Transcript Amino Acids - Biology Learning Center

Last day to drop without a
th
‘W’ is September 16 (this
upcoming Sunday)
Review about bases
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They need to be very specific because they
contain ALL the information for telling the cell
how to function, so if they were flexible and
changeable there would be problems
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Nucleotides (bases) are RIGID/INFLEXIBLE
because of the double bonds that make up the
rings
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Means that the H-bond donors and acceptors are
always in the same place = specificity
How?
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Why?
Transcription:
Writing again
Translation:
Changing
languages
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Cytosine cries out
for Guanine
GUANINE
http://en.wikipedia.org/wiki/Guanine
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Today
we’ll go
from
here...
We can do
anything
Text
To here
Off to see the wizard...
Sending ‘messages’ out from DNA
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DNA replication
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both strands => new DNA
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=> new cell
Transcription
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1 strand => new RNA
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=> new protein
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Transcription: seeing it
http://www.hhmi.org/biointeractive/media/DNAi_transcription_vo1-lg.mov
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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...?
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Amino Acids
• How are they similar?
• How are they different?
• What do the differences mean
in terms of “feel”?
• How many are there?
• Possible?
Amino Acids
• You & partner have an amino
acid; which is it? (StructViewer or
homepage => left column ‘big
twenty’ amino acids)
Nucleic Acids
• How are they similar?
• How are they different?
• What do the differences mean in terms
of “feel”?
• Which is more diverse in terms of
shape and ‘feel’?
• Which would allow for more diverse
shapes and surfaces when
‘connected’?
Different tools; different jobs
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In what ways are all bases identical? Different?
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In what ways are all amino acids identical? Different?
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Which set is more diverse in terms of ‘feel’?
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Which more diverse in terms of shape?
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Which would allow you to build more diverse shapes &
surfaces?
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How does a codon ‘mean’
an amino acid?
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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
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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
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VELCRO: a bond that can be cheerfully broken/re-made during
lab
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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
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
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Wielding the Power
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‘Recall’ that ribosome assembly is the result of methionine
tRNA finding a match on mRNA in presence of small ribosome
subunit
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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’!
Walk-through with 1 tRNA
• Everybody watches visits to
synthetase, ribosome
• In the real world, everything is
happening all the time; all is
happenstance
Roles--for single
mRNA
5’ end is pointy/spiky
3’ end is soft/furry
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4 tRNA (1-2 people)
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4 pairs to be synthetases
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1 small ribosomal subunit x 2
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1 large ribosomal subunit x 2
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2 to be (RNA polymerase & the RNA it makes )
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1 termination factor (1-2 people)
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Roles--for TWO
mRNA
5’ end is pointy/spiky
3’ end is soft/furry
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4 tRNA
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4 synthetases
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1 ribosome
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1-2 to be (RNA polymerase & the RNA it makes )
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1 termination factor
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Learning your ‘lines’
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Handout: Each group find questions related to their role;
answer them
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Lab manual, textbook, internet OK as sources
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Meet your blocks-- 5’ is the end that sticks to hair, socks,
shirts
5’ end is pointy/spiky
3’ end is soft/furry
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Choreographing
translation
A play of many parts, many players, no
brains
PLAYERS
tRNA
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Amino
Acid is the
yellow bit
synthetase
Ready…. Go!
• 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 Includes ‘didn’t work’
• Go until a protein happens
Who knows the code?
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What happens if a tRNA carries the wrong amino
acid?
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What happens if the mRNA contains a copy error
relative to DNA?
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What happens if a tRNA has a mutated anticodon
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Review movie
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(in TA desktop folder)
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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/Brownian motion
**Worth 10 pts on next week’s quiz
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Meet your
semester-long
interest
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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