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

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…


• Paper made of…

If THIS is true…


• 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

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

Where we are


Hb made of fourprotein chains


Where we are


Hb made of fourprotein chains

2 alpha chains2 beta chains


Where we are


Each Hb moleculehas four Heme groups


Where we are


Oxygen IS molecular, so TWO oxygen atoms


Where we are



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


You’ve seen this before:Amino Acid sequence


How is this determined?

You’ve seen this before:Amino Acid sequenceAlpha Helix


You’ve seen this before:Amino Acid sequenceAlpha Helix



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


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



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


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”

Documents

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