AP Bio Unit 1

matter

• takes up space; has mass

• C, H, O, N make up 96% living matter

atoms

smallest unit of any periodic table element

3 components of an atom

neutrons, protons, electrons

neutrons

neutral, in center/nucleus of atom, have atomic weight ~1

protons

positive charge, in center/nucleus of atom, have atomic weight ~1

electrons

negative charge, found in electron cloud/orbitals, no critical mass

orbitals

• areas of space around nucleus

• lower orbital # = closer to nucleus

valence electrons

• # of electrons in outermost orbital

• 1st orbital can hold 2 electrons (1 pair), all other hold 8 (4 pairs)

• # of valence electrons impact how many bonds/types of bonds an atom can make (atoms want full outer ring to be stable)

atomic mass

proton # + neutron #

atomic number

proton #

isotope

• element w/ unusual # of neutrons

• atomic weight different from normal weight of that element

• ex: carbon 13 (1 extra neutron)

molecules

made of more than one atom bonded together

bonding

an attraction b/t 2 atoms/molecules

covalent bonds

electrons are shared b/t atoms in molecule; found in outer orbital of both atoms

polar vs. nonpolar

• polar covalent bond: electrons are not shared evenly, pulled farther from nucleus of one atom & closer to the other

• result: polar molecule w/ uneven distribution of charge

ionic bonds

• electron(s) are transferred between atoms, resulting in the formation of ions that are attracted to each other

• cations & anions

cation vs. anion

cation: positive ion, has lost 1 or more electrons

anion: negative ion, has gained 1 more electrons

hydrogen bonds

weak attractive force b/t 2 polar molecules

water formula/structure

H₂O (bent, 2 hydrogens, 1 oxygen)

water polarity

• oxygen is more electronegative, pulls shared electrons closer so it has a more negative side

• hydrogens are less electronegative, the shared electrons are pulled away from them and are are more positive

water properties: cohesion

• hydrogen bonding b/t molecules of the same substance

• water molecules are attracted to each other, allowing for surface tension and water droplet formation

water properties: adhesion

• hydrogen bonding b/t molecules of different substances

a. water molecules are attracted to other polar or ionic molecules

b. with cohesion allows for capillary action, movement of water through plants

specific heat

amount of heat that needs to be applied to a substance to raise the temperature 1 degree

water properties: high specific heat

• water has high specific heat, requiring lots of applied heat to raise temp.

• prevents body temp. of organisms from (made mostly of water) from fluctuating rapidly

• prevents temp. of planet from changing rapidly (oceans=major heat sink)

structure of ice vs. liquid

as water cools and freezes the hydrogen bonds become more stable and molecules space out to maximize the number of hydrogen bonds they can form, so ice is less dense than liquid water

solid vs. liquid: non-water substances

as substances cool the molecule movements slow down, most substances increase in density because molecules are bouncing off each other less

ice floats

• ice floats on water, bodies of water float from the surface down

• leaves liquid below ice layer

• ice insulates water below; organisms survive winter under ice

water pH

• in any aqueous solution at 25°, the concentration of hydrogen ions multiplied by the concentration of hydroxide ions is = 10^-14

• pH = -log[H⁺]

• If given pH then [H⁺] = 10^(-pH)

pH continued

• Water can (but rarely does) dissociate evenly into H⁺ and OH^- so its pH = 7 (neutral) 

  • Important for enzymes/proteins, many work in an ideal pH range close to neutral and will denature if in an extreme pH (acidic or basic)

carbon properties

• 6 protons, 6 neutrons, 6 electrons

• 4 valence electrons, can form 4 single bonds, up to 2 double bonds, or one triple bond (plus one single bond to another atom)

• Found in all organic molecules

monomer

smallest unit of a macromolecule

polymer

made of multiple monomers linked together

Condensation/Dehydration Synthesis Reaction

• links two monomers (or a monomer and a polymer) together by removing a Hydrogen (H)  from one and a hydroxide (OH) from the other

• the two larger molecules bond in the area that is now available and the Hydrogen and Hydroxide bond to form a molecule of water

Hydrolysis Reaction

• Breaking down a polymer and water, a water molecule breaks down to form a hydrogen and hydroxide and a bond between two monomers in a polymer breaks

• the hydrogen bonds to one of the larger molecules and the hydroxide to the other

functional groups

1. hydroxyl

2. carbonyl

3. carboxyl

4. amino

5. sulfhydryl

6. phosphate

7. methyl

hydroxyl

• formula: OH

• properties: polar, can bond to a hydrogen ion to form water, found in alcohols (compound names ending in -ol)

carbonyl

• Formula/Structure: - CO (with 2 open bonds off carbon) 

• Properties: compounds are called Ketones if carbonyl is in the middle of a skeleton, compounds are called aldehydes if carbonyl is at the end of a carbon skeleton

carboxyl

• Formula/Structure: - COOH or -CO₂H

• Properties: tends to ionize, acidic (releases a H+)

amino

• Formula/Structure: - NH₂

• Properties: acts as a base (can pick up a H⁺), found in all amino acids

Sulfhydryl

• Formula/Structure: - SH

• Properties: forms disulfide bridges in proteins (tertiary structure) between cysteines (Amino Acids)

phosphate

• Formula/Structure: - OPO₃^2-

• Properties: found in nucleic acids (including ATP), repel each other producing lots of stored energy in ATP (energy is released when bond between a phosphate and ADP is broken)

methyl

• Formula/Structure: - CH₃ 

• Properties: can affect gene expression when on DNA or proteins bound to DNA

isomers

Molecules that have the same chemical formula

structural isomers

differ structurally in the arrangement of covalent bonds

cis-trans isomers

found in molecules that have a double bond between carbons

• Cis = atoms attached to carbons involved in double bond are on the same side

• Trans = atoms attached to carbons involved in double bond are on opposing sides