Ch. 2: Chemistry Flashcards
Atom
nucleus of positively charged protons and neutrally charged neutrons with negatively charged electrons outside nucleus
Molecules
groups of two or more atoms held together by chemical bonds,
formed by interaction of their electrons
Electronegativity
ability of an atom to attract electrons,
plays large part in determining kind of bond formed
Ionic Bond
electrons transferred,
electronegativities v different and one atom has much stronger pull on electron (high electronegativity)
Ion
atom with charge;
gain electron –> (-) lose electron –> (+)
Covalent Bond
electrons between atoms shared,
electronegativities between atoms are similar
Nonpolar Covalent
electrons shared equally,
electronegativities are equal and atoms pull equally, (O2)
Polar Covalent
electrons shared unequally, atoms have different electronegativities so one pulls electron more
Pole
during polar covalent bond, atom with greater electronegativity holds electrons closer and produces a negative charge (pole); other atom forms positive pole
Example: H20 (O more electronegative)
Hydrogen Bond
weak bonds between molecules form when (+) charged H atom in one covalent molecule is attracted to a (-) area of another covalent molecule in water (+) H forms H bond w/ (-) O of another molecule
Properties of water
excellent solvent high specific heat capacity ice floats has strong cohesion and high surface tension has strong adhesion
Water as solvent
ionic substances soluble in water bc poles of water molecules separate them into ions, polar covalent molecules work similarly
so many molecules dissolve in water –> universal solvent
Hydrophilic
“water loving,” dissolve in water because are charged
Hydrophobic
“water fearing,” nonpolar covalent substances lack charged poles and do not dissolve in water
Solute
substance that dissolves solvent
Aqueous solution
water is the solvent
Specific heat
degree to which a substance changes temperature in response to gain or loss of heat
Water’s high specific heat
changes temperature v slowly w/ changes in heat content have to add large amounts of energy to warm water or remove lots to cool evaporative cooling (sweat)
Water changing state
when heated (solid-->liquid-->gas) energy is absorbed and breaks H bonds, keeping temp. constant when cooled this is reversed, and H bonds are formed with the released energy
Heat of fusion
energy requited to change water from solid to liquid
Heat of vaporization
energy required to change water from liquid to gas
Ice floats
water expands as it freezes and becomes less dense than the liquid form
weak H bonds constantly break and reform in liquid state while in ice, H bonds between water molecules become rigid in a honeycomb arrangement
Implications of ice floating
if ice didn’t float it would sink and remain frozen due to the insulating protection of the overlaying water so would profoundly affect the survival of the organisms living at the bottom of the water
Water has strong cohesion and surface tension
H bonds cause cohesion and water sticks together, this forms high surface tension so creating a water surface firm enough to allow many insects to walk upon w/out sinking
Water has strong adhesion
water attracts to unlike substances as its poles attract to poles of other substances (wetting finger to turn pages)
demonstrates capillary action (plants)
Capillary action
water’s adhesion to the walls of narrow tubing or absorbent solids like paper it rises up, defying gravity
Organic molecules/ macromolecules
have carbon, easy to bond w/ bc 4 electrons available to form covalent bonds
straight lines or rings
monomers made from polymers
Hydroxyl group
-OH
Ex.: alcohols (ethanol), glycerol, sugars
polar, hydrophilic
Carboxyl group
-C–O/-OH
Ex.: acetic acid, amino acids, fatty acids, sugars
polar, hydrophilic, weak acid
Amino group
-N-H/-H
Ex.: amino acids
polar, hydrophilic, weak base
Phosphate group
-P–O/-O(-)/-O(-)
Ex.: DNA, ATP, phospholipids
polar, hydrophilic, acid
Methyl group
-C-H/-H/-H
Ex.: fatty acids, oils, waxes
nonpolar, hydrophobic
Monosaccharide
simplest kind of carbohydrate w/ one sugar molecule
glucose, fructose
Sugar molecule formula
(CH2O)N
Disaccharide
carbohydrate w/ 2 sugar molecules linked by glycosidic linkage
glucose + fructose = sucrose (table sugar)
glucose + galactose = lactose (milk)
glucose + glucose = maltose (breakdown of starch)
Glycosidic linkage
joins carb molecules
formed by dehydration reaction that causes water molecule to be lost
broken by hydrolysis reaction that requires water when
Polysaccharide
series of connected monosaccharides –> polymer
Ex.: starch, glycogen, cellulose, chitin
Starch
polymer of alpha glucose molecules
principle energy storage molecule in plant cells
Glycogen
polymer of alpha glucose molecules
differs from starch by its pattern of polymer branching
major energy storage molecule in animals
Cellulose
polymer of beta glucose molecules
structural molecule in walls of plant cells and wood
Chitin
polymer similar to cellulose but each beta glucose has nitrogen-containing group attached to ring
structural molecule in walls of fungus cells and in exoskeleton of insects, arthropods and mollusks
Alpha-glucose vs. beta-glucose
alpha glucose: starch (alpha-glycosidic linkages all OH on same side) can easily be broken down (digested) by humans and animals –> helical structure
beta glucose: cellulose (beta-glycosidic linkages every other OH flipped) can only be broken down in specialized organisms –> unbranched sheets that form H bonds
Lipid solubility
insoluble in water but highly soluble in nonpolar substances
3 major groups of lipids
Triglycerides (triaglycerols), phospholipids, steroids
Triglycerides (triaglycerols)
fats and oils
3 fatty acids (hydrocarbon chain w/ -COOH) attached to a glycerol (C2HO)
Fatty acid
hydrocarbons with a carboxyl group (-COOH) at one end of the chain
vary in structure by # of carbons and placement of single and double covalent bonds between carbons
Saturated fatty acid
have only single bonds between carbons so saturated w/ hydrogen
as a result can pack together more tightly –> higher melting temps and solid at room temp (fats)
Unsaturated fatty acid
have double bonds between carbons which creates a bend at bond, spreading triglyceride apart
so have lower melting temp and liquid at room temp
Monounsaturated fatty acid
one double covalent bond
Polyunsaturated fatty acid
2+ double covalent bonds
Phospholipid
triglyceride but w/ phosphate group (-PO3^2-) in place of one of fatty acid chains
fatty-acid “tails” are nonpolar & hydrophobic
phosphate “head” is polar and hydrophilic
oriented so that tails on inside and heads on outside, making cell membranes
Steriod
4 carbon ring backbone
Ex. cholesterol (component of cell membranes), hormones like testosterone and estrogen
Types of proteins
structural, storage, transport, defensive, enzymes
Structural protein
Ex. keratin in hair and horns, collagen in connective tissue, silk in spider web
Storage protein
Ex. casein in milk, ovalbumin in egg white, zein in corn
Transport protein
found in membranes of cells that transport materials into and out of cells and as oxygen-carrying hemoglobin in red blood cells
Defensive protein
antibodies that provide protection against foreign substances in animals
Enzymes
regulate rate of chemical reactions
Protein structure (bonds)
chain of covalently bonded amino acids
bonds called peptide bonds to form polypeptide by dehydration synthesis (one H20 released in forming every bond)
Amino acid general form
Amino group (-NH2), Carbon w/ H, Carboxyl group (-CdoublebondOOH), R group which determines properties
Primary protein structure
order of amino acids
Secondary protein structure
3D shape of protein from H bonding between amino and carboxyl groups of nearby amino acids
Spiral alpha helix bc H on one side only of Beta pleated sheets bc alternating H so H bonds form
Tertiary protein structure
additional 3D shaping
often dominates shape of globular proteins
caused by: H bonding/ ionic bonding between R groups in amino acids, hydrophobic effect that occurs when hydrophobic R moves toward center of protein, disulfide bridges
Disulfide bonds
sulfur atom in amino acid cysteine bonds to sulfur atom in another cysteine
helps maintain folds of amino acid chain
Quaternary structure
protein made from 2+ separate peptide chains
Ex. hemoglobin that’s made of 4 peptide chains held by H bonds and interactions among R groups
DNA
polymer of nucleotides
nitrogenous base, deoxyribose sugar, phosphate group
4 DNA nucleotides each w/ its own nitrogenous base (A, T, C, G)
Purines
double ringed nitrogenous bases
Adenine and Cytosine
Pyrimidines
single ringed nitrogenous bases
Thymine and Guanine
Difference between RNA and DNA
- sugar in RNA is ribose
- uracil replaces thymine (U-A)
- single stranded
Activation energy
energy needed for chemical reaction to take place (trigger formation of new bonds)
Catalyst
speeds up chemical reaction by lowering activation energy
does not participate in reaction so is not altered and can be re-used
Metabolism
chemical reactions that occur in biological systems
Catabolic (break-down) and Anabolic (formations)
driven by chemical equilibrium
Substrate
substance upon which enzyme acts
Ex. enzyme amylase catalyzes breakdown of substrate amylose (starch)
Enzymes
substrate specific (lock-and-key), unchanged in reaction, can catalyze rxn in both forward and backward direction, efficiency affected by temp. and pH (denaturation)
Induced-fit model
describes how enzymes work
enzyme has active site with which reactants (substrates) readily interact, substrate causes conformational change of enzyme that places substrate in a more favorable position to react
Cofactors
nonprotein molecules that assist enzymes
Coenzymes: organic cofactors that accept/ donate e-, vitamins
Inorganic cofactors: metal ions like Fe2+ and Mg2+
ATP
source of activation energy for metabolic reactions
when ATP releases energy, hydrolysis reaction breaks off a P to form ADP
reverse is phosphorylation
Reaction regulation
enzymes, feedback inhibition, competitive inhibition, noncompetitive inhibition, cooperativity
Allosteric effector/ Noncompetitive inhibition
binds to allosteric site on protein (NOT ACTIVE SITE) to cause conformational change in enzyme
activator vs. inhibitor
sometimes permanent sometimes reversible
Feedback inhibition
end product of a series of rxns acts as allosteric inhibitor, shutting down one of the enzymes catalyzing the rxns
Competitive inhibition
substance that mimics substrate inhibits enzyme by binding to active site so preventing substrate binding
Cooperativity
enzyme becomes more receptive to additional substrate molecules after one substrate attaches to
