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The Molecules of Life
Chapter 2
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• Review of chemical bonds (covalent, ionic,
hydrogen bonds)
• Small molecules important for life
– Water (properties, pH, buffer)
– Other small molecules
• Macromolecules
–
–
–
–
Protein
Lipid
Polysaccharide
Nucleic acid
Atoms and Elements
• Atoms
– Basic unit of all matter
– three major
components
• Protons
• Electrons
• Neutrons
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
orbital
• Each orbital contain a certain number of electrons
• Each orbital must be filled before electrons occupy
the next
• Orbitals farthest from the nucleus have the highest
energy
• most stable when the outer orbital contains the
maximum number of electrons
– 2, 8, 8 etc.
Chemical Bonds and the
Formation of Molecules
• To fill outer orbitals atoms form bonds with other
atoms
– Bonds :sharing or the gain or loss of electrons
– Molecules are formed when atoms bond together
• Valence: the number of electrons that an atom must gain or
lose to fill its outer orbital.
• types of chemical bonds (vary in strength)
– Covalent bonds
– Ionic bonds
– Hydrogen bonds
Covalent Bonds
• Formed by sharing of
electrons between atoms
– Strong (difficult to break)
• Requires significant energy
– Enzyme
– can be polar or non-polar
Covalent Bonds
– Non-polar covalent
• Equal attraction
– H-H or C-H
– Organic compound
» C-C bond
Covalent Bonds
– Polar covalent
• Unequal attraction
– Produces a slight charge
within the molecule
» O-H
Ionic Bonds
• gaining or losing
electrons
– Loss and gain of electrons
leads to charged atoms
(ions)
• Cation
• Anion
• 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
• Important among weak forces holding
biological molecules together
Hydrogen Bonds
• Weak bonds formed between polar molecules
– Most commonly between hydrogen and oxygen or nitrogen
– Hydrogen bonds occur between molecules such as
water and DNA
• Covalent bonds are formed within the molecules
– Covalent bonds hold atoms together
– Hydrogen bonds hold molecules together
Hydrogen Bonds
• Weakest of the biological bonds
– Constantly being formed and broken at room
temperature
– Large numbers of hydrogen bonds can hold
molecules together firmly
• Important for molecule-molecule such as enzymesubstrate interaction.
questions
• What is atomic number?
• Cation is formed by:
– Lose electron
– Share electron
– Gain electron
• Which is the strongest chemical bond?
– Ionic bond
– Hydrogen bond
– Covalent bond
Small molecules of the Cell--water
• 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 water
molecules
Bonding Properties of Water
• Water is a great solvent.
– Polar nature accounts for
ability
– Molecules dissolved must
contain charged atoms
– Ions become surrounded
by water
• Na+ and Cl- ions no longer
able to bond to each other
Important Property of solution--pH
• Acidity is measured as pH
– Defined as concentration of H+ ions
• potential Hydrogen
• Measured on logarithmic scale of 0
to 14
– Neutral is pH 7 (H+ and OH- ions are
equal solution)
– acid
– base
• [H+] x [OH-]=10-14
• Buffer system: help to maintain
neutral pH.
Other Small Molecules in the Cell
• small organic and inorganic molecules
– ~ 1% of dry weight of bacteria composed of inorganic
ions
• Na+, K+, Mg2+, Ca2+, Fe2+, Cl-, PO43- and SO42– 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
– Proteins
– Polysaccharides (carbohydrates)
– Lipids
– Nucleic acids
Macromolecules and Their
Component Parts
• All macromolecules
are polymers
– Poly = many
– formed by joining
smaller subunits
together
• dehydration reaction
Macromolecules and Their
Component Parts
• Macromolecules are
broken down into
smaller subunits
• hydrolysis
questions
• What is pH?
• What is the function of buffer?
• Macromolecules are formed by___
reaction of the subunits.
hydrolysis
dehydration
Proteins and Their Functions
• 50% of cell dry weight
• Made up of amino acid subunits
• Most versatile
– Some responsibilities include
• Catalyzing reactions
• Composition and shape of certain bacterial
structures
• Gene regulation
• Nutrient procurement
Amino Acid Subunits
• 20 different types of
amino acids
• common features for
amino acids
– The side chain
differentiates the amino
acids
• Hydrophilic
• Hydrophobic (contain
methyl group)
– Stereoisomers
• L, D amino acid
Peptide Bonds and
Their Synthesis
• peptide bonds
– Formed between
carboxyl group of one
amino acid and the
amino group of the
following amino acid
– Release water
molecule
Protein Structure
• Protein function depends
on the shape of the
protein
– Protein shape depends on
the sequence of amino
acids
• Proteins have four
structures
–
–
–
–
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
– Results from weak
bonds formed between
amino acids
• Certain sequences of
the aa leads to distinct
secondary structures
Protein Structure
• Tertiary structure
– 3 dimensional structure
– 2 major shapes
• Globular
• Fibrous
– Becomes functional protein
– Tertiary structure depends
on primary structure and
interaction with water.
• Hydrophobic interaction
• S-S bond (covalent)
Protein Denaturation
• Specific shape for proper
function
– breaking bonds within the
protein disrupt structure
• protein stop functioning
• Denaturation can be
reversible or irreversible
– Environment determines
reversibility
• Heat
• chemical
Substituted Proteins
• Proteins that has other kind of molecules
covalently bond to side chain of amino
acid.
– Glycoprotein: sugar attached
– Lipoprotein: lipid bond.
questions
• How many kinds of amino acid are there in
a protein?
• What is the primary structure of a protein?
• What determine the shape of a protein?
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
– CH2O
• Monosaccharide
– Classified by number of carbons in molecule
– Most common monosaccharides
• 5 and 6 carbon sugars
Carbohydrates
• Disaccharides
– two monosaccharides joined 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
• Carry genetic code in all cells
– RNA
• Decodes sequence of DNA to produce proteins
– Subunits of nucleic acids are nucleotides
DNA
• DNA are composed of 4
kinds of nucleotides.
– Five carbon sugar
• Deoxyribose
– Phosphate molecule
– Nitrogenous base
• 4 kinds of base: A, T, G, C
• DNA sequence are
represented by base
sequence
DNA
• Nucleotides joined
through covalent
bonding to form a
DNA strand
– phosphate of one
nucleotide join the
sugar of the adjacent
nucleotide
• Results in a sugar
phosphate backbone
• Direction 5’ to 3’
DNA
• double stranded helical
molecule
– hydrogen bonding
between bases from
each strand
• Specific pairing between
bases A-T, G-C
• Bases are
complementary
RNA
• Involved in decoding DNA
• Structure is similar to DNA
– Uracil replace thymine
– ribose in place of deoxyribose
– RNA is generally shorter
– Single stranded.
questions
• What is the subunit of DNA?
• What is the difference between DNA and
RNA?
Lipids
• Critical component of the cell membrane
– Membranes act a gatekeepers to the cell
• Heterogeneous group of molecules
– Made up of different subunits
• Defining feature
– Insoluble in water
• Can be divided into two general classes
– Simple lipids
– Compound lipids
Simple Lipids
• Contain only carbon,
hydrogen and oxygen
• Most common are
called fats
– Made of glycerol and
fatty acid
• Triglyceride
• Fatty acids bond to glycerol
covalently through dehydration
synthesis
Simple Lipids
• Steroids are also
considered simple
lipids
• insoluble in water
• Sterol (with OH in one
ring)
– Example: cholesterol
Compound Lipids
• fatty acids, glycerol and
other elements
• Phospholipid most
important compound lipid
– a phosphate and two fatty
acids attached to a glycerol
molecule
• Amphiphilic molecule
Compound Lipids
• Phospholipids
– Major component in lipid
cell membrane
• bilayer of phospholipids
• orientation
• a barrier to the entry and
exit of cellular substances
questions
• What is the major component of cell
membrane?
• What is the defining feature of lipid?