Unit 1 - The Chemistry of Life

Ch. 1-5

4 properties of water

cohesion/adhesion, expansion upon freezing, universal solvent, moderation of temperature

miller-urey experiment

experiment that simulated early Earth conditions to test the origin of life by creating amino acids from simple molecules

isomers

compounds with the same atoms but different properties and structural arrangements

structural isomers

isomers that differ in the arrangement of atoms in space but have the same molecular formula

cis-trans isomers

isomers that differ in the arrangement of atoms across a double bond, affecting their properties

enantiomers

isomers that are mirror images of each other, often affecting biological activity

thalidomide (comes in R and S enantiomers)

R-thalidomide was a drug that was used as a sedative to alleviate morning sickness for pregnant women; S-thalidomide is a teratogen that causes severe birth defects; lots of birth defects in the 1960s

common functional groups

basic definition of ATP

adenosine triphosphate, primary energy-transferring molecule

buffers

substances that minimize changes in pH and pOH in a solution (e.g. blood acidity)

carbohydrates (monomer, polymer, bond)

monosaccharides, polysaccharides, glycosidic linkages

lipids (monomer, polymer, bond)

fatty acids, triacylglycerols, ester linkages

proteins (monomer, polymer, bond)

amino acids, polypeptides, peptide bonds

nucleic acids (monomer, polymer, bond)

nucleotides, polynucleotides, phosphodiester linkages

maltose & sucrose

maltose = glucose + glucose (1-4)
sucrose = glucose + fructose (1-2)

alpha vs beta glycosidic linkages

glucose polysaccharides

starch (amylose - unbranched, amylopectin - somewhat branched), glycogen (extensively branched), cellulose (unbranched)

cellulose

1-4 beta glycosidic linkages, human enzymes can’t digest, insoluble fiber

chitin

found in arthropod exoskeletons and fungi cell walls, also a strong polysaccharide

lipids (quality & types)

hydrophobic, 3 most important types: fats, phospholipids, steroids

fats (structure, types, function)

triacylglycerol: 3 fatty acids joined to a glycerol by an ester linkage

saturated: no double bonds in fatty acid chain
unsaturated: one or more double bonds
trans: created through hydrogenation, converting unsaturated fats to saturated fats by adding hydrogen - creates saturated fats with trans double bonds

function: energy storage

Humans and other mammals store fats in adipose cells, which cushion vital organs and insulate the body

phospholipids (structure, function)

two fatty acids and a phosphate group are attached to a glycerol

AMPHIPATHIC

when phospholipids are added to water, they form a lipid bilayer - cell membrane

steroids (structure, example)

carbon skeleton with 4 fused rings

e.g. cholesterol is a component in animal cell membranes (maintains stability by reducing fluidity at moderate temperatures and reducing packing at low temperatures)

• high levels of cholesterol may contribute to cardiovascular disease

amino acid structure

alpha carbon connected to H, amino group on left, carboxyl group on right, R group

all the amino acids (20)

nonpolar hydrophobic:

• glycine; gly; g - alpha helix breaker

• alanine; ala; a

• valine; val; v

• leucine; leu; l

• isoleucine; ile; i

• methionine; met; m - sulfur

• phenylalanine; phe; f - rings, UV light-absorbing

• tryptophan; trp; w - rings, UV light-absorbing, precursor of serotonin biosynthesis

• proline; pro; p - alpha helix breaker

polar hydrophilic:

• serine; ser; s

• theronine; thr; t

• cysteine; cys; c - sulfur, disulfide bridges

• tyrosine; tyr; t - rings, UV light-absorbing, CHEESE

• asparagine; asn; n

• glutamine; gln; q

charged hydrophilic:

• acidic:

  • aspartic acid; asp; d

  • glutamic acid; glu; e

• basic:

  • lysine; lys; k

  • arginine; arg; r

  • histidine; his; h

4 levels of protein structure

primary: polypeptide, peptide bonds

secondary: alpha helices and beta pleated sheets, hydrogen bonding between backbone

tertiary: polypeptide folding via side chain interactions and hydrophobic interactions

quaternary: interactions between polypeptide chains

sickle-cell disease

Glutamine → Valine (change in primary structure) leads to sickle cell beta subunit, sickle cell hemoglobin, oxygen carrying capacity is greatly decreased

chaperonins

protein molecules that assist the proper folding of other proteins, parts: cap and hollow cylinder

protein denaturation

alterations in pH, salinity, temperature, or other environmental factors can cause proteins to denature → biologically inactive

x-ray crystallography

commonly used to determine 3D structure of proteins

nucleic acids

construct genes which code for proteins, DNA and RNA

nucleotides

monomers of nucleic acids, pentose sugar + phosphate + nitrogenous base, link via phosphodiester bonds (between 3’ OH- group and 5’ phosphate) forming sugar-phosphate backbone

nitrogenous bases

adenine, thymine, cytosine, guanine, uracil

A and G are purines - double ring
C, U, T are pyrimidines - single ring

Chargaff’s rule

A with T or U, 2 hydrogen bonds
C with G, 3 hydrogen bonds