Rutherford's experiment used gold foil to scatter a-particles by hitting the atomic nucleus

. atoms are electrically neutral: #protons = #electrons = atomic number

. any substance that can’t be broken down by chemical means is called an element

. mass is the amount of substance, and it is the same on earth or moon

. weight is different on earth than on moon, is the force gravity exerts on a substance

. mass of proton = mass of neutron = 1 dalton. 1 gram = 6.02 x 10²³ daltons

. a cation has more protons than electrons. Anion has more electrons than protons

. isotopes are atoms of the same element with different numbers of neutron: C12, C13..

. radioactive isotopes are unstable and decay at constant rate measured as half-life

. chemical nature of atom is dictated by electrons in the outermost orbital (valence orbital)

. electrons occupy discrete energy levels K, L.. inside orbitals, each orbital with 2 electrons max

. electronegativity is the affinity of an atom for electrons. O = 3.5, N = 3.0, C = 2.5, H = 2.1

. electronegativity makes H2O a polar molecule with oxygen being partially negative

. because of water’s polarity hydrogen bonding is favored with O-acceptors and H-donors

. when water molecules stick to each other at the surface, it’s called cohesion

. when water molecules stick to other polar molecules, such as glass, that’s adhesion

. water causes hydrophobic molecules to aggregate or assume shapes like monolayers, micelles, etc.

. water is almost neutral: 1 molecule in 10,000,000 ionizes. Acids are proton donors, bases are acceptors

. strong acids dissociate completely in water, weak acids partially dissociate in water

.  a buffer is a mixture of a weak acid + its salt that resists changes of pH, such as acetic acid + Na acetate

. the buffering comprises 1 pH unit above and 1 pH unit below the pKa of the acid

. primary functional groups are hydroxyl, carbonyl, carboxyl, amino, sulfhydryl and phosphate

. secondary functional groups are ester &thioester, ether & thioether, amide, anhydride

. structural isomers differ in structure of carbon skeleton

. stereoisomers differ in how groups attached. Enantiomers are chiral and mirror image

. polymers such as carbohydrates, nucleic acids & proteins are made of monomers

. macromolecules, including polymers, are made by dehydration & broken by hydrolysis

. monosaccharides: simple sugars with 3 – 9 carbons, have a carbonyl and hydroxyl groups

. oligo- and polysaccharides are also called glycans. Linear D-glucose has 4 stereocenters

. When D-glucose cyclize forms one more stereocenter with 2 orientations a and b

. D-glucose and D-fructose are structural isomers. D-galactose is a stereoisomer of D-glucose

. aD-glucose +a D-fructose makes sucrose. aD-glucose + aD-glucose makes maltose

. starch, a polymer of glucose, has linear amylose (1-4 link) and branched amylopectin (1-4 & 1-6)

. cellulose is a linear polymer of bD-glucose

. a nucleotide has a sugar + nitrogenous base + phosphates

. DNA has deoxyribose, RNA has ribose, and both have only one phosphate.

. nucleic bases are purines (adenine & guanine) and pyrimidines (cytosine, thymine and uracil)

. purines are present in both RNA and DNA as well as cytosine. DNA has thymine, RNA has uracil

. DNA encodes information for protein synthesis, has double helix with H-bonding: A:T and C:G

. RNA uses information in DNA to specify sequence of amino acids in proteins. RNA is single strand

. ATP is the primary energy currency of the cell; NAD+ and FAD are electron carriers

. there are 20 a amino acids that DNA codes in protein synthesis. All amino acids are L

. there are four levels of protein structure: 1^a is the sequence, 2^a can be a-helix or b-sheet mainly

. the 3^a structure is the final shape of a globular or fibrous protein; 4^a has 2 or more 3^a structures

. hydrogen bonding, disulfide bridge, ionic bond & hydrophobic interactions give shape to proteins

. motif is a folding pattern; domain is a unit of the protein that has a function, such as catalysis

. the functional form of a protein is called native state. Folding a protein requires chaperones

. the primary structure of a protein determines its tertiary structure

. fats, oils, waxes, terpenes, steroids and other materials insoluble in water are called lipids

. triglycerides are esters of glycerol with 3 fatty acids. Fatty acids are acids with 12 to 20 carbons

. animal unsaturated fatty acids are cis. Phospholipids have glycerol + 2 fatty acids + phosphate

. phospholipids are amphiphilic (surfactants, soaps) with a polar head and non-polar tail

. cells are the basic unit of an organism, arise from previous cells; most are less than 50 mm

. Robert Hooke in 1665, was the first to observe cells using a microscope

. microscopes are: light (resolve structures 200nm) and electronic (resolve structures 0.2 nm apart)

. light microscopes have 2 magnifying lenses (compound) and are limited to lights’ wavelengths

.  electronic, beam of electrons and can be transmission (through sample) or scanning (on the surface)

.  basic structures of all cells: nucleoid or nucleus, cytoplasm, ribosomes and plasma membrane

. prokaryotes, the simplest organisms, have no-membrane nucleoid, DNA, and cell wall in 2 domains

. in archaea domain walls have sugars/protein, in bacteria domain walls have peptidoglycans

. some prokaryotes have organelles and infoldings in plasma membrane for chemical reactions

. bacteria have microcompartments with semipermeable protein shell for metabolic processes

. prokaryotes have actin- and tubulin-like structures, but cell shape is given by cell wall

. some prokaryotes have pili and flagella that rotate using a proton gradient similar to ATP synthase

. the peptidoglycan (sugars + polypeptides) cell walls of bacteria is susceptible to antibiotics

. cell wall of archaea has saturated hydrocarbons attached to glycerol that gives them thermal protection

. animal and plant cells have in common: plasma membrane, most of the same organelles + cytoskeleton

. plant cells have in addition: cell wall, chloroplasts, vacuoles and glyoxysome for fat to sugar conversion

. the eukaryotes nucleus has DNA divided in linear chromosomes that with protein is called chromatin

. eukaryotes nucleus has nucleolus for RNA synthesis and 2-phospholipid bilayer membrane with pores

. nuclear pores allow the passage of ions and small molecules, control passage of large RNA complexes

. largest internal membrane is the endoplasmic reticulum (ER) which divides the lumen from cytoplasm

. rough ER (RER) has ribosomes that make proteins for export that can be tagged to form glycoproteins

. smooth ER (SER) is a network of tubules and sacs with enzymes to make sugars, steroids and lipids

.  SER assembles membrane lipids, stores Ca ions and modifies foreign substances for detoxification

. Golgi sorts and modifies proteins/ lipids received in cis face from RER/ SER and send those on trans face

. lysosomes (organelles buddings from Golgi) have enzymes for degradation of many internal substances

. peroxisomes, organelles bud off from ER, oxidize fatty acids and get their name from hydrogen peroxide

. vacuoles in plants serve as storage for food or toxins, maintain osmotic pressure via water channels

. osmotic pressure is the force required to stop flow from dilute to concentrated side on a membrane

. an isotonic solution has equal concentrations on both sides of semipermeable membrane

. mitochondria are semiautonomous and have inner-membrane enzymes for oxidative phosphorylation

. chloroplasts of plants have two membranes and make sugars using CO2 as the source of carbon

. cell cytoskeleton has 3 types of proteins: actin, microtubules and intermediate filaments

. centrioles occur in pairs in animal cells and most protist, but not in plants or fungi. They have tubulin

. eukaryotic flagella and cilia have 9 microtubule pairs surrounding 2 microtubules used for movement

. eukaryotic cell walls have cellulose in plants and protists, and chitin or N-acetyl glucosamine in fungi

. instead of cell wall, animals have collagen, elastin and proteoglycan in the extracellular matrix (ECM)

. cell surface has glycolipids and MHC protein: markers (blood types), cell recognition (immune system)

. Cell connections are: 1) adhesive junctions 2) tight junctions and 3) communicating junctions

. plasmodesmata in plants are gaps in cell walls that connect ERs of two cells by a central tube

. cellular membranes have: lipids, integral proteins, interior protein network & cell surface markers

. membrane lipids are glycerophospholipids, sphingolipids and sterols such as cholesterol

. saturated fatty acids are present in warm temperatures, unsaturated FA are present in cold

. membrane transport can be: passive, facilitated and active which requires energy from ATP

. in passive transport, molecules move from high to low concentration with no energy needed

. in facilitated diffusion solute move through channel and carrier proteins from high to low concentration

. osmosis is the diffusion of water across a membrane toward a higher solute concentration

. primary active transport requires ATP and move substances from low to high concentration

. 2^a active transport uses energy of 1^a active transport to move another against concentration gradient

. bulk transport can be endocytosis (into the cell) or exocytosis (discharge of materials out of the cell)

. endocytosis is: phagocytosis (solids), pinocytosis (liquids) or receptor mediated, for specific molecules

. one calorie is the heat required to raise 1^oC to 1 gram of water

. oxidation is the loss of electrons, reduction is gain of electrons and has higher energy than oxidation

. enthalpy (H) is the heat exchange between a system and its surroundings at constant pressure

. entropy (S) is the degree of disorder of a system and increases in an isolated system (2^nd law)

. free energy, DG, is the portion of energy available to do work at constant T & P:  DG = DH - TDS

. if DG is negative, the products have less free energy than reactants and reaction can be spontaneous

. activation energy is the energy required to destabilize bonds to initiate a chemical reaction

. the rate of a reaction depends on the activation energy (Ea) required; the lower Ea the faster the rate

. a catalyst influences chemical bonds to lower Ea. Enzymes are protein catalysts, but some are RNA

. ATP is 1^a energy currency of a cell, good for short-term storage. For long energy storage: fats & sugars

 . the enzyme active site is a pocket or clef for precise fit binding of a substrate

. inhibitors can bind enzyme at active site (competitive) or at a different site (allosteric site)

. cofactors assist enzymes in function; can be metal ions (Zn, Mn, etc.) or coenzymes such as vitamins