Transcript Pencils made of….

Groups for semester project
• Carly , Alexandra , Lindsay
• Natalia , Cara , Tyler
• Rachyl , Candice. Nicole , Angel
• Michaela , Jacob , Katherine
• Jessica , Jordann , Hailey
• Keionna , Tamilla , Kathryn
Groups for semester project
• Kelly , Gina , Samuel
• Wesley , Alexia , Clayton
• May , Philip , Gustavo
• Christopher , Colby , Benjamin
• Neal , Donald , Taylor
• Marissa , John , Nicole
• Jennifer , Karling
Some words on group projects
• ‘Divide and conquer’ is fine, BUT everyone
in your group MUST read and approve the
entire final submission
• If you name is on it, it means that you
contributed to the work as much as any
other group member
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Things to clarify/review for translation
(questions about these will be on next
week’s quiz)
What is the role of diffusion/Brownian
motion - Are the molecules ‘seeking’
partners, or is just random chance?
What exactly is the role of the Ribosome?
Who/what determines if a tRNA matches
the codon on the mRNA? (Hint – think
about ‘feels’
WHAT is the termination factor?
Strings to Blobs
(chains of amino acids -> folded
proteins)
Hemoglobin
What Matters Today?
• How do we go from ‘string’ of mRNA
to a MACHINE (protein)?
• How do you build a machine that builds
a machine?
• Machine = 3D object that does stuff =
protein
• How do we get the shape (the fold)?
From there to here
• Week 2: How DNA can ‘mean’
anything; how it can pass that
meaning on (replication)
• Week 3: How DNA can send
out a ‘message’
(transcription); how that
‘message’ can be ‘translated’
into amino acids
• Now: How a string of amino
acids is formed into a
functional shape
“Building Blocks”
• There are ~ 4 ways molecular
surfaces can ‘feel’
• What are they?
• Amino acid ‘Easter egg hunt’ –
find the one(s) that…
• Homepage -> “Sources”
• Internet
Your Turn
• You ‘fold’ a protein: ProFolder
(Bio181L_Go)
• Show me each solution (Q3)
• Leave 2nd on screen
Profolder Features
• Destinations (lower right) => Folding
• Top: amino acid string
• Squares: places amino acids could go. Note
‘Undo last’ button
• Two spots--use one to improve upon what
you did in the other
• Bottom: note that when you mouseOver an
amino acid, it’s structure & ‘feel’ are shown
How does yours compare?
Inside and Outside
• Protein folding, oil/water, m-brane
formation all same principle
• Protein folding- individual units attached
to a pair of neighbors
• Many proteins need no further
‘instruction’ than sequence & water
If THIS is true…
• Pencils made of….
http://www.nano-enhanced-wholesaletechnologies.com/faq/carbon-forms.htm
If THIS is true…
• Pencils made of….
• Paper made of…
If THIS is true…
•
•
•
•
Pencils made of….
Paper made of…
Oil and water…
Pencils, paper, oil, water…
Again, WHY was this the
best?
Other ‘rules’ of folding (for
last question on W.S.)
(+)
(-)
19
How to hydrogen interactions (H-bonds) contribute to
alpha-helix and beta-sheet?
Other ‘rules’ of folding
(+)
(-)
21
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
2
2
Now let’s “Hemoglobin”
Where we are
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Where we are
Hb made of four
protein chains
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Where we are
Hb made of four
protein chains
2 alpha chains
2 beta chains
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Where we are
Each Hb molecule
has four
Heme groups
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Where we are
Oxygen IS molecular, so
TWO oxygen atoms
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Where we are
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Hb made of four
Protein chains
2 alpha chains
2 beta chains
You’ve seen this before:
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-MolecularBiology
You’ve seen this before:
Amino Acid sequence
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-MolecularBiology
You’ve seen this before:
Amino Acid sequence
How is this
determined?
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-MolecularBiology
You’ve seen this before:
Amino Acid sequence
Alpha Helix
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-MolecularBiology
You’ve seen this before:
Amino Acid sequence
Alpha Helix
How is this
determined?
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-MolecularBiology
You’ve seen this before:
Amino Acid sequence
Alpha Helix
Folded peptide
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-MolecularBiology
You’ve seen this before:
Amino Acid sequence
Alpha Helix
Folded peptide
How is this
determined?
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-MolecularBiology
You’ve seen this before:
Amino Acid sequence
Alpha Helix
Folded peptide
Aggregation of peptides
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-MolecularBiology
Hemoglobin
Hemoglobin
• How hemoglobin’s amino acid sequence
generates its structure
Hemoglobin
• How hemoglobin’s amino acid sequence
generates its structure
• Why hemoglobin is a tetramer (gang of
four)
What today will look
like:
• 30% Worksheet – Easter egg hunt
• 60% Hb Tutorial
• 10% Hb mini research
Running the Tutorial
• Turn OFF Wi-Fi; QUIT safari (not close
window)
• READ the instructions on the intro...
• READ the instructions on each
question...
• READ the instructions on the
webpage...
• READ all the words of each question...
Do it with ‘feeling’
“Mini Research”
• Spend about 10 minutes on your
question
• I need a ‘link’
• 2-3 sentence summary of findings
• Search words that were most affective
• Brief comment on ‘interestingness’
and accessibility
Your Disease
• Genetic disease part 2
• Follow the rubric
Things you already “know”