# General Biology/Getting Started/Matter

General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material

## Matter

Matter is defined as anything that has mass (an amount of matter in an object) and occupies space (which is measured as volume).
* Particles, from smallest to largest and amal is the greatest
** Subatomic particles
*** Electrons
*** Protons
*** Neutrons
** Atoms
** Molecules
** Macromolecules
* Origin of matter
** Big Bang, about 13.7 billion years ago
** Hydrogen, helium
** Heavier elements formed in suns, super nova
*** Earth's matter predates formation of sun, 4.5 billion years ago
* All matter consists of atoms, which are composed of : electrons, protons, neutrons

## The atom

* Example: Hydrogen
** The simplest element
** One proton (+)
** One electron in orbit (-)
* Built by adding one proton (and one electron) at a time
* Number of protons determines atomic number and number of electrons
* Neutrons
** Neutral charge
** Contribute mass
** May decay
* Oxygen
** 8 protons (mass)
** 8 electrons
** 8 neutrons (mass)

## Mass and isotopes

* Atomic mass
** Sum of masses of protons and neutrons
** Measured in daltons or AMU (Atomic Mass Unit)
** An AMU is 1/12 the mass of Carbon-12
** proton ~1 AMU or dalton
** 6.024 x 10$^{23}$ daltons/gram
* Atoms with same atomic number belong to same element
* Isotopes
** Same atomic number but different atomic mass
** Some are radioactive
** Uses of isotopes
*** Radioactive: 3H, 14C, 32P, 35S
**** Tracers in biochemical reactions
**** Detection of molecules in recombinant DNA technology (genetic engineering)
**** Half-life: dating of rocks, fossils
*** Non-radioactive (N, C, O)
**** Diet of organisms (including fossils)
**** Biochemical tracers

## Electrons

* Negative charge
* Held in orbit about nucleus by attraction to positively charged nucleus
* Atom may gain or lose electron, altering charge
** Cation: loses electron, positive charge
*** Na$^+$
** Anion: gains electron, negative charge
*** Cl$^-$
* Determine chemical properties of atoms
** Number
** Energy level

## Chemical bonds

* Form molecules
* Enzymes: make, break, rearrange chemical bonds in living systems
* Ionic
* Covalent
** Sharing of one or more pairs of electrons
*** Called single, double, or triple
** No net charge (as in ionic bonds)
** No free electrons
** Give rise to discrete molecules
** Hydrogen

## Chemical reactions

* Formation and breaking of chemical bonds
* Shifting arrangement of atoms
* Reactants -> products
* Reactions are influenced by:
** Temperature
** Concentration of reactants, products
** Presence of catalysts (enzymes)
* Oxidation:reduction

## Water

* Essential for life
* ~75% earth's surface is water
* Life evolved in water
* Solvent for many types of solutes
* High specific heat
* High polarity
** Creates a slightly negative Oxygen and a Slightly positive hydrogen
** allows formation of Hydrogen Bonds

### Hydrogen bonding

* A type of polar interaction
* Critical for:
** Protein structure
** Enzymatic reactions
** Movement of water in plant stems
* Weak and transient
* Powerful cumulative effect
** Solubility of many compounds
** Cohesion (capillary action)
** Lower density of ice
* Formed between molecules other than water
** Protein structure
** DNA, RNA structure
Water organizes nonpolar molecules
* Nonpolar molecules: no polarity (+/-) charges
* Hydrophobic: exclude water because they don't form hydrogen bonds with it
* Consequences:
** Membranes
** Protein structure
* Hydrophilic: polar substances associate with water
Ionization of water: H$_2$O -> H$^+$ + OH$^-$
* Forms a Hydrogen ion (H$^+$), hydroxide ion (OH$^-$)
* Due to spontaneous breakage of covalent bond
* At 25 °C, 1 liter of water contains 10-7 moles of H$^+$ ions: 10-7 moles/liter
pH
* A convenient way of indicating H$^+$ concentration
* pH = -log[H$^+$]
* For water, pH = -log[10-7] = 7
* Since for each H$^+$ in pure water, there is one OH$^-$, pH of 7 indicates neutrality
* Logarithmic scale
Buffer
* Reservoir for H$^+$
* Maintains relatively constant pH over buffering range

## References

This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the Cleveland State University.