Slide 1Slide 2Slide 3pH ScaleWeak Acids and Bases in BiologyIonization of Weak AcidspKaWeak Acids and Bases in BiologySlide 9Ionic Bonds in Proteins are Affected by pHA Very Brief History of GeneticsA Brief History of GeneticsThe State of Genetics around 1945Slide 14Slide 15Slide 16Slide 17Slide 18Clicker QuestionThe Discovery that Genes are DNA was SurprisingSlide 21Original Model of the Double Helix (1953)Slide 23DNA StructureSlide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Chargaff’s Rules (1951-’52)Slide 33Slide 34Conventions in writing DNA/RNA sequencesSlide 36Slide 37Summary of B-DNA Structural FeaturesWhat forces are responsible for DNA structure?Slide 40Ligase is an organization that works to incite a passion andcuriosity for biological phenomena in students from anydiscipline through core MCB tutoring, exposure to research in workshops, and an introduction to life science applications in real-world contexts via journal clubs and more.•Tutoring Monday, Tuesday 5-8PM, and Thursday 5-7PM at UGL Upper Level•Biweekly Journal Clubs will be held Thursday 7-8PM at Burrill 135If you’re interested in any of these opportunities or would like more information email us at: [email protected] can also check us out on Facebook by searching MCB Ligase at UIUCUndergraduate Research Information Session Tues. September 2nd, 2014 5:00pm - 6:00pm 124 Burrill HallPlanning to go to professional school or graduate school? How are you going to stand out from the competition? Learn how to get involved with research on campus, work with renowned professors and gain the distinction and credit you deserve!MCB 250 - Lecture 3Some Chemical Fundamentals (Conclusion)DNA is the Genetic MaterialDNA StructurepH ScaleWeak Acids and Bases in BiologyA Carboxylic Acid Group – Weak AcidAn Amino Group – Weak BaseWeak acid Conjugate base OH C O O - C + H+ O O C + H+ O=Ka H N + H+ H H N+ H HKaConjugate acidWeak baseIonization of Weak AcidsHA H+ + A-Ka = [H+][A-] [HA][H+] = Ka [HA] [A-]pH = pKa + log [A-] [HA]Henderson-Hasselbach EquationSo when pH = pKa, [A-] = [HA]. When the pH is one unit above the pKa [A-]/[HA] = 10, and when pH is one unit below the pKa [A-]/[HA] = 0.1 [A-] [HA]When [HA] = [A-] then [A-] [HA]= 1 and log= 0KapKa H N+ H H H N H O C O OH C O14pKa1pH% Deprotonated50pKaHA H+ + A-Ka[H+][H+]Weak Acids and Bases in BiologyThe pKa is affected by the local environment. The pKa of an amino acid side chain in the interior of a protein may differ from the pKa of the same side chain on the surface of a protein.The charge of a protein or peptide at neutral pH is determined by how many glutamic acid, aspartic acid, lysine and arginine residues it has.Glu, Asp (pKa approx. 4) Essentially 100% negatively charged at neutral pH.Lys (pKa approx. 10.5), Arg (pKa approx. 12).Essentially 100% positively charged at neutral pH.Ionic Bonds in Proteins are Affected by pHLysine AspartateCH2-CH2-CH2-CH2-NH3+ HOOC-CH2CH2-CH2-CH2-CH2-NH3+ - OOC-CH2CH2-CH2-CH2-CH2-NH2 - OOC-CH2pH Attraction?<27>12NoYesNoA Very Brief History of Genetics•From ancient times: “Like begets like.”•Mendel (1865, rediscovered 1900)–Inheritance of some traits can be explained by simple laws (see Text, Ch. 1). Mendel’s work leads to the idea that there are genetic elements (genes) that can exist in different forms (alleles) that somehow determine observable traits (phenotypes).A Brief History of Genetics•T. H. Morgan (1910) (Nobel Prize 1933)–Genes are located on chromosomes. Chromosomes can be observed directly by microscopy. (See Text p. 11)•Beadle and Tatum (1941) (Nobel Prize 1958)–Genes somehow determine individual proteins. “One gene, one enzyme.” (See Text p. 16)The State of Genetics around 1945•By the 1940’s we knew a lot about how genes behave (they get passed from parents to offspring as part of chromosomes) and we had some idea of what they do (they determine proteins) but a deeper understanding required learning what genes are. •We needed to know the chemical composition and the chemical structure of the gene.What is the nature of the genetic material ?Frederick Griffith-1928, transformation of Streptococcus pneumoniaeSee Text- Page 22SmoothColonyRoughColonyCapsule No CapsuleHeat KilledRecoveredThe mutant pneumococcus was “transformed” by some substance from the dead wild type bacteria.Smooth(Capsule+)Rough(Capsule-)Smooth(Capsule+)HeatKilledSomething is taken up that transforms the rough strain to smooth and the smooth trait is inherited by future generations.Avery et al. carefully purified the “transforming principle” and found that it did not contain protein, carbohydrates, RNA, or lipids. Instead it contained, as far as they could determine, only deoxyribonucleic acid, DNA.We still use the term “transformation” to indicate living cells taking up external DNAWhat is the “something” that transfroms rough pneumococci to smooth?Smooth(Capsule+)Rough(Capsule-)Smooth(Capsule+)BreakCellsPure DNA transforms rough to smooth.The Transforming Material is DNA(Avery, MacLeod, and McCarty, 1944)Purify Transforming Principle - it’s DNA!Fig 2-3 DNA is the Hereditary Material (Alfred Hershey and Martha Chase, 1952Nobel Prize 1969 )Hershey and Chase radioactively labeled the E. coli virus (bacteriophage) T2The protein coat was labeled with 35SThe DNA was labeled with 32PThey showed that after infection, they could strip off the protein. Only the DNA entered the cells and these infected cells gave rise to progeny phage.Clicker Question•There are several types of Strep. pneumoniae that have chemically different polysaccharide capsules (Avery’s previous work) called S1, S2, S3, etc. •Experiment: Dead S1 cells + Live Rough (S2) cells–What is the capsule of the bacteria recovered from the mice?A. S2B. S1C. A mixture of S1 and S2D. The experiment won’t work – the mice will live•The chemical composition (but not the structure) of DNA was known. •DNA is pretty boring. A single sugar, phosphate, and 4 bases couldn’t contain enough information to specify all the proteins in the cell, could they?•Proteins are made of 20 different amino acids with an enormous variety of possible structures. So if the gene is DNA how does it work? •We need to know the chemical structure of DNA to solve this problem.•Enter Wilkins and Franklin, and Watson and Crick