Download Translation & Proteins

Translation & Proteins
Lab manual objectives
• Witness once again how molecular rules
influence higher order structure!
• Explore how monomers function to make
molecules.
• Why does A go with T and C with G again?
• Consider how DNA is dislike/like any other
protein.
• Think about how these molecules function
in our bodies!
Biochemical Properties of
Macromolecules
 In
lab today we will:
 Look
at physical models of these
molecules.
 Use computer software to
understand the feel of these
molecules and how their surfaces
interact with the world
Big Rigs – from DNA to protein
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We have a busy day!!! Let’s try to work together
to make it go faster!
We have a “play” (not my idea… ahem)
A oil/water and carbon exercise, a “identify”
amino acids exercise (this will be quick).
And an in-class Assessor exercise.
If anyone has ideas on how to bang this out
faster… speak up! We can do the hemoglobin
work first, ditch the powerpoint until later etc… this is YOUR class, so let me know!
Revisiting AA - So lets begin with 20
toys… pass ‘em out
 EVERY one has a blue part. Chem name?
 EVERY one has a red part. Chem name?
 Thus these are all...?
 How many are there? Uhhhh….
: matcmadison.edu/.../labManual/chapter_2.htm
Amino acid power
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Like this, the right handed side of the picture is called the
native state, the right is the result of the process of largely
hydrogen bonding, resulting in a three-dimensional
structure determined by a sequence of amino acids.
Different tools; different jobs
 Your group has an amino acid; which is it?
 In what ways are all bases identical? Different?
 In what ways are all amino acids identical?
Different?
 Which group is more diverse in terms of ‘feel’?
 Which is more diverse in terms of shape?
 Which would allow you to build more diverse
shapes & surfaces?
 How many?
Tah Dah! But of
course! There have to
be 20, not including
start and stop codons.
And these amino acids
lead the way to all
kinds of protein fun
and folding.
While I talk….
• Lets make things go quicker today..
• I talk, listen – but while doing so, take a
pencil and follow the instructions on the
next slide.
• What’s in a pencil?
• Graphite!
• What’s graphite? – all allotropes of carbon
Get the oil and water…
• Use the pencils (sideways) to make an
area on the cards where you can punch
out about 6 or so little circles.
• Make sure the penciled region is thick
enough and then drop those little suckers
into the oil/water mixture, mix ‘em up.
• Do this while I jabber away – I’m not
offended!
So…
• ‘hiding greasy spots’ is the primary
driver in protein folding
• maximizing the number of charge-
charge and H-bonding interactions
matters
• Tell me about your results and carbons
role !
So now, why should I bother with
this?
• Therapy
• Drug design
• Natural products & chemistry
• Like - green fluorescent protein (GFP)
Comes from a fluorescent jellyfish!
• This protein has become one of the most
important tools in contemporary
bioscience. Using GFP, researchers have
developed ways to watch processes that
were previously invisible, like the
development of nerve cells or how cancer
cells spread!
• These guys won a Nobel Prize for this
discovery!
So how do we get here from there?
Or anywhere…
• These are a lot of new terms. This
language can be bizarre. These concepts
could even be a little overwhelming at first.
• In a slide or two we will remind you that
this can all really be as simple as a process
the cells in your body undergo every day.
Now. And now. And again.
• Lets review the “Central Dogma” one more
time.
Blinding you with Science
 mRNA: messenger RNA; the 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: a protein machine that
adds a specific amino acid to tRNAs it recognizes
 Termination factor: ‘reads’ UAA et al., causes
ribosome to cut loose the peptide and fall apart
Dogma, Dogma…
www.answers.com
www.cbs.dtu.dk/.../roanoke/central_dogma.gif
So the amino acids do what?
serc.carleton.edu/.../research_methods/genomics
Transcription &
Translation have
many players.
Now lets tackle the
nomenclature, so we
all know the right
words.
Then, I think this
process/concept
becomes more
manageable.
More “central dogma”
And then the proteins are made…
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So it all boils down to this…
But we have to start somewhere…
• And then we can understand…
The importance of mutation: easy to
understand (and foundational to today &
to general understanding of disease,
evolution...)
Mutations on a larger scale - DNA
Livable mutations too!
Smaller scale – proteins like
hemoglobin
Then it all fell apart...
Hartl & Jones, Genetics: Analysis of Genes and Genomes, Figure 7-35
*Moby, “Extreme ways” (theme from Bourne II & III)
We will be looking at this in depth
pretty darn soon…
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But a little more on protein folding and the like
first.
acid + milk, boiling eggs, making cheese all
good examples of charge/phobicity =>
folding & structure
but most have seen these, and other than geewhiz, is there a way to tie to this week’s
concepts?
But to talk about these we gotta go
way back to where we began, much
like my little friend here…
And that
“somewhere” was
here!
This amino acid chain being “built”
ultimately participates in the shaping
and folding of proteins in water (which
we are mostly made up of!)
Proteins are about 50% of the dry
weight of most cells, and are the most
structurally complex macromolecules
known. Each type of protein has its
own unique structure and function.
Polymers are any kind of large
molecules made of repeating identical
or similar subunits called monomers.
The starch we previously saw in action
are polymers of glucose, which in that
case, is the monomer. Proteins are
polymers of about 20 amino acids
(the monomer).
tRNA hangs on
to the AA chain
Two important
things happen
here re: joining
up