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Chapter 30

BIOCHEM 2B03 Chapter Notes - Chapter 30: Ribonucleoprotein, Hydrolase, Hydrophobe


Department
Biochemistry
Course Code
BIOCHEM 2B03
Professor
Margaret Fahnestock
Chapter
30

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Biochem 2B03
2012
1
8Part 4: Information Transfer
Chapter 30: Protein Synthesis
Refer to Chapter 29 Notes 29.3-29.4
RPB1 and its C-Terminal Domain (CTD)
CTD of RPB1 is essential to the function of RNAP II
YSPTSPS repeated 60 times (human)
RNAP II only initiates transcription when the CTD is not phosphorylated
Elongation proceeds only after phosphorylation of CTD, suggesting phosphorylation triggers initiation to elongation
conversion
Following termination, a phosphatase recycles RNAP II for initiation
CTD also play a prominent role in orchestrating subsequent events for processing the transcript (Capping, splicing,
Polyadenylation)
General structure of amino acids
o Cα is a chiral center (with one exception)
The 20 Common Amino Acids
Non-polar amino acids (hydrophobic)

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Biochem 2B03
2012
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Polar, uncharged amino acids
Acidic amino acids
Basic amino acids
Peptide Bond Formation
How is the nucleotide sequence of an mRNA molecule translated into the amino
acid sequence of a protein molecule?
30.1 What is the Genetic Code?

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Biochem 2B03
2012
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What is the nature of the code?
Genetic experiments demonstrated a triple code
RNA has four bases C, G, A, U
42 ways of combining these in pairs
43 ways of combining these in triplets
In 1960 you couldn’t sequence DNA but could sequence protein
Three bases codes for one amino acid
Code is not overlapping
Base sequence is read from a fixed starting point without punctuation
Code is degenerate (each amino acid can be coded for by several triplets)
In vitro transition reactions
Prime them with synthetic RNAs of defined sequence
o
The Genetic Code
Note: termination codons, start codon, redundancy: Trp has the only unique codon
Codons triplets of bases in mRNA; read 5’3’
All codons have meaning; of 64 codons, 61 code for particular amino acids, 3 are nonsense codons serving as termination
codons (stop signal)
Genetic code is
o Unambiguous each codon only codes for one amino acid
o Degenerate each amino acid (exception to Trp and Met) is coded for by more than one codon; synonymous
codons
Codons representing the same amino acid or chemically similar amino acids tend to be similar in
sequence
Eg/ GGx codons Gly; UCx codons Ser
Codons with pyrimidine as 2nd base likely contain hydrophobic side chain
Codons with purine as 2nd base likely contain polar or charged amino acids
Mutations due to single base changes are less harmful
RNA Sequence
Protein Produced
UUUUUUUUU….
Phe Phe Phe Phe…
AAAAAAAAA…
Lys Lys Lys Lys
GGGGGGGGG…
Gly Gly Gly Gly…
CCCCCCCCCC…
Pro Pro Pro Pro…
UAUAUAUAU…
Tyr Ile Tyr Ile…
UAUUUUUAUUUU
Tyr Phe Tyr Phe
UUU
AAA
GGG
CCC
UAU
Phe
Lys
Gly
Pro
Tyr
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