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Biology 1
Mr. Greene
Unit 2
BIOCHEMISTRY
Bellringer
Look at the different substances and write down which
substances you think are composed of elements and
which are composed of compounds.
Key Ideas
 What makes up matter?
 Why do atoms form bonds?
 What are some important interactions between
substances in living things?
Atoms
 Every living and nonliving thing is
made of matter. Matter is anything
that has mass and takes up space.
 All matter is made of very small
particles called atoms. An atom is the
smallest unit of matter that cannot be
broken down by chemical means.
 100 million atoms would make a row
about 1 cm long
 these are represented by chemical
symbols
 H - hydrogen
 N – nitrogen
He - helium
O - oxygen
Atoms
 The nucleus of an atom
is made up of:
 positively charged
protons
 uncharged neutrons.
 Negatively charged
electrons have very
little mass and move
around the nucleus in a
large region called the
electron cloud.
 As a whole, atoms have
no electrical charge.
Elements
Elements
 An element is a substance made up of atoms that
have the same number of protons.
 For example, each atom of the element carbon has
six protons.
 Atoms of an element may have different numbers of
neutrons.
 These atoms are called isotopes of elements.
Atomic Structure
An Element in the Periodic Table
6
C
Carbon
12.011
atomic number - number of protons/ electrons too if neutral
mass number - number of protons and neutrons
Ions and Isotopes
ions
 atoms that have either lost or gained electrons.
 if there are more protons than electrons = positive ions
 if there are more electrons than protons = negative ions
isotopes
 atoms of the same element that have different
numbers of neutrons
 they have the same chemical properties because the have
the same number of electrons
Isotopes of Carbon
Section 2-1
Nonradioactive carbon-12
6 electrons
6 protons
6 neutrons
Nonradioactive carbon-13
6 electrons
6 protons
7 neutrons
Radioactive carbon-14
6 electrons
6 protons
8 neutrons
Chemical Bonds
 The electron cloud of an atom may have levels.
 Electrons in the outermost level, or shell, are called
valence electrons.
 Atoms tend to combine with each other such that
eight electrons will be in the valence shell.
 When atoms combine, a force called a chemical bond
holds them together.
Chemical Bonds
 Chemical bonds form between groups of atoms
because most atoms become stable when they have
eight electrons in the valence shell.
 When atoms of different elements combine, a
compound forms. A compound is a substance made
of the bonded atoms of two or more elements.
Chemical Bonds
Covalent Bonding
 One way that atoms bond is by sharing valence
electrons to form a covalent bond.
 A molecule is a group of atoms held together by
covalent bonds.
 A water molecule, H2O, forms when an oxygen
atom forms covalent bonds with two hydrogen
atoms.
Covalent Bonding
Visual Concept: Covalent
Bonding
Chemical Bonds
Ionic Bonding
 Atoms can achieve a stable valence level by losing or
gaining electrons, resulting in a positive or negative
charge.
 An ion is an atom or group of atoms that has an
electric charge because it has gained or lost
electrons.
 The attractive force between oppositely charged
ions is an ionic bond.
Visual Concept: Ion
Ionic Bonding in Salt
Click to animate the image.
Energy Levels and Ionic Bonding
Polarity
 In some covalent bonds, the
shared electrons are
attracted more strongly to
one atom than to the other.
 As a result, one end of the
molecule has a partial
negative charge, while the
opposite end has a partial
positive charge.
 Molecules with partial
charges on opposite ends
are said to be polar.
Polarity
Solubility
 The partially charged ends of polar molecules attract
opposite charges.
 Because of this behavior, polar molecules can
dissolve other polar molecules and ionic compounds.
For example, water can dissolve sugar and salt.
 Nonpolar substances, such as oil, grease, and wax,
do not dissolve well in water.
Ionic Compounds in Water
Polarity
Hydrogen Bonds
 When bonded to an oxygen,
nitrogen, or fluorine atom, a
hydrogen atom has a partial charge
nearly as great as a proton’s charge.
 It attracts the negative pole of
other nearby molecules. This
attraction, called a hydrogen bond,
is stronger than attractions
between other molecules, but not
as strong as covalent bonds.
 Hydrogen bonding plays an
important role in many of the
molecules that make up living
things.
Summary
 All matter is made up of atoms. An atom has a
positively charged nucleus surrounded by a
negatively charged electron cloud.
 Chemical bonds form between groups of atoms
because most atoms became stable when they have
eight electrons in the valence shell.
 Polar attractions and hydrogen bonds are forces that
play an important role in many of the molecules that
make up living things.
Bellringer
Write what you think an acid and a base are and why.
Guess if the following substances are acids or bases,
and give a reason for your choice:
lemon juice, water, household ammonia, blood, soda
pop, milk, antacid, shampoo
Can you find any similar characteristics between acids
and bases?
Key Ideas
 What makes water a unique substance?
 How does the presence of substances dissolved in
water affect the properties of water?
Properties of Water
 Water has many unique properties that make it an
important substance for life.
 Most of the unique properties of water result because
water molecules form hydrogen bonds with each other.
 Water heats more slowly than most other substances
 It also retains its temperature longer than other
substances
 When water freezes, the crystal structure formed due to
hydrogen bonding makes ice less dense than liquid
water.
Properties of Water
 Water can absorb a large amount of heat without
changing temperature. This property can help
organisms maintain a constant internal
temperature.
 The attraction of particles of the same substance,
such as water, is called cohesion. Cohesion keep
water from evaporating easily; thus, water is a liquid
at ordinary temperatures.
 Water molecules also stick to other polar molecules.
This attraction between particles of different
substances is called adhesion.
Visual Concept: Comparing
Cohesion and Adhesion
Solutions
 A solution is a mixture in which ions or molecules
of one or more substances are evenly distributed
in another substance.
 solute – the substance that is dissolved
 solvent – substance in which the solute is dissolved
 Many substances are transported throughout
living things as solutions of water. Dissolved
substances can move more easily within and
between cells.
 Water dissolves many ionic and polar substances
but does not dissolve nonpolar substances.
solution
Solutions
Acids and Bases
 Some water molecules break apart to form
hydronium and hydroxide ions.
 In pure water, hydronium and hydroxide ions are
present in equal numbers.
 Acids and bases are compounds that change the
balance of these ions.
Solutions
Solutions
Acids and Bases
 Acids are compounds that form extra hydronium
ions when dissolved in water.
 Bases are compounds that form extra hydroxide
ions when dissolved in water.
 When acids and bases are mixed, the extra
hydronium and hydroxide ions react to form water.
Visual Concept: Acids
Visual Concept: Bases
Solutions
pH and Buffers
 pH is a measure of how acidic or basic a solution is.
 Each one-point increase in pH represents a 10-fold
decrease in hydronium ion concentration.
 Pure water has a pH of 7. Acidic solutions have a pH
below 7, and basic solutions have a pH above 7.
pH Scale
Section 2-2
Increasingly Basic
Oven cleaner
Increasingly Acidic
Neutral
Bleach
Ammonia
Soap
Sea water
Human blood
Pure water
Milk
Rain
Acid rain
Tomato
juice
Lemon
juice
Stomach acid
Visual Concept: pH
Solutions
pH and Buffers
 The pH of solutions in living things must be stable.
 For a stable pH to be maintained, the solutions in
living things contain buffers.
 A buffer is a substance that reacts to prevent pH
changes in a solution.
Summary
 The hydrogen bonding between water molecules
explains many of the unique properties that make
water an important substance for life.
 Acids and bases change the concentration of
hydronium ions in aqueous solutions. The pH of
solutions in living things must be stable.
Bellringer
Look at all the different foods that are shown. Write
down what you think all of these substances have in
common.
Key Ideas
 What are the chemicals of life made from?
 What is the role of carbohydrates in cells?
 What do lipids do?
 What determines the function of proteins?
 What do nucleic acids do?
Compounds in Living Organisms
Two Main Categories of Compounds in Living Organisms
1) Inorganic
 don't contain carbon (except carbon dioxide)
 can't be produced by organisms
 except water, carbon dioxide, and oxygen
2) Organic




always contain carbon
carbon - element most closely associated to life
has four electrons in the outermost shell
likes to bond to elements in a variety of ways
 molecules with C-C bonds are called organic molecules (i.e.
the backbone)
 can be made biologically and synthetically
Building Blocks of Cells
 The parts of a cell are made up of large, complex
molecules, often called biomolecules.
 Large, complex biomolecules are built from a few
smaller, simpler, repeating units arranged in an
extremely precise way.
 The basic unit of most
biomolecules contain atoms
of carbon. Carbon atoms can
form covalent bonds with as
many as four other atoms.
Carbon Bonding
Carbohydrates
 Carbohydrates are molecules
made of sugars.
 A sugar contains carbon,
hydrogen, and oxygen in a
ratio of 1:2:1.
 Compounds with the basic
formula, CH2O
 they can be a multiple of the
formula (C6H12O6)glucose
 Glucose is a common sugar
found in grape juice.
Carbohydrates
 Glucose is a monosaccharide, or
“single sugar.”
 Two sugars can be linked to make a
disaccharide.
 Many sugars can be linked to make
a polysaccharide.
 Monosaccharides and disaccharides
are considered simple
carbohydrates. Polysaccharides are
considered complex carbohydrates.
Visual Concept:
Carbohydrates
Carbohydrates
 Cells use carbohydrates
for sources of energy,
structural materials,
and cellular
identification.
 Carbohydrates are a
major source of energy
for many organisms,
including humans.
Carbohydrates
 Chitin and cellulose are complex
carbohydrates that provide support.
 Chitin is found in the shells of insects and the cell
walls of mushrooms.
 Cellulose is found in the cell walls of plants.
 In a complex organism, cells recognize
neighboring cells by the short, branched
chains of varying sugar units on their outer
surface.
Lipids
 Lipids are another class of biomolecules, which
includes fats, phospholipids, steroids, and waxes.
 Lipids consist of chains of carbon atoms bonded to
each other and to hydrogen atoms. This structure
makes lipids repel water.
 The main functions of lipids include storing energy
and controlling water molecules.
Lipids
 The main purpose of fats is to store energy.
 Fats can store energy even more efficiently than carbohydrates.
 The cell’s boundary is made of phospholipids. The structure of
cell membranes depends on how this molecule interacts with
water.
 Waxes, found on the surfaces of plants and aquatic bird feathers,
help prevent evaporation of water from the cells of the organism.
 Steroid hormones such as testosterone and pigments (retinal in
eyes and chlorophyll in plants) are made of lipids.
Lipids
Types of Fats
 saturated - most carbons
are bonded to 2 hydrogens
 unsaturated - there are
some C=C
 Lipids surround taste buds
and the food mixes with
them to give the taste.
Visual Concept: Types of
Lipids
Proteins
 Proteins are chains of amino acids that twist and fold
into certain shapes that determine what the proteins
do.
 There are many types of proteins that perform many
types of functions.
 Proteins may be involved in structure, support,
movement, communication, transportation, and
carrying out chemical reactions.
Proteins
Amino Acids
 A protein is a molecule made up of amino acids, building
blocks that link to form proteins.
 Every amino acid has an amino group and a carboxyl
group. Units of amino acids can form links called peptide
bonds.
 The side group gives an amino acid its unique properties.
Twenty different amino acids are found in proteins. The
human body only makes 12, we must get the other 8
through dietary intake.
Amino Acids
Amino
group
Carboxyl
group
General structure
Alanine
Serine
Visual Concept: Proteins
Visual Concept: Amino Acid
Uses of Proteins
 structure – cartilage, skin, ligaments, and
tendons ---> collagen
 horns of rhinoceros and hair ---> keratin
 enzymes
 a catalyst that increases rate of chemical reactions
 fight infection - antibodies
Nucleic Acids
 A nucleic acid is a long chain of nucleotide units.
 A nucleotide is a molecule made up of three parts: a
sugar, a base, and a phosphate group.
 Nucleotides of deoxyribonucleic acid, or DNA,
contain the sugar deoxyribose.
 Nucleotides of ribonucleic acid, or RNA, contain the
sugar ribose.
A phosphate group
deoxyribose (sugar)
nitrogen-containing molecule,
called a base
Nucleic Acids
DNA - deoxyribonucleic acid
 two interlocking, coil-shaped strands

(a spiral staircase/double helix)
 unicellular ---> long strands
 multicellular ---> compact bundles called
chromosomes
RNA - ribonucleic acid
 variety of shapes depending upon function
 three types - messenger, transfer, ribosomal
Visual Concept: Nucleic Acid
Nucleic Acids
Energy Carriers
 Some single nucleotides have other important roles.
 Adenosine triphosphate, or ATP, is a nucleotide that
has three phosphate groups and supplies energy to
cells.
 Energy is released in the reaction that breaks off the
third phosphate group.
 Other single nucleotides transfer electrons or
hydrogen atoms for other life processes.
Organic
Compounds
Carbon
Compounds
include
Carbohydrates
Lipids
Nucleic acids
Proteins
that consist of
that consist of
that consist of
that consist of
Sugars and
starches
Fats and oils
Nucleotides
Amino Acids
which contain
Carbon,
hydrogen,
oxygen
which contain
Carbon,
hydrogen,
oxygen
which contain
which contain
Carbon,
hydrogen,
oxygen, nitrogen,
phosphorus
Carbon,
hydrogen,
oxygen,
nitrogen,
Summary
 Large, complex biomolecules are built from a few
smaller, simpler, repeating units arranged in an
extremely precise way.
 Cells use carbohydrates for sources of energy,
structural materials, and cellular identification.
 The main functions of lipids include storing energy
and controlling water movement
Summary, continued
 Proteins are chains of amino acids that twist and fold
into shapes that determine what the protein does.
 Nucleic acids store and transmit hereditary
information.
Bellringer
Write down as many different kinds of energy that you
can think of and give an example of each.
Key Ideas
 Where do living things get energy?
 How do chemical reactions occur?
 Why are enzymes important to living things?
Changing Matter
 Living things are made of matter, which consists of a
substance with a form.
 Changes constantly occur in living things.
 A physical change occurs when only the form or
shape of the matter changes.
 A chemical change occurs when a substance
changes into a different substance.
Changing Matter
 Matter is neither created nor destroyed in any
change. This observation is called the law of
conservation of mass.
 The ability to move or change matter is called
energy.
 Energy exists in many forms and can be converted
from one form to another.
 Every change in matter requires a change in energy.
Visual Concept: Energy
Changing Matter
 Energy may change from one form to another, but
the total amount of energy does not change. This
observation is called the law of conservation of
energy.
 The total amount of usable energy decreases
because some energy is given off to the
surroundings as heat.
 Living things use different chemical reactions to get
the energy needed for life processes.
Chemical Reactions
 Changing a substance requires a chemical reaction.
During this process, bonds between atoms are
broken, and new ones are formed.
 A reactant is a substance that is changed in a
chemical reaction
 A product is a new substance that is formed.
 Sometimes products can reform reactants.
Chemical Reactions
Activation Energy
 Chemical creacions can only occur under the right
conditions.
 To form new bonds, the particles must collide fast
enough to overcome the repulsion between their
negatively charged electron clouds.
 The activation energy of a reaction is the minimum
kinetic energy required to start a chemical reaction.
Visual Concept: Activation
Energy and Chemical
Reactions
Chemical Reactions
Alignment
 Even if enough energy is available, the product still
may not form.
 When the reactant particles, the correct atoms must
be brought close together in the proper orientation.
 Chemical reactions can only occur when the
activation energy is available and the correct atoms
are aligned.
Reaction Conditions
Biological Reactions
 In living things, chemical reactions occur between
large, complex biomolecules.
 Many of these reactions require large activation
energies.
 Many of these reactions would not occur quickly
enough to sustain life without the help of enzymes.
CO2 + H2O
H2CO3
Biological Reactions
Enzymes
 An enzyme is a molecule that increases the speed of
biochemical reactions.
 Enzymes hold molecules close together and in the
correct orientation. An enzyme lowers the activation
energy of a reaction.
 By assisting in necessary biochemical reactions,
enzymes help organisms maintain homeostasis.
Effect of Enzyme on
Activation Energy
Biological Reactions,
continued
Enzymes
 Each enzyme has an active site, the region where
the reaction takes place.
 The shape of the active site determines which
reactants, or substrates, will bind to it. Each
different enzyme acts only on specific substrates.
 Binding of the substrates causes the enzyme’s shape
to change. This change causes some bonds in the
substrates to break and new bonds to form.
Enzyme Action
Click to animate the image.
Biological Reactions
Enzymes
 Many enzymes are proteins. Changes in temperature
and pH can change a protein’s shape.
 If an enzyme changes shape, it won’t work well.
 Most enzymes need a certain range of temperatures,
pH, and substrate concentration.
Effect of Enzymes
Reaction pathway
without enzyme
Activation energy
without enzyme
Reactants
Reaction pathway
with enzyme
Activation
energy
with enzyme
Products
Biological Reactions
Metabolism
 Cells get most of the energy needed for metabolism
by breaking down food molecules.
 The release of energy from food molecules occurs in
a series of reactions using many enzymes to capture
energy in the form of ATP molecules.
 The enzymes reduce the activation energy so much
that only a little energy is needed to start the
reactions. In this process, very little energy is lost as
heat.
Other Necessary Terms
 Coenzyme
 an organic molecule that assists an enzyme
 Inhibitor
 a molecule that slows down or stops the action of
an enzyme
 Denaturation
 changing the shape of an enzyme due to heat or
extreme pH
Summary
 Living things use different chemical reactions to get
the energy needed for life processes.
 An activation energy is needed to start a chemical
reaction. The reactants must also be aligned to form
the product.
 By assisting in necessary biochemical reactions,
enzymes help organisms maintain homeostasis.
Enzymatic Reactions