Receptor Structure and Function

what are drug receptors, structurally?

folded proteins

which elements do proteins contain?

hydrogen, carbon, nitrogen, oxygen, phosphorus, sulfur, selenium

small molecules in nature also include halogens (F, Cl, Br, I)

carbon general information

can form vast numbers and varieties of compounds

vital to organic and life processes

carbon chemical properties

can form 4 covalent bonds

often seen in covalent interactions in hydrophobic regions

nitrogen general information

critical for many biological molecules

ammonia often the starting compound for many nitrogen compounds

nitrogen chemical properties

can form 3 covalent bonds

often seen in covalent or hydrogen-bonded interactions

oxygen general information

very reactive, combines with most elements

component of many organic compounds

oxygen chemical properties

can form 2 covalent bonds

hydrogen general information

binds to C, N, O atoms

not very reactive

hydrogen chemical properties

can form 1 covalent bond

participates in H-bonds

phosphorus general information

very reactive

key element in energy currency in biology

phosphorus chemical properties

can form 3 or 5 covalent bonds

sulfur general information

similar to O, very reactive and combines with most elements

found in 2 essential amino acids

sulfur chemical properties

can form 2, 4, or 6 covalent bonds

why does configuration, conformation, and chirality matter?

shape of biological molecules influence folding and stability

recognition and function of biological molecules depend on binding and interactions

configuration

spatial arrangement of atoms in a molecule

changing this requires bond breakage

defines the molecule’s chemical reactivity and type of bonding it participates in

conformation

spatial arrangement of atoms in a molecule that can be obtained by rotation of the atoms about a single bond

no bond breakage required to change this

chirality

property of a molecule that makes the molecule and its mirror image non-superimposable

if there are none of these centers in the molecule, it does not possess this property

protein atoms

C, H, N, O, S

protein building blocks

amino acids

protein polymer bonds

peptide bonds

protein intra-molecular interactions

covalent (S-S), H-bonds, charge based, van der waal’s

protein functional role in cells

enzymes, structural proteins, sensors, receptors, etc

nucleic acid atoms

C, H, O, N, P

nucleic acids building blocks

nucleotides

nucleic acid polymer bonds

phosphodiester bonds

nucleic acid intra-molecular interactions

H-bonds, stacking interactions

nucleic acid functional role in cells

storage of genetic information, enzymes, ribozymes

carbohydrate atoms

C, H, O, N

carbohydrate building blocks

simple sugars

carbohydrate polymer bonds

glycosidic linkages of various types

carbohydrate intra-molecular interactions

H-bonds

carbohydrates functional role in cells

storage of energy, structural, recognition, interactions

lipids atoms

C, H, O

lipids building blocks

fatty acids, glycerol

lipids polymers and bond type

none, forms various di-, triglycerides

lipids intra-molecular interactions

van der waal’s

lipids functional role in cells

membrane signaling, energy storage, small molecule hormones

interactions in biological molecules

covalent bonds—peptide, phosphodiester, disulfide

non-covalent bonds—H-bonds, eletrostatic/ionic, hydrophobic, van der waal’s, metal coordination, pi based interactions (stacking)

weak hydrogen bonding

reversible bond

CH is donor, acceptor is lone pair N or O

dipoles

found across a molecular bond, bond property based on electronegativity

occurs in a covalent bond between atoms with different electronegativity

on the left side of the periodic table,

less electronegative atoms, allows electrons to be pulled away, atom becomes partially positive

on the right side of the periodic table

more electronegative atoms, attract electrons, atom becomes partially negative

what do dipoles cause?

charge separation—results in partial positive atoms and partial negative atoms

also called electrostatics

which bonds have the strongest dipoles?

H-halogen bonds

polar covalent bond

two atoms with vastly different electronegativities share a pair of bonding electrons (>0.4)

the more electronegative element pulls an unequal share of the electron density in the shared pair, bears a partial negative charge

less electronegative element bears partial positive charge

C-H bonds

have a weak dipole, polarize towards the carbon

C-Cl bonds

have a relatively strong dipole polarized toward chlorine

aromatic rings

have pi-bond dipoles

they are flat and planar in one dimension

each C-H gives a week dipole resulting in the H edge being partial positive and the carbons neutral

the orbitals result in partial negative charge near the center of the ring