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The Molecules of Life
Chapter 2
Atoms and Elements
 Atoms
 Basic unit of all matter
 Made up of three
major components
 Protons
 Positively charged

Electrons
 Negatively charged

Neutrons
 Uncharged
Atoms and Elements
 Atom
 Protons and neutrons are found in the nucleus

Account for the “weight” of the atom
 Atomic mass

Electrons orbit the nucleus

Have relatively little mass
 Do not contribute to the mass of the atom
 Approximately 2,000 electrons = 1 proton

Protons and electrons are equal in a
uncharged atom
Atoms and Elements
 Elements

Substance that consists of a single type of
atom

92 naturally occurring elements
 99% of all living matter by weight made up of four
 Carbon
 Hydrogen
 Oxygen
 Nitrogen
 Phosphorus and sulfur make up additional 0.5%
Atoms and Elements
 Each element is identified by two numbers

Atomic number

Number of protons occupying the nucleus
 In an uncharged element this also equals the number
of electrons

Atomic mass

Number of protons plus the number of neutrons
Atoms and Elements
 Electrons of each element are arranged in
orbitals

Each orbital differs in energy

Each orbital can contain a certain number of
electrons
 The first orbital (closest to the nucleus) can hold a
maximum of 2 electrons
 The next two orbital can have a maximum capacity of 8
electrons each


Each orbital must be filled before electrons occupy
the next
Orbitals farthest from the nucleus have the highest
energy
Chemical Bonds and the
Formation of Molecules
 Atoms are most stable when the outer orbital
contains the maximum number of electrons

2, 8, 8 etc.
 To fill outer orbitals atoms form bonds with
other atoms to fill outer orbitals

Bonds are formed with the sharing or the gain
or loss of electrons

Molecules are formed when atoms bond together
Chemical Bonds and the
Formation of Molecules
 There are several types of chemical bonds

They also vary in strength
 Chemical bonds include



Covalent bonds
Ionic bonds
Hydrogen bonds
Covalent Bonds
 Achieve stability through the
sharing of electrons between
atoms


Creates a strong bond
Difficult to break
 Requires significant energy
usually in the form of heat
 Never break spontaneously at
physiological temperatures
 Enzyme required to break at
lower temperature

Bonds can be polar or non-polar
Covalent Bonds
 Non-polar and Polar
 Covalent bonds may have
an equal or unequal
attraction for the shared
electrons
 Non-polar covalent
 Bonds formed between
identical atoms or
between atoms that
have similar attraction
 H-H or C-H
Covalent Bonds
 Non-polar and Polar
 Polar covalent
 One atom has a greater
attraction to the electrons
than the other
 Produces a slight charge
within the molecule
 One part of the
molecule with be
slightly negatively
charged and one
molecule with by
slightly positively
charged
 O-H
Ionic Bonds
 Formed by gaining or losing
electrons
 Electrons completely leave first
atoms and become part of
outer orbital of second atom

Loss and gain of electrons
leads to charged atoms
(ions)
 Atom that loses electrons
becomes positively charged
 Atom that gains electron
becomes negatively charged
 Charged atoms are attracted to
each other and form a bond
between ions
 Ionic bond
Ionic Bonds
 Ionic bonds are weaker than covalent bonds

Bonds dissociate in water


Easily broken at room temperature
Approximately 100 time weaker than covalent
bonds
 Important among weak forces holding
biological molecules together
Hydrogen Bonds
 Weak bonds formed from the attraction of positively charged
hydrogen atoms
 Hydrogen atoms in polar molecules are attracted to
negatively charged atoms or molecules


Most commonly oxygen or nitrogen
Hydrogen bonds occur between molecules such as water
and DNA

Covalent bonds are formed within the molecules
 Hydrogen bonds hold molecules together
 Covalent bonds hold atoms together
Hydrogen Bonds
 Weakest of the biological bonds



Constantly being formed and broken at room
temperature
At room temperature the average lifetime of a
single hydrogen bond is a fraction of a second
Large numbers of hydrogen bonds can hold
molecules together firmly

Like numerous stitches in clothing
 One stitch won’t hold a shirt together but numerous
stitches will
Chemical Compounds of the Cell
 Most important molecule is water


Makes up over 70% of all living organisms by
weight
Importance of water depends on it unusual
bonding properties
Bonding Properties of Water
 Bonding properties of
water


Hydrogen bonds form
between positively
charged hydrogen of
one molecule and
negatively charged
oxygen of another
Hydrogen bonding
produces a polar
molecule
Bonding Properties of Water
 Polar nature accounts for ability to
dissolve numerous compounds
 Water is known as universal
solvent
 Molecules that dissolve in water
must contain charged atoms
 NaCl readily dissolves in water
forming Na+ ions and Cl- ions
 Ions become surrounded by
water

Na+ and Cl- ions no longer
able to bond to each other
pH
 Acidity is measured as pH

Defined as concentration of H+ ions

potential Hydrogen
 Measured on logarithmic scale of 0 to 14
0 highly acid
 14 highly alkaline (basic)
 Acidity based on ionization of water to H+
and OH- ions
 When H+ and OH- ions are equal
solution is neutral



High H+ = acid
High OH- = base
Small Molecules in the Cell
 All cells contain small organic and inorganic
molecules

Approximately 1% of dry weight of bacteria composed
of inorganic ions
+
+
2+
2+
2+
3- and SO 2 Na , K , Mg , Ca , Fe , Cl , PO4
4
 Certain enzymes require positively charged ions for proper
functioning
 Negatively charged phosphate ions are essential in energy
metabolism

Small organic molecules act as precursor metabolites
 These are converted to the building blocks of
macromolecules
Macromolecules and Their Component
Parts
 Macromolecules are very large

Macro = large
 Biological macromolecules are divided into
four classes



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Proteins
Polysaccharides (carbohydrates)
Lipids
Nucleic acids
Macromolecules and Their Component
Parts
 All macromolecules are
polymers
 Poly = many
 Large molecules formed
by joining smaller
subunits together

Joining subunits
together involves
dehydration reaction
 H2O is removed
during chemical
reaction
 Reaction termed
dehydration
synthesis
Macromolecules and Their Component
Parts
 Macromolecules are
broken down into
smaller subunits

Instead of removing
H2O, a molecule of
H2O is added
 Reaction termed
hydrolytic reaction or
hydrolysis
Proteins and Their Functions
 Constitute over 50% of cell dry weight
 Made up of amino acid subunits
 Most versatile

Some responsibilities include

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
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Catalyzing reactions
Composition and shape of certain bacterial
structures
Gene regulation
Nutrient procurement
Amino Acid Subunits
 Proteins are composed of numerous
combinations of 20 amino acids
 Protein function depends on the shape of the
protein

Protein shape depends on the sequence of
amino acids
Amino Acid Subunits
 All amino acids have
the following shared
features

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

A carboxyl group
(COO-)
An amino group (NH2+)
A central carbon
A side chain
 The side chain
differentiates the
amino acids
• Amino acids are subdivided
based on similarities of the
side chain
Peptide Bonds and
Their Synthesis
 The amino acids that form
proteins are held together by
peptide bonds
 Unique type of covalent
bond

Formed between the
interaction of the
carboxyl group of one
amino acid and the
amino group of the
following amino acid
 Reaction causes the
release of water and
the formation of a
peptide bond
Protein Structure
 Proteins have four
structures

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Primary
Secondary
Tertiary
Quaternary
Protein Structure
 Primary structure
 Sequence of amino acids
 In large part determines other protein features
Protein Structure
 Secondary structure
 Primary structure folds
into new configuration
 Helical structure
 Alpha (α) helix

Pleated structure
 Beta (β) sheet

New configuration
results from weak
bonds formed between
amino acids
Protein Structure
 Tertiary structure
 3 dimensional
structure
 2 major shapes
 Globular
 Fibrous
 Becomes functional
protein
Protein Denaturation
 Proteins must have specific
shape to have proper
function
 Environmental conditions
can break bonds within
the protein

Causes shape change
 Shape change causes
protein to stop
functioning
 Called
denaturation
 Denaturation can be
reversible or irreversible
 Environment determines
reversibility
Carbohydrates
 Carbohydrates are diverse group of
molecules with various sizes
 Play important roles in all organisms including



Common source of food and energy
Form part of nucleic acids
Form part of bacterial cell wall
Carbohydrates
 Carbohydrates contain carbon, hydrogen and oxygen
in 1:2:1 ratio

Each carbon atom is bound to two hydrogen atoms
and one oxygen atom
 CH2O
 Polysaccharide
 large molecules made of carbohydrate molecules
 Oligosaccharide
 short chains of carbohydrates
 Monosaccharide
 Single carbohydrate molecule
Carbohydrates
 Monosaccharide


Classified by number of carbons in molecule
Most common monosaccharides

5 and 6 carbon sugars
 5 carbon sugars = pentose
 Ribose and deoxyribose
 6 carbon sugars = hexose
 Glucose, fructose and galactose
Carbohydrates
 Disaccharides


Produced by joining two monosaccharides
through dehydration synthesis
Lactose and sucrose most common in nature



Glucose + galactose = lactose
Glucose + fructose = sucrose
Maltose less common

Glucose + glucose = maltose
Carbohydrates
 Polysaccharides
 Serve different function
 Cellulose most abundant organic molecule on earth
 Polymer of glucose molecules
 Principle constituent in plant cell wall
 Glycogen is carbohydrate storage molecule of animals
and some bacteria
 Polymer of glucose subunits
 Dextran storage molecule for carbon and energy for
some bacteria
 Polymer of glucose subunits
Nucleic Acids
 Two types of nucleic acid

DNA


RNA


Carrie genetic code in all cells
Decodes sequence of amino acids to produce
proteins
Sub units of nucleic acids are nucleotides
DNA
 Master molecule
Determines specific
properties of the cell
 Nucleotides are composed of
three units
 Nitrogen containing ring
compound


Nitrogenous base
 Purine
 Adenine and
guanine
 Pyrimidine
 Thymine and
cytosine

Five carbon sugar molecule


Deoxyribose
Phosphate molecule
DNA
 Nucleotides are joined through
covalent bonding
 Bond created between
phosphate of one
nucleotide and sugar of the
adjacent through
dehydration synthesis

Phosphate molecule acts
as a bridge between the
number 3 (3’) carbon of
one sugar and the
number 5 (5’) carbon of
the adjacent
 Results in a sugar
phosphate backbone
DNA
 DNA in living organisms is a double stranded
helical molecule

Strands are held together by hydrogen
bonding between the nitrogen bases

Specific pairing between bases
 Adenine binds to thymine
 A-T or T-A
 Guanine binds to cytosine
 G-C or C-G

Bases are complementary
RNA
 Involved in decoding DNA
 Structure is similar to DNA

Differs in a number of ways

Thymine is replaced by uracil
 There is no thymine base in RNA

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The sugar is ribose in place deoxyribose
RNA is generally shorter
Exists as a single stranded molecule not double
stranded
Lipids
 Critical component of the cell membrane
 Membranes act a gatekeepers to the cell
 Often determines what enters or leaves the cell
 Heterogeneous group of molecules
 Made up of different subunits
 Defining feature
 Insoluble in water
 Smallest of the four macromolecules
 Can be divided into two general classes
 Simple lipids
 Compound lipids
Simple Lipids
 Contain only carbon, hydrogen
and oxygen
 Most common are called fats
 Solid at room temperature
 Made of glycerol and fatty
acids


Fatty acids are long
hydrocarbon chains plus
an acid group (COOH) at
the end
Glycerol is carbon
hydrogen chain with
three hydroxyl (OH)
groups attached
 Allows for the binding of
three fatty acids to one
glycerol
 Triglyceride
• Fatty acids bond to glycerol
covalently through dehydration
synthesis
Simple Lipids
 Steroids are also considered
simple lipids
 Differ from fats in structure
and function
 Structure consists of fourmembered ring
 Classified as lipid because
steroids are insoluble in
water
 If one of the rings has a
hydroxyl (OH) group
attached it is classified as a
sterol
 Example: cholesterol
Compound Lipids
 Contain fatty acids, glycerol and
other elements
 Phospholipid most important
compound lipid

Phospholipid is made up of a
phosphate and two fatty acids
attached to a glycerol molecule
 Phosphate head is polar and
soluble in water
 Hydrophilic

Fatty acids are non polar and
insoluble in water
 Hydrophobic
Compound Lipids
 Phospholipids

Major component in lipid
cell membrane

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

Membrane is a double or
bilayer of phospholipids
Hydrophilic heads orient
towards internal and
external environments
Hydrophobic tails orient
themselves away from
aqueous environment
towards each other
Membrane acts as a barrier
to the entry and exit of
cellular substances