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Title: Basics of Life Chemistry


1
CHAPTER 2
  • Basics of Life Chemistry

2
INTRODUCTION
  • All living things are composed of and use
    chemicals
  • Chemicals used for
  • communication,
  • defense,
  • aggression,
  • reproduction etc.

3
Introduction
  • Human composed of the chemicals
  • O, C, H, N, C, etc
  • All chemicals known as matter

4
MATTER
  • Any substance that has mass and occupies space

5
Features of matter
  • Energy all matter has energy
  • Kinetic energy
  • Potential energy

6
Features of matter
  • First law of thermodynamics
  • Energy is never created or destroyed but can be
    converted from one form to the other.

7
States of Matter
  • Solid
  • Molecules tightly packed strongly attracted to
    each other
  • Kinetic energy lt liquids
  • Fixed shape and volume under
  • Liquid
  • Molecules slightly further apart but strongly
    attracted
  • Fixed volume under ordinary Ability to flow

8
States of Matter
  • Gas
  • Molecules highly energetic
  • Their collisions move them further apart
  • Gas expands to fill container

9
Composition of Matter
  • Element
  • Pure substances
  • Atom (e.g. H, O)
  • Smallest particle of an element

10
Structure of an atom
  • Bohr Model
  • Nucleus
  • Protons (ve charge)
  • Neutrons (no charge)
  • Electrons (-ve charge)
  • Orbits/energy levels
  • insignificant weight
  • form chemical bonds

11
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12
compound -
  • atoms combined in a fixed ratio
  • E.g water H2O

13
molecule -
  • smallest part of a compound
  • water - H2O
  • sucrose C12H22O11

14
Periodic Table of the Elements -
  • arrangement of elements by properties
  • chemical symbol for each element
  • atomic number -gt of protons
  • of protons of electrons
  • atomic weight protons neutrons
  • atomic weight - atomic number neutrons

15
Isotope -
  • element containing a different number of neutrons

16
model of an atom Bohr Model
  • electrons travel in energy levels
  • level 1 lowest amount of energy
  • filled by 2 electrons
  • level 2 electrons with more energy
  • levels 2 filled by 8 electrons
  • Octet rule

17
why do chemical bonds form?
  • atoms with unfilled energy levels are unstable
  • energy levels are filled by electrons thru
  • sharing covalent bond
  • donating ionic bond

18
covalent bonds
  • electron sharing
  • two atoms share a pair of electrons
  • H H
  • one pair -gt single bond

19
Covalent bonds (cont)-
  • form proteins, carbohydrate, lipids (fats) and
    nucleic acids

20
hydrogen -
  • atomic number is 1
  • has 1 proton 1 electron
  • energy level 1 needs 2 electrons
  • forms 1 covalent bond
  • only H2 exists naturally
  • H-H -gt structural formula
  • H2 -gt empirical

21
helium
  • atomic number is 2
  • 2 electrons
  • energy level 1 filled
  • noble gas

22
carbon
  • atomic number is 6
  • 6 electrons
  • energy level 1 filled
  • energy level 2 has 4 Forms
  • 4 covalent single bonds
  • 2 covalent double bonds
  • 1 covalent double bond, 2 covalent single bonds

23
oxygen
  • atomic number 8
  • 8 electrons
  • energy level 1 filled
  • energy level 2 has 6
  • forms 2 covalent single bonds
  • 1 covalent double bond

24
nitrogen
  • atomic number 7
  • 7 electrons -
  • energy level 1 filled
  • energy level 2 has 5
  • forms 3 covalent single bonds
  • 1 double, 2 singles

25
ionic bonds -
  • one atom donates an electron to another atom
  • results in forming ions - atoms with an
    electrical charge
  • cation -gt atom that has lost an electron ()
    charge
  • anion -gt atom that has gained an electron (-)
    charge

26
sodium chloride -
  • chlorine - 7 electrons in the outer orbit
  • sodium - 1 electron in the outer orbit
  • Na Cl- -gt sodium chloride NaCl

27
Calcium chloride -
  • Calcium - 2 electrons in the outer orbit
  • Chloride - 7 electrons in the outer orbit
  • Cl- Ca2 Cl- -gt CaCl2

28
hydrogen bonds (not really)
  • Linkage that nearly always pairs hydrogen with
    either nitrogen or oxygen
  • Connect molecules
  • Represented as !
  • weak force / strong in number

29
strength of bonds
  • covalent gt ionic gt hydrogen

30
chemical reactions -
  • change in energy
  • energy is stored in the chemical bonds
  • breaking a bond releases energy
  • creating a bond requires energy
  • rearrangement of molecular structure

31
HCl NaOH -gt NaCl H20
  • chemical equation
  • reactants are listed on the left
  • products are listed on the right
  • -gt indicates a chemical reaction has occurred
  • equation must be balanced

32
IONIC COMPOUNDS
  • ACIDS
  • Releases hydrogen ions (H) in solution
  • Strong acids HCL, H2SO4
  • Weak acids Carbonic acid

33
IONIC COMPOUNDS
  • BASES
  • Release hydroxide ion (OH-) negatively charged
  • Alkaline substances
  • Feels slippery on skin
  • Sodium Hydroxide Na(OH-) strong base
  • Sodium bicarbonate Weak base

34
pH Scale -
  • Measurement of acidity /alkalinity
  • measures H ion conc.
  • pH Scale - ranges from 0 to 14
  • pH 7 neutral

35
pH Scale -
  • high H low pH / acid
  • lt 7
  • low H high pH / base
  • gt7

36
IONIC COMPUNDS
  • SALTS
  • Ionic compounds that do not release H or OH ions
  • Neither acids or bases
  • Result from reaction of an acid and a base
  • Chemical reaction is called neutralization

37
Summary
  • Atom
  • Element
  • Molecule
  • Compound
  • Atomic mass unit
  • Atomic number
  • Chemical symbol
  • Atomic nucleus
  • Atomic weight
  • Acids
  • Bases
  • Salt
  • pH
  • Proton
  • Electron
  • Neutron
  • Ion
  • Cation
  • Anion
  • Kinetic energy
  • Chemical reaction
  • Ionic Bond
  • Covalent Bond
  • Hydrogen Bond

38
Organic Chemistry, The Chemistry of Life
  • - Chapter 3

39
Inorganic molecules -
  • do not contain carbon
  • ex water, salt, sodium hydroxide

40
Organic molecules-
  • organic organ (living)
  • must contain carbon

41
4 classes of organic molecules
  • proteins
  • lipids (fats)
  • carbohydrates
  • nucleic acids

42
Carbon / central atom
  • can form 4 covalent bonds
  • bonds spaced evenly
  • -- C --

43
Carbon skeleton / backbone
  • linear or a ring (fig 3.3)
  • attached are functional groups
    ________________

44
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45
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46
Functional groups -
  • clusters of atoms attached to the carbon skeleton
  • determines the chemical property of the molecules
  • Figure 3.8

47
Functional groups -
  • Amine group -
  • -NH2
  • found in amino acids and proteins
  • Phosphate group
  • PO4
  • found in phospholipids

48
Formation of organic molecules-
  • monomer single unit
  • amino acid
  • glucose

49
Formation of organic molecules-
  • polymer / macromolecules
  • monomers joined together
  • Sucrose
  • glucose fructose
  • Starch
  • glu-glu-glu-gluglu

50
Dehydration / Synthesis -
  • the linking together of monomers
  • molecule of water removed
  • covalent bond links the monomers together
  • energy requiring

51
Hydrolysis-
  • unlinking of monomers
  • water molecule added at the junction
  • energy releasing

52
Carbohydrates - sugars and starches -
  • function -
  • provides energy - glucose, glycogen
  • support cellulose

53
Consist of C, H, O
  • consist of carbon, hydrogen, and oxygen
  • empirical formula -gt CxH2xOx
  • equal of carbon and oxygen double hydrogen

54
Name ends in ose
  • name ends in ose
  • triose, 3 carbons
  • pentose, 5 carbons -gt fructose
  • hexose, 6 carbons -gt glucose, galactose

55
Monosaccharides
  • Form complex CHO
  • glucose (dextrose)
  • fructose
  • galactose-

56
Disaccharides - two sugar monomers
  • lactose (milk sugar) -gt
  • glucose galactose
  • sucrose (table sugar) -gt
  • glucose fructose
  • Maltose (malt sugar)
  • Glucose glucose

57
Polysaccharides - complex carbohydrates -
  • many monomers arranged in branches or chains
  • combined by dehydration / synthesis

58
Starch -
  • branched polymer of glucose
  • energy storage in plants
  • Amylopectin amylose

59
Glycogen -
  • tree shaped polymer of glucose
  • energy storage in animals
  • quickly hydrolyzed to glucose
  • found in muscle and liver cells
  • provides rapid bursts of energy

60
Cellulose -
  • Polysaccharide
  • Cell walls of plant cellulose
  • Cannot be digested by humans no calories
  • Digested by ruminants

61
Carbohydrates
  • may be a component of another organic molecule -
  • DNA (deoxyribonucleic acid) -gt deoxyribose sugar
  • RNA (ribonucleic acid) -gt ribose sugar
  • ATP (adenosine triphospate) -gt ribose sugar

62
Lipids (fats)
  • 3 sub-groups
  • true fats
  • phospholipids
  • steroids

63
Consist of C, H, small amounts of O -
  • large, non-polar molecules
  • can not dissolve in water
  • oil water dont mix!
  • formed by dehydration / synthesis

64
Fat vs- oil -
  • fat -gt lipid solid at room temperature
  • oil -gt lipid liquid at room temperature

65
True (neutral) fats function -
  • insulation -
  • prevents loss of body heat
  • cushion internal organs
  • energy storage -
  • fat -gt 9 calories per gram
  • sugar -gt 4 calories per gram

66
Structure of true fats -
  • 1, 2, or 3 fatty acids attached to glycerol

67
Fatty acid-
  • long carbon chain
  • carboxyl (-COOH) group attached to the end

68
FATTY ACID Fig. 3.21
69
Glycerol
  • 3 carbon skeleton
  • 3 alcohol groups attached
  • See page 56

70
Triglycerides-
  • three fatty acids one glycerol
  • most abundant true fat in the body

71
Triglyceride Fig. 3.22
72
Saturated Fatty Acid
  • no double bonds / contains the maximum of
    hydrogen atoms
  • from animal products
  • Solid at room temp
  • examples butter, lard

73
Unsaturated Fatty Acid
  • contains double bonds / limits the of hydrogen
    atoms
  • from plants
  • usually liquid at room temperature

74
polyunsaturated
  • more than one double bond
  • Ex olive oil, soybean oil

75
Omega -3 fatty acids
  • double bond found after the 3rd carbon
  • many are essential
  • hormones
  • cell growth
  • ex fish oil, soybeans

76
Hydrogenation -
  • add hydrogen to an unsaturated fat
  • solidifies the fat
  • ex margarine

77
Phospholipids -
  • structure - two fatty acids, one glycerol, one
    phosphate group
  • function - component of cell membranes

78
Steroids -
  • lipids without fatty acids
  • interlocking rings
  • cholesterol -
  • component of cell membranes
  • converted into bile salts (emulsify fat)
  • vitamin D
  • hormones -
  • estrogen
  • testosterone

79
Proteins -
  • function
  • structural -
  • cell membranes
  • muscle cells
  • tendons
  • Hemoglobin

80
Protein function (cont) -
  • regulation -
  • enzymes (organic catalysts)
  • hormones- insulin, oxytocin
  • antibodies - fight infection

81
Protein function (cont) -
  • carriers -
  • lipoproteins - transport non polar molecule
  • cholesterol
  • triglycerides
  • Phospholipids

82
Consist of
  • made of monomers of amino acids (20 exist)
  • amino group on one end
  • carboxyl group on the other end
  • R-group - functional group that determines
    properties

83
Formed by dehydration / synthesis -
  • peptide bonds between amino acids
  • polypeptide - chain of linked amino acids

84
Four levels of protein organization -
  • primary - polypeptide chain
  • secondary - polypeptide chain twists-
  • alpha helix (coil) - formed by hydrogen bonds
  • beta pleated sheet - formed by hydrogen bonds

85
Protein organization (cont) -
  • tertiary - 3 dimensional
  • side chains (R-groups) bond together
  • quaternary - interactions of individual
    polypeptides

86
Changes in protein structure -
  • sickle-cell anemia-
  • hemoglobin consist of 4 polypeptides
  • two alpha, two beta
  • change in one amino acid causes the protein
    molecules to unwind sickle under increased
    oxygen demand

87
Denaturation-
  • breaking of hydrogen bonds due to heat, light, or
    pH
  • change in structure
  • not reversible
  • you can not unfry an egg!

88
Nucleic acids-
  • function - component of DNA RNA
  • DNA - genetic code
  • RNA - manufacturer of protein

89
Structure of nucleic acids -
  • made up of nucleotides

90
Nucleotides -
  • 5- carbon simple suger
  • deoxyribose (DNA)
  • ribose (RNA0
  • phosphate group
  • nitrogenous base
  • Adenine
  • Guanine
  • Thymine
  • Cytosine
  • Uracil

91
NUCLEIC ACIDS
  • DNA
  • Genetic material
  • Nucleotides building blocks
  • 5-C sugar, deoxyribose
  • Phosphate
  • Nitrogenous Base
  • Adenine,Guanine,Thymine, Cytosine

92
NUCLEIC ACIDS
  • DNA
  • Double helix structure
  • Sugar-phosphate backbone
  • Bases complimentary paring
  • A-T, C-G
  • Coding strand
  • Protein synthesis

93
NUCLEIC ACIDS
  • RNA
  • Protein synthesis
  • Ribose sugar
  • Uracil base and no Thymine
  • Pairing A-U, G-C
  • 3 forms of RNA
  • Messenger RNA mRNA
  • Transfer RNA tRNA
  • Ribosomal RNA rRNA

94
SUMMARY
  • Chemistry of living things
  • Based on Carbon
  • C atoms all organic molecules
  • Structure of OM related to function
  • Common OM
  • CHO, Pns, Lipids, Nucleic acids
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