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The Chemistry of Life
Chapter 2
Units of Matter
• All matter is built from very small units
• Atoms and molecules – smallest particles
that retain chemical properties of their type
of matter
• Element –
– Matter made from only one type of atom
– 92 elements found in nature
– Periodic Table
Twelve Most Common Elements in
Living Organisms
Element
Symbol
Number of Protons
Hydrogen
H
1
Carbon
C
6
Nitrogen
N
7
Oxygen
O
8
Sodium
Na
11
Magnesium
Mg
12
Phosphorus
P
15
Sulfur
S
16
Chlorine
Cl
17
Potassium
K
19
Calcium
Ca
20
Iron
Fe
26
Units of Matter
• Molecules
– Made of two or more atoms
– Differ in size, shape, and behavior
– Largest molecules in plant cell are the DNA
– CH4 – composed of
• 1 carbon atom
• 4 hydrogen atoms
• Compound
– Matter made from molecules
Atoms
• Smallest unit of matter to enter into
chemical reactions
• Formed from three types of particles
– Protons
– Neutrons
– Electrons
Atomic Particles
Particle
Charge
Mass Units
Location
Proton
+
1
Nucleus
Neutron
No
electrical
charge
1
Nucleus
-
Negligible
(0.0005
units)
Orbitals
around
nucleus
Electron
Protons
• Found in nucleus of atom
• Carry positive charge
• 1 atomic mass unit
– Approximately = to mass of neutron
• Number of protons = number of electrons
in electrically neutral atom
Protons
• Electrostatically attracted to electrons
• Determine chemical characteristics of
atom and its identity
Neutrons
• Found in nucleus of atom
• No electrical charge
• 1 atomic mass unit
– Approximately equal to mass of proton
• Only slightly influences chemical
characteristics of atom
Atomic Number
Determined by the number of protons in the
nucleus of the atom
Atomic Weight
Equal to the number of
protons + the number
of neutrons in an
atom
Element
Number
of
protons
Number
of
neutrons
Atomic
mass
Cl
17
17
34
K
19
20
39
H
1
0
1
Isotopes
• Different atomic forms of the same
element
• Same atomic number but differ in number
of neutrons
• Radioactive decay
– Unstable atoms
– Decompose
– Rare among elements making up living
organisms
Isotopes of Carbon
12C
13C
14C
Atomic number
6
6
6
Atomic mass
12
13
14
Number of
protons
6
6
6
Number of
electrons
6
6
6
Number of
neutrons
6
7
8
Electrons
•
•
•
•
Negative charge
Almost no mass
Move around nucleus in orbitals
Number of electrons = number of protons
in electrically neutral atom
Electron Orbitals
• Represent energy levels
• Atom most stable with two electrons in
each orbital
• Inner shell
– Lowest energy level
• Outer shell
– Highest energy level
Chemical Bonding
Types of bonds
• Ionic
• Covalent
Ionic Bonds
• Atoms give up or take on electrons in
order to achieve complete outer shell
• Ions – electrically charged
– Anion (- charge)  Cl– Cation (+ charge)  Na+
Ionic Bonds
• Oxidation-reduction (redox) reaction
– Oxidation  loss of an electron (LEO)
– Reduction  gain of an electron (GER)
• Salt
– Formed by anion ionically bonding to cation
– Cl- + Na+  NaCl
Covalent Bonds
• Nuclei share bonding atoms
• Strongest type of chemical bond
– Strong attraction to nucleus
– Mutual repulsion minimized
Covalent Bonds
• Single bond
– Atoms share two electrons
– Represented by single line (-) in structural
formula
H
H–C-H
H
Methane
Covalent Bonds
• Double bond
– Share four electrons
– Represented by double line (=) in structural
formula
H–C=C-H
H
H
Ethylene
Covalent Bonds
• Triple bond
– Share six electrons
– Represented by triple line () in structural
formula
– Rare in molecules found in cells
Ways to Represent Covalent Bonds
•
•
•
•
Orbital diagram
Ball and stick model
Structural formula
Composition formula
Water
• Most abundant molecule in living
organisms
• Important characteristics
– Ability to dissolve many compounds
– Remains liquid over wide temperature range
– Forms weak hydrogen bonds with itself and
other molecules
Water
• Polar molecule
– local regions of positive, negative, or both
charges
– Electronegativity
• Expresses tendency of nucleus to attract electrons
• High electronegativity of O nucleus attracts
electrons
Slight negative
charge
Slight positive
charge
O
H H
Hydrogen Bonds
•
•
•
•
Form between polar molecules
Represented by dotted line O ….. H
About 1/16 as strong as covalent bond
Large numbers of H bonds among water
molecules makes water more stable (less
volatile)
Hydrogen Bonds
• Hydrogen bonds also form in other
molecules
– Occurs when H nucleus that is sharing
electrons with O or N comes close to another
O or N
– Many biological molecules may also form
hydrogen bonds with each other
• Carbohydrates
• Nucleic acids
Water Dissolves Polar and Ionic
Substances
• Excellent solvent for polar (hydrophilic)
molecules
• Property due to polarity of water molecule
and its ability to form hydrogen bonds
• Solvent + solute = solution
Water Dissolves Polar and Ionic
Substances
• Nonpolar molecules (hydrophobic)
insoluble in water
– Hydrocarbons insoluble in water
– Hydrophobic bond
Acids and Bases
• Acids
– Molecules that donate an H nucleus
– Often associated with sour taste
• Lemon juice (citric acid)
• Bases
– Molecules that accept an H nucleus
– Often bitter and feels slippery
• Sodium hydroxide
Acids and Bases
• pH scale
– Measure of hydronium
ion concentration
– Hydronium ion usually
abbreviated as H+
pH
pH below 7
acidic
pH above 7
Basic or alkaline
pH 7
Neutral
Organic Compounds
• Contain primarily carbon
• Bio-organic molecules
– Actually occur in cells
– Based on C skeleton
– Generally include oxygen and hydrogen
– Often contain nitrogen, phosphorus, and/or
sulfur
Functional Groups
• Smaller part of larger molecule
• Participates in chemical reactions
R – COOH
Carboxyl group
R – OPO3H2
Phosphoryl group
R – NH2
Amino group
Types of Biological Molecules
Class
Components
Polymer
Role
Carbohydrate
Simple sugars
Starch,
glycogen,
cellulose
Energy storage
structure
Protein
Amino acids
Polypeptide
chain
Catalysis, structure,
movement
Lipid
Fatty acids,
glycerol,
phosphate, or
sugar
Phospholipid,
glycolipid,
triglyceride
Membrane
structure, energy
storage
Bases adenine,
thymine, guanine,
cytosine, or uracil,
sugar, phosphate
DNA, RNA
Information
storage, protein
synthesis
Nucleic acid
Carbohydrate
• Simple sugars
– CnH2nOn (n = 3-7)
– Example: glucose C6H12O6
• Oligosaccharides
– Small chains of two or more simple sugars
• Polysaccharides
– Long chains of simple sugars
Examples of Polysaccharides
Example
Function
Forms strong cables in cell wall, keeps cell from bursting
Cellulose under pressure
Pectin
Acts as glue, holds cells together in tissues
Starch
Energy storage compound, polymer of glucose, made and
stored in green plants
Polymer of glucose, larger and more highly branched than
Glycogen starch, made and stored in some algae and in animals
Lipids
• Any oil-soluble
(nonpolar) substance
in cell
• Two classes of lipids
– phospholipids,
glycoproteins
Watersoluble
(polar,
hydrophilic)
functional
group
Phosphate
Phospholipids
group
Glycolipids
Sugars
Water
insoluble
(nonpolar,
hydrophobic)
components
Hydrocarbon
ends of fatty
acids
Hydrocarbon
ends of fatty
acids
Fatty Acids
• Hydrocarbon chain attached to a fatty acid
– unsaturated hydrocarbon chain
• One or more double bonds
– Saturated hydrocarbon chain
• All single bonds
Phospholipids and Glycolipids
• Provide structural basis for cell
membranes
• Form sheets two molecules thick
• Hydrophobic hydrocarbon part of molecule
positioned toward middle (away from
solvent water)
• Hydrophilic components exposed to
solvent water
Structure of Phospholipids and
Glycolipids
Sterols
•
•
•
•
Large, multi-ringed hydrocarbon
Keep cell membrane flexible
Prevent membrane from cracking
Cholesterol
– Primary sterol in animals
– No cholesterol in plants
• Ergosterol
– Primary sterol in plants
Triglycerides
• Energy storage compounds
• Three fatty acid molecules attached to
glycerol connector
• Insoluble in water
• Form lipid bodies in plant cells
Fats and Oils
• Triglycerides extracted from plant organs
Oils
Fats
Physical State
at Room
Temperature
Fatty Acids
Examples
Liquid
Shorter, with
more double
bonds
Salad oils
Solid
Longer with
fewer double
bonds
Palm “oil”,
coconut “oil”,
cocoa butter
Proteins
• Large molecules
• 100 – several hundred amino acids strung
together in long, unbranched chain
Proteins
• Amino acid – fundamental building block
of proteins
– Backbone containing an amino group, central
carbon, and carboxyl (carboxylic acid) group
– 20 different amino acids
– Amino acid and carboxylic acid group give
amino acid its name
– All amino acids have same backbone
• Differ in side chain attached to central carbon
Protein Synthesis
• Amino group of one amino acid attached
to carboxyl group of next amino acid
• Peptide bond
– Bonds linking amino acids
• Polypeptide chain
– Chain of amino acids
Levels of Protein Organization
• Primary structure
– Sequence of amino acids
– Genetically determined
• Secondary structure
– Folding of protein
– Hydrogen bonds between parts of backbone
Levels of Protein Organization
• Tertiary structure
– Ionic, hydrogen, and hydrophobic bonds
between side chains of different amino acids
• Quaternary structure
– Large structural complex
– Protein molecules may associate with each
other or other types of molecules
Functional Properties of Proteins
• Properties depend on 3-D shape of
molecule
– Give cell form
– Direct movement within cell
– Provide scaffold for chemical reactions
• High energy compound
– Enzymes – catalyze chemical reactions
– May be stored for energy (ex. Seeds)
Functional Properties of Proteins
• Denatured
– Heating protein solution to 50ºC or more
breaks bonds between side chains
– Changes shape of protein molecule
– Protein no longer functional
Nucleic Acids
• Two types
– DNA (deoxyribonucleic acid)
– RNA (ribonucleic acid)
• Nucleotide monomers
– 5-C sugar
– Phosphate group
– One or two ringed base
Comparison of DNA and RNA
DNA
RNA
Sugar
Deoxyribose sugar
Ribose sugar
Phosphate group
Phosphate group
Phosphate group
Bases
Adenine, thymine,
guanine, cytosine
Adenine, uracil, guanine,
cytosine
Structure
Double-strand (double
helix) of nucleotides
Single-strand of
nucleotides
Function
Stores genetic
information
Direct protein synthesis
Fundamental DNA Structure
S - CG - S
P
P
S - T= A - S
S = sugar
T = thymine
P = phosphate
C = cytosine
A= adenine
G = guanine
Structure of DNA
DNA
• May have several million nucleotides
• Genetic code
– Set of three bases specified one amino acid
• Gene
– Unit of inheritance
– DNA sequence transcribed as a single unit
and codes for a single polypeptide
DNA Replication
• Must be replicated to pass genetic
information on to next generation
– Synthesize new copies of DNA base
sequences
– Original DNA chains serve as templates for
formation of new DNA
– Replication occurs when cell produces copy
of DNA identical to original DNA double helix