Notes

• mRNA, in eukaryotes, consists of a 5' cap, a 3' polyA tail, and no introns.
• Codons are triplets of the nucleotides (adenine, guanine, cytosine, and uracil).
• There are 64 possible codons.
• The start codon is AUG, and it codes for the amino acid methionine.
• The three stop codons are UGA, UAA, UAG
• At the 3' end of tRNA, there is the amino acid holding domain, or CCA.
• Anticodons are triplets that are complementary to the codon in mRNA. For instance, if the codon is AUG, the anticodon is UAC.
• The characteristics of the genetic code are that it is commaless (except viruses), non overlapping, and redundant or degenerative.
• Redundancy in the genetic code is seen when multiple codons code for the same amino acid. For example, AUA, AUC, and AUU all code for isoleucine.
• Some exceptions to the redundancy of the genetic code is that methionine is coded by AUG and tryptophan is coded by UGG.
• The wobble effect is when the last part of the anticodon triplet has ionisine. Ionisine can pair with adenine, uracil, and cytosine. This decreases the risk of mutation.
• tRNA

  A) A A binding domain

  B) T arm

  C) Variable arm

  D) Anticodon arm

  E) Anticodon

  F) D arm

  
• The 3' CCA, or A A binding domain, holds an amino acid.
• The T arm tethers the tRNA to the ribosome.
• The D arm identifies the amino acids by tRNA synthesase or amino acyl tRNA sythesease.
• tRNA needs to charge. Here, ATP binds to the amino acid and releases PPI. This leads to an amino acyl AMP. The D arm then puts the charged amino acid into the 3' CCA. This releases the AMP (degrades the energy).
• In eukaryotes, the large ribosomal subunit is 60s and the small subunit is 40s. The total weight is 80s.
• In prokaryotes, the large ribosomal subunit is 50s and the small subunit is 30s. The total weight is 70s.
• Ribosomes are rRNA and proteins.
• Aminoglycosides, like gentamycin, and tetracyclines, like doxycyclin, are antibiotics that target the 30s ribosomal subunit in prokaryotes.
• Macrolids, like erythromycin, target the 50s ribosomal subunit of prokaryotes.
• In prokaryotes, the Shine Delgano sequence (AU rich) occurs before AUG.
• In prokaryotic initiation, initiation factors identify the Shine Delgano sequence and bind the small ribosomal unit about eight nucleotide units down. Then the start codon, AUG, codes for N-formylmetionine. Then, the large ribosomal subunit binds to initiation factors. This requires energy in the form of GTP hydrolysis. The large subunit then binds to the small subunit, with the first tRNA (with fmet) in the P site. Then, the hydrolysis of GTP removes the initiation factors.
• In eukaryotes, EIF IV (eukaryotic initiation factors), bind to the small ribosomal subunit. This then binds to AUG, the start codon. The brings in tRNA with methionine. EIFII then binds to the large ribosomal subunit through GTP hydrolysis. The large subunit them binds to the small subunit, with the tRNA in the P site. GTP hydrolysis causes the removal of EIF.
• Large ribosomal subunit is made up of the A, P and E site.
• The A site, or amino acyl site, is the amino acid arrival site.
• The P site id the peptidyl site, where the peptide forms.
• The E site is the exit.
• In elongation, the first tRNA is already in the P site. GTP and elongation factor I bring the next tRNA with the correct anticodon into the A site. GTP hydrolysis puts the tRNA in the A site. Peptidyl transferase causes the N group of the amino acid in the A site to attack the C group of the amino acid in the P group. This lengthens the peptide chain. Translocation occurs, where elongation factor two and GTP hydrolysis move the ribosome further down the chain. The tRNA in the E site is then kicked out and begins charging.
• In termination, a stop codon comes to be bottom of the A site. This causes release factor to bind to the A site. This stops translation and cuts the peptide.
• Proteins made in the rough ER are secreted, incorporated into the cell membrane, or are lysosomes.
• Once mRNA leave the nucleus, it may contain a signal sequence that is 9 to 10 units. This means that it needs to go to the rough ER. Then, signal recognition particle recognizes the signal sequence and binds to it. Then, the signal recognition particle binds to the signal recognition particle receptor on the rough ER.
• After mRNA is bound to the signal recognition particle receptor GTP then binds to the signal recognition particle and the signal recognition particle receptor. The hydrolysis of these GTPs causes the translocon on the rough ER to open. The signal receptor particle dissociates. The ribosome on the mRNA goes over the top of that translocon and the polypeptide goes down it. Then signal peptidase in the rough ER lumen degrades the signal sequence. Once the stop codon is reached, the ribosome dissociates, the translocon closes, and the peptide is released.
• Free ribosomes produce cytoplasm proteins, nuclear proteins, mitochondrial proteins, and peroxisomal proteins.
• Post-translational modifications include adding sugars, lipids, phosphate groups, hydroxyl groups, methyl, acetyl, and cutting.
• Glycosylation is post-translational modification of a polypeptide with sugar. An example of this is antigens and red blood cells.
• Lipidation is the post translational modification of a polypeptide with lipids. An example of this is with cell and organelle membranes.
• Phosphorylation is post translational modification of a polypeptide with a phosphoryl group. An example of this is protein kinase A, where a phosphoryl group activates it.
• Hydroxylation is the post translational modification of a polypeptide with a hydroxyl group. An example of this is collagen.
• Methylation is the post transcriptional modification of polypeptide with a methyl group. This binds to histone, making it tighter and decreasing transcription.