Chapter 2

an atom (ex. carbon) bonded to four dissimilar atoms or groups in a nonplanar configuration

has a tetrahedral orientation of bonds; can be arranged in two different ways

a property of molecules that are mirror images of each other

molecules that exhibit chirality, or ones that can be mirror images of each other

the extent of an atom's ability to attract an electron

bonds between atoms with identical or similar electronegativities

the "resonance hybrid" of a molecule is the actual structure of a molecule in the normal quantum state which has the lowest possible value of total energy

• C=O
• C=N
• C=C
• P=O

• 1-5 kcal/mol
• (at 25 degrees C, thermal energy = .6 kcal/mol; the energy required to break a C - C bond is about 140x larger than that)

salts, such as NaCl; weaken/disrupt ionic interactions holding the biomolecules together

directionality!

WEAKER: in the strongest hydrogen bonds the donor atom, hydrogen atom and acceptor atom all lie in a straight line

Hydroxyl group in alcohols (-OH) and amino group ( -NH₂) dissolve in water to high concentrations

• because water molecules cannot form H-bonds with non polar molecules or non polar portions of molecules, they tend to form cages of relatively rigid pentagons and hexagons around such molecules: this state is energetically UNfavorable because it decreases the randomness (entropy) of the population of water molecules
• -to increase entropy (disorder), the nonpolar molecules aggregate with hydrophobic surfaces facing e/a other so less is facing the water -- this means fewer water molecules are needed to form the surrounding cages and more can be free and disorganized

it's a nonpolar solvent; good for dissolving non-polar molecules

a lock-and-key kind of fit between their shape, charges or other physical properties that allow them to form multiple non-covalent interactions at close range

binding dissociation constant; quantitative measure of affinity

linear polymers made up of 10-several thousand AMINO acids linked by PEPTIDE bonds

linear polymers made up hundreds to millions of nucelotides linked by PHOSPHODIESTER bonds

linear OR branched poluers of monosaccharides (sugars, like glucose) linked by GLYCOSIDIC bonds

what takes place in order for a covalent bond to form between two monomers; involves the loss of a H from one monomer and the loss of an OH (hydroxyl) from the other monomer resulting in the net loss of one water

• 1) these are the building block of proteins
• 2) when incorporated into protein polymer they are called residues
• 3) all have a characteristic structure consisting of central α carbon bonded to four different chemical groups

• -central α carbon bonded to four different chemical groups
• 1) an amino (NH₂) group
• 2) a carboxylic acid or carbonyl group (COOH)
• 3) hydrogen (H) atom
• 4) side chain/R group (variable)

• -EXCEPT for glycines
• -these molecules exist in two mirror images of each other called the D (dextro) and L (levo) isomers
• -ONLY the levo (L) forms of amino acids are found in proteins

• those that contain uncharged side chains
• -5 hydrophobic amino acids' side chains consist ENTIRELY of hydrocarbons (except for methionine which has a sulfur); are all noncyclic
• -the other 3 hydrophobic amino acids have cyclic side chains/are bulky and aromatic

-can be broken up into basic, acidic, and just polar amino acids that confusingly have uncharged R groups

• lysine & arginine have positively charged side chains; histidine has a side chain that has a ring with two nitrogens (called imidazole)
• -this ring can shift from being positively charge (basic) to uncharged depending on the acidity of the surrounding environment
• -all 3 are hydrophilic

aspartate and glutamate have negatively charged side chains due to the carboxyl groups within them (their uncharged forms are called aspartic acid and glutamic acid); are all hydrophilic

• -asparagine and glutamine: have polar side chains containing amide groups w/ H-bonding capabilities
• -seine and threonine: have polar hydroxyl groups; can H-bond with other polar molecules

• 1) cysteine: side chain contains a reactive sulfhydryl group (-SH); can oxidize to form disulfide bond w/ another cystine
• 2) glycine: smallest amino acid; R group = single hydrogen atom
• 3) proline: has a ring shaped side chain; is very rigid and creates a kink in a protein chain limiting folding capabilities (also has an H₂N group in stead of a 3 one)

cysteine, tryptophan and methionine; constitute 5% of amino acids in a protein

leucine, seine, lysine and glutamic acid; total 32% of residues in a typical protein

the addition of an acetyl group to the amino group of the N-terminal residue = most common form of amino acid chemical (looks like CH₃ and O (double bonded) to a C); non acetylated proteins are degraded

• -two types: DNA/RNA
• -monomers of nucleic acids are nucleotides
• -nucleotide structure: phosphate group linked via phosphoester bond to pentose (or ribose for RNA, 5-carbon sugar), linked to a base (nitrogen/carbon containing ring)

de-oxy-ribose (DNA) at its 2' carbon has only an H, whereas ribose has an OH at its 2' carbon

adenine and guanine; have a pair of fused rings

cytosine, thymine and uracil; contain only one ring