2-1 The Nature of Matter
• Objective: You will be able to explain an
atom, element, and compound, describe the
types of bonds, explain why bonding is
important, and describe isotopes and their
functions.
Atoms
• Smallest basic unit of matter
• Subatomic particles:
• Protons- positive (+1)
• Neutrons- neutral
• Electrons- negative (-1)
• Nucleus in the middle=protons+ neutrons
Molecules/Compounds
• Substance composed of 2 or more elements
chemically combined.
• H2O= 2 hydrogens, 1 oxygen
Bonding• Bonds hold elements together to make
compounds
• Bonds store energy
• Types:
– Covalent- elements share electrons
– Ionic- electrons are added or taken away from
other elements
– Hydrogen bond- Weak chemical attraction
between a slightly positive hydrogen atom and a
slightly negative atom usually N or O.
Ionic Bonds
• Bond between 2 ions of
opposite charge
• Form ionic compounds
• Ions=charged particle
(gained or lost
electron)
• Metal gives electron to
nonmetal
Covalent Bond• 2 atoms sharing
electrons
– polar=unequal sharing
– Nonpolar=equal sharing
• Form molecules
• Nonmetal + nonmetal
• More than 2 electrons
can be shared (multiple
bonds)
Check for Understanding
• 1. What are the 2 main types of bonds?
• 2. Which bond is found in molecules?
• 3. What type of compound is found between
ions of opposite charge?
• 4. Which bond shares electrons?
• 5. What is created when molecules don’t
share the electrons equally?
• 6. How are positive ions formed? Negative
ions?
Properties of Water
• Objectives:
• List the properties of water
• Explain why water has so many properties
• Discuss how the properties of water affect
living things.
Properties of Water
• Water is the most abundant compound in
living organisms 2/3 of body is water.
• Composed of 2 atoms of hydrogen linked by
covalent bonds to 1 atom of oxygen
• Polar molecule: oxygen is not sharing
electrons nicely/equally with hydrogens
• Oxygen becomes slightly negative, hydrogens
become slightly positive.
Hydrogen Bonding
• Water’s polarity allows
it to form hydrogen
bonds with other
water molecules
• The hydrogen of one
water molecule is
attracted to the
oxygen of another
water molecule.
Properties of Water due to Polarity
and Hydrogen Bonding:• Cohesion- attraction of water molecules to
each other
• Helps create surface tension, beading of water
and animals walking on water.
• 2. Adhesion- attraction
of water to other
charged molecules
• Important for capillary
action- transporting
water from the roots of
plants to their leaves.
• 3. High Specific Heat- water resists a change in
temperature
• All the heat absorbed or released by water
goes 1st to break and for hydrogen bonds
instead of increasing or decreasing
temperature
• Example- water in ocean/lakes stays fairly
stable allowing life to continue
• 4. Universal Solvent- can
dissolve or break apart
many substances
• Will only dissolve polar and
ionic compounds
(hydrophilic)
• Nonpolar does not have any
+ or – ends that the water
would be attracted to in
order to pull them apart
(hydrophobic)
Solutions and Suspensions
–Solutions
–All the components of a solution are evenly
distributed throughout the solution.
–In a salt–water solution, table salt is the solute—
the substance that is dissolved.
–Water is the solvent—the substance in which
the solute dissolves.
Acids, Bases, and pH
•Acids, Bases, and pH• A water molecule can react to form hydrogen and
hydroxide ions.
• Water is neutral because the number of positive
hydrogen ions (H+) produced is equal to the number of
negative hydroxide ions (OH-) produced.
pH
• Measure of H+ ions in a solution
• Scale of 1-14
• More H+=more acidic, Lower pH#
• Less H+= more basic, Higher pH#
• The concentration of H+ and OH- in pure
water is equal= pH7
Acids, Bases, and pH•At a pH of 7, the
concentration of H+
ions and OH- ions is
equal.
•Pure water has a pH
of 7.
Solutions with a pH
below 7 are called acidic
because they have more
H+ ions than OH- ions.
The lower the pH, the
greater the acidity. Acid rain
Tomato juice
Lemon juice
Stomach acids
The pH Scale
Solutions with a pH
above 7 are called basic
because they have more
OH- ions than H+ ions.
The higher the pH, the
more basic the solution.
The pH Scale
Soap
Bleach
Oven cleaner
Ammonia solution
Acids and Bases
• Acids
– Proton Donors
– Release H+ ions in solution
– Ex-HCL
• Bases
– Proton acceptors
– Release hydroxyl ions (OH-)
– Ex-NaOH
Acids, Bases, and pH
–Buffers
•The pH of the fluids within most cells in the human body must generally be kept between 6.5 and 7.5.
• If the pH is lower or higher, it will affect the chemical reactions that take place within the cells.
Acids, Bases, and pH
–*Controlling pH is important for
maintaining homeostasis.
–One of the ways that the body controls
pH is through dissolved compounds called
buffers.
–*Buffers are weak acids or bases that
can react with strong acids or bases to
prevent sharp, sudden changes in pH.
• pH in most organisms needs to be kept within
a very narrow range.
• A small change in pH can disrupt cell
processes
• Buffers within an organism are used to
regulate pH so that pH homeostasis can be
maintained.
– Helps because it can bind to H+ ion when the H+
conc. Is high or release H+ ions when the H+
conc. Is low.
Check for Understanding
• 1. Why is water a polar molecule?
• 2. explain a hydrogen bond.
• 3. Explain the difference between adhesion
and cohesion.
• 4. What causes water to have such a high
specific heat?
• 5. What substances will not dissolve in water?
• 6. Explain why hydrophilic substances will
dissolve in water.
• 7. Explain the differences between the pH of
acids and bases.
• 8. If a cell’s pH increases, what would a buffer
do?
Carbon
• The basic element of organic compounds
– Inorganic compounds=no carbon
• Has 4 valence electrons available for bonding
• Likes to share electrons which causes covalent
bonds.
• Most common bonding partners: hydrogen,
oxygen, nitrogen, or another carbon atom.
• Carbon is important for 2 reasons
1.Carbon has 4 valence electrons that can form
strong covalent bonds.
2.Carbon can bond with itself.
Check for Understanding
Questions• 1. What is an organic molecule?
• 2. How many bonds can a carbon atom make?
• 3. What other atoms does carbon typically
bond with?
Polymerization
• Objectives:
• Describe a polymer
• explain how polymers are formed and broken
down.
Macromolecules•Macromolecules
•Macromolecules are
formed by a process
known as
polymerization.
•The smaller units,
or monomers, join
together to form
polymers.
Dehydration Synthesis
• Joining monomers together by taking the
hydroxyl group of one monomer and
hydrogen of another to form water.
Hydrolysis
• Breaking polymers into monomers by the
addition of water molecules
• -OH and H are restored on monomers
Nucleic Acids
• Objectives:
• Identify the chemical structure of a nucleic
acid.
• Discuss the uses nucleic acids in living things.
Nucleic Acids
•Nucleic Acids-C, H, O, N, P• Nucleic acids are macromolecules containing
hydrogen, oxygen, nitrogen, carbon, and phosphorus.
• *Nucleic acids are polymers assembled from individual
monomers known as nucleotides.
• Monomer=nucleotides
• Made of a 5-carbon sugar, a phosphate group, and a
nitrogen containing molecule/base
• Holds the cell’s genetic information (information for
making and building proteins)
• 2 types of nucleic acids:
• 1. DNA (deoxyribonucleic acid)- stores the
information for making proteins contains
deoxyribose sugar
• 2. RNA(ribonucleic acid)- helps build protein
contains ribose sugar.
Nucleic Acids
•Nucleotides consist of three parts:
• a 5-carbon sugar
• a phosphate group
• a nitrogenous base
•Individual nucleotides can be joined by covalent
bonds to form a polynucleotide, or nucleic acid.
Check for Understanding
• 1. What are the monomers for nucleic acids?
• 2. What are the 2 types of nucleic acids?
• 3. What are the functions of each type of
nucleic acid?
Carbohydrates
• Objectives:
• Identify the chemical structure of a
carbohydrate.
• Discuss the uses of carbohydrates in living
things.
Carbohydrates•Carbohydrates- CHO (carbon, hydrogen,
oxygen) in a 1:2:1 ratio
•Monomer=monosaccharide
•Store and release energy
•Body’s main energy source
•Typically end in –ose
•Glucose, fructose, galactose
•Ex. Sugar, rice, bread, pasta
Carbohydrate functions- Living things use carbohydrates as their main
source of energy.
– structure in plants (cellulose)
–used as fiber for animals.
–The carbon, hydrogen, and oxygen are used for
amino acids and fatty acids.
Carbohydrates
– The breakdown of sugars, such as glucose,
supplies immediate energy for all cell activities.
–Living things store extra sugar as complex
carbohydrates known as starches.
Types of Carbohydrates
• 1. Monosaccharides-simple sugars
• Glucose- most common source of sugar to
make energy
• Fructose- fruit sugar
• Deoxyribose- major component of DNA
• Ribose- major component of RNA
• 2. Disaccharides- two simple sugars joined by
dehydration synthesis
• Lactose(glucose/galactose)- found in mammals
milk
• Sucrose (glucose/fructose)- table sugar; found
in honey, fruits, and vegetables
• 3. Polysaccharides- long chains of simple sugars
joined by dehydration synthesis
• Starch-found in plants (roots), many glucoses joined
together in a long straight chain
• Glycogen- found in animals (liver or muscles)
• Many glucoses joined with branching
• When energy is needed by animals, a glucose is
hydrolyzed
• Cellulose- found in plant cell walls
• Very strong, long chain of glucoses joined together
• Can’t be digested by animal, but important because
stimulates the digestive tract to make mucus for
passage of waste.
Caloric value of Carbohydrates
• The caloric value is dependent on the number
of carbon-hydrogen bonds.
• If you have more carbohydrates than needed
they are converted to fats and stored.
• Lipids have the most caloric value
• Carbohydrates and Proteins have the same
amount.
Check for Understanding Question
• 1. How is a polymer made?
• 2. How is a polymer broken down?
• 3. What is the monomer for carbohydrates?
• 4. What is the function of carbohydrates?
• 5. What elements are found in carbohydrates?
• 6. Which polysaccharides are found in plants?
Animals?
Lipids
• Objectives:
• Identify the chemical structure of a lipid.
• Discuss the uses of lipids in living things.
Lipids
• Fats, oils, waxes, or sterols
• Made of C, H, O
• Nonpolar molecules (hydrophobic) not
soluble in water
• Monomer= glycerol bonded to fatty acids
• Provide insulation, protection, and store
energy long term
• Not the body’s 1st energy source (carbs are)
• Per gram, a lipid has more energy than a
carbohydrate because it has more carbon-
hydrogen bonds; however, it will always use
carbohydrates 1st as its energy source
• Ex- lard, butter, olive oil, peanut oil
• They contain two component molecules
(glycerols and fatty acids).
Lipids
– *Uses of Lipids
1. store energy, protects, insulates
2. important parts of biological membranes
3. waterproof coverings.
4. Production of some vitamins and hormones.
Characteristics of Lipids• 1. Saturated
• All single bonded carbons in fatty acid chain
• Solids at room temperature (fats)
• Ex. Lard, butter, bacon grease
• 2. Unsaturated
• At least one double or triple bonded carbon
• Liquid at room temperature (oils)
• Double/triple bond creates “kinks” or bends in chain which
gives more spacing between fatty acids allowing them to slide
past each other more easily
• Ex. Oilve oil, vegetable oil,
3. Fused rings- ex cholesterol, estrogen, testosterone
Lipids
–Many lipids are formed when a glycerol molecule
combines with compounds called fatty acids.
–*If each carbon atom in a lipid’s fatty acid chains is joined
to another carbon atom by a single bond, the lipid is said
to be saturated.
–*The term saturated is used because the fatty acids
contain the maximum possible number of hydrogen atoms.
lards, solid at room temperature, no double
bonded carbon
Lipids
–*If there is at least one carbon-carbon double
bond in a fatty acid, it is unsaturated.
–*Lipids whose fatty acids contain more than one
double bond are polyunsaturated.
–Lipids that contain unsaturated fatty acids tend
to be liquid at room temperature.
Types of Lipids
• Triglycerides- glycerol
molecule bonded to 3
fatty acids
• Fats and oils
• Long term energy
storage molecule
• 2. Phospholipids-
glycerol bonded to
2 fatty acids and a
phosphate
containing group
• Found in cell
membranes
• 3. Steroids- four fused/interlocking rings with
other functional or hydrocarbon groups
attached.
• Ex. Cholesterol (most abundant steroid- found
in cell membranes, brain), sex hormones
(estrogen, progesterone, testosterone), bile
salts, vitamin D
Caloric Value of Lipids
• Fats have a greater caloric value because fats
contain more energy (ATP) per gram than
carbohydrates or proteins.
Check for Understanding
Questions• 1. What are the functions of lipids?
• 2. What elements make up lipids? Why is this
different than carbs?
• 3. What are the types of lipids?
• 4. Which has more hydrogen, a saturated or
unsaturated lipid?
• 5. A ring shape is characteristic of what type of
lipid?
Proteins
• Objectives:
• Identify the chemical structure of a protein
• Discuss the uses of proteins in living things.
• List the things that affect the
structure/function of a protein
Proteins
•Made of C,H, O, and N
•Monomer= amino acids
•Diverse group with many different functions:
–1. structural-support and maintainance of cell shape
(as connective tissue and keratin in hair and nails).
–2. Contractile- mechanical work (muscles)
–3. Storage- keep essential substances readily
available
• 4. Defensive- provide protection against
foreign matter (antibodies)
• 5. Transport- carry substances through blook
to rest of body (hemoglobin)
• 6. Hormonal- regulate body functions by
sending messengers (insulin)
• 7. Enzymatic- catalyzed/speed up chemical
reactions without being changed itself (ATP
synthase)
Amino Acids• 20 Amino acids
• 12 made by the body, others must be
consumed (meat, nuts, beans)
• All amino acids have a central carbon with 4
different partners
– 1. Carboxyl group 2. Amino group
– 3. Hydrogen 4. R group or side chain varies
Structure
• Amino acids joined
together by dehydration
synthesis to form a
covalent bond called a
peptide bond (-OH from
carboxyl group of one
amino acid and the H
from the amino group of
another amino acid)
• 2 amino acids=dipeptide
• 3 or more=polypeptide
Function of Proteins
–*Some proteins control the rate of reactions and
regulate cell processes.
–*Some proteins are used to form bones and
muscles.
–*Other proteins transport substances into or out
of cells or help to fight disease.
Protein Levels of Structure
• 1. Primary Structure-
linear sequence of
amino acids
• Specific order
determines structure
and specific gene made
• 2. Secondary
Structure- regular
and repeated coiling
and folding.
• Gives the ability to
hydrogen bond
between functional
groups of the amino
acids.
• 3. Tertiary Structure-
folding in on itself due
to interactions between
side chain/R groups
• Held together in 3-D
shape by hydrogen
bonds, disulfide bridges,
ionic bonds, etc.
between side chains
• Globular and soluble
• 4. Quaternary Structure- interaction among
several polypeptide complexes
• Can be the same subunits or different
• Ex- hemoglobin, enzymes
Shape Determines Function• Denaturation- unraveling of protein shape
making them lose their function and becomin
inactive
• pH and temperature- changes in these cause
hydrogen bonds and other bonds between
side chains to be broken.
Check for Understanding
• 1. What are the monomers for proteins?
• 2. What makes amino acids different from one
another?
• 3. What do proteins do?
• 4. How many peptide bonds would you find in
a polypeptide 10 amino acids long?
• 5. What type of protein structure only
involves hydrogen bonding between different
functional groups of amino acids?
• 6. What type of protein structure involves
interactions between amino acid R groups?
• 7. What type of protein structure allows them
to become more soluble?
• 8. What happens when a protein denatures?
•Everything that happens in an organism, growth,
interactions with the environment, reproduction,
and movement Is based on chemical reactions.
•A chemical reaction is a process that changes
one set of chemicals into another set of
chemicals.
Example
• Cells constantly produce chemical
reactions as normal part of their activity.
• CO2 is carried by your blood to your lungs.
• CO2 is not very soluble in H20. Your
blood stream could not dissolve enough
to carry it away from your tissues.
•A chemical reaction takes place.
• CO2+ H2O H2CO3
• Carbonic
acid
•In the lungs the reaction is reversed
•H2CO3 CO2+H2O
•*When chemical bonds are formed or broken energy
is released or absorbed.
Enzymes
•Some chemical reactions that make life possible are
too slow or have activation energies that are too high
to make them practical for living tissue.
1. Enzymes speed up chemical reactions and lower
activation energy.
2. Enzymes are proteins
3. Enzyme ends in ase.
4. Substrates-molecules that change into new
products
–What happens to chemical bonds during
chemical reactions?
–Chemical reactions always involve changes in the
chemical bonds that join atoms in compounds.
–How do energy changes affect whether a
chemical reaction will occur?
–Energy Changes
Chemical reactions that release energy often occur
spontaneously. Chemical reactions that absorb energy will
not occur without a source of energy.
Example
•Remember the reaction in your lungs:
• CO2+H2O H2CO3
•This reaction is so slow that it would build up in your body and be toxic.
•The enzyme carbonic anhydrase speeds up the reaction by a factor of 10 million.
•Every organism must have a source of energy to carry out chemical reactions.
• Plants- from sunlight
• Animals- from eating
•The energy that is needed to get a reaction started is called activation energy.
Enzymes
•*A catalyst is a substance that speeds up the
rate of a chemical reaction.
•*Catalysts work by lowering a reaction's
activation energy.
•*Catalysts are not altered in this process and
can be used over and over again.
•Enzymes are proteins that are used as catalysts.
– Why are enzymes important to living things?
–*Enzymes are proteins that act as biological
catalysts.
–*Enzymes speed up chemical reactions that take
place in cells.
–*Enzymes act by lowering the activation energy.
Enzymes
•*Lowering the activation energy has a dramatic
effect on how quickly the reaction is completed.
Enzymes
–Enzymes are very specific, generally catalyzing
only one chemical reaction.
–For this reason, part of an enzyme’s name is
usually derived from the reaction it catalyzes.
•Enzyme Action• 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 reactants do not have enough energy, no reaction will
take place.
–The Enzyme-Substrate Complex
• *Enzymes provide a site where reactants can be
brought together to react, reducing the energy needed
for reaction.
• *The reactants of enzyme-catalyzed reactions are
known as substrates.
–The substrates glucose and ATP bind to the
active site on the enzyme, hexokinase, forming an
enzyme-substrate complex.
–*The fit is so precise that the active site and
substrates are often compared to a lock and key.
–The enzyme and substrates remain bound
together until the reaction is done and the
substrates are converted to products.
–The products of the reaction are released and
the enzyme is free to start the process again.
–Active site- location on enzyme where substrate
fits.
Enzyme Action
•An Enzyme-Catalyzed Reaction
How is enzyme activity like a lock
and key?• 1. An active site on the enzyme is like the lock
and the substrate is like the key.
• 2. The substrate comes into the enzyme and
fits perfectly on the active site.
• 3. The enzyme then contributes energy to get
the reaction started.
4. Once the reaction is finished, the reactants
leave the active site.
5. The enzyme is free and ready to take on
another substrate.
–Regulation of Enzyme Activity
• Enzymes can be affected by any variable that influences
a chemical reaction.
• Enzymes work best at certain pH values.
• Many enzymes are affected by changes in temperature.
• Buffers within an organism are used to regulate pH so
that pH homeostasis can be maintained. A small
change in pH can disrupt cell processes.
Reaction Types
• Endergonic or
Endothermic – takes in
energy or heat –
reaction vessel will feel
cool to the touch.
• Exergonic or
Exothermic – gives off
energy or heat –
Reaction vessel will feel
warm to the touch, or
light will be seen.
Checking for Understanding
1. How are and enzyme and a catalyst similar?
2. What role does an enzyme have in a
biochemical reaction?
3. Any enzyme (can/cannot) work in any
chemical reaction?
4. What kind of macromolecule is an enzyme?
5. What is the name given to a reaction that
releases chemical energy?