12-5-12Biology Final Exam: Dec 5- ATP – Adenosine triphosphate – energy money for the cello Broken down into ADP + phosphate Phosphate is used to create a phosphorylated intermediate This is how the cell captures the energy released when you hydrolyze ATPo Uses the purine adenine- GTP – guanosine triphosphateo Uses the purine Guanineo Identical to ATPo Initiation of translation uses a GTP as an energy source to complete the assembly of the transcription initiation complex- Elongationo First step The initiation complex has a codon in the A site, a transfer RNAwith an anticodon that is complementary to that codon goes into the A site. Once it is there, a bond transfer occurs connecting a transfer RNA to a polypeptide is broken and an AA is bonded to another. The amino acid in the P site has nothing attached to it and the AA in the A site has the polypeptide attached to it. - Used a GTP Another GTP is used. That energy is used to eject the transfer RNA that was in the P site, which goes back into the cytoplasm where it is recharged with its AA again.- Transfer RNA’s are constantly used and then recharged The transfer RNA with a polypeptide that was in the A site is then ejected and moved to the P site A new transfer RNA is brought into the A site and the same process is repeated again- Occurs in milliseconds- Elongates the strand of amino acids in the polypeptide by adding one AA at a time. Once at the end of the messenger RNA, a stop Codon appears inthe K site- There is no transfer RNA that has an anticodon complementary to the stop codon- To make sure a transfer RNA cant get in there, a protein called a release factor slides in to block the A site. Preventing RNA from accidentally sliding in there.- One the release factor bonds to the A site:o The bond that bonded the polypeptide to the 3 prime position is broken and the completed polypeptide is released12-5-12o Transfer RNA is ejected from the P site, another GTP molecule is used to separate out the two components of the ribosome and messenger RNA Everything is used over and over again- Prokaryotes – transcription and translation is coupled – both happen at the same timeo There is no nucleus so the DNA is translated into a messenger RNA molecule. The instant the RNA molecule is starting to be produced, a ribosome grabs onto the messenger RNA and a polypeptide begins being produced.- Moving proteins to specific destinations in the cello Ribosomes can be free or boundo Free Found in the cytoplasm (cytosol) Proteins produced function in the cytoplasm of the cell- Ex- enzymes of glycolysiso Bound Attached to the endoplasmic reticulum Produce proteins for - Secretion from the cello Transport vesicles Transporting a protein (or anything) to be secreted from the cell The transport vesicles fuse with the plasma membrane of the cell and release that secretion.- Proteins that function in the endomembrane system- Signal Peptide – 20 AA in lengetho All proteins that are going to be secreted or are going to be part of the endomembrane system begin with the same 20 AA AA are always the sameo Signal recognition particle Like a SNURP- SNURPS – ribonucleoproteins  Complex of RNA in proteins Grabs onto a signal peptide and transports the ribosome and mRNA to a protein in the plasma membrane in the endoplasmic reticulum Translation continues- The protein produced during translation either goes to the inside of the ER or stays on the plasma membrane ofthe ER12-5-12- Mutations – change in the base sequence of a geneo Caused by mistakes by DNA polymerases They have proofreading ability, so mistakes are rarely made – 1010 = almost perfecto Mutagen - a thing that causes a mutation Chemical – base analog (Benzene) – common mutagen – similar in structure to the bases of DNA- The DNA polymerases might mistake benzene for adenine- Chemicals that can fool polymerases Radiation – X-Rays- UV (Ultra Violet) Light – Can cause two thymine’s whichare right beside of each other to for a covalent bond together – Thymine Thymine Dimer (bad) - When replication occurs – the daughter strand will get another nucleotide other than A to bond to it.- Mutated Daughter Strando Point Mutation – Involves a single nucleotide change When one of the bases is change – commonly substitutions, butcan be insertions or deletions Substitution point mutations – substitutes one nucleotide for another- Silent – no AA change- Missense - a single AA change- Nonsense – Involves creating a stop codon in the wrong place Sickle Cell Anemia is an example of a Missense – serious- Most common in people from Africa and the middle east- Abnormal form of hemoglobin- The red blood cell will be sickle shaped- Causes pain and tissue damage because it clogs the small blood vesicles.  Silent point mutation- GGC to GGU codon- They both code for Glycine - as a result of changing GGC to GGU, there is no mess up- Silent mutations exist because the genetic code is unambiguous and redundant Missense Point mutation- One amino acid change in the final protein- Sickle cell Nonsense mutation- Creates a stop codon prematurely- A protein product wont be produced at all or it will be so small it doesn’t have a normal function12-5-12 Insertions and deletions- Much more serious than substitutions- They always cause a frame shift- AAACCCGGGUUU  normal- AAAUCCCGGGUUU  U was inserted between A & C- 1st Codon is still AAA – Normal, but the 2nd is now UCC instead of CCC, 3rd is CGG instead of GGG, 4th is now GUU instead of UUU- Codons downstream of the insertion or deletion are always all changed- The protein will either be vastly different and not function or the frame shift will cause a stop codon very quicklyChapter 18 (Last Chapter!) Gene Regulation – turning genes on or off- Prokaryoteso Genes  Constitutive – Genes that are always on- Ex - glycolysis Inducible – Genes that are normally off but can be turned on Repressible – Genes that are normally on but can be turned offo Operons – Page 1 of final – a group of related structural genes and their controlling elements Almost always exclusively in prokaryotes Lactose Operon – Inducible Three related genes – A, B, C Controlling elements – promoter, operator, and terminator. (Promoter)(Operator)(Gene A)(Gene B)(Gene C)(Terminator) - (Line is a strand of DNA – they’re all on