Chemistry AP Biology

Chemical Bonds Electronegativities of Common Elements Hydrogen2.1 Oxygen3.5 Carbon2.5 Nitrogen3.0 Sulfur2.5 Phosphorus2.1 Sodium0.9 Chlorine3.0 Electronegativity = how well an atom “holds its electrons

Bonds within a molecule Bonding between atoms can be organized on a continuum between covalent and ionic bonds Nonpolar CovalentPolar CovalentIonic

Bonds within a molecule Nonpolar covalent bond = electrons are shared evenly between atoms Polar covalent bond = electrons are shared but are more tightly held by one atom Ionic bond = Electrons are not shared due to strong electronegativity differences (one atom “grabs” the electrons from the other)

Bond Type By Electronegativity Electronegativity differenceBond Type < 0.3Nonpolar Covalent Between 0.3 and 1.7Polar Covalent > 1.7Ionic

Hydrogen Bonds This is a type of bond BETWEEN molecules (different from polar covalent bond) Involves the hydrogen of one molecule being attracted to a strongly electronegative atom in another molecule H HO H N -- ++ ++ ++ --

Hydrogen bonds are extremely important in biological systems. We’ll see them again and again: –Proteins –DNA –Enzymes –And more! Img taken without permission from:

Van der Waals Interactions Weak attractions when two molecules are very close together Temporary dipole moments in an atom can cause these tiny attractions Images taken without permission from:

Applications… Stickybot – uses same model as gecko feet! Gecko glue Image taken without permission from

Properties of Water Polar molecule  forms hydrogen bonds Hydrogen bonds give water some special characteristics (not all): –High specific heat –Evaporative cooling –Insulation of bodies of water

Properties of water (cont.) High Specific Heat –Takes a lot of energy to heat up 1 degree –Makes water very stable Evaporative cooling –Water has a high heat of vaporization –Evaporative cooling prevents overheating

Properties of water (cont.) Insulation of bodies of water –Solid water is less dense than liquid water– ice floats! –Ice on top creates a “cover” that keeps water below from freezing – Allows fish and plants underneath to continue to exist.

Buffers Maintain the pH in a solution Typically consist of an H+ acceptor and an H+ donor Why might this be important in living things? Image taken without permission from:

Carbon- a versatile element Each carbon atom can form 4 bonds Carbon is used in (for all living organisms) –Storage compounds –Cell formation

Molecular drawings In some molecular drawings, C and H are left out as a shortcut –Junction between lines = C –Line that ends with nothing at the end = C –Since C makes 4 bonds, unless otherwise noted H is assumed to be there (to make 4 bonds total) 2 ways to draw the same molecule!

Functional Groups Functional groups are groups of atoms –participate in many chemical reactions –Help determine the properties of organic molecules

Alcohol (hydroxyl) –Other forms: HO— Aldehyde –Other forms: -COH –Properties: Polar, Soluble in water Ketone –Other forms: –Properties: Polar, Soluble in water Functional groups CH 2 C O

Functional groups Carboxyl –Other forms: -COOH, -COO - –Properties: Acidic, Polar, Water Soluble Amino –Other forms: -NH 2, - NH 3 + –Properties: Basic, Polar

Functional groups Thiol –Other forms: -SH –Properties: Polar, forms disulfide bridges/bonds in proteins Phosphate –Other forms: -PO 4 2- –Properties: Charged, Polar