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 2 nd 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…. 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:

Where we are Image source: Hb made of four protein chains

Where we are Image source: Hb made of four protein chains 2 alpha chains 2 beta chains

Where we are Image source: Each Hb molecule has four Heme groups

Where we are Image source: Oxygen IS molecular, so TWO oxygen atoms

Where we are Image source:

Hb made of four Protein chains 2 alpha chains 2 beta chains

You’ve seen this before:

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 sequence Alpha Helix

You’ve seen this before: Amino Acid sequence Alpha Helix How is this determined?

You’ve seen this before: Amino Acid sequence Alpha Helix Folded peptide

You’ve seen this before: Amino Acid sequence Alpha Helix Folded peptide How is this determined?

You’ve seen this before: Amino Acid sequence Alpha Helix Folded peptide Aggregation 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”