Chapter 2
The Chemistry of Life
Ch 2-1
O Objectives:
O Describe 3 subatomic particles
O Explain how isotopes are similar and how
O
O
O
O
they are different
List the functions of radioactive isotopes
Explain the relationship between atoms,
molecules, and compounds
Explain how compounds are different from
their component elements
Describe 2 main types of chemical bonds and
how they form
Atoms
O Atom -the smallest component of an
element that still has properties of the
element
O consists of a positively charged nucleus-
center of the atom containing the protons (+)
and neutrons (neutral)
O surrounded by a negatively charged cloud of
electrons
O "+" and "-" charges strongly attract
Subatomic particles
O Proton
O particle in the nucleus
with a positive charge of
+1
O Neutron
O non-charged (neutral)
nuclear particle with the
same mass as the proton
O Electron
O negatively charged
particle (-1) with a mass
1/1840 of that of a
proton
O Orbit the nucleus
O Determine the chemical
properties of the element
Protons, Neutrons, and
Electrons
O Altering the number of any one of the 3
subatomic particles yields different results
O Change the # of protons
O Changes the atom type entirely
O Recall atomic # determines the element
O Change the # of neutrons
O Forms an isotope
O Increases or decreases atomic mass
O Change the # of electons
O Forms an ion (either cation (+) or anion(-))
O Important for ionic bond formation
Elements
O Elements are pure substances made up of
just one type of atom
O Represented by one or two letter symbols
O C, N, H, O, P, S, Fe, Mg (see appendix E)
Isotopes
O Isotopes- atoms of the same element that
Mass
number
differ in the number of neutrons they
contain are known as isotopes
There are 3 isotopes of carbon present
on Earth: Carbon-12, Carbon-13, and
Carbon-14
Atomic Mass
O Atomic mass- typically appears as a decimal
on the Periodic Table because it is the
weighted average of the mass numbers for
each of the isotopes present in nature for a
particular element
O C has an atomic mass of 12.01
O What does the atomic mass of C tell you
about the prevalence of the different
isotopes?
Isotopes
O Some are radioactive
O Their unstable nuclei
break down at a constant
rate giving off radiation
O Uses of isotopes include:
O Analyzing the age of
rocks and fossils
O Treating cancer
O Eliminate bacteria from
food
O “Tracers” to follow
movement of
substances in the body
Radioactive Tracers
O Radioisotopes of hydrogen, carbon, phosphorus,
sulfur, and iodine have been used extensively to trace
the path of biochemical reactions
O In medicine, tracers are applied in a number of tests
in autoradiography and nuclear medicine
O including single photon emission computed tomography
(SPECT)
O positron emission tomography (PET)
O scintigraphy
O The urea breath test for Helicobacter pylori commonly
used a dose of 14C labeled urea to detect H. pylori
infection
O If the labeled urea was metabolized by H. pylori in the
stomach, the patient's breath would contain labeled
carbon dioxide
Electrons
O Atoms have no net charge
O equal numbers of electrons and protons
O The number of electrons determines the chemical
properties of an element
O Electron energy levels
O electrons exist around the nucleus in regions known
O
O
O
O
O
as energy levels
1st level – holds a max. of 2 electrons
2nd level – holds a max. of 8 electrons
3rd level- holds 18 electons
And so on…
The general formula is that the nth shell can in
principle hold up to 2n2 electrons…
http://en.wikipedia.org/wiki/Electron_shell#List_of_elements_with_electrons_per_shell
Electrons
O An atom’s ability to form bonds is
determined by the electrons in the
outermost energy level or “shell”
O We refer to this shell of electrons as valence
electrons
O Valence electrons are the basis for Lewis dot
structures
Electrons
O Valence electrons can be determined easily by
looking at the Periodic Table
O The group number tells us the number of valence eO Often written in Roman numerals above each family
(column)
All in group
I have 1
valence
electron
Compounds
O A chemical compound
is a substance formed
by the chemical
combination of two or
more elements in
definite proportions.
O NaCl (table salt)
O C6H12O6 (glucose)
O properties of a compound
are different from those of
its individual elements
Chemical Bonds
O The atoms in compounds are held together
by chemical bonds
O forces of attraction that hold atoms together
(chemical energy)
O formed or broken during chemical reactions
O energy is usually required to make bonds
O energy usually released when bonds are
broken
O Ex: ATP to ADP
Chemical Bonds
O Form because atoms with unfilled outer
electron shells are unstable
O can react with other atoms
O Reactive atoms form chemical bonds to
stabilize their outer shells
O The main types of chemical bonds are:
O ionic bonds – atoms transfer (give up or accept e-)
O Loss or gain of e- forms ions with opposite charge
O covalent bonds –atoms share electrons with other
atoms
Chemical Bonds
O Ionic bonds- form between ions of metals and
nonmetals, involve the transfer of electrons to
form a positive cation (metal) and negative anion
(nonmetal) which attract due to their opposite
charges and form a bond
Chemical Bonds
O Covalent bonds- form between 2 nonmetals,
involve the sharing of electrons, can result in
the formation of single, double, or even
triple bonds
O The structure that results when atoms are
joined together by covalent bonds is called a
molecule.
Van der Waals Forces
O Sharing of electrons is not
always equal creating
regions on molecules with
slight positive or negative
charges
O When molecules are close
together, a slight attraction
can develop between the
oppositely charged regions
of nearby molecules
Ch 2-2
O Objectives:
O Discuss the unique properties of water
O Explain why water molecules are polar
O Differentiate between solutions and
suspensions
O Describe how the pH scale works
O Explain what acidic solutions and basic
solutions are
O Describe the importance of buffers in living
things
Mixtures
O Mixture – combination of substances in
which the individual components retain
their own properties
O Solution – a type of mixture where ions
are evenly dissolved in a liquid
O Ex: salt water; salt is the solute and water
is the solvent
O Blood is a suspension because it contains
cells and other undissolved particles in
solution
Water
O Water is the strongest solvent known because it
is polar
O Can dissolve both ionic and covalent compounds
O Polarity results from an uneven sharing of
electrons between the oxygen and hydrogen
atoms.
Hydrogen Bonds
O Because of the partial
positive and negative
charges, polar molecules can
attract each other
O Hydrogen bonds form
between the oxygen of one
water molecule and the
hydrogen of another
Cohesion of Water Molecules
O Cohesion is an attraction between
molecules of the same substance.
O Hydrogen bonding causes cohesion in water
molecules
Adhesion
O Adhesion is an attraction between molecules of
different substances.
Heat Capacity
O Because of the many hydrogen bonds
between water molecules, it takes a great
amount of heat energy to change its
temperature
O Organisms living in large bodies of water are
protected from drastic temperature changes
Water has a Neutral pH
O A water molecule is neutral, but can
dissociate to form hydrogen and hydroxide
ions.
H2O   H+ + OH-
pH Scale
O Chemists devised a measurement system
called the pH scale to indicate the
concentration of H+ ions in solution.
O The pH scale ranges from 0 to 14.
pH Scale
O At a pH of 7, the
concentration of H+
(hydrogen) ions is
equal to the
concentration of OH(hydroxide) ions
O Acids: [H+]>[OH-]
O The more [H+], the
lower the pH value
O Bases: [H+]<[OH-]
O The more [OH-], the
higher the pH value
pH scale
O The pH scale is a logarithmic scale , so a difference
of 1 in pH is 10 times greater in acidity or basicity
O For example, pH 2 is 10^5, or 100,000 times, more
acidic than pH 7
Acids
O An acid is any compound that forms H+ ions
in solution.
H+
Cl-
H+
OH-
Bases
O A base is a compound that produces
hydroxide ions (OH- ions) in solution
O H
Na
Na+ OHH+
OH-
Indicators
O Change color with pH
O Color change is unique to indicator
O Indicators may have a specific pH range in which
they operate
Buffers
O The pH of the fluids within most cells in the
human body must generally be kept
between 6.5 and 7.5.
O Important for maintaining homeostasis
Buffers
O Buffers are weak acids or bases that can
react with strong acids or bases to prevent
sharp, sudden changes in pH
2-2
A molecule in which the charges are unevenly
distributed is called a
a.
b.
c.
d.
polar molecule.
cohesive molecule.
hydrogen molecule.
covalent molecule.
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2-2
A dissolved substance is called a
a.
b.
c.
d.
solvent.
solution.
solute.
suspension.
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2-2
A compound that produces hydroxide ions in
solution is called a(an)
a.
b.
c.
d.
base.
buffer.
acid.
salt.
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2-2
Hydrogen bonds between water molecules
result from
a.
b.
c.
d.
adhesion between water molecules.
magnetic attractions between water
molecules.
uneven electron distribution in each water
molecule.
ionic bonds in the water molecule.
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2-2
On a pH scale, a value of 2 means that the
solution has
b.
equal concentrations of H+ and OH- ions.
the same concentration of H+ ions as pure water.
c.
higher concentration of H+ than in pure water.
d.
lower concentration of H+ than in pure water.
a.
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2–3 Carbon Compounds
The Chemistry of Carbon
O Organic chemistry is the study of all
compounds that contain bonds between
carbon atoms
O Carbon atoms are found in all biological
molecules
Role of Carbon
O Carbon (C) can form an amazing number of
compounds
O Can form four covalent bonds
O Often bond with hydrogen, oxygen, phosphorus,
sulfur, and nitrogen (CHNOPS)
O Can form single, double or triple bonds with
other carbon
O produces a variety of structurally different
molecules including long chains and rings
Macromolecules
O Macromolecules- “giant molecules”
are formed by a process known as
polymerization.
O Built by joining monomers to form
polymers
O Four classes:
O Carbohydrates
O Lipids
O Proteins
O Nucelic Acids
Biological molecules
O Know the types of atoms
O Know the building blocks (monomers) or
key structural components
O Types of bonds that link monomers, if
applicable
O Know their role in living things
Carbohydrates
O Carbo: carbon
-hydrate: water, H2O
O Most have 1:2:1 ratio of C:H:O
O ex: glucose C6H12O6
O Major energy source for living things
O Structural molecules of plants
O Cellulose (plant fiber)
Different Sizes of
Carbohydrates
O Monosaccharides
O Disaccharides
O Polysaccharides
Carbohydrates
O Monosaccharides
O single sugar
O Ex: glucose, fructose
O Monomers (building blocks) for
larger carbohydrates
(polysaccharides)
O glycogen
O starch
O cellulose
Glucose
Carbohydrates
O Disaccharides
O Two sugars
O Ex – Sucrose (table sugar), lactose (milk)
O Formed by a condensation reaction- a bond is
formed by removing a water molecule
Carbohydrates
O Polysaccharides- many monosaccharides chained
together
O Animals store sugar as glycogen (energy storage in liver)
O Plants store sugar as starch (energy storage)
O Plant cell walls made of cellulose
O All 3 are glucose polymers
Lipids
O Insoluble in water
O Fats, oils, waxes and steroids
O Stored energy reserves
O Biological membranes and
waterproof coverings
O Saturated fats – solid at room
temp.
O No double bonds between
carbon atoms
O Unsaturated fats – liquid at
room temp.
O One or more double bonds
between carbon atoms
These are chains of C
and H
Lipids
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Nucleic Acids
O Nucleic acids store and
transmit hereditary, or
genetic, information.
O Two types
O ribonucleic acid (RNA) and
deoxyribonucleic acid (DNA)
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Nucleic Acids
O Nucleic acids are polymers
assembled from individual
monomers known as
nucleotides.
O 5 nucleotides make up nucleic
acids
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Nucleic Acids
Nucleotides consist of three parts:
O a 5-carbon sugar
O a phosphate group
O a nitrogenous base
O adenine
O guanine
O cytosine
O thymine
O uracil
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Nucleotides
O Not all nucleotides are building blocks for
nucleic acids (polynucleotides)
O ATP (adenosine triphosphate) plays an
important role in capturing and transferring
chemical energy
Proteins
O Contain N, C, H, and O
O Important in chemical reactions, structures,
transport of small molecules, and fighting disease
O Made of amino acids (monomers)
O 20 different amino acids in humans
O Amino acids joined by peptide bonds
O aka-polypeptides
(many amino
acids)
Peptide bond
Proteins
• The portion of each amino acid that is different is a side chain called an
R-group
• R-groups can be acidic, basic, polar, nonpolar, and/or contain
carbon rings
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Proteins
O Amino acids are linked via peptide bonds
O Bond forms between the amino group of one
amino acid and the carboxyl group of the
neighboring a.a.
Proteins
O Instructions for arranging
amino acids into proteins is
stored in DNA
O 4 levels of organization
O Primary- a.a. sequence
O Secondary- folding or
twisting of polypeptide
chain
O Tertiary- chain itself is
folded
O Quaternary- multiple folded
chains interact
O Protein shape maintained by
Van der Waals forces and
hydrogen bonds
2–4 Chemical Reactions and Enzymes
O Describe the outcome of breaking bonds in
chemical reactions.
O Explain how energy changes affect how
easily a chemical reaction will occur.
O
Contrast energy absorbing and energy releasing
reactions.
O Explain the function of activation energy in
chemical reactions.
O Explain the role of enzymes in chemical
reactions and their importance to living
things.
Chemical Reactions
O A reaction occurs when chemical bonds are
broken or formed
O One set of chemicals is changed into
another set of chemicals
2H2 +O2
2H2O
Energy Sources
O Organisms must have a source of energy to
use to carry out chemical reactions
O Source varies depending on organism
Energy-Releasing Reactions
O Reactions that release
energy often occur
spontaneously
O energy products can
be heat, light, and/or
sound
Energy-Absorbing Reactions
O If the reaction absorbs
energy, it needs an
input of energy to
occur (Ex: heat,
stirring)
O Heat necessary to
start reactions in cells
would kill cells
O Cells must lower
activation energy
Activation Energy
O Activation energy is the energy needed to start
reaction
O Often required in both types of reactions
O Difference between peak energy in reaction and
energy of reactants
Cellular Reactions
Reaction pathway
without enzyme
Activation energy
without enzyme
Reactants
Reaction pathway
with enzyme
Activation
energy
with enzyme
Products
Enzymes are proteins that lower the activation energy
• act as biological catalysts by speeding up the rate of chemical reactions
Enzymes
O Name is usually dervied from the reaction
it catalyzes
O Dehydrogenase- removes the hydrogen from
NAD+ in cellular respiration
O Lipase- digests fats in the small intestine
O RuBP carboxylase (rubisco)- responsible for
CO2 fixation in photosynthesis
See the naming trend???
Enzyme Action
O Enzyme function is dependent on collisions
with the substrate
O Must collide with enough energy that
bonds can be broken and new bonds
reformed
O Substrates are reactants in an enzyme-
catalyzed reaction
O Bind at specific active sites on enzyme
O Often fit like “lock and key”
Figure 2-22 Enzyme Action
Enzyme
(hexokinase)
Glucose
Substrates
Products
ADP
Glucose-6phosphate
Products
are released
ATP
Active site
Enzyme-substrate
complex
Substrates
are converted
into products
Substrates
bind to
enzyme
Figure 2-22 Enzyme Action
Enzyme
(hexokinase)
Glucose
Substrates
Products
ADP
Glucose-6phosphate
Products
are released
ATP
Active site
Enzyme-substrate
complex
Substrates
are converted
into products
Substrates
bind to
enzyme
Figure 2-22 Enzyme Action
Enzyme
(hexokinase)
Glucose
Substrates
Products
ADP
Glucose-6phosphate
Products
are released
ATP
Active site
Enzyme-substrate
complex
Substrates
are converted
into products
Substrates
bind to
enzyme
Figure 2-22 Enzyme Action
Enzyme
(hexokinase)
Glucose
Substrates
Products
ADP
Glucose-6phosphate
Products
are released
ATP
Active site
Enzyme-substrate
complex
Substrates
are converted
into products
Substrates
bind to
enzyme
Enzyme Regulation
O Function can be affected by enzyme
concentration, pH, and temperature
O Organism specific
O Human enzymes work best at 37oC
O Enzymes can be controlled at the genetic
level (i.e. repressors block synthesis)
O Can be controlled through feedback
inhibition
Feedback Inhibition of
Enzymes
O noncompetitive
inhibition-end product
of a metabolic pathway
binds to a second site on
the enzyme
O binding alters the shape
of the enzyme's active
site, preventing binding
of the first substrate in the
metabolic pathway
Feedback Inhibition of
Enzymes
O competitive inhibition-
end product of enzymatic
reaction is capable of
reacting with the
enzyme's active site
O prevents the enzyme from
binding its normal
substrate
O As a result, the end
product is no longer
synthesized