1- Basic Molecular Structure1 Chapter 2: The Nature of Molecules Topics you are not responsible for: molar concentration End of Chapter questions: Understand: all Apply: all Synthesize: 1 & 3 Do all mQuiz Questions

1- Basic Molecular Structure2 What is PET (Positron Emission Tomography)? What is it used for? cancer heart disease brain function How does it work? Cell metabolic activity FDG (2-Deoxy-2-[18F]fluoro-D-Glucose) How is the image created? PET Image from PetNet solutions

1- Basic Molecular Structure3 What is the basic structure of atoms? Where is energy held in an atom? Nuclear Electrons

1- Basic Molecular Structure4 What does an electron ‘orbital’ diagram depict? What does an electron ‘energy level’ diagram depict? -- electron shells -- “valence shell” Why are orbitals and energy levels Important to chemical reactivity? Orbital overlap ‘Octet rule’ Helium Nitrogen

1- Basic Molecular Structure5 Which atoms are most important to organisms?

1- Basic Molecular Structure6 Why are some atoms radioactive? What is an isotope? Unstable isotopes will ‘decay’ -- gamma rays -- beta particles -- positrons Rate of decay as ‘half-life’ 18 F ~ 2 hours 32 P ~ 14 days 3 H ~ 12 years 14 C ~ 5,760 years 239 Pu ~ 24,000 years Number of: Protons 66 Neutrons 68 Electrons C 14 C Shorthand 12 C Animation

1- Basic Molecular Structure7 What are the principal types of molecular bonds? Covalent Ionic Hydrogen van der Waals

1- Basic Molecular Structure8 What are covalent bonds? How do they form? -- e- shared to stabilize octet -- orbital orientation Where are they found?

1- Basic Molecular Structure Why do atoms form ‘polar’ vs non-polar covalent bonds? Electronegativity reflects the tendency to donate, share or ‘grab’ electrons Atoms may differ in electronegativity In general… If Δ < ~0.8 = nonpolar If Δ ~ = polar atoms have partial ( δ ) charges What if Δ is > 2? δ + δ —

1- Basic Molecular Structure10 What are ionic bonds? How do ‘ions’ form? -- Large Δ in electronegativity -- loss or gain of e- = Oxidation and reduction -- yields Octet stabilization Ions have full + or – charge Na + O 2- Ca 2+ polar covionic

1- Basic Molecular Structure11 What are hydrogen bonds? How do they form? Where are they found? van der Waals bonds -- due to weaker charge fluctuations Hydrogen bonds image from Michael Muller’s web page at exf04am.htm

1- Basic Molecular Structure12 How do properties of water influence cellular properties? -- there is abundant Hydrogen bonding “Stickiness” cohesion & adhesion High solubility Temperature change moderation “Specific heat” Salt in water

1- Basic Molecular Structure13 What determines the ‘pH’ of water? What is pH? pH = - Log [H+] Scale is logrithmic Water ionizes H 2 O ↔ H + + OH -

1- Basic Molecular Structure14 Why is pH important to molecules and cells? -- Properties of proteins -- Enzyme activity Hemoglobin and the “Bohr Effect” Decreasing pH lowers affinity for O 2 Why hemoglobin binds O 2 in lungs and releases it in tissues? How does exercise increase O 2 release in tissues? Hydrolytic enzymes and the lysosome Enzymes destroy proteins, lipids, etc. -- produced in Golgi apparatus (pH 7.5) -- transported to lysosome (pH 5.5) What would be the consequence if hydrolytic enzymes had a pH optimum of 5.5?

1- Basic Molecular Structure15 What are pH ‘buffers’? Stabilize pH Various natural buffers NaPO 4 NaHCO 3 citrate, etc What happens if you add a strong acid to a solution containing a pH buffer? The buffering range Depends upon the type of buffer used