How?
Why?
From strings to blobs
Hemoglobin I
LAB 5
2
From there to here
• Week 3: How DNA can ‘mean’
anything; how it can pass that
meaning on (replication)
• Week 4: 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
What do to with my
string of blobs?
4
Common ‘rules’ of folding
(+)
(-)
6
Images of 3D
7
Grease & beyond
• ‘hiding greasy spots’ is the primary driver
in protein folding
• maximizing the number of charge-charge
and H-bonding interactions matters
8
Great experiments
Scrambled ribonuclease
9
Humpy Dumpy (the more
tragic version)
Sulfur + Sulfur = SulfurSulfur
• In a protein chain (a.k.a.
polypeptide), nearby
sulfur sidechains may be
covalently joined
http://guweb2.gonzaga.edu/faculty/cronk/biochem/images/disulfide_bond_formation.gif
11
Like & unlike an egg
• Break disulfide (Cys-Cys
through their sulfurs)
• Denature with heat
• Cool fast, allow disulfides
to reform
• It ‘locks in’ to inactive
states
Biochemstry, 5th ed.
Berg, Tymoczko & Stryer
12
Like & unlike an egg
• Disconnect the disulfides
• Allow to re-discover its
‘comfy’ shape (re-fold on
its own)
• Allow disulfides to re-lock
• Function!
13
Biochemstry, 5th ed. Berg, Tymoczko & Stryer
What matters today?
• How do we go from the ‘ticker tape’ of an
mRNA to a machine?
– machine = 3D object that does stuff
• Who shapes proteins into their shapes?
Terminology: ‘folding’
• Where does new functionality come from?
What are the consequences of mutation?
14
How does it feel*
• There are only about 5 ways molecular
surfaces can be
• What are they?
• Amino acid ‘Easter egg hunt’ – find the
one(s) that…
• Homepage -> “Sources”
• Interweb
*Bob15Dylan; Like a Rolling Stone
What today will look like:
• 30% Worksheet – Easter egg hunt
• 60% Hb Tutorial
• 10% Hb mini research
Worksheet
Amino acid Easter egg hunt
17
18
http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg
Question Authority
To your pencils, index cards & oil-water
mixes!
NOT
19
Ooey gooey rich & chewy inside...
• Protein folding, oil not mixing with
water, and membrane formation all
reflect the same principle
• In protein folding, the constraint is that
the individual units are all attached to a
pair of neighbors
• Many proteins need no further
‘instruction’ than their sequence &
water to correctly assume their
superhero identity
20
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…
Your turn
• You ‘fold’ a protein: ProFolderPro
(MCB181M_Go)
• Show me each solution
• Leave the 2nd one on screen
25
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
26
How does yours
compare?
27
How?
Why?
Life’s blood: Hemoglobin
Let’s make sense of how this protein works today…
Life’s blood: Hemoglobin
Hemoglobin: overview
http://www.youtube.com/watch?v=WXOBJEXxNEo&feature=related
30
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
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:
Amino Acid sequence
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
Alpha Helix
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
Folded peptide
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
Hemoglobin: what is it?
Image source: http://themedicalbiochemistrypage.org/hemoglobin-myoglobin.html
45
What you’ll learn today (and
potentially be quizzed on)
• How hemoglobin’s amino acid sequence
generates its structure
• Why hemoglobin is a tetramer (gang of
four)
46
Todays assignments
30% Worksheet: easter egg hunt
60% points hemoglobin tutorial
10% points hemoglobin mini-research
47
How does it feel?*
*If you don’t know who Bob Dylan is, shoot one of us now (preferably the one who’s not me)
Hemoglobin tutorial
• Turn OFF Wi-Fi; QUIT safari (not
close window)
• Read...
– the instructions on each question...
– the instructions on the webpage...
– all the words of each question...
49
What today will look like:
• 30% Worksheet – Easter egg hunt
• 60% Hb Tutorial
• 10% Hb mini research
On the relative likelihood
of accidents...
51
What specifically
causes...
• A lysine to become a serine?
• To your codon tables!
52
Your Disease
• Genetic disease part 2
• Follow the rubric