Biology

Chemistry background and Cells

CHEMISTRY BACKGROUND Elements and Atoms

An element is a substance than cannot be broken down into anything simpler by ordinary means.
An atom is the smallest particle of any element that still has the chemical and physical properties of that element.
Each element is composed of only one type of atom.
Electrically charged atoms are called ions; they can either be positively charged (with missing electrons) or negatively charged (with extra electrons). (Remember that electrons have a negative charge.)
There are 92 naturally occurring elements, of which only a dozen or so are important in biological systems.
- Hydrogen (H) is the lightest element. Pure hydrogen (H₂) is a gas.
  Hydrogen often exists in solutions (or in body fluids) as positively charged ions (H⁺)
  Hydrogen can also form covalent bonds in organic compounds.
- Carbon (C) is the most important element in biological systems because it forms the basis of organic compounds.
  Organic compounds are defined as compounds containing covalently bonded carbon, meaning carbon atoms that share electrons with other atoms, including other carbon atoms. Carbon can form long chains of covalently bonded atoms.
- Oxygen (O) commonly forms covalent bonds in organic compounds. It can also form negative ions, or it can participate with other elements to form polyatomic ions. Pure oxygen (O₂) is a gas that makes up about 21% of our atmosphere.
- Nitrogen (N) also can form covalent bonds in organic compounds, or it can combine with other elements to form polyatomic ions like nitrate (NO₃^-). Pure nitrogen (N₂) is a gas that makes up about 78% of our atmosphere.
- Sulfur (S) and Phosphorus (P) are nonmetals that also occur in many organic compounds, or in polyatomic ions.
- Chlorine (Cl) is an important nonmetallic element that forms negative ions (Cl^-) in biological systems.
  Fluorine, Bromine, and Iodine are similar to chlorine in their chemical properties but much less common.
- Sodium (Na), Potassium (K), and Calcium (Ca) are important metallic elements in biological systems.
  They form positively charged ions (Na⁺, K⁺, Ca⁺⁺) dissolved in body fluids.
- Other metallic elements (including iron, magnesium, cobalt, zinc, etc.) occur only in very small amounts in biological systems.
  They are essential for life, but only in very small amounts, mostly as "co-factors" in the structure of enzymes.

Compounds and Molecules

A compound is a substance that can be broken down into its constituent elements.
The smallest particle of a compound (that still has the properties of that compound) is called a molecule.
Ionic compounds are composed of positive and negative ions, held together by electrical attraction.
The most common ionic compounds dissolve in water. The ions separate in solution; each is surrounded by water molecules.
Covalent compounds are held together by the sharing of electrons to form covalent bonds.
THE MOST IMPORTANT BIOLOGICAL MOLECULES ARE COVALENTLY BONDED CARBON (ORGANIC) COMPOUNDS.
The vast majority of organic compounds are made of just four elements! Remember to HONC! to remember them:
- H — Hydrogen always forms one covalent bond.
- O — Oxygen always forms two covalent bonds.
- N — Nitgogen always forms three covalent bonds.
- C — Carbon always forms four covalent bonds.
- P.S. — Phosphorus (P) forms five covalent bonds, and Sulfur (S) forms either six or two.
Water (H₂O or H-O-H) is the most abundant compound on Earth, and it makes up 70-90% of most living organisms.
Water is a polar covalent molecule, meaning that the electrons are unequally shared: they spend much more of their time near the oxygen (which is therefore negatively charged) and less time around the hydrogens (which are therefore more positive).
IMPORTANT CONSEQUENCES:
- The separation of positive and negative charges causes water molecules to attract one another, accounting for water's extremely high specific heat.
- Charge separation also allows water to dissolve ionic compounds by forming "hydration shells" around the charged ions.
- Water also dissolves other polar compounds (those with a separation between positive and negative charges). Organic compounds with many O-H bonds (or N-H bonds) are generally polar and thus water-soluble. Organic compounds with mostly C-H bonds and few or no O-H bonds are generally nonpolar and thus insoluble in water.
Important biological molecules: Important biological molecules
- Amino acids have a central carbon atom (C) bonded to an amino group (-NH₂), an acid group (-COOH), a hydrogen, and a "side group". The "side group" differs from one type of amino acid to another, but the other groups are always the same.
- Proteins are made of chains of amino acids. Once formed, these chains twist and fold (usually) into compact shapes, and their function depends on their shape. Many proteins function as enzymes (biological catalysts) that speed up chemical reactions that would otherwise be very slow. Most chemical reactions inside cells are controlled (regulated) by these enzymes, but the enzymes are needed only in very small quantities.
- Lipids are biological compounds that do not dissolve in water. Fats and oils are important lipids, containing long hydrocarbon chains (containing hydrogen and carbon only). Usually three such chains are attached to a molecule of glycerol.
- Carbohydrates (sugars and starches) contain many -O-H groups and are thus usually water-soluble. The most common sugars form ring-like molecules, commonly with 5 or 6 carbons in the ring.

CELLS and ORGANELLES Prokaryotic cells:
Bacteria and Archaebacteria (Archaea) have prokaryotic cells that are simpler than animal or plant cells, and much smaller.
Prokaryotic cells lack internal compartments and most organelles or cytoskeletal features.
A plasma membrane is present, surrounding the cell. A cell wall is also present in most cases.
A single, circular chromosome is present, containing DNA but no surrounding proteins. The chromosome is not set apart from the rest of the cell.

Eukaryotic cells:
Animals, plants, fungi, algae, and various other organisms have larger and more complex eukaryotic cells, about 10 times the size of bacterial cells.
Eukarypotic cells have many internal compartments with specialized organelles and also a cytoskeleton.
Chromosomes contain histone proteins as well as DNA. Multiple chromosomes are present, and they are linear (rod-shaped or spaghetti-shaped).
The region containing chromosomes is set apart from the rest of the cell as a nucleus, enclosed by a double-layered nuclear envelope.

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