1- Basic Molecular Structure 1

Chapter 2:The Nature of Molecules

Topics you are not responsible for:molar concentration

End of Chapter questions:Understand: allApply: allSynthesize: 1 & 3

Do all mQuiz Questions

1- Basic Molecular Structure 2

What is PET (Positron Emission Tomography)?

What is it used for?cancerheart diseasebrain function

How does it work?Cell metabolic activityFDG (2-Deoxy-2-[18F]fluoro-D-Glucose)

How is the image created?

PET Image from PetNet solutionshttp://www.petscaninfo.com/zportal/portals/pat

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What is the basic structure of atoms?

Where is energy held in an atom?

Nuclear

Electrons

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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

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Which atoms are most important to organisms?

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Why are some atoms radioactive?

What is an isotope?

Unstable isotopes will ‘decay’-- gamma rays-- beta particles-- positrons

Rate of decay as ‘half-life’18F ~ 2 hours32P ~ 14 days

3H ~ 12 years14C ~ 5,760 years

239Pu ~ 24,000 years

Number of: Protons 6 6Neutrons 6 8Electrons 6 6

12C 14C

Shorthand 12C

Animation

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What are the principal types of molecular bonds?

CovalentIonicHydrogenvan der Waals

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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 = nonpolarIf Δ ~ 1 - 2 = polar atoms have partial (δ) charges

What if Δ is > 2?

H2.2Li Be B C N O F

0.98 1.57 2.04 2.55 3.04 3.44 3.98Na Mg Al Si P S Cl

0.93 1.31 1.61 1.9 2.19 2.58 3.16K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br

0.82 1 1.36 1.54 1.63 1.66 1.55 1.83 1.88 1.91 2 1.65 1.81 2.01 2.18 2.55 2.96Rb Sr Y Zr Nb Mo Te Ru Rh Pd Ag Cd In Sn Sb Te I

0.82 0.95 1.22 1.33 1.6 2.16 1.9 2.2 2.28 2.2 1.93 1.69 1.78 1.96 2.05 2.1 2.66Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At

0.79 0.89 1.1 1.3 1.5 2.36 1.9 2.2 2.2 2.28 2.54 2 2.04 2.33 2.02 2 2.2

δ+ δ—

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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 +

O2-

Ca2+

polar cov ionic

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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 athttp://www.uic.edu/classes/bios/

bios100/indexf04am.htm

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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

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What determines the ‘pH’ of water?

What is pH?

pH = -Log [H+]

Scale is logrithmic

Water ionizes

H2O ↔ H+ + OH-

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Why is pH important to molecules and cells?-- Properties of proteins-- Enzyme activity

Hemoglobin and the “Bohr Effect”Decreasing pH lowers affinity for O2

Why hemoglobin binds O2 in lungs and releases it in tissues?

How does exercise increase O2 release in tissues?

Hydrolytic enzymes and the lysosomeEnzymes 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?

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What are pH ‘buffers’?

Stabilize pH

Various natural buffersNaPO4 NaHCO3

citrate, etc

What happens if you add a strong acid to a solution containing a pH buffer?

The buffering rangeDepends upon the type of

buffer used