Transcript Translation: Changing languages

How?
1
Why?
Transcription:
Writing again
Translation:
Changing
languages
2
Today
we’ll go
from
here...
We can do
anything
Text
To here
Off to see the wizard...
Sending ‘messages’ out from DNA
•
•
DNA replication
•
both strands => new DNA
•
=> new cell
Transcription
•
1 strand => new RNA
•
=> new protein
3
Transcription: seeing it
http://www.hhmi.org/biointeractive/media/DNAi_transcription_vo1-lg.mov
4
5
Amino acids
From 4 letters of storage/information
to
20 letters of action!!
20 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?
6
aaDancer
•
Why do nucleotides look like nucleotides, while amino
acids look like amino acids?
•
Remember the handshakes
•
What are amino acids ‘for’?
7
8
Different
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?
Mutation--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
9
How does a codon ‘mean’
an amino acid?
10
11
Walking the walk
How bio machines translate the language of
nucleotides into an amino acid string
Biology: because it has to work like that
way
•
12
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
Types of bonds
13
•
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
Roles--for single
mRNA
5’ end is pointy/spiky
3’ end is soft/furry
•
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)
15
Roles--for TWO
mRNA
5’ end is pointy/spiky
3’ end is soft/furry
•
4 tRNA
•
4 synthetases
•
1 ribosome
•
1-2 to be (RNA polymerase & the RNA it makes )
•
1 termination factor
16
Learning 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/spiky
3’ end is soft/furry
17
DNA template strand
5’ CTTAAATCCGAATGCCCATG 3’
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DNA template strand
(alternate version)
5’ CTTAAATCCGAATGCCCATG 3’
5’ end is pointy/spiky
3’ end is soft/furry
19
Special 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’!
20
21
Choreographing
translation
A play of many parts, many players, no
brains
Going 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.)
22
Walk-through with 1 tRNA
•
Everybody watches visits to synthetase, ribosome
•
In the real world, everything is happening all the time;
all is happenstance
23
Who 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
24
Review movie
•
(in TA desktop folder)
25
26
Meet your
semester-long
interest
Exit Condition
1.) Pair up (two in a group)
2.) Write your names and SECTION at the top of
the paper
3.) EXPLAIN the process of TRANSLATION
Include the following in your answer:
tRNA
mRNA
ribosome
UAG codon
RNA Polymerase
aminoacyl tRNA synthetase
termination factor
diffusion
From Emily
28
Homework
StructViewer*--amino acid look & feel**
Begin thinking about your project
Assessor: 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
29
Old/unused
http://www.youtube.com/watch?v=WTRmvnlNVw4
It 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
31
Tools 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: unit
i.e., to form multiples from single units
32
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.