bio 202 unit 1

element

a substance that cannot be broken down to other substances by chemical reactions

compound

a substance consisting of two or more elements in a fixed ratio

isotopes

two atoms of an element that differ in the number of neutrons. can be stable or unstable (radioactive)

• when unstable can decay spontaneously, giving off particles and energy

half-life isotope

a “parent” isotope decays into its “daughter” isotope at a fixed rate

• values vary from seconds to years for some isotopes

electronegativity

atom’s abillity to attract and pull electrons toward itself

• nonpolar covalent bond = small difference (electrons are shared equally, no charge separation) eg. O2

• polar covalent bond = difference (electrons are shared unequally, partial charges form) eg. HCl

• ionic bond = large difference (electrons are transferred, full charges form) eg. KBr

covalent bond

• single bond = sharing of one pair of valence electrons

• double or triple bond = sharing of two or three pairs of valence electrons

• can form between atoms of the same element or atoms of different elements

• nonpolar = atoms ahare the electron equally

• polar = one atom is more electronegative, and the atoms do not share the electron equally

  • unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule

ionic bond

• atoms sometimes strip electrons from their bonding partners

• the two resulting oppositely charged atoms or molecules are called ions

  • postively charged = cation

  • negatively charge = anion

  • cations and anions attract each other, this attraction is an ____

ionic compounds

compounds formed by ionic bonds (salts like NaCl)

• most salts are quite stable when dry, but dissociate easily in water

hydrogen bond

forms when a hydrogen atom covalently bonded to one electronegative atom (are both attracted to each other)

van der waals interactions

occurs due to temporary or permanent shiftes in electrical charges that make nearby particles pull on each other (dipole moment)

weakest type of chemcial bond or intramolecular interaction

induced dipole - dipole interaction

acid

a substance that increase H+ concentration of a solution

base

a substance that increases the OH- concentration of a solution

pH scale

• acidic solutions = >7

• basic solutions = <7

buffers

substances that minimize changes in H+ and OH- by neutralizing the effects of the acid or base added

• typically a weak acid and base that work by absorbing H+ protons when they are in excess or donating them when they are depleted

bonds with carbon

• with 4 valence electrons, carbon can form 4 covalent bonds with a variety of atoms

• allows carbon to form large, complex molecules

• most frequent bonding partners = hydrogen, oxygen, and nitrogen

isomers

compounds with the same molecular formula but different structures and properties

• structural = have different covalent arrangements of their atoms

• cis-trans (geometric) = have the same covalent bonds but differ in their saptial arrangements

• enantiomers = mirror images of each other

chemical groups: hydroxyl

• alcohols

• is polar beacuse of the electrons spending more time near the electronegative oxygen (highly electronegative) atom

• can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars

chemical groups: carbonyl

• compound name: carboxylic acids or organic acids

  • acts as an acid, can donate an H+ because the covalent bond between oxygen and hydrogen is so polar

• ketones = if carbonyl group is within a carbon skeleton (end in -one)

• aldehydes = if carbonyl group is at the end of the carbon skeleton (end in -al)

• both groups are also found in sugars

• both groups may be structural isomers with different properties

chemical groups: amino

• compound name: amines

• acts as a base, can pick up an H+ from the surround solution (water, in living organisms)

• found in cells in the ionized form with a charge of 1+

chemical groups: sulfhydryl

• compound name: thiols

• 2 groups can react, forming a covalent bond

  • this cross-linking helps stabilize protein structure

chemical groups: phosphate

• compound name: organic phosphates

• contribute negative charge to the molecule of which it is a part (2- when at the end of a molecule, 1- when located internally in a chain of phosphates)

• molecules containing phosphate groups have the potential to react with water, releasing energy

chemical groups: methyl

• compound name = methylated compound

• methylation of DNA affects gene expression

• affect the structure and function of biological molecule, including hormones

marcomolecules

have unique properties that arise from the orderly arrangement of their atoms

• 4 classes:

  • carbohydrates (polymer)

  • lipids

  • proteins (polymer)

  • nucleic acides (polymer)

repeating units that serve as building blocks of polymers are monomers

carbohydrates

• includes sugar and polymers of sugars

• simplest = monosaccharides or simple sugars

  • have molecular formulas that are usually multiples of CH2O

  • eg. glucose

• are polysaccrharides, polymers composed of many sugar building blocks

monosaccharides

classified by

• location of carbonyl group (as aldose or ketose)

• the number of carbons in the carbon skeleton

alpha and beta monodsccharides

• the carbon that orginally had C=O now has a newly formed OH group = anomeric carbon

• because the linear carbonyl was planar, the new OH can end up pointing in either of 2 directions when the ring forms

  • alpha = opposite side as CH₂OH

  • beta = same side as CH₂OH

• once one sugar is linked to another, the alpha or bet form is fixed (frozen)

dehydration reaction

occurs when 2 monomers bond together through the loss of a water molecule

hydrolysis

• polymer disassembled to monomers

• a reaction that breaks down the polymer by adding a water molecule, breaking a bond

polysaccrharides

are long polymers composed of many monosaccharide units and have important storage and structural roles

• architecture and function are determined by its sugar monomers and the positions of it glycosidic linkages

energy storage: starch and glycogen

• in a potato tuber cell = plastids containing starch granules

• in muscle tissue = glycogen granules stored

structural support: cellulose

• starch (alpha configuration) is largely helical

• cellulose (beta configuration) is straight and unbranched

• the orientation of Beta-1,4 linkges forms straight polymers which are stabilized by hydroggen bonds

  • gives cellulose fibers the strength to support weight and stress

source: plant

subunit: beta-glucose

bonds: 1-4

branches: NO

starch

amylose

• source: plant

• subunit: alpha-glucose

• bonds:1-4

• branches: NO

amylopectin

• source: plant

• subunit: alpha-glucose

• bonds:1-4 and 1-6

• branches: YES (~per 20 subunits)

glycogen

source: animal

subunit: alpha-glucose

bonds: 1-4, 1-6

branches: YES (~per 10 subunits)