Transcript Ch. 1 The Chemistry of Life

Ch. 1 The Chemistry of Life
 General Chemistry
 Atoms Molecules and Compounds
 The Structure of Atoms
 Reactions in Living Cells
 Reactions in Living Cells
 Chemical Bonds
 Ions and Living Cells
 Biochemistry
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Organic Compounds and Life
Carbohydrates
Lipids
Proteins
Nucleic Acids
 Genetic Coding in the Cells
 The Double Helix
 The Functions of DNA
The Chemistry of Life
 All organisms are composed of
chemicals.
 An understanding of life
requires and understanding of
chemistry.
Atoms, Molecules and Compounds
 Water is an essential chemical
for living organisms (Oceans 
Droplets).
 A molecule of water would be
the smallest unit that would have
the essential properties of water.
 An element is a substance that
cannot be broken down into
simpler substances. (ex:
Hydrogen and Oxygen)
Atoms, Molecules and Compounds
 John Dalton’s experiments
showed elements were
composed of minute particles.
 Atoms are the smallest unit of
an element that still has the
property of that element.
Atoms, Molecules and Compounds
 Molecules are made from atoms
– can be more than one type
(O2 or CO2).
 Chemists have given elements a
symbol – H : hydrogen, C :
carbon etc…
 About 97% of the compounds in
organisms are composed of C,
H, O, N, P and S
Atoms, Molecules and Compounds
 The number of atoms of each
element in a molecule is shown
by the subscript.
 Carbon Dioxide : CO2
 Ammonia : NH3
The Structure of an Atom
 Atoms are built of smaller
subatomic particles:
 Electrons (-)
 Protons (+)
 Neutrons (0)
 Protons and neutrons remain in
the center, or nucleus, of the
atom.
The Structure of an Atom
 Electrons move in electron
shells around the nucleus.
 Shells are separated by levels of
energy - the closer the shell, the
tighter the hold.
 The first shell can hold 2
electrons, the second shell can
hold 8 and the third can hold 8
 H : 1 e-, C: 6 e-, O: 8 e-, etc…
The Structure of an Atom
 Atoms have an equal number of
protons and electrons – thus no
charge.
 Atoms with unfilled shells want
to loose or gain electrons - basis
for chemical reactions.
 Atoms of the same element that
differ in their number of
neutrons are called isotopes.
 Oxygen-16, Oxygen-17, Oxygen-18
Chemical Reactions
 When atoms share or transfer
electrons from their outermost
shell – chemical bonds form.
 Chemical reactions involve
the making and breaking of
these bonds.
2 H2O  2 H2 + O2
 The equation is written to
balance the number of atoms on
both sides of the arrow (Law of
the Conservation of
Matter)
Chemical Reactions
 The arrow in a chemical
reaction points from reactants to
products.
 Activation energy is the
amount of energy needed to get
a chemical reaction started.
 Energy may need to be supplied
from an outside source.
Chemical Bonds
 When electrons move from one
atom to another atom – an ion
will form.
 Ex: Na – Cl
 An ionic bond is the attraction
between oppositely charged
ions: NaCl
Chemical Bonds
 In a covalent bond, two
atoms share one or more pairs
of electrons.
 Ex: H2
 Ex: H2O
Chemical Bonds
 In a water molecule; the
electrons are not shred
equally between the hydrogen
and oxygen molecules.
 The oxygen end is slightly
negative and the hydrogen
end slightly positive – polar
molecule.
 Hydrogen bonds are weak
bonds between polar
molecules.
Structural Formulas
 Structural formulas show the
number and arrangement of
atoms in a molecule.
 If atoms share two electrons a
double bond forms, three, a
triple bond.
 H-H, O=C=O
Ions and Living Cells
 Salt dissolves in water; Na+ is
attracted to the negative end
of water and Cl- is attracted
to the positive end of water.
 Ions are important for
maintaining water balance in
living organisms.
Ions and Living Cells
 When a nonionic compound
like water is converted to ions,
the process is called ionization.
 The result is a positively charged
hydrogen ion (H+) and a
negatively charged hydroxide ion
(OH-)
Ions and Living Cells
 When ionization occurs – the
hydrogen ion will combine with
a water to form hydronium ion
(H3O+) … however, we refer
to the H+ number.
 Ionization is rare 1 in 500
million water molecules.
 Living cells need specific levels
of H+ amd OH-
Ions and Living Cells
 The level of H+ and OH- ions
in a solution is described by the
pH Scale.
 Scale 0 – 14 (logarithmic – pH
of 3 is 10x pH of 4)
 pH of 7 has the same amount of
H+ and OH- ions and is neutral
(pure water).
Ions and Living Cells
 A solution with more H+ ions
is acidic and has a pH less than
7.
 A solution with more OH- ions
is basic (alkaline) and has a pH
greater than 7.
Ions and Living Cells
 The pH of a cell’s interior helps
to maintain the cell’s chemical
reactions – a very specific pH is
often required .
 Blood at 74.4; 6.8 or 8.0 means
death.
 How does the body cope?
Ions and Living Cells
 Buffers are solutions that help
to prevent changes in pH caused
by the addition of an acid or a
base.
 A buffer works by accepting H+
ions when their levels rise and
donating H+ ions when their
levels fall.
Organic Compounds
 Besides water, organic
compounds are most important
to life on Earth.
 Organic compounds are composed
of carbon, hydrogen usually
oxygen and frequently nitrogen,
sulfur, or phosphorus.
 CO2, CO and H2CO3 are not
organic.
Organic Compounds
 Carbon atoms combine in long
chains to form complex
macromolecules.
 Other atoms attach to the
carbon skeleton giving the
macromolecule a specific
structure and function.
Organic Compounds
 A polymer is a long chain of
single building blocks called
monomers.
 Two monomers may attach by
dehydration synthesis in which a
water molecule is removed.
 Two monomers may break apart
by hydrolysis in which a water
molecule is added.
Carbohydrates
 Carbohydrates are sugars
composed of carbon, hydrogen
and oxygen in a 1:2:1 ratio.
 The simplest are monosaccharides,
or simple sugars (3 – 7
carbons).
 Glucose, galactose and fructose are
all monosaccharides which
provide energy for organisms.
Carbohydrates
 In solution, glucose and other
sugars, exist in their ring forms.
 A carbon at every corner.
Carbohydrates
 A disaccharide consists of two
monosaccharides linked by a
covalent bond as the result of
dehydration synthesis.
 Glucose – Glucose: Maltose
 Glucose – Fructose: Sucrose
 Glucose – Galactose: Lactose
Carbohydrates
 Several glucose molecules may
bond to form complex
carbohydrates called
polysaccharides.
 Plants store glucose in long
chains called starch (potatoes,
wheat, corn, etc.)
 Animals store glucose as
branched chains called glycogen
in the liver and muscles (1 days
worth – diabetes)
Carbohydrates
 The polysaccharide cellulose is
used to build the tough walls tat
enclose plant cells.
 Cellulose is made of B-glucose
which is not easily hydrolyzed.
 wood/ cotton
 insoluble fiber, cows/ termites
– prokaryotes
Lipids
 Lipids consist of fats and oils.
 Composed of carbon, hydrogen
and oxygen.
 The main role of a lipid is in
long term energy storage and
building structures.
Lipids
 Lipids will not dissolve in water
because they are nonpolar.
 The building blocks of lipids are
fatty acids and glycerol.
 Three fatty acids and one
glycerol make a simple fat or
triglyceride.
Lipids
 The property of fatty acids
depends on the length of the
carbon chain and the bonds
between the carbons.
 If a single bond connects the
carbons, it is a saturated fat
(solids).
 If a double bond connects
some of the carbons, it is an
unsaturated fat (oils).
Lipids
 Phospholipids forms when a
molecule of glycerol combines
with two fatty acids and a
phosphate group.
 With proteins, phospholipids
form the cell membrane.
 Cholesterol is part of the
membrane structure of animals
– we make steroids etc. from
cholesterol.
Lipids
 A wax is a simple lipid having a
long-chain alcohol and a fatty
acid.
 Found in nature as coatings on
leaves and stems to prevent the
loss of excessive water.
 Carnuba wax is found on the
leaves of Brazilian palm trees
and is used in floor and
automobile waxes.
Nucleic Acids
 Nucleic Acids are macromolecules
that determine the structure and
function of proteins.
 Source of genetic information in
chromosomes.
 A link to generations past.
Nucleic Acids
 Nucleic acids are composed of
simple units called nucleotides.
 3 parts:
 5-carbon sugar (ribose or
deoxyribose)
 Nitrogen base
 Phosphate group
Nucleic Acids
 Ribose containing are called
ribonulceic acids or RNA.
 Deoxyribose containing are
called deoxyrobonucleic acids or
DNA.
 DNA may contain 1 of 4 bases:
adenine, thymine, guanine and
cytosine.
Nucleic Acids
 In RNA the base uracil replaces
the bases thymine.
 RNA is single stranded where as
DNA is double stranded.
 Three types of RNA perform
roles in the production of
proteins.
Proteins
 Proteins are organic compounds
used in building structures,
defense, communication etc..
 Proteins are built from
monomers called amino acids.
Proteins
 Amino acids are composed of C,
H, O, and N (two contain S)
 Carbon atom attached to:
 Hydrogen atom (-H)
 amino group (-NH2)
 acid or carboxyl group (-COOH)
 variable group (R)
 R may be one of 20 groups
(polar/ nonpolar resulting in
hydrophillic/ hydrophobic aa’s)
Proteins
 Amino acids combine when the
carboxyl group of one molecule
bonds with the amino group of
another.
 These are peptide bonds result in
a long chain or polypeptide (503000 aa’s).
 The type, number and sequence
of aa’s determine the proteins
structure and function.
Proteins
 The sequence of aa’s is the
primary structure.
 Folds in the chain form secondary
structures (a-helices, b-sheets).
 Complex folding forms the
tertiary structure (spherical).
 Multiple tertiary structures
form a quaternary structure.
Proteins
 Hydrophobicity helps to
determine structure.
 This is determined by the
varying polarities of the Rgroups in the structure.
Genetic Coding in Cells
 The four nucleotides in DNA
differ only in their nitrogen
bases.
 Single ring pyrimidines:
 Thymine (T)
 Cytosine (C)
 Double ring purines:
 Adenine (A)
 Guanine (G)
Genetic Coding in Cells
 Nucleotides are joined when
the sugar of one nucleotide
connects to the phosphate
group of another.
 This forms a sugar-phosphate
backbone.
Genetic Coding in Cells
 Scientists Franklin, Watson and
Crick discovered that DNA
exists as a double helix.
 A double helix is like a twisting
ladder.
Genetic Coding in Cells
 The pairing of bases are due
to their size and ability to
form hydrogen bonds.
 Adenine (A) always pairs with
Thymine (T) and Guanine
(G) always pairs with
Cytosine (C).
 If we know one strand, we
can figure out the
complimentary strand.
Genetic Coding in Cells
 Genes are units of genetic
information passed from parent
to offspring.
 DNA stores information in
three base pair codes called
codons.
 Each codon represents an amino
acid.