Chemical Organization of Life

1
Chemical Organization of Life
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• About 25 of the 92 elements are essential to life
• Carbon, hydrogen, oxygen, and nitrogen make up
  96 of living matter
• Most of the remaining 4 consists of calcium,
  phosphorus, potassium, and sulfur
• Trace elements are those required by an organism
  in minute quantities

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LE 2-3
Nitrogen deficiency
Iodine deficiency
4

• Atoms
• same number of protons
• may differ in number of neutrons
• Isotopes
• Most isotopes are stable
• some are radioactive, giving off particles and
  energy

5

• Application of radioactive isotopes in biological
  research
• Dating fossils
• Tracing atoms through metabolic processes
• Diagnosing medical disorders

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LE 2-6
Cancerous throat tissue
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Bonding

• covalent bond
• sharing of a pair of valence electrons by two
  atoms
• shared electrons count as part of each atoms
  valence shell
• molecule
• single covalent bond (single bond)
• sharing of one pair of valence electrons
• double covalent bond (double bond)
• sharing of two pairs of valence electrons

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• nonpolar covalent bond
• atoms share the electron equally
• polar covalent bond
• one atom is more electronegative
• atoms do not share the electron equally

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LE 2-12
?
O
H
H
?
?
H2O
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Bonding

• Ionic Bonds
• transfer of an electron from atom to another
• Create charged particles
• Cation ()
• Anion (-)
• ionic bond is an attraction between an anion and
  a cation
• forms ionic compounds, or salts
• Ex. sodium chloride (table salt)

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LE 2-13
Na
Cl
Na
Cl
Sodium atom (an uncharged atom)
Chlorine atom (an uncharged atom)
Sodium ion (a cation)
Chlorine ion (an anion)
Sodium chloride (NaCl)
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Bonding

• hydrogen bond
• forms when a hydrogen atom covalently bonded to
  one electronegative atom is also attracted to
  another electronegative atom
• the electronegative partners are usually oxygen
  or nitrogen atoms

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LE 2-15
?
?
Water (H2O)
?
Hydrogen bond
?
Ammonia (NH3)
?
?
?
14

• Covalent strongest bonds
• Form most molecules that make up cells
• Ionic hydrogen weak bonds

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LE 2-UN44

• Chemical reactions
• Reactants
• products

2 H2O
O2
2 H2
Reactants
Reaction
Products
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• Ex. Photosynthesis
• sunlight powers the conversion of CO2 and H20 to
  glucose (C6H12O6) and O2

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• Some chemical reactions go to completion
• All reactants are converted to products
• Most chemical reactions are reversible
• Products of the forward reaction become
  reactants for the reverse reaction
• Chemical equilibrium is reached when the forward
  and reverse reaction rates are equal

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Water
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Water

• All living organisms require water more than any
  other substance
• Most cells are surrounded by water, and cells
  themselves are about 70-95 water

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• Four of waters properties that facilitate an
  environment for life
• Cohesive behavior
• Ability to moderate temperature
• Expansion upon freezing
• Versatility as a solvent

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• hydrogen bonds hold water molecules together
• Cohesion
• Creates surface tension
• helps the transport of water against gravity in
  plants
• Adhesion of water to plant cell walls also helps
  to counter gravity

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LE 3-2
Hydrogen bonds
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LE 3-3
Water-conducting cells
100 µm
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• Moderation of Temperature
• absorbs heat from warmer air
• releases stored heat to cooler air
• can absorb or release a large amount of heat with
  only a slight change in its own temperature

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• The solvent of life
• Solution
• liquid that is a homogeneous mixture of
  substances
• Solvent
• dissolving agent of a solution
• Solute
• substance that is dissolved

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• Water is a versatile solvent due to
• its polarity
• Readily forms hydrogen bonds
• aqueous solution
• water is solvent

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• hydrophilic
• affinity for water
• hydrophobic
• does not have an affinity for water

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• Most biochemical reactions occur in water
• Rate generally depends on concentration of
  reactants

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• A hydrogen atom in a hydrogen bond between two
  water molecules can shift from one to the other
• The hydrogen atom leaves its electron behind and
  is transferred as a proton, or hydrogen ion (H)
• The molecule with the extra proton is now a
  hydronium ion (H3O)
• The molecule that lost the proton is now a
  hydroxide ion (OH-)

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• Acid
• substance that increases the H concentration of
  a solution
• pH less than 7
• Base
• substance that reduces the H concentration of a
  solution
• pH greater than 7
• Most biological fluids have pH values in the
  range of 6 to 8
• Cell pH is close to 7

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LE 3-8
pH Scale
0
1
Battery acid
2
Digestive (stomach) juice, lemon juice
Vinegar, beer, wine, cola
3
Increasingly Acidic H gt OH
4
Tomato juice
Black coffee
5
Rainwater
Urine
6
Neutral H OH
Pure water
7
Human blood
8
Seawater
9
10
Increasingly Basic H lt OH
Milk of magnesia
11
Household ammonia
12
Household bleach
13
Oven cleaner
14
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• Acid Precipitation
• rain, snow, or fog
• pH lower than 5.6
• caused by the mixing of different pollutants with
  water in the air
• can damage life in lakes and streams
• Changes soil chemistry
• contributing to the decline of some forests

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LE 3-9
0
More acidic
1
2
Acid rain
3
4
5
Normal rain
6
7
8
9
10
11
12
13
More basic
14
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• Decomposition Reactions
• In chemical notation
• AB A B
• Releases covalent bond energy
• HydrolysisDecomposition reaction with HOH
• E.g., food digestion
• Synthesis Reactions
• In chemical notation
• A B AB
• Absorbs energy
• Formation of new bonds
• Dehydration synthesis
• Removal of HOH between molecules

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Organic Compounds

• Carbohydrates
• sugars and the polymers of sugars
• monosaccharides, or single sugars
• molecular formulas that are usually multiples of
  CH2O
• Ex. Glucose
• Classified based on number of carbons
• 5 pentose
• 6 hexose
• macromolecules polysaccharides
• Disaccharides chain of 2
• Ex . Sucrose (table sugar)

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• Monosaccharides
• major fuel for cells
• raw material for building molecules
• In aqueous solutions they form rings
• Form disaccharides through dehydration synthesis

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LE 5-4
Linear and ring forms
Abbreviated ring structure
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LE 5-5
Dehydration reaction in the synthesis of maltose
14 glycosidic linkage
Glucose
Glucose
Maltose
Dehydration reaction in the synthesis of sucrose
12 glycosidic linkage
Glucose
Fructose
Sucrose
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Organic Compounds

• Formation and Breakdown of Complex Sugars

Figure 2-11 (a), (b)
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• Polysaccharides
• Ex. Starch
• storage polysaccharide of plants
• made of glucose monomers
• surplus starch stored as granules within
  chloroplasts and other plastids
• Ex. Glycogen
• storage polysaccharide in animals
• Stored in liver and muscle cells
• Ex. Cellulose
• major component of the tough wall of plant cells
• polymer of glucose

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LE 5-7
a Glucose
b Glucose
a and b glucose ring structures
Starch 14 linkage of a glucose monomers.
Cellulose 14 linkage of b glucose monomers.
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• Polymers with alpha glucose are helical
• Polymers with beta glucose are straight
• H atoms on one strand can bond with OH groups on
  other strands
• Ex. Cellulose
• Grouped into microfibrils strong building
  materials for plants

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LE 5-8
Cellulose microfibrils in a plant cell wall
Cell walls
Microfibril
0.5 µm
Plant cells
Cellulose molecules
b Glucose monomer
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• Chitin
• structural polysaccharide
• found in the exoskeleton of arthropods
• structural support for the cell walls of many
  fungi
• used as surgical thread

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Lipids

• do not form polymers
• have little or no affinity for water
• Are hydrophobic
• consist mostly of hydrocarbons, which form
  nonpolar covalent bonds
• Include fats, phospholipids, and steroids

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• Fats
• Made up of glycerol and fatty acids
• Glycerol three-carbon alcohol with a hydroxyl
  group attached to each carbon
• fatty acid carboxyl group attached to a long
  carbon skeleton
• separate from water
• water molecules form hydrogen bonds with each
  other and exclude the fats
• three fatty acids joined to glycerol by an ester
  linkage triglyceride

Animation Fats
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LE 5-11a
Fatty acid (palmitic acid)
Glycerol
Dehydration reaction in the synthesis of a fat
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• Fatty acids
• vary in length
• vary in number and locations of double bonds
• Saturated fatty acids
• Have maximum number of hydrogen atoms possible
• no double bonds
• Make up saturated fats
• Animal fats
• Solid at room temperature
• Can contribute to cardiovascular disease (plaque
  deposits)
• Unsaturated fatty acids
• have one or more double bonds
• Make up unsaturated fats
• Plant and fish fats
• Liquid at room temperatures
• Called oils
• fats energy storage

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LE 5-11b
Ester linkage
Fat molecule (triacylglycerol)
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LE 5-12a
Stearic acid
Saturated fat and fatty acid.
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LE 5-12b
Oleic acid
cis double bond causes bending
Unsaturated fat and fatty acid.
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• Phospholipids
• two fatty acids and a phosphate group are
  attached to glycerol
• fatty acid tails are hydrophobic
• phosphate group and its attachments form a
  hydrophilic head
• When added to water, they self-assemble into a
  bilayer, with the hydrophobic tails pointing
  toward the interior
• Make up bilayer of cell membranes

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LE 5-13
Choline
Hydrophilic head
Phosphate
Glycerol
Hydrophobic tails
Fatty acids
Hydrophilic head
Hydrophobic tails
Structural formula
Space-filling model
Phospholipid symbol
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LE 5-14
WATER
Hydrophilic head
Hydrophobic tails
WATER
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• Steroids
• carbon skeleton consisting of four fused rings
• Ex. Cholesterol
• component in animal cell membranes
• High levels in the blood may contribute to
  cardiovascular disease

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Proteins

• Proteins account for more than 50 of the dry
  mass of most cells
• Protein functions include
• structural support
• Storage
• Transport
• cellular communications
• Movement
• Defense against foreign substances

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• Enzymatic Proteins
• acts as a catalyst
• Speeds up chemical reactions
• can perform their functions repeatedly
• Digestive enzymes catalyze the hydrolysis of
  polymers in food
• Suffix -ase

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LE 5-16
Substrate (sucrose)
Glucose
Enzyme (sucrose)
Fructose
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• Structural Proteins
• Support
• Ex. Silk
• Fibers in cocoons and webs
• Ex. Collagen elastin
• Connective tissues in animals
• Ex. Keratin
• Hair, horns, feathers

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• Storage Proteins
• Store amino acids
• Ex. Ovalbumin
• Egg whites
• Source of amino acids for developing chick embryo
• Ex. Casein
• Milk protein
• Source of amino acids for baby mammals
• Plants have storage protein in seeds

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• Transport Proteins
• Transport other substances
• Ex. Hemoglobin
• Contains iron
• In vertebrate blood
• Transports oxygen
• Other transport proteins transport molecules
  across cell membranes

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• Hormonal Proteins
• Coordination of organisms activities
• Ex. Insulin
• Secreted by pancreas
• Regulate concentration of glucose in blood of
  vertebrates
• Causes cells to increase absorption of glucose

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• Receptor Proteins
• Response of cell to chemical stimuli
• Built into cell membrane
• Contractile and Motor Proteins
• Movement
• Ex. Actin Myosin
• Movement in muscles
• Other proteins allow for movement of cilia and
  flagella

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• Defense Proteins
• Protection against disease
• Ex. Antibodies

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• Amino Acids
• organic molecules with carboxyl and amino groups
• Amino acids differ in their properties due to
  differing side chains, called R groups
• Cells use 20 amino acids to make thousands of
  proteins
• linked by peptide bonds

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LE 5-UN78
a carbon
Amino group
Carboxyl group
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• Polypeptides
• polymers of amino acids
• range in length from a few monomers to more than
  a thousand
• Each has a unique linear sequence of amino acids
• A protein consists of one or more polypeptides

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• 4 levels of protein structure
• primary structure
• Its unique sequence of amino acids
• Secondary structure,
• found in most proteins
• consists of coils and folds in the polypeptide
  chain
• Tertiary structure
• determined by interactions among various side
  chains (R groups)
• Quaternary structure
• results when a protein consists of multiple
  polypeptide chains

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LE 5-20
b pleated sheet
H3N Amino end
Amino acid subunits
? helix
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LE 5-20a
Amino end
Amino acid subunits

• Primary Structure
• Determined by inherited genetic information

Carboxyl end
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• Secondary Structure
• result from hydrogen bonds between repeating
  constituents of the polypeptide backbone
• alpha helix
• beta pleated sheet

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LE 5-20b
b pleated sheet
Amino acid subunits
? helix
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• Tertiary structure
• Determined by interactions between R groups

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LE 5-20d
Hydrophobic interactions and van der
Waals interactions
Polypeptide backbone
Hydrogen bond
Disulfide bridge
Ionic bond
76

• Quaternary structure
• results when two or more polypeptide chains form
  one macromolecule
• Ex. Collagen
• fibrous protein consisting of three polypeptides
  coiled like a rope
• Ex. Hemoglobin
• globular protein consisting of four polypeptides
  two alpha and two beta chains

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LE 5-20e
Polypeptide chain
b Chains
Iron
Heme
a Chains Hemoglobin
Polypeptide chain
Collagen
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• Changes in protein
• Can change conformation
• Ex. Sickle-cell disease
• an inherited blood disorder, results from a
  single amino acid substitution in the protein
  hemoglobin

10 µm
10 µm
Red blood cell shape
Normal cells are full of individual hemoglobin mol
ecules, each carrying oxygen.
Red blood cell shape
Fibers of abnormal hemoglobin deform cell into
sickle shape.
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affe
LE 5-21b
Normal hemoglobin
Sickle-cell hemoglobin
Primary structure
Primary structure
Val
His
Val
Leu
Thr
Pro
Glu
Glu
His
Leu
Thr
Pro
Val
Glu
1
2
3
4
5
6
7
1
2
3
4
5
6
7
Exposed hydrophobic region
Secondary and tertiary structures
Secondary and tertiary structures
b subunit
b subunit
a
?
a
?
Quaternary structure
Normal hemoglobin (top view)
Quaternary structure
Sickle-cell hemoglobin
a
?
?
a
Function
Molecules do not associate with one another
each carries oxygen.
Function
Molecules interact with one another
to crystallize into a fiber capacity to carry
oxygen is greatly reduced.
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• Protein conformation
• Protein shape
• Primary structure
• pH
• salt concentration
• Temperature
• loss of a proteins native conformation is
  denaturation
• A denatured protein is biologically inactive

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LE 5-22
Denaturation
Denatured protein
Normal protein
Renaturation
82

• Nucleic Acids
• Genetic information
• two types
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)
• polymers called polynucleotides
• monomers called nucleotides
• nitrogenous base,
• pentose sugar (either ribose or deoxyribose)
• phosphate group

83

• There are two families of nitrogenous bases
• Pyrimidines have a single six-membered ring
• Purines have a six-membered ring fused to a
  five-membered ring

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LE 5-26b
Nitrogenous bases
Pyrimidines
Uracil (in RNA) U
Cytosine C
Thymine (in DNA) T
Purines
Adenine A
Guanine G
Pentose sugars
Deoxyribose (in DNA)
Ribose (in RNA)
Nucleoside components
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• DNA
• provides directions for its own replication
• directs synthesis of messenger RNA (mRNA)
• through mRNA, controls protein synthesis
• Protein synthesis occurs in ribosomes
• The amino acid sequence of a polypeptide is
  programmed by a unit of inheritance called a gene
• Genes are made of DNA

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• RNA
• Important in protein synthesis
• 3 types
• Ribosomal RNA (rRNA)
• Messenger RNA (mRNA)
• Transfer RNA (tRNA)

87

• DNA
• has two polynucleotides spiraling around an
  imaginary axis, forming a double helix
• the two backbones run in opposite 5 to 3
  directions from each other, an arrangement
  referred to as antiparallel
• The nitrogenous bases in DNA form hydrogen bonds
  in a complementary fashion
• A always with T
• G always with C

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LE 5-27
5 end
3 end
Sugar-phosphate backbone
Base pair (joined by hydrogen bonding)
Old strands
Nucleotide about to be added to a new strand
5 end
New strands
5 end
3 end
5 end
3 end