BIOLOGY
UNIT 3 CHAPTER 2
Biochemistry
CHAPTER 2 SECTION 1
Basic
Chemistry

A cell is made up of atoms, elements,
compounds, and molecules.
The chemical processes of
an organism takes place
inside the organism’s
individual cells.
Living and nonliving things
are made up of tiny units
called atoms.




An element cannot be
broken down into any
other substance or matter.
Pure silver (Ag) is an element.
It is made up of only silver
atoms.
When you break down a silver
atom, you get subatomic
particles of electrons, protons,
and neutrons.
Element
Symbol
Carbon
C
Hydrogen
H
Oxygen
O
Nitrogen
N
Sulfur
S
Phosphorus
P
Magnesium
Mg
Iodine
I
Iron
Fe
Calcium
Ca
Sodium
Na
Chlorine
Cl
Potassium
K
Zinc
Zn

A compound is formed when two or
more elements combine chemically.




The properties (or characteristics)
of compounds are quite different
from the properties of the elements
from which they are composed.
For example, table sugar (sucrose)
is made up of the elements
carbon, hydrogen, and oxygen.
Carbon is a black solid, and
hydrogen and oxygen are
colorless gases.
However, when they combine
chemically, they form a white
granular substance.



A molecule of a particular compound
is made up of definite numbers and
kinds of atoms bonded, or joined,
together.
A molecule of water contains two
hydrogen atoms and one oxygen atom
bonded together (H20).
Two atoms of hydrogen bond
together to form a molecule
of hydrogen (H2).
When two or more atoms of the same
element combine, the resulting substance is
called a molecule of that element.
When two oxygen atoms combine they
for a molecule of oxygen gas (O2).
When two or more different kinds of atoms
bind, they form molecules of a compound.
Two hydrogen atoms combine with one
oxygen atom to form the compound
water (H2O).

Chemical bonding is the
process by which elements
combine to form compounds.
The formation of a chemical
bond can be
 1.) an ionic bond which
involves the transfer of
electrons from one atom to
another, or
 2.) a covalent bond which
involves the sharing of
electrons between atoms.

The basic types of chemical bonds are:

ionic bonds -- involve a transfer of electrons

covalent bonds – involve molecules that share

hydrogen bonds – a weak bond between polar

peptide bonds – a type of bond that joins amino
usually between molecules that have opposite
charges
electrons
molecules
acids together to make a protein molecule
Chemical Bonding


An ionic bond is a
chemical bond formed
when atoms lose or gain
electrons.
Sodium chloride (NaCl)
is an example of an
ionic compound held
together by ionic bonds.
Sodium loses one
electron to chlorine
when the bonding
process occurs.
Ionic bonds usually
form between a metal
(+) and a nonmetal (-).



Covalent bonds are formed when atoms
produce compounds by sharing electrons.
When making hydrogen
gas, one molecule of
hydrogen gas is formed
when two hydrogen atoms
join by sharing electrons (H2).
Covalent bonds usually form
when nonmetals (-) share
electrons.

A hydrogen bond is a weak chemical
attraction between polar molecules.

Polar molecules are molecules with an

Water is an example of a polar molecule.


unequal distribution of electrical charge.
The partially positive end of one water
molecule is attracted to the negative end of
another water molecule.
The attraction between two water
molecules is an example of a hydrogen
bond, and is what holds water molecules
together.



Peptide bonds are a type
of bond that joins amino
acids together to make a
protein molecule.
Polypeptides are formed
from many amino acids
bonded together.
Proteins are made up of
long polypeptide chains.
CHAPTER 2 SECTION 2
WATER
AND SOLUTIONS

Cohesion is an attraction between
substances of the same kind.

Because of cohesion, water and other
liquids form thin films and drops.

Surface tension is a condition that
occurs when molecules at the surface
of water are linked together
(cohesively)by hydrogen bonds, and
prevent the surface of water from
stretching or breaking easily.
Because of cohesion,
water and other liquids
form thin films and
drops.
Surface tension prevents
the surface of water from
stretching or breaking
easily.
Once the surface
tension is broken,
the objects will sink.

Adhesion is an attraction between different

Adhesion powers a process known as capillary
action.

Capillary action is a process where water


substances.
molecules move upward through a narrow tube
such as the stem of a plant.
The attraction of water to the walls of the tube
sucks the water up more strongly than gravity
pulls it down.
Water moves upward through a plant from roots to
leaves through a combination of capillary action,
cohesion, and other factors.
Water moves upward through a plant from roots to leaves
through a combination of capillary action, cohesion,
adhesion, and other factors.


A solution is a mixture in which one or more
substances are evenly distributed in another
substance.
A solution is made up of the solute and the
solvent.

A solute is the substance that is dissolved in
a solution.

The solvent is the substance that dissolves
another to form a solution.



Water is often called the “universal
solvent” because it dissolves so
many substances.
Many important substances in the
body have been dissolved in blood or
other aqueous fluids.
The polarity of water enables many
substances to dissolve in water.

Ionic compounds and polar molecules
dissolve best in water.

Nonpolar molecules do not dissolve well
in water.


When nonpolar substances, such as oil, are
placed in water, the water molecules are
more attracted to each other than to the
nonpolar molecules.
This explains why oil clumps or beads in
water.
ABOVE: Water on the
hydrophobic surface of
grass. Hydrophobic
molecules tend to be nonpolar and thus prefer other
neutral molecules and
nonpolar solvents.



Acids are compounds that release
hydrogen ions (H+) when dissolved in
water.
Acids have a sour taste, can dissolve
many metals, and turn litmus paper red.
Examples of acids in the body are
hydrochloric acid (produced by stomach
cells that aids digestion), acetic acid
(vinegar), and carbonic acid (in sodas).




Bases are compounds that reduce the
concentration of hydrogen ions in a solution.
Many bases release hydroxide ions (OH-)
when dissolved in water.
Bases are bitter and slippery and turn litmus
paper blue.
Examples of common bases are baking soda,
Milk of magnesia, ammonia, bleach,
detergents, and most soaps.



The pH scale
measures whether a
solution is acid, basic
or neutral.
The scale runs from
0 to 14.
A pH of 7 indicates
that the solution is
neutral. This means
that the solution is
neither an acid nor a
base.
The lower the pH
number, the more
acidic the solution.
The higher the pH number,
the more strongly basic the
solution.
A pH below 7 indicates
that the solution is acidic.
A pH above 7 indicates that
the solution is basic.



Each successive change of 1 pH unit
represents a tenfold change in hydrogenion concentration.
A solution with a pH of 6 has 10 times as
many hydrogen ions as a solution with a pH
of 7.
A pH of 3 indicates a 10,000-fold (10 X 10 X
10 X 10) increase in hydrogen-ion
concentration.
CHAPTER 2 SECTION 3
Chemistry of Cells
.



A chemical formula represents the
chemical makeup of a compound.
It shows the numbers and kinds of atoms
present in a compound.
It is a type of “shorthand” that scientists
use.
C6H12O6 = CCCCCCHHHHHHHHHHHHOOOOOO
 The chemical formula for sugar is C6H12O6
(glucose).
 This means that in one molecule of sugar,
there are six carbon atoms, twelve
hydrogen atoms and six oxygen atoms.





H2O (water)
SO2 (sulfur dioxide)
CO2 (carbon dioxide)
CaCO3 (calcium carbonate)
C6H10O5 (cellulose)

Equations are used to describe chemical reactions.

Reactants are the substances that start the
reaction.

The reactants are placed on the left side of the
equation.

Products are the substances formed by the
reaction.

The products are placed on the right side of the
equation.

The arrow means “yields,” “to make,” or “to form”.

Reactions may be represented either by words
or formulas.

The word equation for aerobic respiration is:
SUGAR + OXYGEN  ENERGY + CARBON DIOXIDE + WATER

A chemical equation is an equation that uses
formulas instead of words.

The chemical equation for aerobic respiration
is:
C6H12O6 + 6O2

ATP + 6CO2 + 6H2O

Living things are made up of inorganic and
organic compounds.

Inorganic compounds are compounds that

do not contain both carbon and hydrogen.
The principal inorganic compounds found in
living things are:
 water
 salts
 inorganic acids
 inorganic bases


Organic compounds are compounds
that contain both carbon and hydrogen.
The main classes of organic compounds
(macromolecules) found in living things
are:
 1. carbohydrates (CHO)
 2. lipids
(CHO)
 3. proteins
(CHON)
 4. nucleic acids (CHONP)




Organic compounds can be:
monomers: compounds made up of
single units
polymers: compounds made up of
many units joined together
isomers: compounds with the same
molecular formula, but different
structural formulas




Carbohydrates are the main source of energy
for cell activities.
Two main types of carbohydrates are sugars and
starches.
Carbohydrates are made
up of the elements carbon,
hydrogen, and oxygen
(CHO).
Generally, there are
twice as many hydrogen
atoms as oxygen atoms in
carbohydrates (2:1 ratio).




The simplest carbohydrates
are called monosaccharides,
or simple sugars.
Monosaccharides are called the
“building blocks” of carbohydrates,
or the subunits of carbohydrates.
A common monosaccharide
is glucose (C6H12O6). Fructose is
another example of a
monosaccharide sugar.
Glucose is the plant sugar formed
during photosynthesis.

A disaccharide sugar, or double sugar, is
formed when two simple sugars combine.

Maltose (C12H22O11) is an example of a common

disaccharide.
Maltose is formed when two glucose molecules
chemically combine (glucose + glucose).

Lactose is a disaccharide sugar composed of

Sucrose is a disaccharide sugar composed of
glucose and galactose.
glucose and fructose.
lactose
sucrose

Polysaccharides are long chains of

Starch and cellulose are important polysaccharides

Glycogen is an important polysaccharide found in
monosaccharides (sugar molecules) bonded together.
found primarily in plants.
animals.



Starch, or amylum, is a carbohydrate
consisting of a large number of glucose
units joined together by glycosidic bonds.
Starch is the energy storage molecule for
plants.
Starch is the most common carbohydrate
in the human diet, and is contained in
large amounts in such staple foods as
potatoes, wheat, maize (corn), and rice.



Cellulose is the structural component of
the cell walls of green plants, and is a
complex polysaccharide composed of
glucose monomers.
Cellulose is the most common organic
compound on Earth.
About 33% of all plant matter is cellulose
(the cellulose content of cotton is 90%
and that of wood is 40–50%).
The chemical
formula
for cellulose is
C6H10O5 and it
consists of
a linear chain of
several hundred
to over ten
thousand
glucose units.




Glycogen is a polysaccharide that serves as
short-term energy storage for animals.
Glycogen is made primarily by the liver and
the muscles.
Muscle cell glycogen appears to function as
an immediate reserve source of available
glucose for muscle cells.
When it is needed for energy, glycogen is
broken down and converted again to glucose.
Lipids are insoluble organic
compounds that contain the
elements carbon,
hydrogen, and oxygen (CHO).
 Lipids include fats, oils,
waxes, and sterols, and some
fat-soluble vitamins.

 Fatty acids and
glycerol are the
building blocks,
or subunits, of
lipids.




Fats store energy and contain
three fatty acids bonded to a
glycerol molecule backbone.
Glycerol is a three-carbon
organic molecule.
A fatty acid is a long chain of
carbon atoms with hydrogen
bonded to them.
Because bonds between carbon
and hydrogen are rich in energy,
fats can store a lot of energy.

Two types of lipids are fats and
oils.
 Fats are solids at room
temperature.
 Oils are liquids at room
temperature.


Lipids form part of the structure of
cell membranes in living organisms.
Extra food that is not immediately
needed as a source of energy is
changed to fat and stored, so lipids
are a source of stored energy in
living organisms.


Unsaturated fats form double bonds in their hydrocarbon chains,
which causes them to bend. This prevents the molecules from being able to
“stack” or “pack” themselves tightly. Thus, unsaturated fats remain
in a liquid state at room temperature such as oils.
Saturated fats do not form double bonds, and form straight
hydrocarbon chains instead, so they pack themselves close together. Thus,
saturated fats form a solid at room temperature such as
animal fat, butter, tallow, or lard.



Proteins are organic molecules that form important
cell products such as enzymes, hormones, antibodies,
and hemoglobin.
Proteins also play an important role in cell repair and
growth, and can be found in the cell membranes of
most cells.
Proteins are made
up of carbon, hydrogen,
oxygen, and nitrogen.
(CHON)

Some proteins also
contain sulfur and
phosphorus.

Amino acids are the building blocks, or subunits

There are 20 amino acids found in all living things.


(monomers) of proteins.
Amino acids can be
joined together in any
sequence and combination.
Because of this, there are
a very large number of
different proteins that can
be formed.

Structure: building structural components of
organisms (collagen, elastin, keratin, microtubules,
microfilaments)

Regulation of metabolic processes: hormones such as
insulin, or hemoglobin which carries oxygen in the blood

Carrying out of metabolic processes: enzymes



Membrane component: carrier proteins, protein
pumps, transport of materials through membrane
phospholipid layers
Self and non-self recognition: major histocompatibility
complexes (tissue rejection, immune responses such as
with antibodies)
Membrane receptors: hormone receptors and
neurotransmitter receptors
All amino acids are made up of an amino group, a
carboxyl group, and an R side chain.
The R side chain is different for each amino
acid, making each amino acid unique.





Amino acids that form proteins are
held together by peptide bonds.
A dipeptide is formed from two amino
acids that are bonded together.
Polypeptides are formed from many
amino acids bonded together.
Proteins are made up of
long polypeptide chains.
Proteins fold into compact shapes
determined partly by how the amino
acids interact with water and each
other.



Nucleic acids are very large
macromolecules made up of carbon,
hydrogen, oxygen, nitrogen, and phosphorus
(CHONP).
A nucleotide is the simplest subunit, or
building block, of nucleic acids.
Nucleotides are
composed of
a sugar molecule,
a nitrogen base, and
a phosphate group.

Nucleotides are composed of a sugar
molecule, a nitrogen base, and a phosphate
group.



DNA and RNA are two kinds of nucleic acids.
DNA makes up genes and is involved in
heredity.
RNA is involved in the making of proteins.

DNA, or deoxyribonucleic acid, consists of two
strands of nucleotides that spiral around each
other in a shape that is known as a double helix.
Chromosomes contain long
strands of DNA, which store
hereditary information.
DNA is located in the nucleus
of all living cells.



RNA, or ribonucleic acid,
usually consists of a single
strand of nucleotides.
RNA plays many key roles
in the manufacture of
proteins, and the
replication of DNA.
RNA can also act as an
enzyme, promoting the
chemical reactions that
link amino acids to form
proteins.
DNA bases: T-A, G-C
Deoxyribose sugar
Original information
for making proteins
RNA bases: U-A, G-C
Ribose sugar
Working copy for
making proteins
One form or type
Variety of forms:
m-RNA, t-RNA, r-RNA
Found primarily in the
nucleus and forms
chromosomes during
cell division
DNA is a large
molecule that is a
double helix.
Found in nucleus and
throughout the cell
RNA is made of smaller
molecules and is singlestranded.

1. CARBOHYDRATES: contain the elements
carbon, hydrogen, and oxygen (CHO) in a 2:1
ratio

Carbohydrates are the main source of energy
for cell activities.

Two main types : sugars and starches.
Carbohydrates can be simple
monosaccharides such as glucose and fructose
 disaccharides such as maltose or lactose or
 polysaccharides such as starch and cellulose.


2. LIPIDS: contain the elements carbon,

Fats - solids at room temperature

Oils - liquids at room temperature

Lipids form part of the structure of cell
membranes (phospholipid bilayer).

Lipids are a source of stored energy in living
organisms.

Lipids contain two or three fatty acids
bonded to a glycerol molecule backbone.
hydrogen, and oxygen (CHO) and include fats
and oils

3. PROTEINS: made up of carbon, hydrogen,

Proteins form enzymes, hormones, antibodies,
and hemoglobin.

Proteins play an important role in cell repair and
growth.

Proteins are composed of simpler subunits
called amino acids (CHONPS).

Proteins can form dipeptide bonds or polypeptide
bonds.
oxygen, and nitrogen (CHON) and sometimes
sulfur


4. NUCLEIC ACIDS: composed of carbon,
hydrogen, oxygen, nitrogen, and phosphorus
(CHONP)
Nucleotide - simplest subunit of nucleic acid
made up of a sugar molecule, a nitrogen
base, and a phosphate group

DNA and RNA: two kinds of nucleic acids

DNA – double-stranded, makes up genes,
located in the nucleus, involved in heredity

RNA – single-stranded, able to move about
cell, involved in the making of proteins
Name the compound.
glucose
nucleotide
sucrose
amino acid
lipid
Name the compound.
cellulose
starch
RNA
maltose -- disaccharide
CHAPTER 2 SECTION 4
Energy and
Chemical
Reactions



Energy is the ability to move or change
matter.
In chemical reactions, energy is
released or absorbed when chemical
bonds are broken and new ones are
formed.
Activation energy is the energy needed
to start a chemical reaction.




Each chemical reaction that occurs in a
living thing is controlled by an enzyme.
Enzymes are large, complex protein
molecules that control the rate of
chemical reactions.
Enzymes are the organic catalysts in
cellular chemical reactions.
A catalyst is a substance that causes or
accelerates a chemical reaction without
itself being affected.



Catalysts can speed up or slow down
a chemical reaction.
An enzyme (acting as a catalyst) can
increase the speed of a chemical
reaction by reducing the activation
energy needed by the reaction, thus
conserving energy.
Enzymes are not consumed by the
reactions they catalyze—they can take
part in many reactions.


A substrate is the molecule at the beginning of a
chemical reaction on which an enzymes acts.
An enzyme acts only on a specific substrate
because only that substrate fits into the enzyme’s
active site.

Active sites are the pockets formed from the

An enzyme’s shape determines its activity.

folds on an enzyme’s surface.
Typically, an enzyme is a large protein with one or
more deep folds on its surface.


In organisms, enzymes allow the chemical reactions
of metabolism to take place more efficiently than
they otherwise would at body temperature.
For example, amino acids are produced from protein
digestion. The enzymes needed for this reaction are
not changed, but must be present for the reaction
to occur.
Some examples of enzymes affecting
reactions that you may be familiar
with:


Enzymes in biological washing
powders break down protein or fat
stains on clothes.
Enzymes in meat tenderizers break
down proteins, making the meat
easier to chew.
B12

Some enzymes have a nonprotein part called a
coenzyme.

Many coenzymes are vitamins.

If a vitamin is missing from the human body, a
certain enzyme cannot function.

If an enzyme doesn’t function, one or more metabolic
reactions cannot occur.

This is one of the reasons why it is important that
you eat a well-balanced diet every day.

Without coenzymes (vitamins) needed by the body,
the chemical processes necessary for proper
metabolism cannot take place.


The rate of enzyme action is influenced by
several factors:
 Temperature
 Relative concentrations of enzyme and
substrate
 pH
Each enzyme has an optimum temperature
and pH at which it functions most
efficiently and its rate of activity (or
action) is the greatest (think of Goldilocks
-- not too hot, not too cold, just right).



At temperatures below the optimum, the rate
of enzyme activity (action) is low.
Enzyme activity increases with increasing
temperature up to the
optimum temperature.
Above the optimum
temperature, the rate
of enzyme activity
decreases.



At pH levels below the optimum, the rate
of enzyme activity (action) is low.
Enzyme activity increases with increasing
pH up to the optimum
pH.
Above the optimum pH,
the rate of enzyme
activity decreases.

ATP or adenosine triphosphate is an
important molecule because it is the
molecule that stores energy for chemical
and mechanical processes in the body.

The energy in ATP is stored within the
high energy phosphate bonds.

If a phosphate bond is formed, energy is
stored.

If a phosphate bond is broken, energy is
released.

ATP is a modified form of the nucleotide adenine,
plus two phosphate groups.

Splitting the glucose molecule releases energy.

Glycolysis, the breaking down of the sugar


glucose, produces a net of two molecules of ATP.
Glycolysis is a process that occurs during
cellular respiration -- the chemical reactions
that break down food.
ATP is like a “rechargeable battery” because it
can be recycled and used over and over again.




The human body uses about 1 million molecules of
ATP per second per cell.
There are more than 100 trillion cells in the human
body.
That is about 1 X 1020, or
100,000,000,000,000,000,000 ATP molecules used in
the body each second.
ATP is an extremely important molecule because it is
the molecule that stores energy for chemical and
mechanical processes in the body (such as skeletalmuscular movement). Without ATP, those processes
would not occur.
The End!
One final thought…