Biochemistry 1

Water molecules form _____

dipoles

dipole

a molecule with electric charge distributed asymmetrically about its structure
responsible for water’s high dielectric constant

hydrogen bond

partially unshielded nucleus bound to an

electron-withdrawing oxygen or nitrogen atom + unshared electron pair on another oxygen or nitrogen atom

covalent bonds

strongest force that holds molecules together

hydrophilic

water-loving

hydrophobic

water-hating

amphiphatic

possess regions rich in charged or polar functional

groups and regions with hydrophobic character

hydrophobic interactions

tendency of nonpolar compounds to self-associate in an aqueous environment

second law of thermodynamics

the optimal free energy of a hydrocarbon-water mixture is a function of both maximal enthalpy and highest entropy

salt bridges

electrostatic interactions between oppositely charged groups within or between biomolecules

van der Waals forces

• a.k.a.1-ondon dispersion forces

• arise from attractions between transient dipoles

  generated by the rapid movement of electrons of all neural atoms

nucleophiles

- electron-rich molecules

electrophiles

electron-poor molecules

enzymes

protein catalysts that accelerate the rate of hydrolytic reactions when needed

proteases

catalyze the hydrolysis of proteins into their component amino acids

nucleases

catalyze the hydrolysis of the phosphoester bonds in DNA and RNA

water, in the presence of an acid, it acts as a proton ___; in the presence of a base, it acts as a proton ___.

In the presence of an acid, it acts as a proton acceptor; in the presence of a base, it acts as a proton donor.

pH

negative log of the hydrogen ion concentration - decreases as [H+] increases

pH of blood

7.0

pH of stomach acid

1.0

pH of saliva

6.0

acids

proton donors

bases

proton receptors

weak acids

dissociate only in partially acidic solutions

strong acids

e.g. HCl, H2SO4
completely dissociate into anions and protons even in strongly acidic solutions (low pH)

weak bases

completely dissociates even at high pH

Henderson-Hasselbach equation

• describes the behavior of weak acids and buffers

buffering

• ability to resist a change in pH following addition of

  strong acid or base

entropic forces

macromolecules expose polar regions to an aqueous interface and bury nonpolar regions

atoms

• basic building blocks of matter

law of constant composition

in a given compound, the relative numbers and kinds of atoms are constant

law of conservation of mass

the total mass of materials present after a chemical reaction is the same as the total mass present before the reaction

law of multiple proportions

if two elements A and B combine to form more than one compound, the masses of B that can combine with a given mass of A are in the ratio of small whole numbers

atomic number

the number of protons or electrons in an atom of any particular element
- shown by the subscript

mass number

shown by the superscript,

number of protons plus neutrons

isotopes

atoms with identical atomic numbers but different mass numbers

ionization energy

• minimum energy needed to remove a valence

  electron (electrons in the outermost orbit, farthest

  from the nucleus)

electron affinity

the energy change upon adding an electron to an atom, in a gas phase forming an anion.

metallic character

• characteristic luster, and they are good conductors of

  heat and electricity

diatomic molecule

a molecule made up of two atoms

molecular compounds

compounds composed of molecules contain more than one type of atom

molecular formulass

chemical formulas that indicate the actual numbers of atoms in a molecule

empirical formula

chemical formulas that give only the relative number of atoms of each type in a molecule

cation

ion with a positive charge

anion

ion with a negative charge

lewis symbol

consists of the element’s chemical symbol plus a dot for each valence electron

octet rule

• atoms tend to gain, lose, or share electrons until they

  are surrounded by eight valence electrons

IONIC BONDING

transfer of electrons

covalent bonding

sharing of electrons

bond polarity

a measure of how equally or unequally the electrons in any covalent bond are shared

nonpolar covalent bond

one in which the electrons are shared equally

polar covalent bond

one of the atoms exerts a greater attraction for the bonding electrons than the other

electronegativity

• the ability of an atom in a molecule to attract

  electrons to itself

The _____ the difference in electronegativity between two atoms, the more polar their bond.

The greater the difference in electronegativity between two atoms, the more polar their bond.

three types of intermolecular attractions:

• -  dispersion forces

• -  dipole-dipole attractions

• -  hydrogen bonding

intermolecular interactions

electrostatic, involving attractions between positive and negative species, much like ionic bonds

dispersion forces

tend to increase in strength with increasing molecular weight and with decreasing distance between molecules

polarizability

• the ease with which the charge distribution is

  distorted in a molecule

• -  measure of the “squashiness”

repulsion

can occur when the positive or negative ends of two molecules are in close proximity

ion-dipole forces

exists between an ion and a polar molecule
- the magnitude of the attraction increases as either the ionic charge or the magnitude of the dipole moment increases

Group transfer reaction

a functional group will be transferred from one molecule that serves as the donor molecule that will be the acceptor molecule

Phosphorylation

the process through which a phosphate group is transferred from one molecule to a protein, usually within a biological system

kinase

• the enzyme involved in phosphorylation

dephosphorylation

process through which a phosphate group is removed

hydrogenation

a molecule of hydrogen (H2) is added across a C-C double, reducing it to a C-C single bond

hydrolysis

water is added to a molecule to break it apart to two molecules

dehydration

removal of water to join molecule together; also condensation

oxidation

reduction reactions, loss of electrons

redeuction

reverse reaction of oxidation, gain of electrons

primary alcohol (R-OH)

oxidized to an aldehyde (R-COH)

aldehyde (R-COH)

oxidized to a carboxylic acid (R-COOH)

aldehyde (R-COH)

reduced to a primary alcohol (R-OH)

carboxylic acid (R-COOH)

reduced to an aldehyde (R-COH)

isomerization

a single molecule is rearranged such that it retains the same molecular formula but now has a different bonding order of the atoms forming a structural or stereoisomer

biomolecules

• molecules that occur naturally in living organisms

• -  compounds of carbon

• -  macromolecules like carbohydrates, proteins, nucleic

  acids, and lipids

• -  small molecules like primary and secondary

  metabolites

monomer

smallest functioning unit of a biomolecule

dimer

two monomers together

polymer

several monomers together

carbohydrates

• major source of energy for the body

• -  most abundant organic molecules in nature

• -  contain three elements: C,H,O

empircal formula of carbohydrates

(CH20)n

glucose

• most important carbohydrate

three subtypes of carbohydrates:

●  monosaccharides

●  disaccharides

●  polysaccharides

monosaccharides

• -  simplest sugars

• contains 3-7 carbons and one aldehyde or ketone

  group

• classified as trioses, tetroses, pentoses, hexoses or

  heptoses

• glucose, fructose, galactose

disaccharides

• consist of 2 monosaccharides

glucose+glucose =

maltose

glucose +galactose =

lactose

glucose+fructose=

sucrose

polysacharrides

condensation products of more than ten monosaccharide units
- starches and dextrins

starch

major metabolic fuel in diet

glycogen

the storage polysaccharide in animals

inulin

polysaccharide of fructose

protein

synthesized sequence of amino acids linked together in a linear polypeptide structure

primary structure

sequence of amino acids in a polypeptide chain

secondary structure

folding of short (3-30 residue), contiguous segments of polypeptide into geometrically ordered units

tertiary structure

overall 3 dimensional shape of proteins

quaternary structure

number and types of polypeptide units of oligomeric proteins and their spatial arrangement

nucleic acids

- macromolecules consisting of a large number of linked nucleotides (polymer of nucleotides joined by a 3’-5’ phosphodiester bond)
- Biopolymers essential in all forms of life - Most important of all biomolecules

- Encode and store information that will be transmitted and expressed outside the cell

nucleotides

building blocks of nucleic acids

DNA

chemical basis of heredity

RNA

direct and regulates protein synthesis