Transcript Pencils made of…. - Biology Learning Center

Strings to Blobs
Hb One
What Matters Today?
• How do we go from ‘string’ of mRNA to
a MACHINE?
– machine = 3D object that does stuff
• How do proteins get the shape?
– Term: ‘folding’
• How specific aminos and protein
shapes = operational machines
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 ~ 5 ways molecular
surfaces can ‘feel’
• What are they?
• Amino acid ‘Easter egg hunt’ – find
the one(s) that…
• Homepage -> “Sources”
• Interweb
Freeman, Scott. Biological
Science. 4th Edition.
Your Turn
• You ‘fold’ a protein: ProFolder
(Bio181L_Go)
• Show me each solution (Q4)
• 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?
Other ‘rules’ of folding
(+)
(-)
Images of 3D
Q. 4
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…
Now let’s “Hemoglobin”
Small capillary
(blood vessel)
Scale & role
Tetramer:
4 protein chains
(~145 amino acids)
Heme:
C34H32O4N4Fe
Oxygen molecule
2 atoms
17
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-Molecular-Biology
You’ve seen this before:
What is it?
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
You’ve seen this before:
Amino Acid sequence
How is this
determined?
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
You’ve seen this before:
Amino Acid sequence
What is it?
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
You’ve seen this before:
Amino Acid sequence
Alpha Helix
How is this
determined?
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
You’ve seen this before:
Amino Acid sequence
Alpha Helix
What is it?
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
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-Molecular-Biology
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-Molecular-Biology
What will we learn about Hb?
• How hemoglobin’s amino acid sequence generates
its structure
What will we learn about Hb?
• 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 (Hemo
one)
• 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...
Running the Tutorial (Hemo
one)
• 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 effective
• Brief comment on ‘interestingness’ and
accessibility
Your Disease
• Genetic disease part 2
• Follow the rubric
• Your mutations linked on course
calendar
Things you already “know”