Transcript Amino acid
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 2 Your questions • Partial charges and “feels” • Assessors and Programs • Lab reports vs. write-ups Strings to Blobs Hb One What Matters Today? • 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? 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-wholesaletechnologies.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 Hb made of four protein chains Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease Where we are Hb made of four protein chains 2 alpha chains 2 beta chains Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease Where we are Each Hb molecule has four Heme groups Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease Where we are Oxygen IS molecular, so TWO oxygen atoms 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 four Protein chains 2 alpha chains 2 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 How is this determined? http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology You’ve seen this before: Amino Acid sequence Alpha Helix http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology You’ve seen this before: Amino Acid sequence Alpha Helix How is this determined? http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology You’ve seen this before: Amino Acid sequence Alpha Helix Folded peptide http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology You’ve seen this before: Amino Acid sequence Alpha Helix Folded peptide How is this determined? http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology You’ve seen this before: Amino Acid sequence Alpha Helix Folded peptide Aggregation of peptides http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology Hemoglobin 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) What today will look like: • 30% Worksheet – Easter egg hunt • 60% Hb Tutorial • 10% Hb mini research Running the Tutorial • 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... Do it with ‘feeling’ “Mini Research” • 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 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? Your Disease • Genetic disease part 2 • Follow the rubric Things you already “know”