Transcript Understanding Biochemistry

Chapter 2
The Chemistry of Life
Section 1: The Nature of
Matter
Objectives
• What three subatomic particles make up
atoms?
• How are all the isotopes of an element
similar?
• What are the two types of chemical
bonds?
The Big Idea
• Life Depends on chemistry
• Chemical reactions keep you
alive
Atom
• Basic unit of matter
Democrites
Subatomic particles
• Protons - Positively charged (+)
• Neutrons - Not charged (neutral)
• Electrons - Negatively charged (-)
Electrons
Bind together
to form the
nucleus
Protons
Nucleus
Neutrons
Element
• A pure substance that consists
of just one type of atom
An elements atomic number = number of
protons
6
C
Carbon
12.011
Atomic number
Isotope
• Atoms of the same element
that differ in the number of
neutrons they contain
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
Radioactive isotopes
• Can be dangerous
• Can be used
practically
–Radioactive dating
–Treat cancer
–Kill bacteria
What is the atomic mass?
• The weighted average of the
masses of an elements isotope is
called its atomic mass
Compounds
• A substance formed by the
chemical combination of two or
more elements in definite
proportions
• Ex) H2O, NaCl
Ionic Bonds
• Formed when one or more
electrons are transferred from
one atom to another
The Sum of protons and neutrons in the nucleus of an
atom is its mass number
6
C
Carbon
12.011
Mass number
What is an Ions?
• Positively and negatively
charged atoms
• If an atom loses an electron it
becomes positive + (Cations)
• If an atom gains an electron it
becomes negative - (Anions)
Sodium atom (Na)
Chlorine atom (Cl)
Sodium ion (Na+)
Chloride ion (Cl-)
Protons +11
Electrons -10
Charge
+1
Protons +17
Electrons -18
Charge
-1
Transfer
of electron
Protons +11
Electrons -11
Charge
0
Protons +17
Electrons -17
Charge
0
Covalent Bonds
• Forms when electrons are
shared between atoms
Molecule
• The structure that results when
atoms are joined together by a
covalent bond
• Smallest unit of most compounds
Van der Waals Forces
• A slight attraction that
develops between the
oppositely charged regions of
nearby molecules due to
unequal sharing of electrons
Questions
1. Describe the structure of an atom.
Atoms are made up of protons and
neutrons in a nucleus. Electrons are
in constant motion in the space
around the nucleus.
2. Why do all isotopes of an element
have the same chemical properties
They have the same number of
electrons
3. What is a covalent bond?
A bond formed when electrons are
shared between atoms
4. What is a compound? How are they
related to molecules
A compound is a substance formed
by the chemical combination of two or
more elements in definite proportions.
A molecule is the smallest unit of
most compounds
5. How do Van der Waals forces
hold molecules together?
When the sharing of electrons
are unequal, a molecule has
regions that are charged. An
attraction can occur between
oppositely charged regions of
nearby molecules
6. How are ionic bonds and Van
der Waals forces similar? How
are they different?
In both cases, particles are
held together by attractions
between opposite charges.
The difference is that ionic
charges are stronger
Section 2: Properties of
Water
Objectives
• Why are water molecules polar?
• What are acidic solutions? What
are basic solutions?
The Big Idea
• Much of our planet is covered in
water
• Water is necessary for life to exist
• If life exists on other planets,
there most likely is water present
• Water has many properties that
make life possible
Polarity
(-)
The oxygen atom has
a stronger attraction for
electrons
(+)
Hydrogen Bonds
• Because of waters partial
charges, they can attract each
other and create hydrogen bonds
• Not as strong as covalent or ionic
bonds
• Waters ability to create multiple
hydrogen bonds gives it many
special properties
Cohesion
• Attraction between molecules of
the same substance
Adhesion
• Attraction molecules of different
substances
Mixture
• Material composed of two or more
elements or compounds that are
physically mixed but not
chemically combined
• Ex.) salt & pepper, earths
atmosphere
Solutions
• Mixture of two or more
substances in which the
molecules are evenly distributed
• Ex.) salt water
• Settles out over time
Solutions
Cl-
Cl-
Na+
Na+
Water
Water
Solute
• Substance that is dissolved
• Ex.) salt
Solvent
• The substance that does the
dissolving
• Ex.) Water
Suspensions
• Mixture of water and nondissolved materials
• Ex.) sugar solution, blood
• Separate into pieces so small,
they never settle out
The pH scale
• Indicated the concentration of
hydrogen ions in a solution
Acid
Neutral
Base
Acids
• Any compound that forms H+
(hydrogen) ions in solution
Base
• A compound that produces OH(hydroxide) ions in solution
Buffers
• Weak acids or bases that can
react with strong acids or bases
to prevent sharp, sudden pH
changes
Questions
1. Use the structure of a water
molecule to explain why its polar
Oxygen atom has greater
attraction for electrons, therefore
the oxygen atom is negative and
the hydrogen end is positive
2. Compare acidic and basic
solutions in terms of their H+ ion
and OH- ion concentrations
Acid have more H+ ions than OHions, and bases have more OHions than H+ ions
3. What is the difference between a
solution and a suspension?
In a solution, all components are
evenly distributed. In a
suspension, un-dissolved
particles are suspended
4. What does pH measure?
The concentration of H+ ions in a
solution
5. The strong acid hydrogen floride
(HF) can be dissolved in pure
water. Will the pH of the solution
be greater or less than 7?
less than 7
Section 3: Carbon Compounds
Objective
• What are the functions of each
group of organic compounds?
Interest Grabber
Section 2-3
Life’s backbone
• Most of the compounds that make up living
things contain carbon. In fact, carbon makes
up the basic structure, or “backbone,” of these
compounds. Each atom of carbon has four
electrons in its outer energy level, which
makes it possible for each carbon atom to
form four bonds with other atoms.
• As a result, carbon atoms can form long
chains. A huge number of different carbon
compounds exist. Each compound has a
different structure. For example, carbon chains
can be straight or branching. Also, other kinds
of atoms can be attached to the carbon chain.
Methane
Acetylene
Butadiene
Benzene
Isooctane
Macromolecules “giant molecules”
• Formed by a process called
polymerization
Monomers
• Smaller units
Polymers
• Linked up monomers
Carbohydrates
• Compounds made up of carbon,
hydrogen, and oxygen atoms
usually in a ratio of 1:2:1
• Main source of energy
• The monomers of starch are
sugars
• Single sugar molecules are called
monosaccharides
• The large macromolecules
formed from monosaccharides
are known as polysaccharides
Starch
Glucose
Lipids
• Made mostly from carbon and
hydrogen atoms
• Used to store energy
Lipid
Fatty Acids
Glycerol
Proteins
• Macromolecules that contain
nitrogen as well as carbon,
hydrogen, and oxygen
• Proteins are polymers of
molecules called amino acids
Amino Acids
Carboxyl group
General structure
Alanine
Serine
• More than 20 different amino
acids, can join to any other amino
acid
• The instructions for arranging
amino acids into many different
proteins are stored in DNA
• Each protein has a specific role
• The shape of proteins can be very
important
Proteins
Amino
Acids
Nucleic Acids
• Macromolecules containing hydrogen,
oxygen, nitrogen, carbon, and
phosphorus
Double
Helix
Nucleotides
• Consists of 3 parts: 5-carbon sugar,
phosphate group and nitrogen base
Nitrogen Base
Phosphate
group
5-Carbon Sugar
2 kinds of nucleic acids
• RNA (ribonucleic acids) –
contains sugar ribose
• DNA (deoxyribonucleic acid) –
contains sugar deoxyribose
Questions
1. Name four groups of organic compounds
found in living things
carbohydrate, lipid, protein, nucleic acids
2. Describe at least one function of each
group of organic compounds
carbohydrates – energy
lipids – store energy
proteins – form tissue
nucleic acids – transmit hereditary
information
3. Compare the structures and
functions of lipids and starches
Lipids are made from carbon and
hydrogen. Starches are made of
carbon, hydrogen and oxygen.
They both can be used to store
energy
Section 4: Chemical
Reactions and Enzymes
Objectives
• What happens to chemical bonds
during chemical reactions?
• How do energy changes affect
whether a chemical reaction will
occur?
• Why are enzymes important to
living things?
The Big Idea
• Living things are made up of
chemical compounds
• Everything that happens to an
organism is based on chemical
reactions
Chemical Reactions
• A process that changes or
transforms one set of chemicals
into another
Reactants
• Elements or compounds that
enter into a reaction
Products
• Elements or compounds
produced by a chemical reaction
Example Reaction: Getting
rid of carbon dioxide
• In the blood
CO2 + H20  H2CO3 (carbonic acid)
• In the lungs
H2CO3  CO2 + H2O
Released as you
breathe
Energy in reactions
Energy-Absorbing Reaction
Energy-Releasing Reaction
Activation
energy
Products
Activation energy
Reactants
Reactants
Products
Activation Energy
• The energy that is needed to get
a reaction started
Enzymes
• Some chemical reactions are too
slow or have activation energies
that are too high to make them
practical for living tissue
• These chemical reactions are
made possible by catalysts
Catalyst
• Substance that speeds up the
rate of chemical reactions
• Work by lowering a reactions
activation energy
Enzyme
•
•
•
•
•
Biological catalysts
Speed up reactions in cells
Very specific
Named for the reaction is catylzes
Enzyme names always end in ase
Reaction pathway
without enzyme
Activation energy
without enzyme
Reactants
Reaction pathway
with enzyme
Activation
energy
with enzyme
Products
Substrates
• The reactants of enzyme
catalyzed reactions
• The active site of the enzyme and
the substrate have
complementary shapes
• Fit like a lock and key
Enzyme Action
Enzyme – substrate complex
ADP
Enzyme
(hexokinase)
Glucose
Substrates
Products
ATP
Glucose-6phosphate
Products
are released
Active site
Enzyme-substrate
complex
Substrates
are converted
into products
Substrates
bind to
enzyme
Regulation of Enzyme Activity
• Enzymes are affected by any
variable that affects chemical
reactions
1. pH
2. Temperature
3. Concentration
of enzyme
Questions
1. What happens to chemical bonds
during chemical reactions
Bonds are broken in reactants and
new bonds are formed in products
2. Describe the role of energy in
chemical reactions
some chemical reactions release
energy, and other chemical
reactions absorb energy. Energy
changes determine how easily a
chemical reaction will occur
3. What are enzymes, and how are
they important to living things?
Enzymes are biological catylasts.
Cells use enzymes to speed up
virtually every important chemical
reaction that takes place in cells
4. Describe how enzymes work,
including the role of the enzyme
substrate complex
Substrates, the reactants of an
enzyme-catylzed reaction, attach
to the enzyme at an active site
and form an enzyme – substrate
complex. Once the complex is
formed, the enzyme helps convert
substrate into product
5. A change in pH can change the
protein. How might a change in pH
affect the function of an enzyme such
as hexokinase (hint: think about the
analogy of the lock and key)
A change in pH could change the
shape of hexokinase. This change
would diminish the ability of glucose
and ATP to bind to the active site of
the enzyme.