Water

• the special properties of water are due to its bent shape

• water is polar

polar molecules:

• partial positive and partial negative charge

• uneven distribution of electrons

• a molecule is polar if it has sulfur, oxygen, or nitrogen in it (most electronegative)

• polar molecules attract to other polar molecules and this is called hydrogen bonding

• polar dissolves in polar due to hydrogen bonding

• nonpolar dissolves in nonpolar due to van der waals

• alcohol dissolves in both water and oil because it has polar and nonpolar parts. polar parts can form hydrogen bonds with the water and the oil mixes through van der waals

hydrogen bonding:

• form between polar molecules only

• different from covalent bonds: not within the molecule

• can break these bonds by adding heat

properties of water:

• cohesion****: linking together of like molecules (water sticks to water)

  • high specific heat: it takes a lot for water to change 1 degree celcius

  • high heat of vaporization: high energy needed to break hydrogen bonds before water can evaporate

  • high surface tension: molecules on the surface of water form a tight network making it difficult to penetrate the surface

  • less dense as a solid: water molecules form stable hydrogen bonds creating a crystal

• adhesion: the clinging of one substance to another (water sticks to other objects)

  • capillary action: liquid floats into narrow space

  • versatile solvent: charged regions on water attract ions and charged areas in polar compounds

ice floats:

hydrogen bonding causes ice to have a crystalline lattice structure, making it less dense than water

important because if ice didn’t float all bodies of water would freeze solid

acids and bases:

• water has a pH of 7 (10 to the negative 7)

• Acid: a substance with a pH less than 7

  • release H+ in H2O (releases hydrogen into the solution) H usually in front

    • ex. HCl

  • more hydrogens, the more acidic it is

• Base: pH greater than 7

  • accept H+ and takes them out of the solution. usually OH at the end

    • ex. NaOH

  • more hydrogens, the less basic it is

• Buffer: substances that prevent large fluctuations in pH

  • will increase or decrease H+ ions in order to lower or higher the pH

Carbon

organic compounds:

• contain carbon and hydrogen

• carbs, lipids, proteins, nucleic acids

• made by living thing

• C,H,O,N

inorganic compounds:

• do not contain carbon or hydrogen

• water, minerals, O2, CO2

• carbon had 4 valence electrons- can make 4 covalent bonds

hydrocarbons: composed of only carbon and hydrogen, always nonpolar and hydrophobic

functional groups:

• hydroxyl group : -OH

  • polar: allows H-bonding in that region

• carbonyl group: c double bond O

  • aldehydes and ketones (found in sugars)

• carboxyl group: -COOH

  • organic acid

• animo group: -NH2

  • acts as a base

• phosphate group: -PO4

  • very electronegative

  • found in ATP

  • lots of hydrogen bonding

  • found in DNA

• sulfhydryl group: -SH

  • found in proteins (more SH groups means more stable protein)

  • amino acid w/ SH is called cysteine

    • polar, will form H-bonds

    • used to regulate DNA expression

dehydration synthesis:

• synthesizing a polymer

• pull out H2O and add it to the end of the reaction

hydrolysis:

• breaking down a polymer

• add H2O to split the molecule

stanley miller’s experiment:

miller identified a variety of organic molecules that are common in organisms. he proved that these molecules, which are now only made by living things, were around when the earth was created because its climate was somewhat like the conditions he set in his experiment.

isomers and isotopes:

• isomer: 2 or more compounds w/ the same formula but different arrangement of atoms and difference properties

  • structural isomers: differ in covalent arrangement and locations of double bonds vary

  • cis-trans isomers: one is cis and one is trans

  • enantiomers: mirror images of each other.

    • ex. albuterol is medicine that works but its enantiomer R-albuterol does nothing

• isotopes: 2 or more types of atoms that have same atomic number and position but differ in neutron number

Carbs

• contain elements: carbon, hydrogen, oxygen

• monomer: monosaccharide

• hydrogen and oxygen are in a 2:1 ratio

immediate energy:

• comes from simple sugars: monosaccharides and disaccharides

• ex. of monosaccharides: glucose, sucrose, lactose

• ex. of disaccharides: maltose, sucrose, lactose

• glucose monomers are held together by glycosidic linkages

stored energy:

• comes from long chains or glucose called starches

• animal starch: glycogen

  • stored in muscle, liver

  • more long term energy

• plant starch: amylose

  • must be broken down through hydrolysis and then built up in our bodies

  • ex. pasta, bread, potato

  • stored chains sugar

solving the chemical formula:

if number of units is 15, subtract 14 H2O from the unit (28 H, 14 O)

cellulose:

• structural polysaccharide

• found in plant cell walls

• passes through our digestive system as fiber

• and 1,4 beta glycosidic linkages- cannot break down unlike alpha

• chitin: not used for energy, found in cell walls of fungi

Lipids

• contain carbon, hydrogen, and oxygen (little)

hydrophobic: insoluble in water (nonpolar)

triglycerides:

• stored energy, heat insulation stored under skin over the muscle

• 1 glycerol, 3 fatty acids

• ester bond: bond between oxygen and carbonyl group

• saturated fatty acids:

  • single bond

  • solid at room temp

  • animal sources

  • less healthy (butter. lard)

• unsaturated fatty acids

  • double bond

  • liquid at room temp

  • plant sources

  • trans unsaturated fats: worst kind, hydrogens on opposite sides of the carbon

    • hurt cholesterol, cause heart disease

    • created in hydrogenation

cholesterol:

• soft, waxy substance made up in liver

• used to make steroid hormones (testosterone, estrogen, cortisone)

• found in animal products

• basic structure has 4 carbon rings and a hydrocarbon chain

  • if missing hydrocarbon chain, then it is a steroid

• atherosclerosis: hardening of ther arteries from accumulation of cholesterol over time

phospholipids:

• make up a major part of cell membrane

• nonpolar

• 1 glycerol, two fatty acids, one phosphate group

• hydrophilic heads, hydrophobic tails

Proteins

• carbon, oxygen, hydrogen and nitrogen (sometimes sulfur)

• monomer: amino acid

• two animo acids = dipeptide

• peptide bond: colvalent bond between the carboxyl group of one amino covalentacid and the animo group of the next amino acid

functions of proteins:

• enzymes: speed up chemical reactions by lowering the activation energy

• motor/contractile proteins: muscle (actin + myosin), movement of cilia and flagella. responds to chem stim

• immune defense: antibodies are special proteins made by white blood cells that inactivate and destroy viruses and bacteria

• transport proteins: carry molecules into or out of the cell membrane (transmembrane proteins) or throughout the body

• structural proteins: collagen (skin, wounds, tendons), keratin makes up hair and nails

• storage proteins: storage of amino acids

• hormones/signaling: allows coordination of an organism’s activity

  • insulin: regulates sugar in blood stream

  • receptors: built into the membrane of a nerve cell to detect signaling molecules released by other cells

structure of a protein:

1. primary structure

   1. stabilized by peptide bonds

   2. specific sequence of amino acids

   3. denaturation cannot change the structure

2. secondary structure

   1. specific shape

   2. polypeptide is either alpha helix of pleated sheet

   3. mutation cannot change this structure

3. tertiary structure

   1. the overall 3-D shape

   2. becomes a protein that can function

   3. results from the interactions among (hydrophobic, hydrogen bonds, covalent bonds, ionic interactions, etc.)

4. quaternary structure

   1. proteins that contain 2 or more polypeptide chains to make the whole protein

   2. held together by hydrogen/covalent bonds

   3. hemoglobin contains 4 polypeptides each

causes of protein denaturation:

1. temperature

   1. too hot can permanetely denature protein

   2. too cold can slow down the functioning of a protein, but not denature

2. changes in pH

3. salts

• mutations: inherited change in DNA

• denature: environmental influences change the shape/function of proteins

Nucleic Acids

• organic molecule

• carbon, hydrogen, oxygen, phosphorus, and nitrogen

• serve as the blueprints for proteins

• DNA is transcripted into mRNA which is translated into a polypeptide

• phosphodiester bond: covalent bond that holds DNA and RNA together

  • hold one strand of nucleotides together

• 5’ prime starts at phosphate then goes to 3’. then switches on other side

DNA:

• found inside the nucleus of every eukaryotic cell

• sugar: deoxyribose

• shape: double helix

• nitrogen bases:

  • adenine (purine) w/ thymine (pyrimidine)

  • guanine (purine) w/ cytosine (pyrimidine)

  • purine bonds with a pyrimidine, cannot do purine-purine bond

RNA:

• reads and copies genes and synthesizes the proteins from the genetic code

• every 3 bases is called a codon and codes for a single amino acid

• sugar: ribose

• shape: single strand

• nitrogen bases:

  • adenine, guanine, cytosine, uracil (pyrimidine)