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http://www.youtube.com/watch?v=4Tc6RserFvI. How?. Why?. From strings to blobs. 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’

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From strings to blobs

How?

Why?

From strings to blobs


What matters today
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’

  • How specific amino acids and protein shapes give rise to operational machines that perform body tasks


From there to here
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


Meet the building blocks
Meet the building blocks

  • There are only about 5 ways molecular surfaces can be

  • What are they?

  • Amino acid easter egg hunt--find the one(s) that...


Youtube watch v 4tc6rserfvi

http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svghttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg


Ooey gooey rich chewy inside
Ooey gooey rich & chewy inside...http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

  • 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


Question authority
Question Authorityhttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

  • To your pencils, index cards & oil-water mixes!


Your turn
Your turnhttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

  • You ‘fold’ a protein: ProFolder (Bio181L_Go)

  • Show me each solution (Q. 3)

  • Leave the 2nd one on screen


Profolder features
Profolder featureshttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

  • 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
How does yours compare?http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

11


Other rules of folding

(+)http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

(-)

Other ‘rules’ of folding


Images of 3d
Images of 3Dhttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

Q. 4


Life s blood hemoglobin

How?http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

Why?

Life’s blood: Hemoglobin


Hemoglobin overview
Hemoglobin: overviewhttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

http://www.youtube.com/watch?v=WXOBJEXxNEo&feature=related


Scale role

Small capillaryhttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

(blood vessel)

Tetramer:

4 protein chains

(~145 amino acids)

Heme:

C34H32O4N4Fe

Oxygen molecule

2 atoms

Scale & role

Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease


1 2 3 4 protein
1-2-3-4 protein!http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology


Hemoglobin what is it
Hemoglobin: what is it?http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

Image source:http://themedicalbiochemistrypage.org/hemoglobin-myoglobin.html


What you ll learn today
What you’ll learn todayhttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

  • How hemoglobin’s amino acid sequence generates its structure

  • Why hemoglobin is a tetramer (gang of four)


Todays assignments
Todays assignmentshttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

  • 30% Worksheet: easter egg hunt

  • 60% points hemoglobin tutorial

  • 10% points hemoglobin mini-research


Hemoglobin tutorial
Hemoglobin tutorialhttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

  • 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...

  • Ask yourself: will you be the monkeys at the typewriter, or Shakespeare?


How does it feel
How does it feel?*http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

*If you don’t know who Bob Dylan is, shoot one of us now


On the relative likelihood of accidents
On the relative likelihood of accidents...http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg


What specifically would it take for
What http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svgspecifically would it take for...

  • A lysine to become a glycine?

  • To your codon tables!

  • How often is that going to happen?


More on your disease
More on your disease!http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

  • See the calendar for links


Homework
Homeworkhttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg