What we have to learn to do, we learn by doing Aristole Welcome to Biology: A Molecular Approach Bio 7505 Professors: JM Crisman, PhD EJ Lehning, PhD

Lecture Block- Basic Chemistry

Basics of Quantum Mechanics Protons, neutrons and electrons Atomic number- total # of protons Atomic mass- protons + neutrons - dalton is the unit of atomic mass

Potential Energy- Energy is Stored Kinetic Energy- Energy is released Potential Energy vs. Kinetic Energy (stored) vs. (released) X miles Calories For Bonds Use Kilocalories (kcals) Free nrg (  G) What do the words “potential” and “kinetic” mean?

Atoms store nrg and release nrg 1)Movement of electrons between nrg (energy) levels (e.g. fluorescence) 2) Forming and breaking bonds 3) Radioactive Decay- Nrg is also released when some atoms release subatomic particles

Fig. 2.3

Fig. 2.4 Radioactive Half-life Radioactive Isotopes Decay

electrons occupy different energy levels Nucleus K L M Lowest nrg Highest nrg Nrg = energy

Fig. 2.5

Fig. 2.8

Fig. 2.6 Nrg in nrg levels can be use to create fluorescence

Atoms can absorb energy (potential energy) and release energy (kinetic energy)Nucleus K LM Lowest nrg Highest nrg Nrg = energy Absorb nrg Release nrg An Example

Ionic Bonds- AKA electrovalent bonds - Atoms are in close association and electrons are donated and change the charge of the atom.

Cations- ions with positive charge (e.g. Na + ) Anions- ions with negative charge (e.g. Cl - ) Ions: Number of electrons does not equal the number of protons….. So there is a charge

Redox Reactions e- can be gained and lost during chemical reactions (rxns). Gain of e- ---reduction Loss of e- ---oxidation LEO SAYS GER Used for energy transfer in biochemical reactions Redox = reduction/oxidation reactions

Bonds and Basic Reactions Covalent bonds- pairs of electrons are shared between atoms Strong bonds that require significant amounts of energy to break Bonds store energy Atoms interact to form molecules by forming bonds

These bonds take tons of nrg to form! -So cells use molecules called enzymes that make reactions go faster! Explain the example of making a protein from amino acids When chemical combine they form an intermediary state called a transition state….takes a ton of energy to get there…and when achieved the transition state allows bonds to break and new bonds to form Enzymes lower the amount of energy needed to break and reform New bonds…they hold reactants close together and move electrons themselves!...usually within their own molecular structures!

Chemical reactions pass through a transition state and enzymes speed-up reactions by lowering the nrg needed to get there + Free nrg (  G) kcal reactants products Activation nrg (Ae)- nrg needed to get to the transistion state from transistion state from reactant nrg level A + BC Enzymes are biological catalysts that lower the Ae What is an enzyme? Use the example of two amino acids!!!!!!

Besides true bonds, there are other ways atoms interact with each other Van der Waal forces Hydrogen bonds (H Bonds) Hydrophobic interactions Low nrg associations - are like velcro individually these interactions are weak but collectively they are very strong

Van der Waals Interactions Within a certain radius atoms attract each other. If they get too close…they repel each other Molecules naturally attract each other Van der Waal Radius Distance that atoms of a molecule will stably interact individually these interactions are weak but are stronger collectively

H Bonds DIPOLE Water (H 2 O) HOH H O H H O H   O and N can form Hydrogen bonds -very weak individually but collectively strong In fact the DNA double helix is stabilized by these interactions Polar Molecule

Hydrophobic Interactions Hydrophobic molecules (i.e. do not interact with water…and thus tend to interact with each other… to “drive” water out Very important to stabilize many molecular structures (e.g. cell membranes, some protein structure) What does “hydro” and “phobic” mean?