Unit 1: Chemistry of Life

matter

matter

anything that takes up space and has mass

element

substance that cannot be broken down into other substances by chemical reactions

compound

substance consisting of 2 or more elements combined in a fixed ratio

carbon, hydrogen, oxygen, nitrogen

which substances make up 96% of living matter?

atoms

smallest units of an element that retain the property of the element

protons

positively charged particles found in the nucleus of the atom

electrons

negatively charged particles that are found in electron shells around the nucleus

electrons

what subatomic particle determines the chemical properties and reactivity of the element?

neutrons

particles with no charge

nucleus

where are neutrons found?

isotopes

forms of an element with differing numbers of neutrons

atomic number

number of protons an element possesses; unique to every element

mass number

sum of an element’s protons and neutrons

chemical bonds

interactions between the valence electrons of different atoms

molecules

atoms are held together by chemical bonds to form _____

covalent bond

occurs when valence electrons are shared by 2 atoms

nonpolar covalent bond

occurs when the electrons being shared are shared equally between the two atoms

electronegativity

a tendency to attract electrons of a covalent bond

polar covalent bonds

1 atom has greater electronegativity than the other, resulting in an unequal sharing of the electrons

ionic bonds

chemical bonds resulting from the attraction between oppositely charged ions

hydrogen bonds

weak chemical interactions that form between the partial positively charged hydrogen atom of 1 molecule and the strongly electronegative oxygen/nitrogen of another molecule

van der waals interactions

very weak, transient connections that are the result of asymmetrical distribution of electrons within a molecule; contribute to the 3D shape of molecules

chemical reaction

make and break chemical bonds, shows reactants with an arrow to indicate their conversion into the products

reactants

starting materials in a chemical reaction

products

ending materials in a chemical reaction

negative

the oxygen region of water has a partial _____ charge

positive

the hydrogen regions of water have a partial _____ charge

4

each water molecule can form a maximum of _____ hydrogen bonds at a time

cohesion

linking of like molecules; causes surface tension

adhesion

clinging of 1 substance to another

transpiration

movement of water molecules up the thin xylem tubes and their evaporation from the stomata in plants

cohesion; adhesion

water molecules cling to each other by _____ and to the walls of the xylem tubes by _____

specific heat

the amount of heat required to raise/lower the temperature of a substance by 1 ºC

solvent

substance that something is dissolved in

solute

substance being dissolved

solution

combination of the solvent and solute

hydrophilic

substances that are water soluble; includes ionic compounds, polar molecules, some proteins

hydrophobic

substances that are nonpolar and do not dissolve in water

1. cohesion

2. adhesion

3. high specific heat

4. less dense as a solid than a liquid

5. important solvent

properties of water that result from hydrogen bonds

pH scale

runs between 0-14 and measures the relative acidity and alkalinity of aqueous solutions

acids

have an excess of H+ ions and a pH below 7

acids

[H+] > [OH-]

bases

have an excess of OH- ions and a pH above 7

bases

[H+] < [OH-]

buffers

substances that minimize changes in pH by accepting H+ when they are in excess/donating H+ when they are depleted

carbonic acid (H2C03)

an important buffer in living systems; moderates pH changes in blood plasma and the ocean

carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus

major elements of life (P.S. COHN)

carbon

all organic compounds contain _____

• 4 valence electrons - 4 covalent bonds

• can form single, double, or triple bonds

• large molecules

• chains, rings, and branches

why is carbon unparalleled in its ability to form large, complex molecules?

isomers

molecules that have the same formulas but differ in their arrangement of the atoms

structural isomers

isomers that differ in the covalent arrangements of their atoms

cis-trans isomers

isomers where carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds

enantiomers

isomers that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon

asymmetric carbon

carbon that is attached to 4 different atoms/groups of atoms

hydroxyl group (-OH)

• compound name: alcohol (specific name usually ends in -ol)

• properties: polar, helps dissolve molecules like sugars

• examples: ethanol, methanol

carbonyl group (>CO)

• compound name: ketone/aldehyde

• properties: acid (tends to ionize), source of H+ ions

• examples: acetone, propanol, sugars

carboxyl group (-COOH)

• compound name: carboxylic acid/organic acid

• properties: polar, acidic b/c it tends to ionize, source of H+ ions

• examples: acetic acid, fatty acids, sugars, carboxylate ions

amino (-NH2)

• compound name: amine

• properties: acts as base

• examples: amino acids (e.g. glycine)

sulfhydryl group (-SH)

• compound name: thiol

• properties: slightly polar, forms disulfide bridges in proteins

• examples: cysteine

phosphate group (-OPH3 2-)

• compound name: organic phosphate

• properties: highly hydrophilic, acidic

• examples: ATP, DNA, phospholipids

methyl group (-CH3)

• compound name: methylated compound

• properties: highly stable/unreactive, affects expression of genes

• examples: 5-methylcytosine (component of DNA)

polymers

large chain molecules made of repeating subunits called monomers

monomers

repeating subunits that make up polymers

dehydration reactions

reaction that create polymers from monomers, where 2 monomers are joined by removing 1 molecule of water

hydrolysis

reaction that occurs when water is added to split large molecules; reverse of dehydration

carbohydrates

serve as fuel and building material; include both simple sugars and polymers; have a ratio of 1 C:2 H:1 O

monosaccharides

monomers of carbohydrates; contains carbonyl group and multiple hydroxyl groups, e.g. glucose, fructose, galactose, ribose

polysaccharides

polymers of monosaccharides; e.g. starch, cellulose, glycogen

what is the structure of starch?

1-4 alpha glycosidic linkages (this makes it digestible)

what is the structure of cellulose?

1-4 beta glycosidic linkages (this means humans cannot digest it)

what are the functions of polysaccharides?

energy storage, structural support

what are examples of energy storage polysaccharides?

starch, glycogen

starch

storage polysaccharide found in plants (e.g. in potatoes)

glycogen

storage polysaccharide found in animals (within vertebrate muscle & liver cells)

what are examples of structural support polysaccharides?

cellulose, chitin

cellulose

structural polysaccharide that is a major component of plant cell walls

chitin

structural polysaccharide that is found in the exoskeleton of arthropods (lobsters, insects) and the cell walls of fungi; similar to cellulose but has a nitrogen-containing attachment

fats/triglycerides

made up of a glycerol molecule and 3 fatty acid molecules

fatty acids

include hydrocarbon chains of variable lengths; nonpolar/hydrophobic

saturated fatty acids

• no double bonds between carbons

• pack solidly at room temp

• linked to cardiovascular disease

• commonly produced by animals

• e.g. butter, lard

unsaturated fatty acids

• have some carbon double bonds - result in kinks

• liquid at room temp

• commonly produced by plants

  • e.g. corn oil, olive oil

glycerol

alcohol made up of 3 carbons, each with a hydroxyl group

what are the functions of lipids

energy storage, protection, insulation

phospholipids

• major component of cell membranes

• hydrophilic head w/ phosphate group

  • 2 hydrophobic fatty acid tails

steroids

lipids with a carbon skeletons of 4 rings fused together

cholesterol

steroid; common component of animal cell membranes

estrogen, testosterone

steroid hormones

proteins

polymers made up of amino acid monomers

amino acids

contain central carbon bonded to carboxyl group at one end, an amino group at the other end, an H atom, and an R group

peptide bonds

link amino acids; formed by dehydration synthesis between amino and carboxyl groups of adjacent monomers

primary structure (proteins)

unique sequence in which amino acids are joined

secondary structure (proteins)

refers to 1 of 2 3D shapes that are the result of H bonding between members of the polypeptide backbone (not amino acid side chains)

alpha helix

coiled shape, like slinky, of proteins

beta pleated sheet

accordion shape of proteins

tertiary structure (proteins)

complex globular shape resulting from interactions between R groups (H bonds, hydrophobic interactions, van der Waals interactions, disulfide bridges)

quaternary structure

refers to the association of 2 or more polypeptide chains into 1 large protein

denatured protein

protein loses its shape and ability to function because of heat, a change in pH, or some other

functions of proteins

enzymes, defense, storage, transport, hormones, receptors, contractile/motor, structural

3 parts of nucleotides

nitrogenous base, pentose sugar, phosphate group

dna

• molecule of heretidy

• double stranded helix

• A, T, C, G

• A bonds to T

  • C bonds to G