groups for semester project carly, alexandra, lindsay natalia, cara, tyler rachyl, candice. nicole,...

Groups for semester project

• Carly , Alexandra , Lindsay

• Natalia , Cara , Tyler

• Rachyl , Candice. Nicole , Angel

• Michaela , Jacob , Katherine

• Jessica , Jordann , Hailey

• Keionna , Tamilla , Kathryn

Groups for semester project

• Kelly , Gina , Samuel

• Wesley , Alexia , Clayton

• May , Philip , Gustavo

• Christopher , Colby , Benjamin

• Neal , Donald , Taylor

• Marissa , John , Nicole

• Jennifer , Karling

Some words on group projects

• ‘Divide and conquer’ is fine, BUT everyone in your group MUST read and approve the entire final submission

• If you name is on it, it means that you contributed to the work as much as any other group member

Things to clarify/review for translation (questions about these will be on next

week’s quiz)• What is the role of diffusion/Brownian

motion - Are the molecules ‘seeking’ partners, or is just random chance?

• What exactly is the role of the Ribosome?

• Who/what determines if a tRNA matches the codon on the mRNA? (Hint – think about ‘feels’

• WHAT is the termination factor?

Strings to Blobs

Hemoglobin

(chains of amino acids -> folded proteins)

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

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

• Machine = 3D object that does stuff = protein

• How do we get the shape (the fold)?

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 ~ 4 ways molecular surfaces can ‘feel’

• What are they?

• Amino acid ‘Easter egg hunt’ – find the one(s) that…

• Homepage -> “Sources”

• Internet

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

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…

Again, WHY was this the best?

19

Other ‘rules’ of folding (for last question on W.S.)

(+)

(-)

How to hydrogen interactions (H-bonds) contribute to alpha-helix and beta-sheet?

21

Other ‘rules’ of folding

(+)

(-)

22Mutation--not always

bad• While the comparison is often made, proteins

are not sentences

• An amino acid is a collection of properties; changing from one to another changes a region of the protein by (little/some/a lot/completely)

• It’s an exaggeration, but think of amino acids more like different vacuum cleaner nozzles

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 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”

• Genetic disease part 2

• Follow the rubric

Your Disease

Things you already “know”

groups for semester project carly, alexandra, lindsay natalia, cara, tyler rachyl, candice. nicole,...

Documents

screen slide

kathryn slide

karling slide

sequence water slide

group member slide

functional shape slide

string of amino acids

places amino acids