Course objective

The big question: what is life ?

Assuming that we consist of nothing else but common compounds what makes us tick ?

Why are we alive but a rock is not ?

We metabolize energy, reproduce, evolve, a rock ... ('n rolls). But how does this come about ?

Therefore, let's examine the relationships in this mixture of substances to discover their function.

Course structure

Life exists as an inverted pyramid of complexities: the "simple" relationships of atoms leading to "complex" relationships of organs e.g. the brain.

Course philosophy

The underlying motif of all lectures will be on the structure-function relationship of molecular interactions. In other words, how particular functions stem from the structures of the molecules themselves or from molecular complexes.

This course provides a basis for most of the biological and biochemical courses you will take in your careers. Therefore, the stress will be on the understanding of concepts and mechanisms, rather than on the memorization of facts.

Course organization

Physics/Chemistry

All matter, living or not, obeys the physical and chemical rules. We have to learn these rules.

Biochemistry

Biochemistry is a subset of chemistry present in living systems. It is a molecular society where molecules help other molecules and reactions are ordered.

Cell Biology

A cell is not an amorphous soup in which chemical reactions take place.

Reactions are organized in metabolic pathways and pathways are compartmentalized within a cell.

Organelles are specialized intracellular compartments, each with well defined functions. Some are factories, others are recycling plants, yet others are libraries.

Molecular Biology

Science of sex life on a molecular level.

How is information transferred from genes to protein ?

Cell / Systemic Physiology

High level organization of cells and tissues.

How do organisms go about their bodily functions: respiration, circulation, motility, nerve conduction ?

Atoms

Elements

An element is a substance that can't be broken into simpler substances in a chemical reaction.

Common elements

105 (92 naturally occurring) of elements are known but only 20 are used by living organisms. Five of them account for 99% of all body mass.

ElementSymbolAbundance
OxygenO65%
CarbonC19%
HydrogenH10%
NitrogenN3%
CalciumCa2%

Trace elements

The remaining 1% of mass is made of trace elements necessary to carry out catalytic functions, e.g. Fe, Zn, Mg, Cu

Atom

The atom is the smallest unit of an element retaining its properties. Atoms can be subdivided into sub- atomic particles but these don't have properties of the element.

Atom size

objectsize
atoms0.1 nm
organelles0.1 mm
cells0.1 mm
organs1 - 100 cms

Structure

Nucleus

The nucleus is the center of an atom, it contains 2 major subatomic particles: neutrons and protons.

Protons
Proton's mass is 1 atomic mass unit ( 1.7 x 10-24 g), and they have 1 positive electrical charge.

All atoms of the same element have the same number of protons

The number of protons defines atomic number and chemical properties

Neutrons
1 atomic mass unit (same as a proton) but no electrical charge;

The number of neutrons can vary in the same element giving rise to isotopes. Isotopes have the same chemical properties because the number of protons is the same but different physical properties like mass, radioactivity or magnetic properties.

Example: carbon isotopes:

Isotopepropertyabundance
12Cnatural
13Cmagneticv. rare
14Cradioactiveeven rarer
Atomic mass is the total mass of the atom. It equals (approximately) the mass of the nucleus or the sum of the proton and neutron masses. The superscript in front of an element's symbol denotes its atomic mass.

Electrons

Electrons are very light: 1/1700 smaller mass than that of a proton.

Electric charge of an electron is -1.

In an atom the number of electrons equals the number of protons, thus atoms are electrically neutral.

Electrons orbit around the nucleus. The centrifugal force of motion balanced by the attraction of the positive nucleus. The electrons paths are called orbitals.

Orbitals
Orbitals near the nucleus have lower energy and the electrons will try to occupy first these.

When electrons occupy the lowest energy orbitals the atom is said to be in its ground state.

Energy absorption (e.g. light absorption) can cause an electron to jump to a higher energy orbital. Such an excited state is unstable and the electron relaxes back to the ground state often radiating light (fluorescence, phosphorescence).

Fig. 2.5

Orbitals have different shapes: s orbitals are spherical; p orbitals are dumbbell-like.

Orbitals of different type contain different number of electrons: s (2 electrons); p (6 electrons), d (10 electrons).

Fig. 2.7, 2.8

Electrons exist with 2 different spin orientations (± ½ ). Electrons in one orbital want to be paired up with a partner with opposite spin thus forming an electron pair.

Shells
Orbitals are arranged into shells. The first (innermost) K shell can hold 2 electrons, the second (L) 8, the third (M) 18 electrons, the fourth (N) 32.

Aufbau Prinzip
In 1924 Pauli discovered that no two electrons can occupy the same orbital and have the same spin, this principle is called the Pauli Exclusion principle.

The Pauli exclusion principle explains how elements are formed: first the s orbital of K shell is filled with two electrons, then the s orbital of the L shell followed by 6 electrons of p orbital. Once L shell is filled, M shell fills up following the same pattern: s, p and d orbitals.

ShellKLM
Element1s2s2p3s3p3d
H 1 - - - - -
He 2 - - - - -
Li 2 1 - - - -
Be 2 2 - - - -
B 2 2 1 - - -
C 2 2 2 - - -
N 2 2 3 - - -
O 2 2 4 - - -
F 2 2 5 - - -
Ne 2 2 6 - - -
Na 2 2 6 1 - -
In a periodic table, elements in neighboring columns differ by one electron, while elements in the rows differ by the a shell.

Atom stability: octet rule

Atoms are most stable when the outermost shell has 8 electrons (with exception of H and He). Atoms will attempt to loose or gain electrons to have 8 electrons in the outermost shell.

Valency

Number of electrons to loose or gain to obtain an octet of electrons defines an element's valency:
monovalent (1 electron): Na, K, Cl
divalent (2 electrons): Ca, Mg, O
trivalent (3 electrons): Fe, Al

They all want to achieve the number of electrons of the column 8 (noble gases) of the same or preceding row of the periodic table.

Atoms loosing electrons have a positive valency; negative for atoms gaining electrons.

P. Fajer Atoms 7/5 Chem-1 12/30/95 11:32 PM 7