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Chapter 2
The chemical Basis of Life
Introduction
Why study chemistry in an Anatomy and
Physiology class?
• body functions depend on cellular functions
• cellular functions result from chemical
changes
• biochemistry helps to explain physiological
processes, and develop new drugs and
methods for treating diseases
Introduction cont.
• Chemistry = the study of matter
• Biochemistry= the study of the chemistry of
life
• Matter = anything that occupies space and
has mass
– composed of elements
– (i.e. solids, liquids, gases)
Structure of Matter
Structure of Matter
• Elements – composed of chemically identical
atoms
– bulk elements – required by the body in large
amounts
– trace elements – required by the body in small
amounts
• Atoms – smallest particle of an element
– the least complex level of organization
Subatomic Particles
• Proton =
a positively charged particle in
the nucleus of an atom
– Mass=1
• Neutron = an electrically neutral particle in
the nucleus of an atom
– Mass=1
• Electron = an electrically negative particle
that revolves around the nucleus
– Mass = 0
Elements
•
•
•
•
Element = a basic chemical substance
composed of atoms
Elements are represented by a 1 or 2 letter
symbol
120 elements exist in nature
Approximately 26 are naturally occurring in
humans.
– most abundant=carbon (C), Hydrogen (H),
Oxygen (O) Nitrogen (N), Phosphorus (P) =
CHONP
– Referred to a bulk elements (Know Table 2.2
and 2.3 for the test)
Elements You need to Know
Know this table
Elements cont.
• Atoms are neutral in charge
- The number of protons is
equal to the number of
electrons.
• The Atomic Number (A#) of
an atom represents the
number of protons in its
nucleus.
• The Atomic Mass (AM) of an
atom is equal to the number of
protons plus the number of
neutrons in its nucleus
– Average weight of common
isotopes
Isotopes
• Isotopes = atoms of an element that have the
same A#'s but different AW's (i.e. same # of
protons, different # of neutrons)
– Any sample of an element is likely to contain
multiple isotopes
– The nuclei of some isotopes are stable
– The nuclei of other isotopes are unstable and
break apart to become more stable
• When the nucleus of an atom breaks apart, it releases
radioactive energy
• Radioactive isotopes have many biological uses (i.e.
Carbon Dating)
Molecules and Compounds
• Molecule – particle formed when two or more
atoms chemically combine
• Compound – particle formed when two or
more atoms of different elements chemically
combine
• Molecular formulas – depict the elements
present and the number of each atom present
in the molecule
– water (H2O), glucose (C6H12O6)
Bonding of Atoms
• The electrons of an atom are arranged in
orbits, shells, or energy levels around the
central nucleus
• A characteristic number of electrons fill each
shell
– 2 electrons fill the first shell (closest to nucleus)
– 8 electrons fill the second shell
– 8 electrons fill the third shell
Bonding of Atoms cont.
• The way in which atoms react with one
another (i.e. their chemical properties) is
based on the electrons in their outermost shell
= Valence Electrons
• The outermost shell of an atom is called its
valence shell
Electron Shells (valence)
Bonding of Atoms cont.
• Atoms form bonds with other atoms to fill their
outermost or valence electron shell (energy
level)
– "Rule of Octets" = except for the first energy
level (which contain 2 electrons), atoms react with
other atoms so they will have 8 electrons in their
valence shell
– All 8 slots filled=inert, non reactive
– Less that 8 slots filled= atom seeks a stable
energy level with a full shell
Example Problem #1
Fluorine has an Atomic Number of 9. Draw an
atom of fluorine. How and why will fluorine
react?
Example Problem #1
Fluorine has an Atomic Number of 9. Draw an
atom of fluorine. How and why will fluorine
react?
Since atoms are
stable with 8
electrons in their
valence
shell,
+
9p
fluorine will tend to
0
9n
bind with atoms
that have one
electron to donate
-
Example Problem #2
Argon has an Atomic Number of 18. Draw an
atom of argon. How and why will argon
react?
Example Problem #2
Argon has an Atomic Number of 18. Draw an
atom of argon. How and why will argon
react?
Since
Argon
has
a
full valence shell, it
- will not tend to
bond
to
other
+
18p
atoms and be
0
18n
relatively inert
-
-
-
-
-
-
Ions
• Ions = atoms that have lost or gained
electrons to fill their valence shell
– anion = a negatively charged ion (Cl-)
– cation = a positively charged ion (Na+)
– An attraction exists between oppositely charged
ions and an ionic bond results (i.e. Na+Cl-)
• Formed when electrons are transferred from
one atom to another
Ionic Bond
• An ionic bond results due to the attraction
that exists between oppositely charged ions
and (i.e. Na+Cl-)
– They are formed when electrons are transferred
from one atom to another
Ionic
Bond
Covalent Bond
• A covalent bond is formed by the equal
sharing of electrons between atoms
– very strong bond
– i.e. H2 and O2
• Atoms tend to make the same number of
covalent bonds
– Same number of slots on the valence shell
– Structural formula
– More than one elector can be bound
• Double, triple bonds
Covalent Bond
•
•
•
•
Hydrogen atoms form single bonds
Oxygen atoms form two bonds
Nitrogen atoms form three bonds
Carbon atoms form four bonds
H―H
O=O
N≡N
O=C=O
Covalent Bond
Structural Formula
Structural formulas show how atoms bond and
are arranged in various molecules
Polar Bond
• Polar Bond=A polar covalent bond is formed
by the unequal sharing of electrons between
atoms
– strong bond
– results in molecules that are polar
• one end of the molecule is slightly positive, one end of
the molecule is slightly negative
– i.e. water (H2O)
Hydrogen Bond
• Hydrogen Bonds= a weak attraction
between the positive end of one polar
molecule and the negative end of another
polar molecule
– formed between water molecules
– important for protein and nucleic acid structure
– Examples include interaction between water
molecules and DNA chains
– These bonds are easily broken and put back
together (very weak)
Types of Chemical Reactions
• Synthesis Reaction – more complex chemical
structure is formed
A + B  AB
• Decomposition Reaction – chemical bonds
are broken to forma simpler chemical
structure
AB  A + B
Types of Chemical Reactions cont.
• Exchange Reaction – chemical bonds are
broken and new bonds are formed
AB + CD  AD + CB
• Reversible Reaction – the products can
change back to the reactants
A + B ↔ AB
Acids, Bases, and Salts
• Electrolytes – substances that release ions in water
NaCl  Na+ + Cl-
• Acids – electrolytes that dissociate to release
hydrogen ions in water
HCl  H+ + Cl-
• Bases – substances that release ions that can
combine with hydrogen ions
NaOH  Na+ + OH-
• Salts – electrolytes formed by the reaction between
an acid and a base
HCl + NaOH  H2O + NaCl
Acid and Base Concentrations
• pH scale - indicates the
- concentration of hydrogen ions in
- solution
• Neutral – pH 7
- indicates equal concentrations of H+ and OH-
• Acidic – pH less than 7
- indicates a greater concentration of H+
• Basic or alkaline – pH greater than 7
- indicates a greater concentration of OH-
Chemical Constituents of
Cells
Inorganic Substances
• Inorganic Substances are small compounds
that do not contain both the atoms C and H
– Examples include oxygen, carbon dioxide (CO2)
water, salts, acids & bases
Water
• Water is a polar molecule that demonstrates
hydrogen bonding and therefore it possesses
very unique characteristics
– Water is an excellent solvent (universal?)
– Many solutes are dissolved in our body's water
(i.e. polar substances dissolve in polar water)
– Many ionic compounds (i.e. NaCl) dissociate or
break apart in water
Water cont.
• Water participates in many chemical
reactions (in our cells and fluids)
– Dehydration (synthesis) is when water is
removed from adjacent atoms (of molecules) to
form a bond between them
– Hydrolysis (degradation) is when water is used
to break bonds between molecules
• Water is an excellent temperature buffer
– absorbs and releases heat very slowly
• Water is the most abundant component in
cells (about 70%)
Water cont.
• Water provides an excellent cooling
mechanism
– It requires a lot of heat to change water from a
liquid to a gas (i.e. high heat of vaporization). If
water does change forms and evaporate, it leaves
a cool surface behind
• Water serves as a lubricant
– mucus
– internal organs
– joints
Inorganic Substances cont.
• Oxygen (O2)
– gas that is transported in the blood
– used to release energy from nutrient molecules
• Carbon Dioxide (CO2)
– a by-product of cellular respiration
• Inorganic salts
– Abundant in body fluids
– Source of necessary ions (Na+, Cl-, K+, Ca2+,
etc…)
– Play important roles in metabolism
Organic Substances
• Organic Substances= contains the atoms
carbon (and hydrogen)
• Small molecules (monomers or building
blocks) are covalently bonded together to
form large polymers or macromolecules
• Water is usually involved in the formation and
breakage of bonds between monomers
– Dehydration Synthesis = removal of water to
form a covalent bond between monomers
– Hydrolysis = using water to break bonds
between monomers
Organic Substances cont.
• The four major classes found in cells
include:
– carbohydrates
– lipids
– proteins
– nucleic acids
Carbohydrates
•
•
•
•
•
Provide Energy to cells
Supply materials to build cell structures
Water-soluble
Contain C, H, O
Carbohydrates (sugars)= contains C, H, and
O in a 1:2:1 ratio (usually)
– glucose = C6H12O6
Carbohydrates
• Monomers (building blocks) are
monosaccharides
– glucose, fructose
• Hexoses = simple 6-C sugars
– glucose
– fructose
– galactose
• Polymers are formed by dehydration
synthesis
Monosaccharide
Monosaccharide cont.
Carbohydrates cont.
Disaccharides: 2
monosaccharides
covalently bonded
together
– maltose = glucose +
glucose
– lactose = glucose +
galactose
– sucrose = glucose +
fructose
Carbohydrates cont.
• Polysaccharides:
many glucose
molecules covalently
bonded together
– starch = plant storage
carbohydrate
– glycogen = animal
storage carbohydrate;
stored in liver and
skeletal muscle
– cellulose=plant starch
Carbohydrates cont.
• Polymers are broken down by hydrolysis
resulting in monosaccharides
• Function = energy source / energy storage!
CELLULAR RESPIRATION OVERVIEW
glucose + oxygen
energy + H2O + CO2
(ATP)
Lipids
• Lipids= contain C, H, and O, but much less O
than in carbohydrates
• Soluble in organic solvents
• Insoluble in water
• Types of lipids
– Fats
– Phospholipids
– Steroids
Fats
• Monomers (building blocks) = triglycerides
(glycerol + 3 fatty acids)
• Function = energy store/ energy source
• Saturated fats=have only single bonds
between the carbons in their fatty acid chains
– are solid at room temperature
– are animal fats
– are nutritionally "BAD" fat
– include bacon grease, lard, butter
Fats
• Unsaturated fats= have one or more double
bond between the carbons in their fatty acid
chains
– are liquid at RT (oils)
– are plant fats
– are nutritionally "GOOD" fat
– include corn and olive oil
Fatty Acids
Triglycerides
Phospholipids
• Phospholipids=
triglyceride with the
substitution of a polar
phosphate group (PO4-)
for one fatty acid chain
• One glycerol, 2 fattyacids, 1 phosphate
• Function = major cell
membrane component
Steroids
• Steroids= four
interconnected
carbon rings
– Example is cholesterol
• Function = compose
cell membranes;
chemical
messengers
(hormones)
Proteins
• Monomers = amino acids
– Structure=amino group, carboxyl group, side chain (R
group)
– 20 different types of Amino Acids (R groups differ)
Proteins cont.
• Polymers are formed by dehydration
synthesis between the amino group of one
amino acid and the carboxyl group of a 2nd
amino acid
• Bond formed = a peptide bond
Peptide Bond
Proteins cont.
• Length of amino acid chains may vary
– peptide = 2-100 aa's
– polypeptide = 100-thousands aa's without a
function
– protein = 100-thousands of aa's with a specific
function
Functions of Proteins
•
Structure
–
•
Transport
–
•
hemoglobin
Movement
–
•
keratin in hair, nails
and skin
actin and myosin in
muscles
Chemical messengers
–
–
hormones
neurotransmitters
•
Defense
– antibodies
•
Catalysts
– enzymes=Biological
catalysts, that increase
the rate of chemical
reactions without being
consumed by the
reaction
Denaturation of Proteins
• Denaturation of Proteins= the loss of 3dimensional conformation (shape) of a
protein. This results in loss of function
• Reasons for denaturation
– extreme pH values
– extreme temperature values
– harsh chemicals (disrupt bonding)
– high salt concentrations
Protein Structure
• Primary (1o) = sequence of amino acids
• Secondary (2o) = twisting of amino acid
chain; due to hydrogen bonding;
• Tertiary (3o) = folding of the amino acid chain;
due to ionic bonds, disulfide bridges, and
hydrophobic interactions;
• Quaternary (4o) = interactions between
different amino acid chains (See the four
amino acids chains that compose hemoglobin
on page 518).
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
Nucleic Acids
• Monomers = nucleotides
• Nucleotide structure = 3 parts
– pentose sugar (5-C)
– phosphate group
– nitrogenous base
• purine (double ring)
• pyrimidine (single ring)
• Polymers are formed by bonding between the
sugar of one nucleotide and the phosphate
group of a second nucleotide =
sugar/phosphate backbone
Nucleic Acids
Deoxyribonucleic Acid = DNA
• Structure
– Sugar = deoxyribose
– Bases = adenine (A), thymine (T), cytosine (C),
guanine (G)
– double stranded (resembles ladder); strands
held together by H-bonds between bases on
opposite strands
• A complements T (2 hydrogen bonds)
• C complements G (3 hydrogen bonds)
Nucleotides
DNA cont.
• double helix (ladder is twisted)
• Function = genetic material (i.e. genes,
chromosomes)
• DNA contains all necessary information
needed to sustain and reproduce life!
DNA Structure: One Strand
DNA Structure: Two Strands
DNA Structure cont.
Ribonucleic Acid = RNA
• Structure
– Sugar = ribose
– Bases = A,G,C, and uracil (replaces thymine)
– single stranded.
• Function = transport DNA code during protein
synthesis
RNA vs. DNA