Download Chemical Organization of Life

 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
LE 2-3
Nitrogen deficiency
Iodine deficiency
 Atoms
 same number of protons
 may differ in number of neutrons

Isotopes
 Most isotopes are stable
 some are radioactive, giving off particles and energy
 Application of radioactive isotopes in biological
research:
 Dating fossils
 Tracing atoms through metabolic processes
 Diagnosing medical disorders
LE 2-6
Cancerous
throat
tissue
Bonding
 covalent bond
 sharing of a pair of valence electrons by two atoms
 shared electrons count as part of each atom’s 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
 nonpolar covalent bond
 atoms share the electron equally
 polar covalent bond
 one atom is more electronegative
 atoms do not share the electron equally
LE 2-12
–
O
H
+
H
H2 O
+
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)
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)
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
LE 2-15
–
+
Water
(H2O)
+
Hydrogen bond
–
Ammonia
(NH3)
+
+
+
 Covalent = strongest bonds
 Form most molecules that make up cells
 Ionic & hydrogen = weak bonds
LE 2-UN44
 Chemical reactions
 Reactants
 products
2 H2
O2
Reactants
2 H2O
Reaction
Products
 Ex. Photosynthesis
 sunlight powers the conversion of CO2 and H20 to
glucose (C6H12O6) and O2
 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
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
•
Four of water’s properties that facilitate an
environment for life:
Cohesive behavior
Ability to moderate temperature
Expansion upon freezing
Versatility as a solvent
 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
LE 3-2
Hydrogen
bonds
LE 3-3
Water-conducting cells
100 µm
 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
 “The solvent of life”
 Solution

liquid that is a homogeneous mixture of substances
 Solvent
 dissolving agent of a solution
 Solute
 substance that is dissolved
 Water is a versatile solvent due to:
 its polarity
 Readily forms hydrogen bonds
 aqueous solution
 water is solvent
 hydrophilic
 affinity for water
 hydrophobic
 does not have an affinity for water
 Most biochemical reactions occur in water
 Rate generally depends on concentration of reactants
 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-)
 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
LE 3-8
pH Scale
0
Increasingly Acidic
[H+] > [OH–]
1
Neutral
[H+] = [OH–]
Battery acid
2 Digestive (stomach)
juice, lemon juice
3 Vinegar, beer, wine,
cola
4 Tomato juice
5 Black coffee
Rainwater
6 Urine
7 Pure water
Human blood
8
Seawater
Increasingly Basic
[H+] < [OH–]
9
10
Milk of magnesia
11
Household ammonia
12
13
Household bleach
Oven cleaner
14
 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
LE 3-9
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
More
acidic
Acid
rain
Normal
rain
More
basic
Decomposition Reactions
 In chemical notation:
 AB
A+B
 Releases covalent bond energy
 Hydrolysis—Decomposition reaction with H•OH
 E.g., food digestion
Synthesis Reactions
 In chemical notation:
 A+B
AB
 Absorbs energy
 Formation of new bonds
 Dehydration synthesis
 Removal of H•OH between molecules
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)
 Monosaccharides
 major fuel for cells
 raw material for building molecules
 In aqueous solutions they form rings
 Form disaccharides through dehydration synthesis
LE 5-4
Linear and
ring forms
Abbreviated ring
structure
LE 5-5
Dehydration
reaction in the
synthesis of maltose
1–4
glycosidic
linkage
Glucose
Glucose
Dehydration
reaction in the
synthesis of sucrose
Maltose
1–2
glycosidic
linkage
Glucose
Fructose
Sucrose
Organic Compounds
Formation and Breakdown of Complex Sugars
Figure 2-11 (a), (b)
 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
LE 5-7
a Glucose
a and b glucose ring structures
Starch: 1–4 linkage of a glucose monomers.
Cellulose: 1–4 linkage of b glucose monomers.
b Glucose
• 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
LE 5-8
Cellulose microfibrils
in a plant cell wall
Cell walls
Microfibril
0.5 µm
Plant cells
Cellulose
molecules
b Glucose
monomer
 Chitin
 structural polysaccharide
 found in the exoskeleton of arthropods
 structural support for the cell walls of many fungi
 used as surgical thread
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
 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
LE 5-11a
Fatty acid
(palmitic acid)
Glycerol
Dehydration reaction in the synthesis of a fat
 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
LE 5-11b
Ester linkage
Fat molecule (triacylglycerol)
LE 5-12a
Stearic acid
Saturated fat and fatty acid.
LE 5-12b
Oleic acid
cis double bond
causes bending
Unsaturated fat and fatty acid.
 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
LE 5-13
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
Structural formula
Space-filling model
Phospholipid symbol
LE 5-14
Hydrophilic
head
Hydrophobic
tails
WATER
WATER
 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
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
 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
LE 5-16
Substrate
(sucrose)
Glucose
Enzyme
(sucrose)
Fructose
 Structural Proteins
 Support
 Ex. Silk

Fibers in cocoons and webs
 Ex. Collagen & elastin

Connective tissues in animals
 Ex. Keratin

Hair, horns, feathers
 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
 Transport Proteins
 Transport other substances


Ex. Hemoglobin
 Contains iron
 In vertebrate blood
 Transports oxygen
Other transport proteins transport molecules across cell
membranes
 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
 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
 Defense Proteins
 Protection against disease

Ex. Antibodies
 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
LE 5-UN78
a carbon
Amino
group
Carboxyl
group
 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
 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
LE 5-20
b pleated sheet
+H N
3
Amino end
Amino acid
subunits
a helix
LE 5-20a
Amino end
Amino acid
subunits
 Primary Structure
 Determined by
inherited genetic
information
Carboxyl end
 Secondary Structure
 result from hydrogen bonds between repeating constituents
of the polypeptide backbone


alpha helix
beta pleated sheet
LE 5-20b
b pleated sheet
Amino acid
subunits
a helix
 Tertiary structure
 Determined by interactions between R groups
LE 5-20d
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Hydrogen
bond
Disulfide bridge
Ionic bond
 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
LE 5-20e
Polypeptide
chain
b Chains
Iron
Heme
Polypeptide chain
Collagen
a Chains
Hemoglobin
 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
Red blood Normal cells are
cell shape full of individual
hemoglobin
molecules, each
carrying oxygen.
10 µm
Red blood
cell shape
Fibers of abnormal
hemoglobin deform
cell into sickle
shape.
LE 5-21b
Sickle-cell hemoglobin
Normal hemoglobin
Primary
structure
affe
Val
His
1
2
Leu
Thr
3
4
Pro
Glu
5
6
Secondary
and tertiary
structures
Function
7
b subunit
Primary
structure
Secondary
and tertiary
structures
Molecules do
not associate
with one
another; each
carries oxygen.
His
1
2
Leu
Thr
3
4
Function
Val
Glu
5
6
7
b subunit
Sickle-cell
hemoglobin
b
a
Pro
Exposed
hydrophobic
region
a
Quaternary
structure
b
Val
b
a
Quaternary Normal
hemoglobin
structure
(top view)
Glu
Molecules
interact with
one another to
crystallize into
a fiber; capacity
to carry oxygen
is greatly reduced.
b
a
 Protein conformation
 Protein shape




Primary structure
pH
salt concentration
Temperature
 loss of a protein’s native conformation is =
denaturation
 A denatured protein is biologically inactive
LE 5-22
Denaturation
Normal protein
Denatured protein
Renaturation
 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
 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
LE 5-26b
Nitrogenous bases
Pyrimidines
Cytosine
C
Thymine (in DNA) Uracil (in RNA)
U
T
Purines
Adenine
A
Guanine
G
Pentose sugars
Deoxyribose (in DNA)
Nucleoside components
Ribose (in RNA)
 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
 RNA
 Important in protein synthesis
 3 types



Ribosomal RNA (rRNA)
Messenger RNA (mRNA)
Transfer RNA (tRNA)
 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
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