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Strings to Blobs Hb One

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Page 1: Strings to Blobs Hb One. 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’

Strings to Blobs

Hb One

Page 2: Strings to Blobs Hb One. 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 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

What Matters Today?

Page 3: Strings to Blobs Hb One. 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’

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

Page 4: Strings to Blobs Hb One. 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’

“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

Page 5: Strings to Blobs Hb One. 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’
Page 6: Strings to Blobs Hb One. 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’

Freeman, Scott. Biological Science. 4th Edition.

Page 7: Strings to Blobs Hb One. 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’

Your Turn

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

• Show me each solution (Q4)

• Leave 2nd on screen

Page 8: Strings to Blobs Hb One. 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’

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

Page 9: Strings to Blobs Hb One. 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 does yours compare?

Page 10: Strings to Blobs Hb One. 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’

Other ‘rules’ of folding

(+)

(-)

Page 11: Strings to Blobs Hb One. 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’

Images of 3D

Q. 4

Page 12: Strings to Blobs Hb One. 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’

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

Page 13: Strings to Blobs Hb One. 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’

If THIS is true…

• Pencils made of….

http://www.nano-enhanced-wholesale-technologies.com/faq/carbon-forms.htm

http://www.nano-enhanced-wholesale-technologies.com/faq/carbon-forms.htm
http://www.nano-enhanced-wholesale-technologies.com/faq/carbon-forms.htm
Page 14: Strings to Blobs Hb One. 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’

If THIS is true…

• Pencils made of….

• Paper made of…

Page 15: Strings to Blobs Hb One. 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’

If THIS is true…

• Pencils made of….

• Paper made of…

• Oil and water…

• Pencils, paper, oil, water…

Page 16: Strings to Blobs Hb One. 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’

Now let’s “Hemoglobin”

Page 17: Strings to Blobs Hb One. 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’

17

Scale & role

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

Small capillary(blood vessel)

Tetramer:4 protein chains(~145 amino acids)

Oxygen molecule2 atoms

Heme:C34H32O4N4Fe

http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Page 18: Strings to Blobs Hb One. 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’

Hb made of fourProtein chains

2 alpha chains2 beta chains

Page 19: Strings to Blobs Hb One. 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’

You’ve seen this before:

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

http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
Page 20: Strings to Blobs Hb One. 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’

You’ve seen this before:What is it?

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

http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
Page 21: Strings to Blobs Hb One. 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’

You’ve seen this before:Amino Acid sequence

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

How is this determined?

Page 22: Strings to Blobs Hb One. 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’

You’ve seen this before:Amino Acid sequenceWhat is it?

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

Page 23: Strings to Blobs Hb One. 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’

You’ve seen this before:Amino Acid sequenceAlpha Helix

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

How is this determined?

Page 24: Strings to Blobs Hb One. 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’

You’ve seen this before:Amino Acid sequenceAlpha HelixWhat is it?

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

Page 25: Strings to Blobs Hb One. 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’

You’ve seen this before:Amino Acid sequenceAlpha HelixFolded peptide

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

How is this determined?

Page 26: Strings to Blobs Hb One. 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’

You’ve seen this before:Amino Acid sequenceAlpha HelixFolded peptideAggregation of peptides

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

Page 27: Strings to Blobs Hb One. 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 hemoglobin’s amino acid sequence generates its structure

What will we learn about Hb?

Page 28: Strings to Blobs Hb One. 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 hemoglobin’s amino acid sequence generates its structure

• Why hemoglobin is a tetramer (gang of four)

What will we learn about Hb?

Page 29: Strings to Blobs Hb One. 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’

• 30% Worksheet – Easter egg hunt• 60% Hb Tutorial• 10% Hb mini research

What today will look like:

Page 30: Strings to Blobs Hb One. 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’

• 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)

Page 31: Strings to Blobs Hb One. 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’

• 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)

Page 32: Strings to Blobs Hb One. 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’

Do it with ‘feeling’

Page 33: Strings to Blobs Hb One. 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’

• 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

“Mini Research”

Page 34: Strings to Blobs Hb One. 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’

• Genetic disease part 2

• Follow the rubric

• Your mutations linked on course calendar

Your Disease

Page 35: Strings to Blobs Hb One. 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’

Things you already “know”


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