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UNIT 1:
Biochemistry
THINK ABOUT IT
Think about important news stories you’ve heard. Bird flu
spreads around the world, killing birds and threatening a
human epidemic. Users of certain illegal drugs experience
permanent damage to their brains and nervous systems.
Reports surface about efforts to clone human cells.
These and many other stories involve biology—the science that
employs scientific methodology to study living things. The
Greek word bios means “life,” and -logy means “study of.”
Unit 1 Content Expectations
LIFE Describe the 8 characteristics of life.
B2.4f - recognize and describe that both living and nonliving things are composed of compounds,
which are themselves made up of elements joined by energy-containing bonds, such as those in
ATP.
B2.5A Recognize and explain that macromolecules such as lipids contain high energy bonds.
B2.2B - Recognize the six most common elements in organic molecules (C, H, N, O, P, S).
B2.2A - Explain how carbon can join to other carbon atoms in chains and rings to form large
and complex molecules.
B2.2C - Describe the composition of the four major categories of organic molecules
(carbohydrates, lipids, proteins, and nucleic acids).
B2.2D - Explain the general structure and primary functions of the major complex organic
molecules that compose living organisms.
B2.2E Describe how dehydration and hydrolysis relate to organic molecules.
B2.2f - Explain the role of enzymes and other proteins in biochemical functions (e.g., the protein
hemoglobin carries oxygen in some organisms, digestive enzymes, and hormones).
Unit 1 Big Idea
Living things are made up of energy rich complex chemical
structures.
Unit 1 Core Concepts
Living things are made up of four major types of organic
molecules: carbohydrates, lipids, proteins and nucleic
acids.
Organisms are made up of different arrangements of these
molecules, giving all life a biochemical framework.
Carbohydrates and lipids contain many C-H bonds that store
energy.
Peer Review
Scientists share their findings with the
scientific community by publishing articles that
have undergone peer review.
In peer review, scientific papers are reviewed
by anonymous, independent experts.
Reviewers read them looking for oversights,
unfair influences, fraud, or mistakes in
techniques or reasoning. They provide expert
assessment of the work to ensure that the
highest standards of quality are met.
IN YOUR NOTES
Predict what might happen if an article
is published without undergoing peer
review.
Scientific Theories
What is a scientific theory?
In science, the word theory applies to a well-tested explanation that unifies
a broad range of observations and hypotheses and that enables scientists
to make accurate predictions about new situations.
Scientific Theories
Evidence from many scientific studies may support several related hypotheses
in a way that inspires researchers to propose a scientific theory that ties those
hypotheses together.
In science, the word theory applies to a well-tested explanation that unifies a
broad range of observations and hypotheses and that enables scientists to
make accurate predictions about new situations.
A useful theory that has been thoroughly tested and supported by many lines of
evidence may become the dominant view among the majority of scientists, but
no theory is considered absolute truth.
Science is always changing; as new evidence is uncovered, a theory may be
revised or replaced by a more useful explanation.
Avoiding Bias
The way that science is applied in society can be affected by bias, which is a
particular preference or point of view that is personal, rather than scientific.
Science aims to be objective, but scientists are human, too. Sometimes
scientific data can be misinterpreted or misapplied by scientists who want to
prove a particular point.
Recommendations made by scientists with personal biases may or may not be
in the public interest. But if enough of us understand science, we can help
make certain that science is applied in ways that benefit humanity.
• LIFE
Describe the 8
characteristics of life.
Characteristics of Living Things
Biology is the study of life. But what is life?
No single characteristic is enough to describe a living thing. Also, some
nonliving things share one or more traits with organisms.
Some things, such as viruses, exist at the border between organisms and
nonliving things.
Characteristics of Living Things
Despite these difficulties, we can list characteristics that most living things have
in common. Both fish and coral, for example, show all the characteristics
common to living things.
Characteristics of Living Things
Living things are based on a universal genetic code.
All organisms store the complex information they need to live, grow, and
reproduce in a genetic code written in a molecule called DNA.
That information is copied and passed from parent to offspring and is almost
identical in every organism on Earth.
Characteristics of Living Things
Living things grow and develop.
During development, a single fertilized egg divides again and again.
As these cells divide, they differentiate, which means they begin to look
different from one another and to perform different functions.
Characteristics of Living Things
Living things respond to their environment.
A stimulus is a signal to which an organism responds.
For example, some plants can produce unsavory chemicals to ward off
caterpillars that feed on their leaves.
Characteristics of Living Things
Living things reproduce, which means that they produce new similar
organisms.
Most plants and animals engage in sexual reproduction, in which cells from
two parents unite to form the first cell of a new organism.
Other organisms reproduce through asexual reproduction, in which a
single organism produces offspring identical to itself.
Beautiful blossoms are part of an apple tree’s cycle of sexual reproduction.
Characteristics of Living Things
Living things maintain a relatively stable internal environment, even
when external conditions change dramatically.
All living organisms expend energy to keep conditions inside their cells
within certain limits. This conditionprocess is called homeostasis.
For example, specialized cells help leaves regulate gases that enter
and leave the plant.
Characteristics of Living Things
Living things obtain and use material and energy to grow, develop, and
reproduce.
The combination of chemical reactions through which an organism
builds up or breaks down materials is called metabolism.
For example, leaves obtain energy from the sun and gases from the air.
These materials then take part in various metabolic reactions within the
leaves.
Characteristics of Living Things
Living things are made up of one or more cells—the smallest units
considered fully alive.
Cells can grow, respond to their surroundings, and reproduce.
Despite their small size, cells are complex and highly organized.
For example, a single branch of a tree contains millions of cells.
Characteristics of Living Things
Taken as a group, over generations, organisms evolve, or change over
time.
Evolutionary change links all forms of life to a common origin more than
3.5 billion years ago.
Characteristics of Life video
THINK ABOUT IT...
What are you made of?
Just as buildings are made from bricks, steel, glass, and wood, living things are
made from chemical compounds.
When you breathe, eat, or drink, your body uses the substances in air, food,
and water to carry out chemical reactions that keep you alive.
The first job of a biologist is to understand the chemistry of life.
Atoms
What three subatomic particles make up atoms?
The subatomic particles that make up atoms are protons (+), neutrons(O),
and electrons (-).
Atoms
The study of chemistry begins with the basic unit of matter, the atom.
The concept of the atom came first from the Greek philosopher Democritus, nearly
2500 years ago.
Democritus asked, can you divide a substance without limit, or does there come a
point at which you cannot divide the substance without changing it into something
else?
Democritus thought that there had to be a limit, and he called the smallest
fragment the atom, from the Greek word atomos, which means “unable to be cut.”
Atoms
Atoms are incredibly small. Placed side by
side, 100 million atoms would make a row
only about 1 centimeter long—about the
width of your little finger!
Despite its extremely small size, an atom
contains subatomic particles that are even
smaller.
The subatomic particles that make up atoms
are protons, neutrons, and electrons.
The subatomic particles in a carbon atom
are shown.
Protons and Neutrons
Protons and neutrons have about the same
mass.
Protons are positively charged particles (+)
and neutrons carry no charge at all.
Strong forces bind protons and neutrons
together to form the nucleus, at the center
of the atom.
Electrons
The electron is a negatively charged
particle (–) with only 1/1840 the mass of a
proton.
Electrons are in constant motion in the
space surrounding the nucleus. They are
attracted to the positively charged nucleus
but remain outside the nucleus because of
the energy of their motion.
Electrons
Because atoms have equal numbers of
electrons and protons, their positive and
negative charges balance out, and atoms
themselves are electrically neutral. The
carbon atom shown has 6 protons and 6
electrons.
Elements and Isotopes
A chemical element is a pure substance that
consists entirely of one type of atom.
More than 100 elements are known, but only
about two dozen are commonly found in living
organisms.
Elements are represented by one- or two-letter
symbols. For example, C stands for carbon, H for
hydrogen, Na for sodium, and Hg for mercury
(shown).
Elements and Isotopes
The number of protons in the nucleus of an
element is called its atomic number. Carbon’s
atomic number is 6, meaning that each atom of
carbon has six protons and, consequently, six
electrons.
Chemical Compounds
In what ways do compounds differ from their component elements?
The physical and chemical properties of a compound are usually very
different from those of the elements from which it is formed.
For example, sodium is a silver-colored metal that is soft enough to cut with
knife. It reacts explosively with cold water. Chlorine is a very reactive,
poisonous, greenish gas that was used in battles during World War I.
However, the compound sodium chloride--table salt--is a white solid that
dissolves easily in water, is not poisonous, and is essential for the survival
of most living things.
a
Parts of an Atom Video
• B2.4f
recognize and describe that
both living and nonliving things
are composed of compounds,
which are themselves made up
of elements joined by energycontaining bonds, such as
those in ATP..
Chemical Compounds
A chemical compound is a substance formed by the chemical combination of two
or more elements in definite proportions.
Scientists show the composition of compounds by a kind of shorthand known as a
chemical formula. Water, which contains two atoms of hydrogen for each atom of
oxygen, has the chemical formula =H2O. The formula for table salt, NaCl, indicates
that the elements that make up table salt—sodium and chlorine—combine in a 1:1
ratio.
Chemical Bonds
The atoms in compounds are held together by various types of chemical
bonds.
Bond formation involves the electrons that surround each atomic nucleus.
The electrons that are available to form bonds are called valence electrons.
The main types of chemical bonds are ionic bonds and covalent bonds.
Ionic Bonds
An ionic bond is formed when one or more electrons are transferred from
one atom to another.
An atom that loses electrons becomes positively charged. An atom that
gains electrons has a negative charge. These positively and negatively
charged atoms are known as ions.
Ionic Bonds
Ionic bonds form between sodium and chlorine to form NaCl, table salt.
Ionic Bonds
A sodium atom easily loses its one valence electron and becomes a sodium ion
(Na+).
Ionic Bonds
A chlorine atom easily gains an electron (from sodium) and becomes a chloride
ion (Cl-).
Ionic Bonds
These oppositely charged ions have a strong attraction for each other, forming
an ionic bond.
Ionic Bond Video
Covalent Bonds
Covalent bonds involve electrons being shared by atoms instead of being
transferred.
The moving electrons travel about the nuclei of both atoms, forming a covalent
bond.
When the atoms share two electrons, the bond is called a single covalent bond.
Sometimes the atoms share four electrons and form a double bond. In a few
cases, atoms can share six electrons, forming a triple bond.
Covalent Bonds
The structure that results when atoms are
joined together by covalent bonds is called a
molecule, the smallest unit of most
compounds.
This diagram of a water molecule shows that
each hydrogen atom is joined to water’s lone
oxygen atom by a single covalent bond. Each
hydrogen atom shares two electrons with the
oxygen atom.
Covalent Bonds
When atoms of the same element join together, they also form a molecule.
Oxygen molecules in the air you breathe consist of two oxygen atoms joined by
covalent bonds.
Covalent Bond Video
• B2.5A
Recognize and explain that
macromolecules such as
lipids contain high energy
bonds.
High Energy Bonds
High energy bonds are found in organic molecules such as lipids and ATP.
They are covalent bonds that, when broken, release high amounts of energy.
So, the energy needed for your cells to function is stored in high energy
bonds. When your cell needs energy, it breaks those bonds by breaking down
molecules like carbohydrates, lipids, and ATP.
Why don't we eat rocks?
Our cells break down macromolecules such as lipids and proteins to
get energy. Each bond in a macromolecule holds energy. Bonds
between Carbon and Hydrogen (as well as those in ATP) hold LOTS
of energy and are called HIGH ENERGY BONDS.
We eat food to get energy. Our food is made up of macromolecules.
Our body breaks down those macromolecules to get energy. In other
words, rocks aren't made up of organic macromolecules so we
cannot use them for energy!!!
High Energy Bonds Movie
B2.2B
Recognize the six most
common elements in
organic molecules (C, H, N,
O, P, S).
The Chemistry of Carbon
What elements does carbon bond with to make up life’s molecules?
Carbon can bond with many elements, including hydrogen, nitrogen,
oxygen, phosphorus, and sulfur to form the molecules of life.
B2.2A
Explain how carbon can
join to other carbon atoms
in chains and rings to form
large and complex
molecules.
Carbon videos
The Chemistry of Carbon
Carbon atoms have four valence electrons, allowing them to form strong
covalent bonds with many other elements, including hydrogen, oxygen,
phosphorus, sulfur, and nitrogen.
Living organisms are made up of molecules that consist of carbon and
these other elements.
The Chemistry of Carbon
Carbon atoms can also bond to each other in chains and rings, which gives
carbon the ability to form millions of different large and complex structures.
Carbon-carbon bonds can be single, double, or triple covalent bonds.
Chains of carbon atoms can even close up on themselves to form rings.
B2.2A - Explain how carbon can join to other carbon atoms in chains and
rings to form large and complex molecules.
THINK ABOUT IT
In the early 1800s, many chemists called the compounds created by organisms
“organic,” believing they were fundamentally different from compounds in
nonliving things.
We now understand that the principles governing the chemistry of living and
nonliving things are the same, but the term “organic chemistry” is still around.
Today, organic chemistry means the study of compounds that contain bonds
between carbon atoms, while inorganic chemistry is the study of all other
compounds.
B2.2C
Describe the composition of the
four major categories of organic
molecules (carbohydrates, lipids,
proteins, and nucleic acids).
B2.2D
Explain the general structure and
primary functions of the major
complex organic molecules that
compose living organisms.
Carbohydrates
Carbohydrates are compounds made up
of carbon, hydrogen, and oxygen atoms,
usually in a ratio of 1 : 2 : 1.
Living things use carbohydrates as their
main source of energy. The breakdown of
sugars, such as glucose, supplies
immediate energy for cell activities.
Plants, some animals, and other
organisms also use carbohydrates for
structural purposes.
Carbohydrates
Carbohydrates (like Glucose) are actually many subunits called Sugars that
have been joined together. When an organism needs energy, it breaks down
carbohydrates by breaking the bonds within it. This supplies immediate energy
for the organism's cells.
Lipids
Lipids are a large and varied group of biological molecules. Lipids are made
mostly from carbon and hydrogen atoms and are generally not soluble in water.
The common categories of lipids are fats, oils, and waxes.
Lipids can be used to store energy. Some lipids are important parts of biological
membranes and waterproof coverings.
Steroids synthesized by the body are lipids as well. Many steroids, such as
hormones, serve as chemical messengers.
Lipids
Many lipids are formed when a glycerol molecule combines with compounds
called fatty acids.
The picture below shows one Lipid molecule. It is made up of glycerol and fatty
acids (subunits).
Nucleic Acids
Nucleic acids store and transmit hereditary, or genetic, information.
Nucleic acids are macromolecules containing hydrogen, oxygen, nitrogen,
carbon, and phosphorus.
Nucleic acids are assembled from subunits known as nucleotides.
Nucleic Acids
Nucleotides consist of three parts: a 5carbon sugar, a phosphate group
(–PO4), and a nitrogenous base.
Some nucleotides, including adenosine
triphosphate (ATP), play important roles in
capturing and transferring chemical energy.
Nucleic Acids
Individual nucleotides can be joined by
covalent bonds to form nucleic acid.
There are two kinds of nucleic acids:
ribonucleic acid (RNA) and deoxyribonucleic
acid (DNA). RNA contains the sugar ribose
and DNA contains the sugar deoxyribose.
Protein
Proteins are macromolecules that contain nitrogen as well as carbon,
hydrogen, and oxygen.
Proteins are made of subunits called amino acids.
Proteins perform many varied functions, such as controlling the rate of
reactions and regulating cell processes, forming cellular structures, transporting
substances into or out of cells, and helping to fight disease.
Protein
Amino acids are compounds with an amino group (–NH2) on one end and a
carboxyl group (–COOH) on the other end.
Covalent bonds called peptide bonds link amino acids together to form a
polypeptide.
A protein is a functional molecule built from one or more polypeptides.
B2.2E
Describe how dehydration
and hydrolysis relate to
organic molecules.
Dehydration & Hydrolysis
The four macromolecules we just discussed (Carbohydrates, Lipids, Nucleic
Acids, and Proteins) are made up of subunits. Those subunits join together
to make the macromolecule.
Dehydration is when macromolecule subunits join together, the subunits lose
an H and an OH. The H and OH pair up to form..... WATER! ( H + OH = H2O
) This is called DEHYDRATION because the subunits are losing a water
molecule.
Dehydration & Hydrolysis
The opposite of dehydration is HYDROLYSIS. Hydrolysis is when a
macromolecule breaks into its original subunits and the H and OH are
reattached to the subunits.
Therefore, in HYDROLYSIS, a water molecule is used up to separate a
macromolecule into its subunits.
Dehydration & Hydrolysis
1. For which reaction is water used up?
2. Which reaction makes a macromolecule from its
subunits?
B2.2f - Explain the role of
enzymes and other proteins
in biochemical functions
(e.g., the protein hemoglobin
carries oxygen in some
organisms, digestive
enzymes, and hormones).
Enzymes
What role do enzymes play in living things and what affects their
function?
Enzymes speed up chemical reactions that take place in cells and
facilitate the breakdown of complex molecules by acting as
substrate-specific catalysts.
Temperature, pH, and regulatory molecules can affect the activity
of enzymes.
The Enzyme-Substrate Complex
For a chemical reaction to take place, the reactants must collide with
enough energy so that existing bonds will be broken and new bonds
will be formed.
If the reactants do not have enough energy, they will be unchanged
after the collision.
Enzymes provide a site where reactants can be brought together to
react. Such a site reduces the energy needed for reaction.
The Enzyme-Substrate Complex
The reactants of enzyme-catalyzed
reactions are known as substrates.
For example, the enzyme carbonic
anhydrase converts the substrates
carbon dioxide and water into
carbonic acid (H2CO3).
The Enzyme-Substrate Complex
The substrates bind to a site on the enzyme called the active site.
The active site and the substrates have complementary shapes.
The fit is so precise that the active site and substrates are often
compared to a lock and a key.
The Enzyme-Substrate Complex
Enzyme video 1