Transcript The Chemistry of Life

The Chemistry of Life
Atoms
• All matter is made up of elements, which are
substances that cannot be broken down into
smaller substances in a chemical reaction.
• An atom, the fundamental unit of matter, is
the smallest unit of an element that displays
all of that element’s characteristics.
Continue…
• Atoms contain the following subatomic particles:
– Protons: positively charged particles located with the
atomic nucleus, or core of the atom
– Neutrons: Electrically neutral particles located within
the atomic nucleus.
– Electrons: Negatively charged particles orbiting in a
cloud around the atomic nucleus
electron
neutron
proton
Continue…
• Atoms are described by their atomic number and
mass number
– Atomic number: indicates the number of protons in an
atom.
– Mass number: indicates the combined number of protons
and neutrons in an atom
• Atom’s chemical symbol, the written representation
of an atom includes atomic number, mass number,
any charge on the atom.
Atomic Behavior
• Is largely determined by the number and
arrangement, or electron structure, of
electrons orbiting its nucleus.
• Electrons move about in regions called
orbitals located at varying distances from the
nucleus.
Electron Shells
• All of an atom’s electrons are arranged in
orbitals located at different energy levels,
called electron shells, around the nucleus.
• Shells further away from the nucleus requires
more energy.
• Electrons tend to move toward lower energy
positions and will fill orbitals in the lowest
electron shells before filling orbitals in
electrons shells farther out.
Continue…
• Each electron shell has a maximum number of
orbitals, and therefore electrons that it can hold:
– First electron shell – maximum one orbital- 2 electrons
– Second electron shell- maximum 4 orbitals- 8 electrons
– Third electron shell- maximum 4 orbitals – 8 electrons
– Four electron shell- maximum 4 orbitals- 8 electrons
Valence Electrons
• Occupy the energy shell farthest from the
nucleus.
• Atoms with a full complement of electrons in
their outermost shell are more stable  and
less reactive.
• These valence electrons will help in the
forming of chemical bonds.
Example: Valence Electrons
• Sodium 11Na has 11 electrons. Two electrons in the
first shell, 8 in the second shell and 1 in the last (3rd
shell). To create a full outer shell electrons, a
sodium atom loses the single valence electron from
the third shell.
• In contrast, chlorine, 17Cl has seventeen electrons.
Two in the first orbital, 8 in the second orbital, 7 in
the third orbital. To create a full outer shell
electrons, a chlorine atom gains one electron.
Ions
• An ion is an atom that has acquired a positive or
negative electric charge by gaining or losing electrons.
• There are two types of ions:
– Cation: is an atom that has lost electrons and acquired a
positive charge (Example: Sodium)
– Anion: is an atom that has gained electrons and acquired a
negative charge (Example: Chlorine)
Example: Potassium (K) can lose an electron to become a cation,
K+. Sulfur (S) can lose two electrons to become an anion, S-2
Isotopes
• Are atoms of the same element that have different
number of neutrons and therefore different atomic
masses.
• Example: There are three naturally occurring carbon
isotopes, each with a different atomic number: Carbon
-12, Carbon-13, and Carbon-14. As represented in the
atomic number, carbon-14 has one more neutron than
carbon-13 and two more neutrons than carbon-12
Radioactive Isotopes
• Are highly unstable and spontaneously decay
by losing protons or neutrons along with
energy. The rate of decay is constant for any
given isotopes
• Half-life: is a measure of the amount of time it
takes for half of the atoms in that substance to
decay
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• All living organisms are composed of carbon14 and carbon-12 in a certain ratio, designated
by the variable x.
– Half life of carbon-14 is 5, 730 years and will decay
to nitrogen-14
• Scientist measure the ratio of radioactive
isotopes such as carbon-14 against other
elements present in a fossil to determine the
approximate age of the fossil.
Example of radioactive isotopes
• The age of a bone fossil that contains carbon14 and carbon-12 in a ratio of 1/8 x can be
dtermined using the half-life of carbon-14.
Because one-eighth is (1/2)3, three half-lives
have passed for carbon-14 presnet in this
fossil. Three times 5,730 equals 17, 190;
therefore the fossil is approximately 17, 190
years old
Chemical Bonds
• Are the interactions between the electrons of
two or more atoms.
• Electronegativity- is the strength of the
attraction an atom has for its electrons, helps
determine the nature of the chemical bonds
that atom can form.
– The more attraction electronegative an atom is, the
greater the strength of its attraction for electrons.
Covalent Bond
• Two or more atoms share valence electrons.
• Covalent bonds result in the formation of
molecules, which are strong, stable
associations between two or more atoms
• Atoms joined by covalent bonds may share
one, two, or three electrons resulting in single,
double, or triple bonds.
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• The distribution of shared atoms in a covalent bond
depends on the electronegativities of the atoms.
• Two terms to describe the way electrons are shared:
– Nonpolar covalent bonds: form between atoms that have
similar electronegativity. The electrons in a nonpolar
covalent bond are shared equal between the two atoms.
– Polar covalent bonds: form between atoms that have
different electronegativities. Valence electrons in a polar
covalent bond will be more attracted to the atom of higher
electronegativity, resulting in a partial negative charge on
that atom and partial positive charge on the other atom.
Polar
Vs.
Nonpolar
Ionic Bonds
• Form when electrons are transferred from an atom of low
electronegativity to an atom of high electronegativity.
• The atom that lost an electron becomes positively charged
anion, while the atom that has gained an electron becomes
a negatively charged cation.
• Cations and anions are mutually attracted to one another
by their charges.
• This mutual attraction results in the formation of a crystal,
which is a highly regular and ordered solid whose atoms
are arranged in repeating units.
Hydrogen Bond
• The weakest of all chemical attractions, form when
a hydrogen atoms that is covalently bonded to an
electronegative atom is attracted to another
electronegative atom, generally either oxygen (O) or
nitrogen (N).
• Hydrogen bonds are one of the main forces that
give proteins their 3-D shapes
Water
• Water is the most abundant molecule present
in all living organisms.
• All chemical reactions within an organism take
place in the presence of water.
• Several characteristics unique to water
contribute to its vital importance in the
processes of life, such as its properties as a
solvent and tendency to form ions.
Water as a Solvent
• Solution is a homogeneous mixture of
molecules (Evenly distributed mixture)
– Example: Kool-Aid
• Parts of a solution:
– Solvent: Substances that dissolves other
molecules.
• Water
– Solute: Substance that is being dissolved
• Kool-aid
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• The hydrogen bonds that hold water molecules make water a
versatile solvent that can form a solutions with a polar
(hydrophilic: a molecule that is attracted to water) molecules.
Water can form solutions with nonpolar (hydrophobic: a
molecule that repelled from water) molecules.
• Example: In an aqueous solution of NaCl and water, the
solvent is water and the solute is NaCl. NaCl is ionic, and
therefore hydrophilic and forms an aqueous solution in which
water is the solvent and NaCl is the solute. Oil nonpolar, and
therefore hydrophobic. Oil will not dissolve in water.
Water Ionization
• Water molecules spontaneously ionize, or
break down, into hydroxide ion (OH-) and
hydrogen ions (H+).
• Chemical equation illustrates the explanation:
H2O
OH- + H+
pH Scale
• Ranges 0 to 14, expresses the concentration of
hydrogen and hydroxide ions in a solution.
– This determines if a solution is Neutral, Acidic, or Basic
• Neutral Solution: Have equal number of –OH and
H+ ions in the solution – pH of 7
• Acidic Solution: have a greater concentration of H+
ions in the solution – pH of less than 7
• Basic Solution: have a greater concentration of –
OH –pH of greater than 7
Continue…
• A buffer solution : a solution containing either
a weak acid and a conjugate base or a weak
base and a conjugate acid, used to stabilize
the pH of a liquid upon dilution.
• Buffers are substances that reduce the effect
of acids and bases on the pH of a solution
Calculating pH
• The pH of a given solution expresses the
negative logarithm of the hydrogen ion
concentration
• Equation:
pH = -log [H+]
Isomers
• Are organic compounds that have the same
molecular formula but different structure
– There are three types
• Structural Isomers: differ in their covalent arrangement
• Geometric isomers: differ in their spatial arrangement
around a double bond
• Enantiomers or optical isomers: are mirror images of
each other
Reactions
• There are five types of reactions you should
know for this exam:
• 1- Hydrolysis reaction: a reaction that breaks
down compounds by the addition of H2O
• 2- Dehydration synthesis reaction: A reaction in
which two compounds are brought together with
H2O released as a product.
• 3- Endergonic Reaction: A reaction that requires
input of energy to occur
A + B + energy  C
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• 4- Exergonic Reaction: A reaction that gives off
energy as a product.
A + B  energy + C
5- Redox reaction: A reaction involving the transfer
of electrons
Biological Macromolecules
• Compounds that contains Carbon and usually
Hydrogen.
• Four types of macromolecules
– Nucleic Acid
– Proteins
– Carbohydrate
– Lipds
Continue…
• Most biological macromolecules are polymers,
which are long chains composed of many
monomers, similarly structured subunits
bonded together
Nucleic Acid
• Form polymers of nucleotides, molecules
composed of a phosphate group, a five-carbon
sugar, and a nitrogenous bases (Four
nitrogenouos bases: adenine, guanine, cytosine,
thymine, uracil)
• DNA and RNA are nucleic acids that function in
protein synthesis and the storage and
transmission of genetic transmission
Proteins
• Proteins consist of one or more polypeptides,
polymers of amino acids (building blocks of
proteins) folded into complex 3-D shapes.
• An amino acid is a small molecule made up of a
central carbon atom, an amino group, a carboxyl
group, a hydrogen atom, and functional group
labled “R”
• Twenty different amino acids exist, each formed
with a different R group.
Proteins Continued…
• Polypeptides form when amino acids bond
together in long chains.
• The twenty different amino acids can produce
a diverse range of proteins, including
enzymes, hormones, cell receptors,
antibodies, transport proteins, storage
proteins, motor proteins, and structural
proteins.
Proteins Continue…
• All proteins have either 3 or 4 structural levels
– Primary Structure: Refers to the sequence of amino
acids that form the polypeptides
– Hydrogen bonds single groups in a polypeptide chain
result in a folded region referred as the secondary
structure. Secondary structure includes helices (coils)
and sheets (pleated folds)
– Tertiary structure describes the folding of an entire
polypeptide chain. Interactions between the R groups
of the polypeptide chain determine the overall shape
of the tertiary structure.
Continue…Protein
• Quaternary structure: Interactions between
two or more polypeptides
Enzymes
• Are proteins that act as organic catalyst
– Catalyst: speeds up reactions by lowering the
activation energy needed for the reaction to take
place but are not used in the reaction.
– Substrate: substance that enzymes act on
• Enzymes are selective; they interact only with
particular substrates. It is the shape of the
enzyme that provide the specificy.
– Active Site: The part of the enzyme that interacts
with the substrate
Induced-fit Model
• Of the enzyme-substrate interaction describes
the active site of an enzyme as specific for a
particular substrate that fist its shape (Often
times called the lock and key model)
Enzyme Activate Energy Graph
Enzyme Continue…
• Every enzyme effectiveness (reaction taking
place)
This will
– Temperature
– pH
– Concentration of substrate
– Concentration of the enzyme involved
be helpful
to know
for both
the AP
Exam and
the
Enzyme
Lab
Competitive Inhibition and
Noncompetitive Inhibition
• Competitive Inhibition: an inhibitor molecule
resembling the substrate binds to the active
site and physically blocks the substrate from
attaching.
Continue…
• Noncompetitive inhibition: an inhibitor
molecule binds to a different part of an
enzyme, causing change in the shape of the
active site so that it can no longer interact
with the substrate
Carbohydrates
• Macromolecule that contains Carbon,
Hydrogen, and Oxygen
– Ratio of 1:2:1
• Provides energy for organisms
Monosaccharide
• Simple sugar or simple carbohydrates
– Examples: Glucose (used for cellular respiration),
fructose, and lactose – provides energy for cells
Disaccharide
• Sugar consisting of two monosacharides
bound together
– Sucrose: Table sugar
• Major sugar in plants
• Fructose and glucose bonded together
– Lactose
• Found in diary products
• 2 glucose molecules bonded together
Polysaccharide
• Carbohydrate of bonding three or more
monosaccharide molecules
• Two important molecules for storing energy are:
– Starch : Made up of solely of glucose
• Energy storage for plants
• Corn, Potatoes, Beans
– Glycogen: linking many glucose molecules together
• Animals store their energy
• Found in liver and muscle cells
Continue… Polysaccharides
• Two important structural polysaccharides
– Cellulose: composed of glucose molecules
• Used for in the formation of the their cell walls
– Chitin: Important part of the exoskeletons of
arthropods– such as insects, lobsters, and crabs
Lipids
• Organic compounds used by cells as long-term
energy stores or building blocks
• Hydrophobic and insoluble in water because
they contain a hydrocarbon tail
Fats
• Which are lipids made up of combining
glycerol and three fatty acids
• Used as long term energy stores in cells
• Are not easily metabolized as carbohydrates
Saturated vs. Unsaturated
• Saturated: Contain no double bonds (means it
can be easily broken)
– Associated with heart disease and atherosclerosis
• Unsaturated: contain one (mono-) or more
(poly-) double bonds
Steroids
• Act as chemical messengers in an organisms
• Cholesterol: Component found in cell membranes
• Steroids: the sex hormones
(testosterone, progesterone, and estrogen)
Phospholipds
• Combining a glycerol with two fatty acids and
a phosphate group
• Phospholipds are bilayered structures they
have both hydrophobic tail and hydrophilic
head
• Major component of cell membranes
Functional Groups
• Commonly found in biological
macromolecules
• Share the same chemical properties
Functional Groups
Functional
Group
Class of Compounds
Macromolecule
Amino
Amines
Proteins
Carbonyl
Ketones & aldehydes
Lipids
Carboxyl
Carboxylic acid
Proteins
Alcohols
Carbohydrates
Phosphate
Phosphate
Nucleic Acids
Sulfhydryl
Thiols
Proteins
Hydroxyl
Structural Formula
Notice
the -OH
Functional Group
• Quiz on:
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The End