Download - Translation: Changing languages
11
Translation: Changing languages
Translation: Changing languages
How? Why?
Transcription: Writing againTranscription: Writing again
2
Today we’ll go from here... To here
Text
We can do We can do anythinganything
3Off to see the wizard...
• DNA replication
• both strands => new DNA
• => new cell
• Transcription
• 1 strand => new RNA
• => new protein
Sending ‘messages’ out from DNA
4Transcription: seeing it
http://www.hhmi.org/biointeractive/media/DNAi_transcription_vo1-lg.mov
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Amino acidsAmino acidsFrom 4 letters of
storage/information to
20 letters of action!!
From 4 letters of storage/information
to 20 letters of action!!
620 toys
• EVERY one has a blue part. Chem name?
• EVERY one has a red part. Chem name?
• Thus these are all...?
• How many are there?
7aaDancer• Why do nucleotides look like nucleotides, while
amino acids look like amino acids?
• Remember the handshakes
• What are amino acids ‘for’?
8Different tools; different jobs• You & partner have an amino acid; which is it? (StructViewer
or homepage => left column ‘big twenty’ amino acids)
• In what ways are all bases identical? Different?
• In what ways are all amino acids identical? Different?
• Which set is more diverse in terms of ‘feel’?
• Which more diverse in terms of shape?
• Which would allow you to build more diverse shapes & surfaces?
9Mutation--not always bad
• While the comparison is often made, proteins are not sentences
• An amino acid is a collection of properties; changing from one to another changes a region of the protein by (little/some/a lot/completely)
• It’s an exaggeration, but think of amino acids more like different vacuum cleaner nozzles
10How does a codon ‘mean’ an amino acid?
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Walking the walkWalking the walkHow bio machines translate the
language of nucleotides into an amino acid string
How bio machines translate the language of nucleotides into an amino
acid string
12Biology: because it has to work like
that way
• Von Neumann argued that... [self-reproducing] machines would need to store separately the information needed to make the machine and would need to have a mechanism to interpret that information—a tape and a tape reader. In effect, he abstractly described the gene, the ribosome, and the messenger.
--Matt Ridley in Francis Crick, discoverer of the genetic code
13Types of bonds
• VELCRO: a bond that can be cheerfully broken/re-made during lab
• Duct tape: same at the molecular level, but at the 181L student level, breaking such a bond gets you a zero on this week’s quiz
Blinding you with Science (jargon)
RNA Polymerase: joins RNA links into a chain
mRNA: messenger RNA; RNA string copied (‘transcribed’) from DNA
tRNA: transfer RNA; one of many RNA molecules that carry specific amino acids
ribosome: giant machine (>200 proteins, 4 RNAs (2 > 1000 nucleotides) that oversees the reading of the mRNA and the creation of polypeptide
aminoacyl tRNA synthetase: protein machine adds amino acid to tRNAs
Termination factor: ‘reads’ UAA etc., => ribosome looses the peptide & falls apart
15Roles--for single mRNA
• 4 tRNA (1-2 people)
• 4 pairs to be synthetases
• 1 small ribosomal subunit x 2
• 1 large ribosomal subunit x 2
• 2 to be (RNA polymerase & the RNA it makes )
• 1 termination factor (1-2 people)
5 ’ end is pointy/spiky3 ’ end is soft/furry
16Roles--for TWO mRNA
• 4 tRNA
• 4 synthetases
• 1 ribosome
• 1-2 to be (RNA polymerase & the RNA it makes )
• 1 termination factor
5 ’ end is pointy/spiky3 ’ end is soft/furry
17Learning your ‘lines’
• Handout: Each group find questions related to their role; answer them
• Lab manual, textbook, internet OK as sources
• Meet your blocks-- 5’ is the end that sticks to hair, socks, shirts
5 ’ end is pointy/spiky3 ’ end is soft/furry
18DNA template strand
5’ CTTAAATCCGAATGCCCATG 3’
19DNA template strand
(alternate version)
5’ CTTAAATCCGAATGCCCATG 3’5 ’ end is pointy/spiky
3 ’ end is soft/furry
20Special powers• Recall that ribosome assembly is the result of
methionine tRNA finding a match on mRNA in presence of small ribosome subunit
• Only methionine tRNA (it will ‘know itself’ once crowned by the synthetase that hands out met) can team with small ribosomal subunit & join with the ‘AUG’!
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Choreographing translation
Choreographing translation
A play of many parts, many players, no brains
A play of many parts, many players, no brains
22Going with the flow• mRNA at the central bench
• ribosome assembles around it
• synthetases at bench corners (or ‘diffuse’ opp. direction vs. tRNA)
• tRNAs will ‘diffuse’ by following a path through the room
• When any event first happens*, action stops, molecules involved will announce, explain
• Go until a protein happens
*This includes non-events (rejections, etc.)
23Walk-through with 1 tRNA
• Everybody watches visits to synthetase, ribosome
• In the real world, everything is happening all the time; all is happenstance
24Who knows the code?
• What happens if a tRNA carries the wrong amino acid?
• What happens if the mRNA contains a copy error relative to DNA?
• What happens if a tRNA has a mutated anticodon
25Review movie
• (in TA desktop folder)
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Meet your semester-long
interest
Meet your semester-long
interest
Exit ConditionExit Condition1.) Pair up (two in a group)
2.) Write your names and SECTION at the top of the paper
3.) EXPLAIN the process of TRANSLATIONInclude the following in your answer:
tRNAmRNA
ribosomeUAG codon
RNA Polymeraseaminoacyl tRNA synthetase
termination factordiffusion
1.) Pair up (two in a group)2.) Write your names and SECTION at the top of
the paper3.) EXPLAIN the process of TRANSLATIONInclude the following in your answer:
tRNAmRNA
ribosomeUAG codon
RNA Polymeraseaminoacyl tRNA synthetase
termination factordiffusion
From Emily
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HomeworkHomeworkStructViewer*--amino acid look & feel**
Begin thinking about your projectAssessor: mutation & translation
*As will always be the case in this course, no tricks; focus on the primary idea(s)
**‘SurfaceViewer’ link from Software page may help
...Ch. 3 reading about the immune system is just for fun
StructViewer*--amino acid look & feel**Begin thinking about your projectAssessor: mutation & translation
*As will always be the case in this course, no tricks; focus on the primary idea(s)
**‘SurfaceViewer’ link from Software page may help
...Ch. 3 reading about the immune system is just for fun
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Old/unusedOld/unused
http://www.youtube.com/watch?v=WTRmvnlNVw4
31It Has to Be part II
"The main idea was that it was very difficult to consider how DNA or RNA, in any conceivable form, could provide a direct template for the side-chains of the twenty standard amino acids. What any structure was likely to have was a specific pattern of atomic groups that could form hydrogen bonds. I therefore proposed a theory in which there were twenty adaptors (one for each amino acid), together with twenty special enzymes. Each enzyme would join one particular amino acid to its own special adaptor. This combination would then diffuse to the RNA template. An adaptor molecule could fit in only those places on the nucleic acid template where it could form the necessary hydrogen bonds to hold it in place. Sitting there, it would have carried its amino acid to just the right place where it was needed."
From “What mad pursuit”, Francis Crick’s memoir of his days in the molecular world
32Tools of the times
• while real ribosomes require specific ‘instruction’ and ‘landing pad’, they could be fooled into starting randomly
• biochemists had found an enzyme that would take a pot full of ribonucleotides and polymerize* them willy-nilly (in random sequence)
*poly: multiple mer: uniti.e., to form multiples from single units
Experiments & interpretations
Starting simple. If the only nucleotide you add to the mix is rCTP, what RNA chain will you make?
You add cell extracts that can do translation. You find some protein made, and it consists only of prolines strung together. What do you conclude?
You decide to look into C + A containing codons.