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- 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
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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