groups for semester project carly, alexandra, lindsay natalia, cara, tyler rachyl, candice. nicole,...
TRANSCRIPT
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Groups for semester project
• Carly , Alexandra , Lindsay
• Natalia , Cara , Tyler
• Rachyl , Candice. Nicole , Angel
• Michaela , Jacob , Katherine
• Jessica , Jordann , Hailey
• Keionna , Tamilla , Kathryn
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Groups for semester project
• Kelly , Gina , Samuel
• Wesley , Alexia , Clayton
• May , Philip , Gustavo
• Christopher , Colby , Benjamin
• Neal , Donald , Taylor
• Marissa , John , Nicole
• Jennifer , Karling
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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
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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?
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Strings to Blobs
Hemoglobin
(chains of amino acids -> folded proteins)
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• 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?
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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
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“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
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Your Turn
• You ‘fold’ a protein: ProFolder (Bio181L_Go)
• Show me each solution (Q3)
• Leave 2nd on screen
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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
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How does yours compare?
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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
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If THIS is true…
• Pencils made of….
http://www.nano-enhanced-wholesale-technologies.com/faq/carbon-forms.htm
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If THIS is true…
• Pencils made of….
• Paper made of…
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If THIS is true…
• Pencils made of….
• Paper made of…
• Oil and water…
• Pencils, paper, oil, water…
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Again, WHY was this the best?
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19
Other ‘rules’ of folding (for last question on W.S.)
(+)
(-)
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How to hydrogen interactions (H-bonds) contribute to alpha-helix and beta-sheet?
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21
Other ‘rules’ of folding
(+)
(-)
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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
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Now let’s “Hemoglobin”
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Where we are
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
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Where we are
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Hb made of fourprotein chains
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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
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Where we are
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Each Hb moleculehas four Heme groups
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Where we are
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
Oxygen IS molecular, so TWO oxygen atoms
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Where we are
Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease
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Hb made of fourProtein chains
2 alpha chains2 beta chains
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You’ve seen this before:
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
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You’ve seen this before:Amino Acid sequence
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
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You’ve seen this before:Amino Acid sequence
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
How is this determined?
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You’ve seen this before:Amino Acid sequenceAlpha Helix
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
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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?
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You’ve seen this before:Amino Acid sequenceAlpha HelixFolded peptide
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
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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?
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You’ve seen this before:Amino Acid sequenceAlpha HelixFolded peptideAggregation of peptides
http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology
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Hemoglobin
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• How hemoglobin’s amino acid sequence generates its structure
Hemoglobin
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• How hemoglobin’s amino acid sequence generates its structure
• Why hemoglobin is a tetramer (gang of four)
Hemoglobin
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• 30% Worksheet – Easter egg hunt• 60% Hb Tutorial• 10% Hb mini research
What today will look like:
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• 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
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Do it with ‘feeling’
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• 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”
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• Genetic disease part 2
• Follow the rubric
Your Disease
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Things you already “know”