The Nature of Molecules Chapter 2

Understanding the structure of atoms is critical to understanding the nature of biological molecules. Atoms are composed of
protons = positively charged particles (+1) neutrons = neutral particles (0) electrons = negatively charged particles (-1) protons and neutrons are located in the nucleus electrons are found in orbitals surrounding the nucleus
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Atomic Structure

Every different atom has a characteristic number of protons in the nucleus. atomic number = number of protons Atoms with the same atomic number have the same chemical properties and belong to the same element.
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The Periodic Table

arranges all elements according to their atomic number identifies elements with similar chemical properties

 there are 90 naturally occurring elements only 12 elements are found in living organisms in substantial amounts 4 elements make up 96.3% of human body weight:
carbon hydrogen oxygen nitrogen
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Each proton and neutron has a mass of ~ 1 dalton. Atomic mass = the sum of protons and neutrons Isotopes = atoms of the same element that have different
atomic mass numbers due to different numbers of neutrons

think of isotopes as versions these are all versions of carbon sometimes they are radioactive (C14) but not necessarily
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Isotopes where protons dont equal neutrons tend to be unstable, which causes them to break down (decay) into elements of lower atomic numbers. When they decay they emit radioactivity. Unstable isotopes occur naturally in very small concentrations.
Using very sensitive instruments, we can use radioisotopes for lots of stuff in science, engineering, medicine including the construction of images (as in MRI)
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Neutral atoms have the same number of protons and electrons. Ions are charged atoms (also called electrolytes) cations have more protons than electrons and are positively charged anions have more electrons than protons and are negatively charged
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Atoms vs ions
Na atom: Na+ ion: how many protons? (see Periodic Table) how many electrons? how many protons? how many electrons? How about the neutral chlorine atom vs the charged chlorine ion? How many protons? How many electrons? (what # are you looking up from the Periodic Table?)
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ELECTRONS
very small (1000x lighter than protons or neutrons) orbit nucleus at WICKEDLY fast rate: 1000000000000000x/sec as a result you cant really tell where one is (only that its within this cloud, or orbital) 1-2 electrons per orbital (2 max)

Electrons possess potential energy (energy of position), with electrons far from the nucleus having the most energy.
atomic energy levels not same as electron orbitals energy levels correspond to quanta (s., quantum) orbitals indicate an electrons most likely location

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Electrons moving from one energy level to another provides the energy for life
Electrons often change their orbitals temporarily. The further away from the nucleus, the more energy an electron has. When an electron falls back toward the nucleus, it releases the energy it gained on the trip out. This is the basis of the energy for all life as we know it!!
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Energy levels not same as orbitals

K = the lowest energy level (shell)

nearest the nucleus contains single s orbital (1s) contains 1 or 2 electrons (max 2)

L = the next contains one s and three p orbitals highest referred to as 2s and 2p orbitals energy shell since each orbital has two electrons, can hold up to 8 total

Neon completely filled K and L shells contains 2 + 8 (=10) electrons is a noble gas
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Electrons can be transferred from one atom to another, while still retaining the energy of their position in the atom. oxidation = losing an electron reduction = gaining an electron

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Valence electrons electrons in the outermost energy level of an atom the chemical properties of a specific element depend on interactions between valence electrons of other atoms
atoms with full energy levels are less reactive than atoms with unfilled energy levels.

Octet rule atoms tend to establish completely-full outer energy levels

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molecules = groups of atoms held together in a stable association compounds = molecules containing more than one type of element chemical bonds = the interactions between atoms that hold them together in molecules or compounds

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Chemical bonds =
the interactions between atoms that hold them together in molecules or compounds

Chemical bonds important in biology:

covalent bonds ionic bonds hydrogen bonds hydrophobic interactions van der Waal forces

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Covalent bonds
form when atoms share 2 or more valence electrons covalent bond strength depends on the number of electron pairs shared by the atoms
single bond double bond

p24

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triple bond
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Electronegativity is an atoms affinity for electrons. Differences in electronegativity dictate how electrons are distributed in covalent bonds.
nonpolar covalent bonds = equal sharing of electrons polar covalent bonds = unequal sharing of electrons

compare H2 (or O2 or N2) with water H2O!

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Within a water molecule, the bonds between oxygen and hydrogen are highly polar. Partial electrical charges develop: oxygen is partially negative hydrogen is partially positive

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Ionic bonds
formed by the attraction of oppositely charged ions

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Hydrogen bonds
weak attractions between a partially negative atom and a partially positive hydrogen atom
H bonds readily form between water molecules or between water and another charged molecule

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Van der Waals attractions (or forces)

weakest of all bonds When two nonpolar molecules come together, normally electrons in outer shell would cause atoms to repel each other. In Van der Waals interactions, the orbits set up so they miss each other-allowing them to be closer together.

without Van der Waals

with Van der Waals

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Chemical reactions
involve the formation or breaking of chemical bonds whether a chemical reaction occurs is influenced by
temperature concentration of reactants and products availability of a catalyst chemical reactions are written with the reactants first, followed by the products 6H2O + 6CO2 C6H12O6 + 6O2 reactants products chemical reactions are often reversible C6H12O6 + 6O2 6H2O + 6CO2

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Water Chemistry
all living organisms are dependent on water its chemical structure is the basis for its unique properties ability to readily form hydrogen bonds is crucial to many of its unique properties

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 cohesion: water molecules stick to other water molecules by hydrogen bonding

adhesion: water molecules stick to other polar molecules by hydrogen bonding

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Water is most dense as a liquid

Unlike most substances, solid water (ice) is less dense than liquid water. Water is most dense at 4oC.

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Water is a good solvent: water dissolves polar molecules and ions

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Water organizes nonpolar molecules:

hydrophilic: water-loving hydrophobic: water-fearing Water does not dissolve nonpolar (hydrophobic) substances
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Water can form ions:

H2O OH-1
hydroxide ion

H+1
hydrogen ion

hydrogen ion (H+1) is the basis of the pH scale acids and bases:
greater H+1 concentration lower pH (acidic) lower H+1 concentration higher pH (basic)

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Acids and Bases

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Acid: a chemical that releases H+1 ions Base: a chemical that accepts H+1 ions Buffer: a chemical that accepts/releases H+1 as necessary to keep pH constant
most biological buffers consist of a pair of molecules, one an acid and one a base

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CH2 Bonus Topics

the importance of water (see pp25,26) the significance of Rutherfords experiment (p18)

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