THE MOLECULES OF CELLS

PAGES 18-44

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

AtomComposed 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

Elementa 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

Isotopean atom of an element that differs in the

number of neutrons in the nucleus

e.g. Carbon 12 (12C) and Carbon 14 (14C)both are carbon, must have 6 protons 12C has 6 protons and 6 neutrons 14C has 6 protons and 8 neutrons

Radioactive Isotopean unstable isotope; an atom that will decay

(change) into a different element as subatomic particles are lost from the nucleus

e.g. 14C 14N + 1e-

6p + 8n 7p + 7n

Ionan 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

Moleculea substance composed of two or more atoms;

the atoms may be identical or may be different elements.

e.g. water H2Oglucose C6H12O6

oxygen gas O2

Chemical Bondan attractive force between two atoms

Three different types:IonicCovalentHydrogen

Ionic Bondthe 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 Bondschemical 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 equallyPolar covalent bond – the pair(s) of electrons are not shared equally

Nonpolar covalent bondChlorine atoms share 1 pair of electrons

Fig. 2.6

FIG. 2.6

Polar covalent bondsO and H do not share electrons

equally

O and H have partial charges due to polar covalent bonds

Pg. 26

Hydrogen Bondan attractive force between two atoms with

opposite partial chargesThe 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. glucoseO-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

NADox + e- + H+ NADHre

lower energy higher 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. HCO3- + H+ H2CO3

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.

100 = 1 10-1 = 0.1 10-2 = 0.01 10-14 = 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.

H2O + CO2 H2CO3 HCO3- + 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

compoundsOrganic molecule- a molecule synthesized by living organisms (no longer useful)- a molecule containing 2 or more carbon atoms (What about methane, CH4?) - a molecule containing at least the elements carbon and hydrogen

Functional Groups- parts of organic molecules

Hydroxyl group -OHMethyl group -CH3

Carboxyl (acidic) group -COOHAmino group -NH2

Phosphate group -PO3

Families of Organic Molecules

CarbohydratesLipidsProteinsNucleic Acids

Carbohydrates

Contain only C, H and OLots of hydroxyl groupsThree groups we’ll look at

Monosaccharides – simple sugarsDisaccharides – made from 2 simple

sugarsPolysaccharides – 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 ORatio of these three elements is:

1C : 2H : 1OLots of hydroxyl groups, -O-HDissolve easily in water. Why?

e.g. glucose or fructose, C6H12O6

ribose, C5H10O5

DisaccharidesComposed of 2 simple sugars bonded

togetherC:H:O ratio not quite 1:2:1

e.g. sucrose, C12H22O11, made from joining glucose and fructose, both C6H12O6

Easily digested to simple sugars

PolysaccharidesContain only C, H and ORatio not 1C:2H:1O, but still contains lots

of OSize limits solubility in water

e.g. starch and cellulose are both polysaccharides made from only glucose

starch – easily digestedcellulose – undigestible by most

organisms

LipidsUsually contain only C, H and ORatio of C:H:O nowhere near 1:2:1lots of C and H, relatively little O

• 4 types we’ll look at:Fatty Acids GlyceridesPhospholipids Steroids

Fatty AcidsConsist 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

GlyceridesGlycerol 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 lipidsContain only lots of C, H and little O

Behaves like other lipidse.g. cholesterolAbsolutely necessary – e.g. cell membranes, sex hormones

ProteinsContain nitrogen, in amino groups

Made from long chains of amino acids

Very diverse group of molecules; very diverse functions

Shape is extremely important

Amino AcidsAn amino group and a carboxyl group bonded to the same carbon atom

Differ in the R group attached to the central carbon atom

Amino AcidsAll proteins made from different combinations of the same 20 amino acids

Humans have 8 (children 9) essential amino acids – must be present in diet

PolypeptideA 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?

DenaturationA 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 AcidsAn organic molecule composed of long chains of nucleotides.

e.g. DNA, RNA

NucleotidesAn 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