BIO206H5 Lecture Notes - Lecture 10: Start Codon, Radionuclide, Non-Coding Rna

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30 Oct 2016
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BIO206 Protein Synthesis
- Process that involves the synthesis of a linear sequence of amino acids proteins themselves
are made up of a limited number of 20 L-amino acids
- Protein synthesis process has a directionality to it very discreet, one step at a time process,
one peptide at a time is formed
- Protein begins synthesis at N-terminus, guided by the mRNA which is translated from
the ’ ed to the ’ ed of RNA
- Leads synthesis of protein from N-terminus to C-terminus
- Once the process is finished, there is post-translational modification
Translation (very complicated!)
- Every organism has protein synthesis machinery 100 different macromolecules that are core
requirements for protein synthesis
- Three major types of RNA that participate: mRNA, rRNA, tRNA
- mRNA where information is stored, primary sequence of amino acid is designated is
on this
- rRNA ribosomal RNA catalytic component; formed into large complexes; catalysis of
peptide bonds in sequence determined by mRNA
- tRNA transfer RNA adaptor molecules allowing for 4 letter nucleic acid code to be
converted into 20 letter amino acid code
- Other types of RNA molecules such as noncoding RNA (snRNA involved in spliceosome
complex)
The Genetic Code
- How does a series of four nucleotides code for 20 amino acids?
- A single nucleotide coded for a single amino acid would only result in FOUR amino acids not a
1:1 ratio; similar for a doublet (too small)
- 3 nucleotides (triplet) coding for 64 amino acids (43) is the SMALLEST that can have a
unique combination for 20 amino acids
- Not necessarily right answer but it is a starting point
- Initial experiments involved making synthetic RNA
- Taking uridine residues and making a small RNA molecule, using a cell free system you
would add the artificial RNA into cell free system and add a variety of acids (1 of which
might be radioactive)
- See what fraction the radioisotope is found for instance, when using Poly-U
UUUUUU… the got sall portios of just polPhe phe-phe-phe) so U may code for
phenylalanine
- Poly-A AAAAAA… ol polLs ls-lys-lys)
- Poly-C CCCCCC… ol polpro pro-pro-pro)
- Had to start getting into combinations
- Genetic code is a nonoverlapping, degenerate, comma-free, triplet code
- Codon: group of bases that specifies a single amino acid the code is read in units of 3
nucleotides
- 3 bases per codon (triplet) = 64 combinations
- 44 combinations do NOTHING or are degenerate (amino acids specified by more than one
codon)
- Cysteine has two codons, UGC and UGU
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- Methianine only has ONE CODON but arginine has six different codons that can specify
has a degenerate code
The standard genetic code
- Best portrayed in a table synonyms usually 3rd positios ole
- I.e. CUU, CUC, CUA, CUG all code for leucine the organization of the table in this
format allows us to translate it into amino acids and it helps us identify where the
degenerate codons are
- 61 of 64 codons describe amino acids
- 2nd position if more than 4 synonyms (e.g. Leu)
- Phenylalanine has a degenerate code as well
- AUG (met) is a START CODON codes for the amino acid methionine; only codon that codes for
methionine (also typically the codon that indicates START protein synthesis)
- Only a single codon for methionine because it is a start codon
- What is unique about methionine is it is one of the two sulfur containing amino acids
distinguishes it as the start amino acid
- UAG, UAA, UGA are STOP CODONS happen at the end of an RNA molecule
- Is the degeneracy of the genetic code random or is there some evolutionary advantage?
- The genetic code is NOT a random degenerate code but it is a very specific, highly
selected for process that gives advantage to the cells
Recall: Primary sequence of beta-hemeoglobin the effect of a single change may be huge
- Changes structure of blood cells and oxygen carrying capacity single point mutation can be
very deleterious
- Can lead to non-viable organisms that die before birth or are not viable at all
- Real disadvantage of single-point mutations in the genes
Degenerate code minimizes effect of mutations
- Point mutations occur frequently we have a very elaborate DNA system to get rid of them but
sometimes that fails so now we rely on degeneracy of genetic code to minimize IMPACT OF
THE SINGLE NUCLEOTIDE CHANGE IN DNA
- For instance, AGC ACA causes Ser Arg (going from a polar to a possible charged amino acid
possible deleterious effect)
- BUUUT GCA GCU causes Ala Ala this causes a SILENT MUTATION
- This mutation has been negated by the degeneracy of the code two different codons
used to code for alanine
- Degeneracy many mutations at 3rd odo positio are silet
- XYU XYC all synonyms
- XYA and XYG all synonyms except trp/stop ile/start (met)
2nd Codon Position
- If the purine is in second position, they often code for polar amino acids
- If it is a pyrimidine, it codes for hydrophobic amino acids
- If we switch one purine for another purine, we are MINIMIZING the effect by substituting for
one polar amino acid for another
- Same thing for pyrimidine-pyrimidine swap still hdrophoi; has’t ullified the
mutation but has minimized the effect
1st Codon Position
- UUU = F CUU = L AUU = I GUU = V
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Document Summary

Process that involves the synthesis of a linear sequence of amino acids proteins themselves are made up of a limited number of 20 l-amino acids. Protein synthesis process has a directionality to it very discreet, one step at a time process, one peptide at a time is formed. Protein begins synthesis at n-terminus, guided by the mrna which is translated from the (cid:1009)" e(cid:374)d to the (cid:1007)" e(cid:374)d of rna. Leads synthesis of protein from n-terminus to c-terminus. Once the process is finished, there is post-translational modification. Every organism has protein synthesis machinery 100 different macromolecules that are core requirements for protein synthesis. Three major types of rna that participate: mrna, rrna, trna. Other types of rna molecules such as noncoding rna (snrna involved in spliceosome complex) A single nucleotide coded for a single amino acid would only result in four amino acids not a. 1:1 ratio; similar for a doublet (too small)

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