The Class Notes belongs to Biol 201 at Loyola Marymount University taught by Yiwen Fang in Fall 2016. Since its upload, it has received 5 views. For similar materials see Cell Function in Biology at Loyola Marymount University.

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Date Created: 10/07/16
CELL FUNCTION: Chapter 7 Friday 10/7/16 Translation What is needed for translation? If we are going to make proteins, we need: 1. mrRNa (template) 2. tRNA (translator) 3. rRNA + ribosome (machinery) 4. Building blocks: amino acids 5. Energy Translation is one of the slowest processes we have talked about so far. It is more complicated as well. tRNA  tRNA is used for translating. It links RNA and protein together (about 80 base pairs long) o forms a weird/unique shape, a clover leaf shape *must know shape  three loops and one major stem  Recall: RNA polymerase III makes tRNA genes How does tRNA act as a translator? 1. Reads the codon at the anticodon region by forming a base pair with the codon, in an anti-parallel orientation, 2. Bring the amino acids that correspond to the codon a. Happens at the acceptor stem i. Has a 3’ overhang sticking out that has CCA nucleotides ii. Is on the opposite end of the anticodon region. Step 1:  Need to charge the tRNA. o Covalently link a tRNA molecule with an amino acid o Uses aminoacyl-tRNA synthetase (enzyme)  Charges tRNA by attaching the correct amino acid.  Uses ATP to form covalent bond between the acceptor end (CCA) and the amino acid.  Now tRNA is charged and is able to take the amino acid into the ribosome o How many aminoacyl-tRNA synthetase enzymes do you need?  At least 20 (for each amino acid)  Really about 41 Step 2:  Need to get the ribosomes (machinery) ready o How?  Recall: ribosomes are located in the cytosol and on the E.R.  They are made of rRNA and ribosome proteins.  There are ~ 82 ribosome proteins  Majority of the ribosomes are made of RNA (2/3)  They are made of two units, large and small. o Large = has three species of rRNA o Small = only has one species of rRNA o Ribosome is a ribozyme – an RNA molecule that has catalytic activity  It works as a protein (enzyme) that carries out reactions  rRNA is folded to form a core  Form the catalytic site, a peptidyl transferase  Ribosomal proteins are located on the surface  How does ribosome do all this? o Small and large subunits o Exit site o Peptidyl-tRNA binding site o Amino acyl- tRNA binding site Video explanation of this:  mRNA is translated into protein.  Translation begins when mRNA binds to ribosome  Start codon occupies P site  tRNAs first enter ribosome at A site  Complementary matching on tRNA (anticodon) and codon on mRNA ensure correct sequences  mRNA passing along the ribosome 3 nucleotides at a time  They pass along from A to P to E (e meaning exit)  The amino acid is attached to the chain and the codons leave. Finally, a stop codon is reached and the process ends *METHOD IS SAME FOR BOTH free ribosomes and ER ribosomes Initiation 1. Ribosome finds start codon (AUG), initiation begins. a. Rate of initiation determines how much protein will be made b. Heavy regulated step c. There are a lot of proteins involved called initiation factors i. initiator tRNA is involved as well (carries the amino acid Methionine) ii. Methionine attaches at P site 1. Large subunit attaches 2. Then a new incoming tRNA occupies the A site and the attached amino acid links on to the Methionine via peptide bond Elongation 1. New incoming tRNA always comes to A side and attaches to the polypeptide acid chain 2. tRNA once the amino acid has left and attached to the chain, is no longer needed and is ejected on the E site. Termination Where does it terminate? a. When it encounters the stop codon (UAA, UAG or UGA) b. Stop codon does not code for an amino acid c. No tRNA recognizes the stop codon. i. Instead the cells use release factors that are shaped like tRNA. They’re like fake tRNA. Binds to the A site. ii. Since the release factor doesn’t actually code for anything, the ribosome adds water which adds an H+ to the end of the chain and the amino acid chain, which tells it to release. 1. Water is the signal that the job is done. d. Newly made protein will get bound by a chaperone protein Prokaryotes vs. Eukaryotes More translation factors in eukaryotes Both have polyribosome (“polysomes”): multiple ribosomes attached to mRNA  Efficient translation Bacteria (prokaryotes):  Polycistronic, meaning in one mRNA you carry multiple coding sequences that will be made into multiple proteins o (operon: a unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis.) Eukaryotes  Monocistronic: only one transcript per protein Question: What can you do to stop / interrupt translation artificially? Class Answer: (1) Kill the ribosome (2) Take away the initiator tRNA (3) Make fake tRNA to occupy EPA sites Antibiotics Naturally made compounds that kill bacteria. All inhibit or interrupt protein translation (look at the examples on slide 15)  Tetracycline: No tRNA can get to A site  Streptomycin: Prevent initiation factor, preventing getting to the elongation step Antibiotics can preferentially work on the eukaryotic cells, but also sometimes harm the host bacteria. Protein Degradation / Modification  Once protein is made, if they are damaged or no longer needed they will be degraded o Process called Proteolysis  Cell has such small space, so anything that is not useful needs to be disposed Proteasomes are the large protein machines found in cytosol and nucleus to damage the proteins o How does the proteasome know which ones need to be degraded?  The proteins have tags called ubiquitins at specific sites  Process called ubiquitination  Chains of ubiquitins called polyubiquitin chains o Ubiquitins are re-used / recycled  Once proteins are done sometimes they need to have groups added to them for functional purposes o E.g. Phosphorylation, methylation, etc.


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