BIOL1007 Lecture Notes - Lecture 7: Open Reading Frame, Start Codon, Reading Frame
Explain the unique problems associated with converting the
information as a nucleic acid sequence to an amino acid sequence.
Describe how these issues are overcome, with reference to the
universality and redundancy of the genetic code
Outline the unique problems associated with protein synthesis, with
particular reference to the unfavourable thermodynamics of peptide
bond formation and the requirement for order. Describe the
strategies used by cells to overcome these problems.
Need to convert sequence of nucleotides (with 4 different bases) to a sequence of amino acids
(20 different bases)
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Need to have correct order of amino acids -> order determines fold and function of the
protein
-
Peptide bond formation is very thermodynamically unfavourable
-
Must have precise start and stop for proteins -> extra amino acids may alter the fold and
function
-
Challenges of protein synthesis
4 different bases which use only one position so only 4 possible combinations (A, G, C, T)
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4 different bases BUT 2 positions = 4 x 4 = 16 combinations (e.g. AA, AG, TC)
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We will need a stop code so at least 21 combinations
○
64 is too many
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There is redundancy in the code, so some amino acids have more than one code
○
3 combinations code for stop -> so we have 61 combinations coding for 20 amino acids
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So if we have 20 amino acids -> needs minimum of 3 positions with 4 bases = 4x4x4 = 64
combinations
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The combinations
Codon - Combination of 3 bases which codes for an amino acid (triplet codon)
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Codon sequence is quoted 5' to 3' from the mRNA
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Codon will have the same sequence as the DNA strand that WASN'T copied (non-template
strand)
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Contains uracils instead of thymines (it is RNA)
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Things to know
Stop codons
UAG
UGA
UAA
Start codon
AUG - also condes for methionine (so every protein starts with
methionine)
Leucine (just an
example)
CUU
CUA
CUC
CUG
UUA
The codon
L7 - Making proteins
Thursday, 24 August 2017
8:52 PM
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UUA
UUG
Reading the code
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3 positions -> 3 reading frames
○
We want start and stop codon to be in the same reading frame ie. Open reading frame
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Start codon determines reading frame
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Read codon in triplets
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If you insert or delete downstream -> reading frame shift, so every reading frame downstream
from that changes
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Degenerate/redundant - more codons (61) than amino acids (20), so some amino acids have
more than 1 codon
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Universal - same code is used by all life forms
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Code can be described as…
Structure that bridges the nucleic acid and protein world
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Small RNA molecule, 75-90 nucleotides with lots of intra-strand loops
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3'OH - amino acid attaches
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Anticodon loop - complementary code to the codon in the messenger RNA
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tRNA - the adapter
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How does the correct amino acid get bonded to its matching tRNA?
e.g. leucine tRNA synthase will only bind to leucine
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Different side chain helps with identifying correct amino acid
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Correct amino acid binds to the enzyme
1.
ATP molecule forms
2.
Carboxylic acid reacts with first phosphate, activating the amino acid
3.
Pyrophosphate is released, breaking down into 2 phosphates (thermodynamically favourable),
so removing product drives reaction forward
4.
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Document Summary
Explain the unique problems associated with converting the information as a nucleic acid sequence to an amino acid sequence. Describe how these issues are overcome, with reference to the universality and redundancy of the genetic code. Outline the unique problems associated with protein synthesis, with particular reference to the unfavourable thermodynamics of peptide bond formation and the requirement for order. Describe the strategies used by cells to overcome these problems. Need to convert sequence of nucleotides (with 4 different bases) to a sequence of amino acids (20 different bases) Need to have correct order of amino acids -> order determines fold and function of the protein. Must have precise start and stop for proteins -> extra amino acids may alter the fold and function. 4 different bases which use only one position so only 4 possible combinations (a, g, c, t) 4 different bases but 2 positions = 4 x 4 = 16 combinations (e. g. aa, ag, tc)