Biological Chemistry

EFB325 Cell Physiology

Chemical bonds/ions/redox/pH/properties of water

Elements

atoms composed of protons, neutrons, electrons - # of protons defines the element
electron shells, valance
isotopes have a different mass due to different # of neutrons
ions have a charge due to a varying number of electrons (which carry a negative charge)
there is little correlation between the elemental composition of the Earth's crust and of cells

Compound = has two or more chemically bonded elements

Types of bonds and their strengths

Covalent bonds

outer shells "want" to be filled=octet rule, resulting in shared electron pairs between atoms
double, triple covalent bonds form when more electrons are shared
directional - leads to 3D structure
polar covalent bonds result when one nucleus pulls electrons away from the other nucleus due to difference in electronegativity
covalent bonds with carbon are commonly formed with carbon, nitrogen, oxygen, hydrogen
valence of carbon=4, yields tetrahedral structures

Ionic bonds

dissociation of compounds into ions-cations and anions, so that usually the outer shell is either emptied or filled and the atom is stable in that form
depends on electronegativity of atom
there is an electrostatic interaction between ions - positive charge is attracted to a negative charge
non-directional

Hydrogen bonds

a hydrogen bond is formed when a H is shared between two electronegative atoms
in biology, H is shared between combinations of O or N
when O or N are covalently bound with H, they often form a polar covalent bond - a bond with a dipole moment (- around the O or N; + around the H)
this + polarity around the H interacts with a - polarity on N or O
20X weaker than covalent

van der Waals

attraction between neutral atoms which are very close to each other
brings atoms to a certain optimal distance from one another (repulsion if too close)
fraction of strength of H-bond

Typical chemical groups or structures in biological chemistry

Bonds with C

hydroxyl, carbonyl (aldehyde or ketone), carboxyl (carboxylic acid), ester (acid+alcohol)
amino, amide, sulfhydryl (thiol)
carbon shorthand drawings

Phosphate groups

Oxidation/reduction reactions (redox reactions)

involve the transfer of electrons, so that an atom either stably gains (reduction) or loses (oxidation) one or more electrons [more complex than ionic interactions - does not result in electrostatic bonding]
often when an electron is gained, a H+ is added also - so reductions often involve addition of covalent bonds with H (oxidations involve loss of bonds with H and perhaps more bonds with oxygen)
oxidation number-is decreased by a reduction reaction (increases by oxidation)
cleavage of water to release oxygen- 2H₂O -> 4H⁺ + O₂ + 4e^-
reactions involving NADH (nicotinamide adenine dinucleotide)=transfer of 2 e^- each

Transfer of H⁺ (protons) defines acids and bases

acid=H⁺ donor; base=H⁺ acceptor
pH=-log[H⁺]; high pH value=low [H⁺], low pH value=high [H⁺]
the pK value for a certain group defines the pH at which that group is protonated or not

Properties of water

-water is polar=triangular shape, with a net negative dipole moment on the O, positive polarity on the H

-water has high surface tension, high boiling point, high specific heat, high heat of vaporization

water is an excellent solvent-competes for hydrogen and electrostatic (ionic) bonds

Chemical groups and compounds can be defined as hydrophilic or hydrophobic

hydrophilic=water-loving, have some polarity or charge; a molecule may have no net charge, but has local areas of + and - polarity that makes it hydrophilic
hydrophobic=water-fearing, are neutral, tend to coalesce in water because the water molecules are attracted to one-another

Important example of the interaction of hydrophobic molecules in an aqueous environment are lipids that form biological membranes