Bio: Chemistry of Life Test 1

everything (macromolecules and functional groups)

covalent bond

shares one or more pairs of electrons so their valence shells are full

ionic bond

form when one atom is much more electronegative than the other and a complete transfer of electrons occurs

hydrogen bond

attraction between the partial negative end of one molecule and the partial positive hydrogen of another molecule (not covalent, continually break and form as molecules move)

hydrophobic interactions

in the presence of a polar substance, hydrophobic substances are driven to aggregate with each other

van der Waals forces

attractions between nonpolar molecules that are close together (electrons are always moving around atoms therefore there are moments of partial charges)

polar covalent

electrons spend more time closer to the nucleus of the more electronegative atom

nonpolar covalent

electrons shared equally, atoms have similar electronegativities

ions

electrically charged particles formed when atoms lose or gain one or more electrons (cations lose electrons, anions gain electrons)

cohesion

hydrogen bonds between water molecules cause them to stick together

hydrophilic

polar molecules interact with water, hydrogen bonding, “water loving,” dissolve freely in water

hydrophobic

nonpolar molecules, “water fearing,” associate with one another and not water

pH

0 is acidic with Hplus, 7 is neutral, and 14 is basic

buffer

help maintain a constant pH, small changes in Hplus will not change the pH of solution (Ex: bicarbonate ion, CO3-, carbonic acid, H2CO3

macromolecules

large molecules containing thousands or more atoms, functions depend on functional groups, made up of monomers to make polymers (biological: proteins, lipids, nucleic acids, and carbohydrates)

hydroxyl =>alcohol

aldehyde => aldehyde

keto => ketone

carboxyl => carboxylic acid

amino => amine

phosphate => organic phosphate

sulfhydryl => thiol

methyl => alkyl

condensation reaction

form covalent bonds between monomers to make polymers, water molecule is released

hydrolysis reactions

break covalent bonds between polymers to make monomers, a water molecule is consumed

carbohydrates

made from sugar molecules, store energy, transport stored energy, carbon skeletons, extracellular structures (CH2O)

monosaccharides

the monomers of complex carbohydrates, simple sugars

disaccharides

two simple sugars linked by covalent bonds

oligosaccharides

3-20 monosaccharides

polysaccharides

hundreds or thousands of monosaccharides (linear, branched, highly branched)

pentoses

5-carbon sugars (Ex: ribose, deoxyribose)

hexose

6-carbon sugar (Ex: glucose, fructose)

glycosidic bonds

hold together di-, oligo-, and polysaccharides, formed through condensation reactions, covalent bond

nucleic acids

informed macromolecules, polymers specialized for storage, transmission, and use of genetic information (Ex: DNA, RNA)

nucleotides

monomers for nucleic acid, nitrogen containing (nitrogenous) base, a 5-carbon (pentose) sugar, and phosphate group

nucleoside

just the pentose and nitrogenous base

pyrimidines

nitrogenous base, single ring, “pyramids are sharp so they CUT”, cytosine, uracil, thymine

purines

nitrogenous base, double ringed, “Pure As Gold”, purine, adenine, guanine

Deoxyribose nucleic acid (DNA)

pentose sugar, thymine, adenine, guanine, cytosine, sugar phosphate backbone form a backbone and nitrogenous bases face inwards, double stranded, right-handed double helix

Ribose nucleic acid (RNA)

extra OH group on 2’ carbon compared to DNA, more reactive than DNA, uracil, adenine, guanine, cytosine, single stranded, can form hydrogen bonds with itself resulting in 3D structure

sugar-phosphate backbone

phosphate group always attached to the 5’ carbon and 3’ carbon of the next, links with phosphodiester bonds and condensation reactions

phosphodiester bond

links nucleotides together (5’ carbon + phosphate + 3’ carbon)

polarity and antiparallel double helix

ends of nucleic acids differ, 3’ and 5’ end on each chain, directional asymmetry of linear polymers

hydrogen bonding between nitrogenous bases

thymine and adenine (2 hydrogen bonds)

cytosine and guanine (3 hydrogen bonds)

Chargaff’s Rule

in a DNA sample, %A=%T and %G=%C so %pyrimidines=%purines

minor groove

backbones of the two strands are closer together

major groove

backbones of the two strands are further apart

lipid

insoluble in water, nonpolar hydrocarbons (Ex: fats and oils, phospholipids, carotenoids, steroids, and waxes)

fats and oils

triglycerides that store energy, glyceride and three fatty acids go through a condensation reaction and have ester linkage to become a triglyceride, saturated and unsaturated

glycerol

a 3-carbon alcohol with three -OH groups

fatty acid

long nonpolar hydrocarbon chain and a polar carboxyl group

ester linkage

bond formed when the carboxyl group of a fatty acid reacts with the -OH group of a glyceride (condensation reaction)

saturated

all C-C bonds in the hydrocarbon chain are single bonds, all carbons are saturated with hydrogens (straight fatty acids can pack together tightly) (Ex: fats in animals, solids at room temp, high melting points)

unsaturated

hydrocarbon chains contain more than single bonds, double bonds cause kinks, the kinks prevent close packing (Ex: oils, liquid at room temp, low melting points)

phospholipids

amphipathic with hydrophilic “head” (contains phosphate group) and hydrophobic “tail” (contains two fatty acid chains), form the phospholipid bilayer (form spontaneously) and micelles

carotenoids

light absorbing pigments, composed of repeating branched 5-carbon unit (Ex: Beta-carotene is the pigment the traps light energy in leaves during photosynthesis)

steroids

organic compounds whose multiple rings are linked through shared carbon atoms (Ex: cholesterol is an important component of the cell membrane, hormones are chemical signals that carry messages)

wax

a long-chain alcohol bound to a fatty acid (Ex: wax coatings repel water like on feathers)

proteins

work hard and have diverse functions (Ex: enzymes, structural proteins, signaling proteins, transporters)

amino acids

monomers of proteins covalently linked, have an alpha carbon, amino group, carboxyl group, and side chain R group (R group is different with different functional groups)

types of amino acids

charged hydrophilic side chains, uncharged hydrophilic side chains, nonpolar hydrophobic side chains, or special side chains (cysteine, glycine, and proline)

polypeptide chains

single, unbranched chains of amino acids, has polarity (N-terminus is amino group and beginning, C-terminus is carboxyl group and ending)

peptide bond

covalent link formed by condensation reactions

protein structures

structure dictate function, fold into specific 3D shapes, represented as space-filling, stick, or ribbon

primary structure

the sequence of amino acids in a polypeptide chain, stabilized by peptide bonds

secondary structure

determined and stabilized by hydrogen bonding within the backbone (hydrogen bonding only in backbone with N-H and C=O) of amino acids (N-alpha C-C is repeating unit) (Ex: alpha helix and beta sheet)

alpha helix

coil resulting from hydrogen bonding between N-H and C=O groups in the backbone of the polypeptide

beta pleated sheets

two or more polypeptide chains are aligned, hydrogen bonds form between the chains

tertiary structure

how a protein folds in 3D due to interactions between side chains, stabilized by hydrogen bonds, hydrophobic interactions, disulfide bridges, depend on a weak non-covalent interactions

disulfide bridge

two cysteines can form a covalent linkage

quaternary structure

the association of a polypeptide with other polypeptides, protein only has a quaternary structure if its composed of two or more separate polypeptide chains

amino acid substitutions/mutations

impact structure and functions

denatured

when a protein has lost secondary, tertiary, or quaternary structures (happens with added heat, change in pH, and added chemicals), (when the protein comes back from being denatured it will return to the identical shape it was before because the shape is determined by the sequence of amino acids)

chaperone proteins

protect proteins from folding improperly, safety mechanism for proteins to refold

protein shape

can change as a result of interaction with other molecules (molecules bind to protein) or as a result of covalent modification (have functional groups covalently attached)

shape

there must be a general “fit” between molecules

chemistry

R groups on the surface of the molecules interact through noncovalent interactions (ionic, hydrogen bonding, hydrophobic interactions, van der Waals forces)