Notes 11-11

I. Overview of translation:
a. DNA gene → mRNA transcript → amino acid chain
b. Codon: 3 base long sequence on mRNA nucleotide sequence that codes for specific amino acid
i. Could have up to 64 possible codons
1. Only have 20 different amino acids corresponding to those codons
2. Must have more than 1 for the possible amino acids
ii. Redundant codons – why?
1. The idea that we have more than 1 codon per amino acid
iii. Know how to use table of codons, like the one attached
c. Ribosome binds to mRNA
i. Bind at Shine-Dalgarno sequence – a specific series of bases on mRNA that are complementary to sequence of bases in rRNA
d. AUG = start codon; also, methionine
i. Ribosome moves 1 base at a time down mRNA until it reaches AUG
ii. AUG defines “reading frame” of mRNA
iii. Once our ribosome has bound to the shine-delgarno sequence and moved one base at a time to the AUG – now we really start translating this into an amino acid sequence.
iv. Each of our codons are going to be every 3 bases after this point
v. A lot of the DNA doesn’t even get transcribed into amino acids
e. Transfer RNAs (tRNA) bearing amino acids brought in by ribosome, matched to codons
i. Transfer RNA (tRNA) has anticodon that is complementary to mRNA codon
ii. Clover-leaf shaped with an anticodon on one side, and an amino acid on the other
iii. Ribosomal RNA (rRNA) brings in +RNAs and matches them with codons on mRNA
iv. The ribosome moves down mRNA bringing in tRNAs that are complementary to each codon
1. Each tRNA has amino acids attached to them
f. Amino acids linked into a chain by ribosome
i. Catalyze the bond between the two amino acids hooking them together
1. Continues to attach each amino acid as it goes down the line putting them in a chain
ii. Ribosome also detaches the tRNA from the amino acid
g. At stop codon (UAA, UAG, or UGA), ribosome releases mRNA and amino acid chain
i. Because there is no +RNA with anticodon complementary to stop codons, rRNA pauses at the stop codon
ii. A protein called release factors are complementary to the stop codons and can interact with it instead of the rRNA.
1. They bind with stop codons - catalyze the reaction detaching our amino acid chain from our ribosome and also our ribosome from our mRNA – giving us a beautiful amino acid chain that will go off and do things in the cell

A Story About Gene Expression and Armistice Day (Veteran’s Day)
WWI ended on November 11, 1963

I. Clostridium perfringens
a. Soil bacterium
i. Found very deep in the soil
ii. When it is actively growing it expresses a virulence factor
b. Strict anaerobe
i. Cannot grow in the presence of oxygen – but that’s okay because they’re found deep in the soil where there isn’t any
c. Spore-forming
i. Spores
1. Very hardy non-metabolic state that some gram (+) bacteria can enter into
a. Not very many can, but there are a few that can
ii. Spore-forming sigma factors
1. Sigma factors are only on when the bacteria are around too much oxygen or run out of water
2. High {02} and low in [H2O]
3. They turn on spore-forming genes to make a spore environment to make a spore in the bacteria
II. WWI was ugly because …
a. We had trench fare
i. People living in trenches would get massive wounds and medicines weren’t very good to fix things
ii. Boots would stay on for months at a time – containing CP spores and no oxygen so they became actively dividing bacteria
III. Virulence factors
a. Exotoxins
i. Phospholipase
1. Enzyme that breaks down phospholipids
2. Would kill all of the tissue on people’s bodies
ii. Regulation of phospholipase gene expression
b. Acinteobacter baumanii (“Iraqibacter”)
i. Similar soil bacteria in Iraq that cause very similar mechanisms

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