THE MOLECULES OF CELLS PAGES Chapter 2

- A SUBSTANCE THAT OCCUPIES SPACE AND HAS MASS; - A SUBSTANCE COMPOSED OF ATOMS Matter

- THE SMALLEST UNIT OF AN ELEMENT that possesses all the characteristics of that element - UNIT OF AN ELEMENT THAT IS NOT EASILY DIVISIBLE BY ORDINARY CHEMICAL MEANS Atom

Composed of : 1 or more protons (positive charge), usually 1 or more neutrons (no charge), and 1 or more electrons (negative charge) Often the number of protons and electrons are equal. The resulting atom has no net charge.

Fig. 2.2

Element a pure substance composed of only one kind of atom e.g. hydrogen (H), carbon (C), oxygen (O) (See 1114 webpage for a list of chemical symbols you should know.) Different elements must have a different number of protons in the nucleus

Isotope an atom of an element that differs in the number of neutrons in the nucleus e.g. Carbon 12 ( 12 C) and Carbon 14 ( 14 C) both are carbon, must have 6 protons 12 C has 6 protons and 6 neutrons 14 C has 6 protons and 8 neutrons

Radioactive Isotope an unstable isotope; an atom that will decay (change) into a different element as subatomic particles are lost from the nucleus e.g. 14 C  14 N + 1e - 6p + 8n 7p + 7n

Ion an atom of an element that has gained or lost one or more electrons e.g. H +, Na + - both have lost one electron Cl - - has gained one electron

Molecule a substance composed of two or more atoms; the atoms may be identical or may be different elements. e.g. water H 2 O glucose C 6 H 12 O 6 oxygen gas O 2

Chemical Bond an attractive force between two atoms Three different types: Ionic Covalent Hydrogen

Ionic Bond the chemical bond that results from the attractive force between two oppositely charged ions e.g. table salt Na + - Cl - Ionic bonds are not extremely strong.

Covalent Bonds chemical bonds that result from two atoms sharing one or more pairs of electrons; produces a relatively strong bond Two types of covalent bonds: Nonpolar covalent bond – the pair(s) of electrons are shared equally Polar covalent bond – the pair(s) of electrons are not shared equally

Nonpolar covalent bond Chlorine atoms share 1 pair of electrons Fig. 2.6

FIG. 2.6 Polar covalent bonds O and H do not share electrons equally

O and H have partial charges due to polar covalent bonds Pg. 26

Hydrogen Bond an attractive force between two atoms with opposite partial charges The atoms are not ions, the partial charges result from the atoms being polar covalently bonded to some other atom. weak bonds, but very important in living systems

O forms hydrogen bonds with H BETWEEN water molecules Fig. 2.8

Hydrophilic - the substance is attracted to water; will form H bonds with water; contains some polar covalent bonds Hydrophobic - the substance is repelled by water; will not form H bonds with water; contains mostly nonpolar covalent bonds

Hydrophilic – e.g. glucose O-H bond is polar covalent Fig. 2.17

WILL THIS MOLECULE FORM ANY H BONDS WITH WATER? A fatty acid – all the C-C and C-H bonds are nonpolar covalent Fig. 2.22

Oxidation – the loss of one or more electrons from an atom or molecule Reduction – the gaining of one or more electrons from an atom or molecule Usually linked; referred to as oxidation/reduction reactions

Oxidation/reduction is important in living systems because energy is transferred from molecule to molecule with the electrons. Oxidation – loss of e - and energy Reduction – gaining of e - and energy

NAD ox + e - + H +  NADH re lower energyhigher energy

Acid - a substance that releases hydrogen ions when placed in solution e.g. HCl  H + + Cl - Base - a substance that combines with H + when placed in solution e.g. HCO H +  H 2 CO 3

pH - a measure of the hydrogen ion concentration of a solution - ranges from 0 to 14 0 – the most acidic, lots of H + 14 – the least acidic, very few H + (most alkaline or basic) 7 – neutral, neither acidic or basic

pH is the negative logarithm of the hydrogen ion concentration Based on logarithms, each whole number change represents a 10-fold change in H +. pH 6 is 10X more acidic than pH 7 Negative log is why larger numbers represent lower acidity = = = = 0.000,000,000,000,01

Buffer - a substance, that within a certain range, maintains a constant pH by combining with H + when mixed with an acid, or releasing H + when mixed with a base - Buffers do not necessarily maintain a pH of 7. H 2 O + CO 2  H 2 CO 3  HCO H +  

Organic Chemistry “Organic chemistry nowadays almost drives me mad. To me it appears like a primeval tropical forest full of the most remarkable things, a dreadful endless jungle into which one does not dare enter for there seems to be no way out.” Fredrich Wohler 1835

Organic Chemistry - the study of carbon containing compounds Organic molecule - a molecule synthesized by living organisms (no longer useful) - a molecule containing 2 or more carbon atoms (What about methane, CH 4 ?) - a molecule containing at least the elements carbon and hydrogen

Functional Groups - parts of organic molecules Hydroxyl group -OH Methyl group -CH 3 Carboxyl (acidic) group-COOH Amino group-NH 2 Phosphate group-PO 3

Families of Organic Molecules Carbohydrates Lipids Proteins Nucleic Acids

Carbohydrates Contain only C, H and O Lots of hydroxyl groups Three groups we’ll look at Monosaccharides – simple sugars Disaccharides – made from 2 simple sugars Polysaccharides – polymers of simple sugars

Polymer - a large molecule composed of repeating subunits, monomers e.g. polysaccharides, proteins, DNA, plastics, etc.

Monosaccharides – simple sugars Contain only C, H, and O Ratio of these three elements is: 1C : 2H : 1O Lots of hydroxyl groups, -O-H Dissolve easily in water. Why? e.g. glucose or fructose, C 6 H 12 O 6 ribose, C 5 H 10 O 5

Disaccharides Composed of 2 simple sugars bonded together C:H:O ratio not quite 1:2:1 e.g. sucrose, C 12 H 22 O 11, made from joining glucose and fructose, both C 6 H 12 O 6 Easily digested to simple sugars

Polysaccharides Contain only C, H and O Ratio not 1C:2H:1O, but still contains lots of O Size limits solubility in water e.g. starch and cellulose are both polysaccharides made from only glucose starch – easily digested cellulose – undigestible by most organisms

Lipids Usually contain only C, H and O Ratio of C:H:O nowhere near 1:2:1 lots of C and H, relatively little O 4 types we’ll look at: Fatty AcidsGlycerides PhospholipidsSteroids

Fatty Acids Consist of a carboxyl group and a hydrocarbon chain Fig. 2.22

Saturated Fatty Acids at least 2 H atoms bonded to each of the C in the hydrocarbon chain Common in animal fats; solid at room temperature Fig. 2.22

Unsaturated Fatty Acids One or more C atoms in the hydrocarbon chain have less than 2 H atoms bonded to them. Common in vegetable oils; liquid at room temp. Fig. 2.22

Glycerides Glycerol and 1, 2 or 3 fatty acids (mono-, di-, or triglycerides) How are they synthesized? How do you digest them?

Phospholipids A diglyceride + phosphate group + R group Lipid end is hydrophobic Phosphate and R group end is hydrophilic Form the basic structure of all cell membranes

Steroids Non-fatty acid lipids Contain only lots of C, H and little O Behaves like other lipids e.g. cholesterol Absolutely necessary – e.g. cell membranes, sex hormones

Proteins Contain nitrogen, in amino groups Made from long chains of amino acids Very diverse group of molecules; very diverse functions Shape is extremely important

Amino Acids An amino group and a carboxyl group bonded to the same carbon atom Differ in the R group attached to the central carbon atom

Amino Acids All proteins made from different combinations of the same 20 amino acids Humans have 8 (children 9) essential amino acids – must be present in diet

Polypeptide A small polymer of amino acids; part of a protein molecule. Peptide bonds – a covalent bond between the carboxyl group of one amino acid and the amino group of the following amino acid. Synthesis? Digestion?

Denaturation A change in the shape of a molecule. Shape is very important in organic molecules, especially proteins. e.g. frying an egg; sickle-cell anemia

Nucleic Acids An organic molecule composed of long chains of nucleotides. e.g. DNA, RNA

Nucleotides An organic molecule composed of: 1 or more phosphate groups, a 5-carbon sugar, and a nitrogenous base

Adenosine Triphosphate - ATP A nucleotide involved in most of the reactions in which energy is transferred in living organisms Composed of Adenine (N-base), 5-C sugar and three phosphate groups