Chapter 1 The Chemsitry of Life & Water, the Solvent of Life

matter

anything that takes up space and has mass

element

a substance made up of atoms of one kind that cannot be broken down to other substances by chemical reactions

its property depend on the structure of its atoms

molecule

formed when two or more atoms join together chemically

consists of a well-defined number of atoms bonded together

compound

substance consisting of two or more elements in a fixed ration

has characteristics different from those of its elements

atom

the fundamental, smallest unit of matter that still retains the properties of an element

protons+neutrons (both in atomic nucleus) + particles

this of various elements differ in number of subatomic particles

atomic number

number of protons in its nucleus

all atoms of a particular element have the same nunber of protons in their nuclei

number of protons = number of electron (in neutral atom)

mass number

number of protons + number of neutrons in atomic nucleus

atomic mass, the atom’s total mass, can be approximated by the mass number

neutrons and protons have almost identical masses, close to 1 dalton

isotopes

different atomic forms of the same element that have the same nunber of proton but differ in the nunber of neutron

potential energy

the energy that matter has because of its location or structure

electron shells

energy levels around the nucleus where electrons are found

excited electron

electron that has absorbed energy and moved to a higher energy level

valence electrons

electrons in the outermost shell

orbital

the 3-D space where an electron is found 90% of the time

covalent bond

the sharing of a pair of valence electrons by two atoms

the shared electrons count as part of each atom’s valence shell

electronegativity

an atom‘s attraction for the electrons in a covalent bond

nonpolar covalent bond

atoms share electron equally

polar covalent bond

one atom is more electronegative, and the atoms do not share the electron equally, causing a partial positive or negative charge for each atom or molecule

hydrogen bond

when a hydrogen atom covalently bonded to one electronegative atom is also attracted to anotger electronegative atom (usually oxygen or nitrogen atoms in living cells)

Van der Waals interactions

attractions between molecules that are close together as a result of the asymmetric distribution of electrons in molecules or atoms

ionic bond

an attraction between an anion and a cation

salts are formed by this bond

isomers

compounds with the same molecular formula but different structures and properties

structural isomers

differ in covalent arrangements (may also differ in location of double bonds)

cis-trans isomers

same covalent bond but differ in spatial arrangements due to inflexibility of double bond → affects biological activity

enantiomers

mirror images of each other due to the presence of an asymmetric carbon (:attached to four different atoms or groups of atoms)

functional groups

components of organic molecules that are most commonly involced in chemical reactions

hydroxyl group (OH-)

A functional group consisting of an oxygen atom bonded to a hydrogen atom; often found in alcohols

carbonyl group (C=O)

a functional group consisting of a carbon atom double-bonded to an oxygen atom; found in aldehydes and ketones

Carboxyl group (-COOH)

A functional group consisting of a carbonyl group bonded to a hydroxyl group; found in carboxylic acids

Amino group (-NH2)

A functional grouo consisting of a nitrogen atom bonded to two hydrogen atoms; found in amines and amino acids

Phosphate group(-PO4^2-)

A functional group consisting of phosphorus atom bonded to oxygen atoms, one of which is bonded to four oxygen atoms, one of which is bonded to the carbon backbone; found in nucleotides and phospholipids

Sulfhydryl group (-SH)

A functional group consisting of a sulfur atom bonded to a hydrogen atom; found in thiols and plays a role in protein structure

Methyl group (-CH3)

A functional group consisting of a carbon atom bonded to three hydrogen atoms; often affects gene expression and protein function

cohesion

collectively, hydrogen bonds holding water molecules together

results in high surface tension

helps the transport of water against gravity plants

adhesion

attraction between different substances

thermal energy

kinetic energy associated with random motion of atoms or molecules

heat

thermal energy in transfer from one body of matter to another

specific heat

the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1degrees celsius

evaporation

the transformation from liquid to gas because ’fast‘ molecules depart the liquid and enter the air

heat of vaporization

heat a liquid must absorb for 1g to be converted to gas

hydration shell

when an ionic compound is dissolved in water, each ion is surrounded by a sphere od water molecules called a ___

hydrophilic substance

has an affinity for water

hydrophobic substance

does not have an affinity for water

proton

a hydrogen atom in a hydrogen beteeen two water molecules can leave its electron behind and become transferred as a __ (hydrogen ion, H+)

hydronium ion

molecule with extra proton is now a ___ (H3O+, often represented as H+)

hydroxide ion

molecule that lost proton is now a __ (OH-)

dynamic equillibrium

water is in a state of ____ in which water molecules dissociated at the same rate at which they are being reformed

Acids

substances that release hydrogen ions (H⁺) in solution. They have a sour taste, a pH less than 7, and react with bases to form salts and water. Strong ___ fully dissociate in water, while weak ___ only partially dissociate.

Bases

substances that accept hydrogen ions (H⁺) or release hydroxide ions (OH⁻) in solution. They have a bitter taste, slippery feel, and a pH greater than 7. __ react with acids to form salts and water (neutralization). Strong ___ fully dissociate in water, while weak ___ only partially dissociate.

buffers

substances that minimize changes in [H+] and [OH-] in a solution by accepting H+ when they are in excess, and donating when they are depleted