2 Future regrets (again) At the end of every semester, some students ask: “is there anything I can...

2

Future regrets (again)• At the end of every semester, some students ask:

“is there anything I can do to raise my grade”• The answer is always: Go back in time and be

more committed, go to office hours, earn higher scores

• You are at that time now. Grab it before it goes by

Your questions

• Partial charges and “feels”

• Assessors and Programs

• Lab reports vs. write-ups

Strings to Blobs

Hb One

• How do we go from ‘string’ of mRNA to a MACHINE?

• How do you build a machine that builds a machine?

• Machine = 3D object that does stuff

• How do we get the shape?

What Matters Today?

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

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

Question Authority

• Pencils, paper, water, and oil

If THIS is true…

• Pencils made of….

http://www.nano-enhanced-wholesale-technologies.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”

Where we are

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 fourprotein chains

Where we are

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

Hb made of fourprotein chains

2 alpha chains2 beta chains

Where we are

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

Each Hb moleculehas four Heme groups

Where we are

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

Oxygen IS molecular, so TWO oxygen atoms

Where we are

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

Hb made of fourProtein chains

2 alpha chains2 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

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

How is this determined?

You’ve seen this before:Amino Acid sequenceAlpha Helix

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

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?

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

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

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?

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

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

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)

Hemoglobin

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

What today will look like:

• 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

Do it with ‘feeling’

• 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

“Mini Research”

On the relative likelihood of accidents…

What specifically would it take for…

• A lysine to become a glycine?

• To your codon tables!

• How often is that going to happen?

• Genetic disease part 2

• Follow the rubric

Your Disease

Things you already “know”