ap bio chem of life

Matter

anything that takes up space + mass, made of elements, exists in many forms

Element

substance cannot be broken down to other substances by chemical reactions, recognize 92 elements in nature, each element has symbol

Compound

made of atoms joined by bonds, substance consist of two or more different elements combined in a fixed ratio, properties depend on its atoms + how they are bonded together, has characteristics different from those of its elements

Elements make up most of living matter

Oxygen, carbon, hydrogen, nitrogen, remaining 4% are calcium, phosphorus, potassium, and sulfur

Essential element

organism needs to live a healthy life + reproduce, similar among organisms w/ certain variations, of 92 natural elements 20-25% are essential elements

Trace element

required by an organism in only minute quantities, some needed by all forms of life, others req by certain species only

Atom

smallest unit of matter that still retains the properties of an element, make up elements, different from atoms of any other element, symbolize w/ same abbreviations used for element made up of those atoms

Neutron

subatomic particle, electrically neutral, 1.7 x 10⁻²⁴ g or 1 dalton

Proton

subatomic particle, one unit of postive charge, 1.7 x 10 ⁻²⁴g or 1 dalton

Electron

subatomic particle, one unit of negative charge, very small charge

Atomic nucleus

dense core at center of atom, packed with protons and neutrons, protons give nucleus positive charge and rapidly moving electrons form cloud of negative charge around nucleus, attraction between opposite charges keep electrons in vicinity of nucleus

Atomic number

number of protons in nucleus, unique to each element, subscript to left of symbol, unless otherwise indicated atomic number also \= number of electrons

Atomic mass

total mass of an atom

Mass number

total number of protons and neutrons in nucleus, superscript to left of element's symbol

Electron shells

characteristic average distance and energy level, represented by concentric circles, can only exist at certain levels, not between, move from one shell to another by absorbing/losing amount of energy \= difference in potential energy between its position in the old shell and that in the new shell

Energy

capacity to cause change, ex. by doing work

Isotope

different atomic forms of same element, atoms have same number protons w/ different number of neutrons + thus different mass, behave identically in chemical reactions

Radioactive isotopes

isotope where nucleus decays spontaneously, giving off particles and energy, if changes number of protons transforms atom to different element, used as radioactive tracers, hazardous to life by damaging cellular molecules

Half-life

time it takes for 50% of the parent isotope to decay

Radiometric dating

measure ratio of different isotopes + calculate how many half\=life have passed since organism fossilized or rock was formed

Potential energy

energy matter possesses because of its location or structure, matter has tendency move toward lowest possible state of potential energy, further electron is from nucleus \= greater its potential energy

Chemical behavior determined by:

the distribution of electrons in the atom's electron shell, specifically the number of valence electrons

Valence electrons

number of electrons in its outermost shell

Inert

chemically unreactive elements, those with full valence shells

Orbital

three-dimensional space where an electron is found 90% of the time, never know exact location of an electron, component of electron shell, no more than two electrons can occupy a single orbital, reactivity of atom arises from presence unpaired electrons in 1+ orbitals of atom's valence shell

Chemical bonds

atoms stay close together and held by attractions, strongest kinds are covalent bonds in molecules and ionic bonds in dry ionic compounds

Covalent bond

sharing of pair of valence electrons by two atoms, strong bonds

Molecule

two or more atoms held together by a covalent bond, characteristic size + shape key to function, shape determined by positions of atoms' orbitals

Single bond

pair of shared electrons

Double bond

molecule formed by sharing two pairs of valence electrons

Valence

bonding capacity of an atom, usually equals the number of electrons required to complete the atom's valence shell

Electronegativity

attraction of a particular atom for the electrons of a covalent bond, more electronegative \= more strongly it pulls shared electrons toward itself, in covalent bond between two atoms of same element electrons are shared equally, in organisms most of strongest chemical bonds are covalent

Nonpolar covalent bond

covalent bond between two atoms of same element, electrons shared equally because two atoms have same electronegativity

Polar covalent bond

atom bonded to more electronegative atom, electrons of bond are not shared equally

Ionic bond

cations and anions attract each other, any two ions of opposite charge can form an ionic bond do not need to have acquired their charge by electron transfer with each other, strength affected by environment

Ions

two atoms so unequal in attraction for valence electrons that the more electronegative atom strips an electron completely away from partner, two resulting oppositely charged atoms/molecules, also apply to entire molecules that are electrically charged

Anion

A negatively charged ion

Cation

A positively charged ion

Ionic compounds/salts

compounds formed by ionic bonds, found in nature as crystals, does not consist of molecules - formula is only a ratio

Hydrogen bond

when hydrogen atom covalently bonded to electronegative atom, hydrogen has partial positive charge that allows it to be attracted to a different electronegative atom with a partial negative charge nearby, in living cells electronegative partners are usually oxygen or nitrogen

Van der Waals interactions

even nonpolar covalent bonds may have positively and negatively charged regions, electrons may accumulate by chance in one part of molecule, ever-changing regions of positive and negative charge enable all atoms + molecules stick to each other, individually weak + occur only when atoms/molecules close together, simultaneously are powerful

Weak chemical interaction

reinforce three dimensional shape of molecule, include ionic bonds, hydrogen bonds, and Van der Waals interactions

Molecular shape is crucial because:

Biological molecules bind temporarily to each other by forming weak interactions only if shapes are complementary, endorphins and morphine bind to brain receptors, relieving pain and producing euphoria, shape mimics brain's natural endorphins

Chemical reactions

making and breaking of chemical bonds, leading to changes in composition of matter, matter is conserved, greater the concentration of reactant molecules, more frequently they collide with one another + have opportunity form products

Photosynthesis Equation

6CO2 + 6H2O + light energy --\> C6H12O6 + 6O2

Dynamic equilibrium

reactions still go on in both directions but w/ no net effect on concentrations of reactants + products, not equal in concentration but concentrations stabilized at particular ratio

Polar molecule

molecule with uneven distribution of charges in different regions of molecule, ex. water at one end O has partial negative charges bc O pulls electrons towards itself, at other end H has partial positive charges

Hydrogen bonding

attractions between oppositely charged atoms of different water molecules (partially + H to partially - O), in liquid form bonds fragile, form, break, + reform w/ great frequency, at any instant most water molecules bonded to neighbors, organize molecules into higher level of structural order

Cohesion

linking together of like molecules, often by hydrogen bonding, high surface tension, contribute to transport of water + dissolved nutrients against gravity in plants

Adhesion

clinging of one substance to another, ex. water to cell walls

Calorie

amount of heat to raise the temperature of 1 gram of water by 1 degree Celcius, 1 calorie \= 4.184 Joules

Thermal energy

kinetic energy associated with random movement of atoms or molecules, reflects total KE + depends on volume

Temperature

average kinetic energy of molecules in body of matter regardless of volume

Heat

thermal energy in transfer from one body of matter to another, thermal energy pass from warmer to cooler object until two are same temperature, molecules in cooler object speed up at expense of thermal energy of warmer object

Specific heat

amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1 degree Celcius, water specific heat is 1 cal/(g C) - will change temperature less than other liquids when it absorbs/loses a given amount of heat

Hydrogen bonding + high specific heat of water

Heat must be absorbed in order to break hydrogen bonds, heat also released when hydrogen bonds formed, heat must be used disrupt hydrogen bonds before water molecules can begin moving faster to cause temp change, when temp drops slightly, many additional hydrogen bonds form which releases considerable amount of energy in form of heat

High specific heat + moderation of temperature

Large body of water absorb + store huge amount of heat from sun in daytime/summer
@ night/winter gradually cooling water warms air, moderate air temp in coastal areas, stabilize ocean temp - create favorable environment for marine life, keeps temp fluctuations on land + in water w/in limits that permit life, organisms made of water + better able resist changes in own temp

Evaporation

molecules moving fast enough to overcome attractions can depart liquid and enter air as a gas, transformation from liquid to gas (vaporization), some evaporation occurs at any temperature - temp \= average speed, fastest molecules can evaporate, if liquid heated average KE increases + evaporation occurs more rapidly

Heat of vaporization

quantity of heat liquid must absorb for 1 g to be converted from liquid to gaseous state, water has high heat of vaporization - hydrogen bonds must be broken before molecule can exit from liquid, for 1 g water at 25 C need 580 cal heat (2x for 1 gram alcohol), help moderate Earth's climate, solar heat absorbed by sea consumed during evaporation of surface water, account for severity of steam burns

Evaporative cooling

surface of liquid cools down during evaporation bc molecules with greatest KE change from liquid to gaseous state, contribute to stability of temp in lakes + ponds, prevent terrestrial orgs from overheating

Property of ice floating

Water less dense as solid than as liquid, water expands, at temp above 4 C water behaves like other liquids - expand when warm and contract when cool, from 4 C to 0 C water freeze bc molecules move too slowly to break hydrogen bond, at 0 C molecules locked into crystalline lattice - each water molecules hydrogen bonded to four partners, bonds keep molecules at "arm's length" - far enough make ice less dense than liquid water, if ice sank then bodies of water would freeze solid + making life as we know it impossible, allow aquatic animals live in water over winter, provide solid habitat for some animals, at risk of disappearing due to global warming

4°C is critical temperature for floating ice...

When temp rises bonds break, greatest density at 4 C - begin to expand as molecules move faster, in liquid water bonds constantly breaking + re-forming

Solvent vs. Solute

solvent - dissolving agent of a solution, solute - substance that is dissolved

Solution vs. aqueous solution

solution - liquid that is completely homogenous mixture of 2+ substances, concentration of solute same everywhere in mixture, aqueous - solution were solute is dissolved in water, water \= solvent

Water as solvent

Due to polarity of water molecule, hydration shell - sphere of water molecules around each dissolved ion, working inward toward center of sphere water eventually dissolves all ions, ex. NaCl in water: Na and Cl ions exposed to solvent, ions + partially +/- regions of water molecule attracted bc opposite charges, water surrounds indiv Na and Cl ions, shields them from one another + dissolves all ions, results in Na cations and Cl anions mixed homogenously w/ water, other ionic compounds also dissolve in water (seawater, living cells), polar molecules water soluble, water molecules surround each of solute molecules + form hydrogen bonds, proteins can dissolve if they have ionic + polar regions on surface

Hydrophilic

substance with affinity for water, can be hydrophilic w/o dissolving - cell molecules so large they don't dissolve, cotton

Hydrophobic

substances w/o affinity for water, substances that are nonionic + nonpolar, cannot form hydrogen bonds, repel water - vegetable oil, cell membranes

Molarity

number of moles (6.02 x 10^23 molecules) of solute per liter of solution, used for aqueous solutions

When water dissociates...

Hydrogen atom participating in hydrogen bond between two water molecules shifts from one molecule to another, hydrogen atom leaves electron behind + hydrogen ion transferred, reversible + statistically rare but important, H+ and OH- are very reactive, changes in concentration drastically affect cell's proteins + other complex molecules, Hydroxide ion - OH-, water molecule that lost a proton, charge of 1-, Hydronium ion - H3O+, proton binds to water molecule (by convention H+ used to represent H3O+), reversible reaction that can reach dynamic equilibrium

pH scale

simple numerical method express range of H+ concentrations, compresses wide range of possible concentrations by using logarthms, pH of solution \= negative log (base 10) of H+ concentration, pH decreases as H+ concentration increases, [H+][OH−] \= 10−14

Acid

substance that increases hydrogen ion concentration of a solution, donate addition H+ into solution when dissolved in water, ex. HCl -\> H+ + Cl- (now more H+)

Base

reduces hydrogen ion concentration of a solution, some reduce H+ concentration directly by accepting hydrogen ions, ex. NH3 (ammonia) unshared electron pair in N's valence shell attract hydrogen ion, creates NH4+, others reduce H+ concentration indirectly by dissociating to form hydroxide ions that combine w/ hydrogen ions + form water, NaOH becomes Na+ and OH-

Neutral

solution where H+ and OH- concentrations are equal, double arrows \= reversible reaction + weak, single arrows \= compounds dissociate completely when mixed w/ water + strong

Buffer

substance minimizes changes in concentrations of H+ and OH- in a solution, accept/donate hydrogen ions based on need, usually contain weak acid + corresponding base, ex. carbonic acid dissociates to bicarbonate ion and hydrogen ion, consist of acid + base in equilibriumm w/ each other (most other buffers also acid-base pairs), internal pH of most living cells close to 7, slight change can be harmful bc chem processes of cell sensitive to concentrations of H+ and OH- ions, buffers found in human blood

Ocean acidification

CO2 dissolves in seawater + reacts w/ water to form carbonic acid which lowers pH of ocean, alter balance of conditions for life in ocean, carbonate ion concentration of ocean reduces, marine organisms cannot produce calcium carbonate

Carbon

basis all biological molecules, form four bonds, bond to other carbons, can make carbon skeletons, commonly bonds to H, O, N, properties of C-containing molecule depend on arrangement of C skeleton + chemical groups

Organic chemistry

study of compounds containing C, range from simple molecules to proteins, organic molecules may have been synthesized abiotically on early Earth, overall percentages of major elements of life (C, H, O, N, S, P) quite uniform from one org to another, common evolutionary origin of all life, different species + individuals distinguished by variations in types of organic molecules they make

Carbon structure

Key to atom's chem characteristics is electron configuration, determines kinds + \# of bonds atom will form w/ other atoms, has 6 electrons (2 in first shell, 4 in second shell), 4 valence electrons in shell that can hold up to 8 electrons, each pair of shared electrons constitutes covalent bond, in org molecules usually forms single or double bonds, each C atom acts as intersection point from which molecule can branch off in four directions, w/ four single covalent bonds four hybrid orbitals cause bonds angle toward corners of imaginary tetrahedron, bond angles 109.5

Valence

number electrons req fill valence shell of atom, number covalent bonds it can form, electron config gives covalent compatibility w/ many diff elements, CO2 simple molecule + lacks hydrogen, considered inorganic despite containing C, source of C via photosyntheic organisms for all organic molecules

Carbon chains

C atom can use 1+ valence electrons form covalent bonds to other C atoms, link atoms into chains, C chains form basis most org molecules, skeletons vary in length, can be straight, branched, in rings, some have double bonds which vary in \# + location, variation in chains \= source molecular complexity + diversity, skeletons of bio molecules inclue atoms other elements

Hydrocarbons

org molecules consisting of only C and H, atoms of H attached to skeleton wherever electrons available for covalent bonding, major components of petroleum, not prevalent in most living orgs, fats have long hydrocarbon tails, can undergo reactions that release large amount of energy, gasoline that fuels car, tails of fat are stored fuel for plant embryos + animals

Isomers

compounds w/ same numbers of atoms of same elements but different structures + different properties, number possible isomers increases as C skeletons increase in size

Molecular function

Properties of org molecule dep on arrangement of C skeleton + chem groups attached to skeleton
Participate in chem reactions or contribute to function indirectly by effects on molecular shape

Cis-trans isomer

geometric, C have covalent bonds to same atoms but atoms differ in spatial arrangements due to inflexibility of double bonds, single bonds allow atoms rotate freely around bound axis w/o change compounds, subtle difference in shape can have dramatic effect on biological activities of organic molecules, a) cis isomer - arrangement with both Xs on same side of double bond, b) trans isomer - arrangement with Xs on opposite sides of double bond

Enantiomers

isomers mirror images of each other + differ in shape due to presence of asymmetric carbon that is attached to four diff atoms/group of atoms, essentially left + right handed versions of molecule, left cannot fit into right, only one isomer biologically active bc only that form can bind to specific molecule

Structural isomer

differ in covalent arrangements of atoms, skeleton is straight vs branched, may differ in location of double bonds

Steroids

organic molecules with common C skeleton in form four fused rings, estrogen + testosterone differ only in chem groups attached to rings

Functional groups

special configuration of atoms, chem groups directly involved in chem reactions, certain properties (shape + charge) that cause it participate in chem reactions in characteristic way, hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl, all but methyl chem reactive, of reactive all except sulfhydryl also hydrophilic + increase solubility or org compounds in water, methyl not reactive but serve as recognizable tag on bio molecules

Adenosine triphosphate (ATP)

organic molecule attached to string of three phosphate groups, when three molecules present in series one phosphate may split off in reaction w/ water, ATP -\> ADP (adenosine diphosphate), store potential to react w/ water/other molecules, process releases energy that can be used by cell

Macromolecule

large carbohydrates, proteins, nucleic acids bc of huge size, great diversity of macromolecules, between relatives similar DNA + proteins, molecules constructed from 40-50 common monomers, polymer chains can have 1000s of monomers

Polymer

long molecule consisting of many similar/identical building blocks linked by covalent bonds

Monomer

repeating units that serve as building blocks of polymer, smaller molecule, in addition to forming polymers some have functions of their own, chem mechanisms by which cells make polymers + break them down similar for all large bio molecules

Enzyme

specialized macromolecules that speed up chemical reactions, is not consumed by reaction

Condensation reaction

reaction connect monomer to another monomer/polymer, two molecules covalently bonded w/ each other w/ loss of small molecule

Dehydration reaction

two molecules covalently bonded together w/ loss water molecule, synthesize carbohydrate + protein polymers, each reactant contribute part of water molecule that is released during reaction, repeated as monomers added to chain one by one

Hydrolysis

polymers disassembled to monomers, reverse of dehydration reaction
Bond between monomers broken by addition of water molecule (H attach to one, HO attach to another)
During digestion polymers broken down into monomers + released into bloodstream, cells use dehydration reaction to assemble new polymers

Carbohydrates

include sugar + polymers of sugar

Monosaccharides

simple sugars, simplest carbs, monomers from which more complex carbs built, generally have molecular formulas w/ some multiple of CH2O, glucose most common, has carbonyl group, multiple hydroxyl groups, aldose - aldehyde sugar, carbonyl group @ end of skeleton, ketose - ketone sugar, carbonyl group w/in skeleton, size of skeleton range from 3-7 C long, usually 3 trioses, 5 pentoses, 6 hexoses (like glucose, fructose), provide nutrients for cells, during cell respiration cells extract energy from glucose by breaking down in series of reactions, C skeleton serve as raw material for synthesis of small org molecules (amino acids, fatty acids)

Asymmetric carbon

C attached to four diff atoms/groups, way parts arranged around asymmetric C source of diversity, in aqueous solutions most 5/6 C sugars form rings

Glycosidic linkage

covalent bond formed between two monosaccharides by dehydration reaction, ex. sucrose, lactose, must be broken down into monosaccharides to be used by orgs