Download The Chemistry of Life

The Chemistry of Life
Chapter 2
Section 2.1 The Nature of Matter
Atoms - the basic unit that makes up all matter
• 2 main parts:
• Nucleus – the center of the atom
• Electron cloud – area around the nucleus
• Contains smaller particles called subatomic particles.
• Protons – found in nucleus
• Positively charged
• Mass = 1 atomic mass unit (1 u)
• Neutrons – found in nucleus
• No charge
• Mass = 1 atomic mass unit (1 u)
• Electrons – found in electron cloud
• Negatively charged
• No significant mass (1/1840 mass of proton)
Section 2.1 The Nature of Matter
Element
• Pure substance consisting of one type of atom
• Represented by 1-3 letter symbols
• First letter capitalized
• Other letters lower case
• Examples: H, Na, Uub
• All atoms of the same element have the same
number of protons
• Neutral atoms have the same number of protons and
electrons
• Isotopes
• Atoms of the same element that have different
numbers of neutrons and different masses
• All have the same chemical & physical properties
Section 2.1 The Nature of Matter
Atomic Number
• Equals the number of protons in an element
Mass Number
• Equals the sum of the protons and neutrons in an
element
Atomic Mass
• Weighted average of the masses of an element’s
isotopes
• The abundance of each isotope in nature is
considered when the average is calculated
Section 2.1 The Nature of Matter
Radioactive Isotopes
• Nuclei are unstable and break down at a constant
rate over time
• Radiation released may be dangerous
• Uses for radioisotopes:
• Determination of the ages of rocks and fossils
• Detection and treatment of cancer
• Killing of bacteria that cause food to spoil
• Used as “tracers” to follow the movement of
substances within organisms
Section 2.1 The Nature of Matter
Chemical Compounds
• Substance formed by the
chemical combination of two or
more elements in definite
proportions.
• Chemical formula
• Shows the composition of a
compound by a kind of short
hand
• Examples: H2O, NaCl
• The physical and chemical
properties of a compound are
usually very different from those
of the elements from which it is
formed.
Section 2.1 The Nature of Matter
Section 2.1 The Nature of Matter
Chemical Bonds
• Hold atoms together
• 2 main types:
• Ionic bonds
• Formed when electron(s) transferred from one
atom to another
• Transferred electrons are outer or valence
electrons
• Smallest part: ion
• Charged atom
• Negative ion: atom gains electron(s)
• Positive ion: atom loses electron(s)
• Very strong attraction
• Example: Sodium chloride (table salt)
Section 2.1 The Nature of Matter
Chemical Bonds
• Hold atoms together
• 2 main types:
• Covalent bonds
• Formed when one or more pairs
of valence electrons is shared
between two atoms.
• 1 pair: single bond
• 2 pairs: double bond
• 3 pairs: triple bond
• Smallest part: molecule
• Examples:
• Water (H2O)
• Oxygen gas (O2)
Section 2.1 The Nature of Matter
Chemical Bonds
• van der Waals forces
• Weak intermolecular attraction between
the oppositely charged regions of
nearby molecules
• Not as strong as ionic or covalent bonds
• Helps hold molecules together
• Especially when large
• Named after the scientist who
discovered them
Section 2.2 Properties of Water (pages 40 - 44)
Water Properties:
• Neutral molecule (10 protons and 10 electrons)
• Polar molecule
• Oxygen attracts electrons more than hydrogen
• Oxygen has more protons to attract electrons
• Shared electrons shared unequally
• Has a partial positive area (around hydrogens)
• Has a partial negative area (around oxygen)
• Electrons stay closer to oxygen
• Hydrogen bonds
• Attraction between hydrogen atom on one water
molecule and oxygen atom on another water molecule
• Not as strong as ionic or covalent bonds
• Multiple hydrogen bonds can form
Section 2.2 Properties of Water (pages 40 - 44)
Water Properties due to Hydrogen
bonding:
• Cohesion
• Attraction between molecules of the
same substance
• Causes water molecules to be drawn
together
• Causes “beading” of water drops
• Causes surface tension
• Allows some insects and spiders
to won on the surface of a pond.
Section 2.2 Properties of Water (pages 40 - 44)
Water Properties due to Hydrogen
bonding:
• Adhesion
• Attraction between molecules of different
substances
• Water more attracted to glass of
graduated cylinder than to other water
molecules
• Slight dip in water (meniscus) forms
due to attraction of water to glass
• Water rises in a narrow glass tube
due to attraction of water to glass
• Called capillary action
Section 2.2 Properties of Water (pages 40 - 44)
Water Properties due to Hydrogen bonding:
• High Heat Capacity
• It takes a large amount of heat energy to change
the temperature of water.
• Allows large bodies of water to absorb a great
deal of heat with little temperature change
• Oceans and lakes
• Protects water organisms from drastic
temperature changes
• Allows heat from chemical reactions inside
cells to be absorbed in the water of the cell to
keep cell temperatures regulated.
Section 2.2 Properties of Water (pages 40 - 44)
Mixture:
• Material composed of 2 or more elements or
compounds that are physically mixed together but
not chemically combined
• Solutions
• All parts of the mixture are evenly distributed
throughout the solution
• Solute: part of a solution being dissolved
• Example: sugar in sugar water
• Solvent: part of a solution doing the
dissolving
• Example: water in sugar water
• Water’s polarity gives it the ability to dissolve both
ionic compounds and other polar compounds.
Section 2.2 Properties of Water (pages 40 - 44)
Mixtures:
• Suspensions
• Mixture of water and undissolved material
• Movement of water keeps undissolved materials
suspended so they don’t settle out
• When movement of water stops, materials will settle to
the bottom
• Blood in your body contains solutions and suspensions:
• The liquid part of your blood is mostly water and
contains many dissolved compounds
• Blood also contains cells that do not dissolve in water
and stay suspended as long as the water continues to
move.
Section 2.2 Properties of Water (pages 40 - 44)
Acids, Bases, and pH:
• pH scale
• Ranges from 0 to 14
• Indicates concentration
of hydrogen ions (H+) in
solution
• pH less than 7 is acidic
• More H+ than OH• pH greater than 7 is
basic
• Less H+ than OH• pH equal to 7 is neutral
• Equal amounts H+
and OH-
Section 2.2 Properties of Water (pages 40 - 44) HONORS
pH:
• Means “function of hydrogen
ion concentration”
• Hydrogen ions (H+) can
also be written as
hydronium ions (H3O+)
• As the pH increases, the
concentration of hydrogen
or hydronium ions
decreases
• Each step on the pH scale
represents a negative
power of 10.
Section 2.2 Properties of Water (pages 40 - 44)
Acids:
• Any compound that
forms extra hydrogen
ions (H+) ions in solution
• Sour taste
• pH less than 7
• Strong acids:
• pH = 0 – 3
• Can be corrosive
to skin
• Stomach acid is
HCl (hydrochloric
acid)
Section 2.2 Properties of Water (pages 40 - 44)
Bases:
• Any compound that forms extra
hydroxide (OH-) ions in solution
• Bitter taste
• Used as cleansers because they
dissolve grease
• pH greater than 7
• Strong bases:
• pH = 11 – 14
• Can be corrosive to skin
• Lye is NaOH
• Chemical name is
sodium hydroxide
Section 2.2 Properties of Water (pages 40 - 44)
Buffers:
• Weak acid or base that can react with strong acids or bases to prevent sharp,
sudden changes in pH
• pH of most body fluids usually between 6.5 and 7.5
• Blood normal pH = 7.4
• Buffers found in our bodies keep us from large changes in pH to maintain
homeostasis
• Antacids are sometimes used to buffer stomach acids
Section 2.3 Carbon Compounds (pages 45 - 49)
Carbon Chemistry
• Organic Chemistry
• Study of compounds that contain
bonds between carbon atoms
• Inorganic Chemistry
• Study of all other compounds
• Carbon can combine with many elements
to form the molecules of life
• Including: hydrogen, oxygen,
phosphorus, sulfur, and nitrogen
• Remember CHONPS
• Living organisms are made up of
molecules that consist of carbon and
these other elements
Section 2.3 Carbon Compounds (pages 45 - 49)
Carbon Atoms
• Have 4 valence electrons
• Carbon atoms can bond to each other and other elements
• Can form 4 bonds
• Carbon compounds can form single, double, or triple covalent bonds
• Many different shapes of carbon compounds can be seen
• Chains
• Branched structures
• Ring structures
Section 2.3 Carbon Compounds (pages 45 - 49)
Macromolecules
• Large organic compounds
• Means “giant” molecules
• Most formed by the process of polymerization
• Large compounds being built by joining
smaller ones together
• Monomers are the smaller compounds
• Polymers are the large compounds being
built
• The monomers in a polymer may all be identical
or may be different
• There are 4 groups of macromolecules based on
their chemical composition:
• Carbohydrates, lipids, nucleic acids, proteins
Section 2.3 Carbon Compounds (pages 45 - 49)
Carbohydrates
• Macromolecules
• Made of carbon, hydrogen, and oxygen
• Hydrogen and oxygen in 2:1 ratio
• Means carbon + water
• Functions:
• Main source of energy for organisms
• Structural purposes
• Like the strings in celery
• Polymers
• Made of monomers called simple
sugars or monosaccharides
• Called polysaccharides
Section 2.3 Carbon Compounds (pages 45 - 49)
Section 2.3 Carbon Compounds (pages 45 - 49)
Carbohydrates
• Monosaccharides
• Simple sugars
• Examples: glucose, fructose, galactose
• Disaccharides
• Double sugars
• Made by joining two monosaccharides
• Example: sucrose
• Made of glucose + fructose
• Polysaccharides
• Complex carbohydrates
• Polymers
• 3 main types:
• Starches, glycogen, and cellulose
Section 2.3 Carbon Compounds (pages 45 - 49)
Polysaccharides (Complex sugars)
• Starches
• Polysaccharides used by plants to store
excess sugar
• Cellulose
• Tough, flexible fibers that give plants much of
their strength and rigidity
• Glycogen
• Used by animals to store excess sugars
• We store in our liver
• When blood sugar is low, glycogen is
released into the blood
• Used by muscles for contractions and
movement
Section 2.3 Carbon Compounds (pages 45 - 49)
Lipids
• Macromolecules
• No monomers
• Not a polymer
• Made mostly of carbon and hydrogen
• Few oxygen
• Common categories: fats, oils, and waxes
• Generally not soluble in water
• Functions:
• Store energy
• Important parts of biological membranes
• Waterproof coverings
• Chemical messengers (steroids produced by
the body)
Section 2.3 Carbon Compounds (pages 45 - 49)
Lipids
• Many formed when a glycerol molecule
combines with compounds called fatty acids
• Circulating fats are called triglycerides
• Saturated Fats
• Contain the maximum possible number of
hydrogen atoms
• No double bonds between the carbon
atoms on the fatty acids
• Less healthy
Section 2.3 Carbon Compounds (pages 45 - 49)
Lipids
• Unsaturated Fats
• Have at least one double bond between the
carbon atoms on the fatty acids
• Polyunsaturated fats have more than one
double bond between the carbon atoms on
the fatty acids
• More healthy
• Trans Fats
• Unsaturated fat that has had air whipped into
it until it becomes saturated
• Example: shortening
• Found in some cookies, crackers, and
doughnuts
• Very unhealthy!
Section 2.3 Carbon Compounds (pages 45 - 49)
Lipids
• Fats
• Usually solid at room temperature
• From animals
• Less healthy
• Some plants
• Coconut oil can be solid at
room temp
• More healthy
• Usually saturated fats
Section 2.3 Carbon Compounds (pages 45 - 49)
Lipids
• Oils:
• Usually liquid at room temperature
• Plants
• Usually more healthy
• Usually unsaturated
• Can be monounsaturated or
polyunsaturated
Section 2.3 Carbon Compounds (pages 45 - 49)
Lipids
• Waxes: usually solid at room
temperature
• Sources: Animals and
plants
• Honeycomb, wax on outside
of cucumbers
Section 2.3 Analyzing Data (page 48)
Comparing Fatty Acids
1. Which of the 4 fatty acids is
saturated? Which are
unsaturated?
• Stearic acid is saturated
• The other 3 fatty acids are
unsaturated.
2. How does melting point change as
the number of carbon-carbon
double bonds increases?
• Melting point decreases as the
number of double bonds increases.
Fatty Acid
Number of
Carbons
Number of
Double Bonds
Melting
Point (°C)
Stearic Acid
18
0
69.6
Oleic Acid
18
1
14
Linoleic Acid
18
2
-5
Linolenic Acid
18
3
-11
3. If room temperature is 25°C, which fatty
acid is a solid at room temperature?
Which is liquid at room temperature?
• Stearic acid is solid at room temperature
• The other 3 fatty acids are liquid at room
temperature.
Section 2.3 Carbon Compounds (pages 45 - 49)
Nucleic Acids
• Macromolecules
• Made of hydrogen, oxygen, nitrogen, carbon, and
phosphorus
• Polymers: Nucleic acids or polynucleotides
• Monomers: Nucleotides
• 3 main parts:
• 5-carbon sugar
• Phosphate group
• Nitrogen base (also nitrogenous)
• Function:
• Store and transmit hereditary or genetic information
• 2 main types: DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)
Section 2.3 Carbon Compounds (pages 45 - 49)
Section 2.3 Carbon Compounds (pages 45 - 49)
Proteins
• Macromolecules
• Made of nitrogen, carbon, hydrogen, and
oxygen
• Polymers: Proteins or polypeptides
• Monomers: Amino acids
• Compounds with an amino group (NH2) on one end and a carboxyl group
(-COOH) on the other end
• Linked together by peptide bonds to
form a protein or polypeptide (polymer)
Section 2.3 Carbon Compounds (pages 45 - 49)
Proteins
• Functions:
• Control the rate of chemical reactions
• Regulate cell processes
• Form important cellular structures
• Transport substances into or out of
cells
• Help to fight disease
Section 2.3 Carbon Compounds (pages 45 - 49)
Proteins
• More than 20 different amino acids found in nature
• Since all amino acids have an amino group and a
carboxyl group, they can join to any other amino
acids
• Makes proteins very diverse
• Levels of organization in proteins:
• Primary structure: sequence of amino acids
• Secondary structure: folding or coiling of
polypeptide chain
• Tertiary structure: complete 3-D arrangement
of polypeptide chain
• Quaternary structure: proteins with more than
one chain are arranged in a specific way
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
Chemical Reactions
• Process that changes, or transforms, one set
of chemicals into another.
• Mass and energy are absorbed during
chemical reactions
• Including chemical reactions in living
organisms
• Some reactions happen slowly
• Example: When iron and oxygen react to
form rust
• Some reactions happen quickly
• Example: When baking soda and
vinegar are mixed
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
Chemical Reactions
• Reactants
• The elements or compounds that enter into a
chemical reaction
• Products
• The elements or compounds produced by a
chemical reaction
• Coefficients
• Whole numbers placed in front of elements or
compounds in a chemical equation
• Used to balance chemical equations
• Chemical reactions involve changes in the
chemical bonds that join atoms in compounds.
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
Energy in Reactions
• Energy is released or absorbed whenever chemical bonds are formed or broken
• Chemical reactions involved changes in energy
• Chemical reactions that release energy often occur spontaneously
• Chemical reactions that absorb energy will not occur without a source of energy
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
Energy in Reactions
• With reversible chemical reactions, if the reaction
releases energy in one direction
2H2 + O2  2H2O
• The reaction will absorb energy in the other
direction, and will not occur spontaneously
2H2O  2H2 + O2
Energy Sources
• In order to stay alive, organisms need to carry out
reactions that require energy
• Plants get their energy by trapping and storing
energy from the Sun
• Animals get their energy when they consume
other animals or plants
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
Activation Energy
• Energy needed to get a chemical reaction started
• Needed regardless of whether a reaction releases or absorbs energy
• Energy releasing reactions need a lower activation energy than energy
absorbing reactions
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
• A catalyst is a substance that:
• Speeds up the rate of a chemical reaction
• Does not get used up in a chemical reaction
• Lowers activation energy
• Enzymes
• Proteins that act as biological catalysts
• Speed up reactions that take place in cells
• Lowers activation energy
• Are very specific
• Usually only catalyze one chemical reaction
• Part of the enzyme’s name comes from the reaction it catalyzes.
• Usually ends in –ase
• Example: Carbonic anhydrase gets it name because it catalyzes the reverse
reaction that removes water from carbonic acid
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
• Without carbonic anhydrase, the reaction is very slow
• Carbon dioxide can build up in the blood to dangerous levels
• When carbonic anhydrase is present, the reaction takes place immediately
• Carbon dioxide gets removed quickly from the blood
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
Enzyme-Substrate Complex
• For chemical reactions to occur, reactants
must collide with enough energy so that
existing bonds are broken and new bonds
will be formed.
• If reactants do not have enough energy, they
will not be changed after the collision
• Enzymes provide a site where reactants can
come together to react
• The site reduces the activation energy
• Called the active site
• Reactants of enzyme-catalyzed reactions
are called substrates
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
Enzyme-Substrate Complex
• The substrate and active site on the
enzyme have complementary
shapes
• The fit between the substrate and
active site is so precise, it can be
compared to a lock and a key
• The active site on the enzyme is
the lock
• The substrate (reactant) is the
key
• The “key” will only fit into one
“lock”
Section 2.4 Chemical Reactions and Enzymes (pages 50-53)
Regulation of Enzyme Activity
• Enzymes play essential roles in:
• Controlling chemical pathways
• Making materials cells need
• Releasing energy
• Transferring information
• Factors that affect enzyme activity:
• Change in temperature
• Enzymes work at specific temperatures
• Change in pH
• Enzymes work at specific pH
• Regulatory molecules
• Enzymes cannot work when certain
substances are present