Download I. CHEMICAL BASIS OF LIFE, cont

UNIT II - BIOCHEMISTRY
Big Campbell ~ Ch 2-5
Baby Campbell ~ Ch 2-3
I. CHEMICAL BASIS OF LIFE
• Elements
o Cannot be broken down without losing characteristic
properties
o Six elements in greatest concentration in living things are






Sulfur
Phosphorus
Oxygen
Nitrogen
Carbon
Hydrogen
o Defined by Atomic # which is = #of protons and the #of
electrons in most cases
I. CHEMICAL BASIS OF LIFE, cont
• Atoms
o Smallest unit of matter
that retains properties of
that element
 Protons (+); found in
nucleus
 Neutrons (neutral); found
in nucleus
 Electrons (-); found in
electron clouds.
o Atomic Mass = p + n
o Isotopes – when an
atom has a different
atomic mass, Ex: C12,
C13, C14
I. CHEMICAL BASIS OF LIFE, cont
• Chemical Bonds
o Chemical behavior of atom determined by valence electrons
o Atoms interact with other atoms to complete their valence shells,
either by transferring or sharing electrons
I. CHEMICAL BASIS OF LIFE, cont
• Types of Chemical Bonds
o Ionic – Results when one atom has a much stronger
attraction for electrons than another; one atom has a
greater electronegativity. Electron(s) are transferred
resulting in formation of ions. Bond forms due to charge
attraction. Strength is dependent on environment
I. CHEMICAL BASIS OF LIFE, cont
o Covalent Bonds – More stable;
results from sharing a pair of
valence electrons. Forms a
molecule. One pair of electrons
shared = single covalent bond; two
pair of electrons shared = double
covalent bond.
Non-polar covalent bond –
formed when electronegativity
of atoms is the same
Polar covalent bond – formed
when one atom is more
electronegative; unequal
sharing of electrons results in
slight charges at either end of
molecule
II. WATER
• Properties of Water Due to its
Polarity
o Hydrogen “bonds”
II. WATER
o “Stickiness”
Cohesion
 Surface Tension
Adhesion
Capillary Action
II. WATER, cont
o Regulation of Temperature
 High specific heat
 High heat of vaporization
o Density of “solid” water _<_ density of
liquid water
II. WATER, cont
o
Solvent of Life

Hydrophilic



“Water-loving”
Polar molecules
“pull apart” ionic
compounds &
other polar
molecules
Hydrophobic


“Water-hating”
Non-ionic and
non-polar
substances are
repelled by water
II. WATER, cont
• Dissociation of Water
o Rare, but measurable phenomenon
o (2)H2O → H3O+ + OH- → H+ + OHo In aqueous solution at 25˚C, total conc of [H+] [OH-] = 1x10-14
 Neutral solution → [H+] = [OH-]; therefore [H+] = 1 x 10-7
o pH = Provides a means for a compressed measurement of [H+]
 -log10[H+]
o Acid – Substance that dissolves in water to __increase_ [H+]
 [H+] _>___ 1 x 10-7; pH __<__ 7
o Base - Substance that dissolves in water to _decrease_ [H+]
 [H+] _<___ 1 x 10-7; pH _>_ 7
o pH of Water = 7
II. WATER, cont
o Buffers
Maintain a constant pH by donating, accepting H+
Bicarbonate Buffer System
 Very important buffer system in blood
 pH of blood = _7.4_
III. ORGANIC CHEMISTRY – THE STUDY OF CARBON
• Atomic Structure of C
o Atomic Number of C = 6
 6 protons
 6 electrons
 __4___ valence electrons
o Hydrocarbon – composed
on only C-H; impt in fossil
fuels. Hydrophobic
o Isomer – compounds with
the same #of
elements/atoms, but a
different structural
arrangement. See Ex…
Four Ways Carbon skeletons can
vary
III. ORGANIC CHEMISTRY, cont
Functional Group
Hydroxyl
Structure
Characteristics
-OH may be written as
HO-
Very polar; forms “ –ols”
(alcohols)
C=O, also written -CO
Ketone – if carbonyl group
is within the carbon
skeleton
Carbonyl
Aldehydes – if carbonyl
group is at the end of the
carbon skeleton.
Carboxyl
-COOH; c alled carboxylic
acids
Acts as an acid; donates H+
to solution
III. ORGANIC CHEMISTRY, cont
Functional Group
Structure
-NH2; called amines
Acts as a base; removes H+
from solution
-SH; called thiols
Important in stabilizing protein
structure; forms disulfide
bridges
Amino
Sulfhydryl
Characteristics
Phosphate
Methyl
-OPO3; known as
organic
phosphates
Gives molecule negative
charge; react with water to
release energy
-CH3
Affects the expression of
DNA
IV. THE BIOMOLECULES
• Most are polymers made up of single units called
monomers
• Four Main Groups
 CARBOHYDRATES
 LIPIDS
 PROTEINS
 NUCLEIC ACIDS
IV. BIOMOLECULES, cont
• Dehydration Synthesis
o
o
o
o
o
Also called _CONDENSATION REACTION__
Reaction that occurs to build polymers
Forms __COVALENT_ bond between 2 monomers
_WATER_lost as waste product
Requires energy input, enzymes
IV. BIOMOLECULES, cont
• Hydrolysis
o “__WATER BREAKING/SPLITTING_”
o Covalent bonds between monomers broken Releases energy;
reaction accelerated with enzymes
V. CARBOHYDRATES
•
•
•
•
•
Provide fuel, act as building material
Generally, formula is a multiple of CH2O
Contain carbonyl group & multiple hydroxyl groups
Monomer = monosaccharides
Monosaccharides – usually found as ringed structures
o Pentoses
 Ribose
 Deoxyribose
V. CARBOHYDRATES, cont
o Hexoses
Glucose
Fructose
Galactose
V. CARBOHYDRATES, cont
• Disaccharides
o 2 monosaccharides covalently bonded together through
dehydration synthesis
o Example
 Sucrose
 Lactose
 Maltose
V. CARBOHYDRATES, cont
• Polysaccharides
o Many monosaccharides covalently bonded together
through dehydration synthesis
o Two main groups
 Energy Storage Polysaccharides
Starch – Plants store glucose as starch in cell
structures called plastids. Humans have enzymes to
hydrolyze starch to glucose monomers.
Glycogen – Storage form of glucose in animals. More
highly-branched than starch. In humans, found
mainly in liver, muscle cells
V. CARBOHYDRATES, cont
 Structural polysaccharides
 Cellulose – polymer of glucose. Every other glucose is upside
down – forms parallel strands of glucose molecules held
together with H-bonds
V. CARBOHYDRATES, cont
Structural polysaccharides
• Chitin – found in arthropod
exoskeleton, cell walls of fungi
VI. LIPIDS
•
•
•
•
•
Very diverse group
Non-polar, hydrophobic molecules
Hydro_phobic__
Not true polymers
Four groups




Fats & oils
phospholipids
steroids
waxes
VI. LIPIDS, cont
• Fats& Oils
o Composed of
glycerol + 3 fatty
acids
o Glycerol = 3-C
alcohol
o Fatty acids – long
hydrocarbon
chains ending with
carboxyl group
o AKA triglycerides
o Used for energy
storage
VI. LIPIDS, cont
 Saturated fats – “Saturated
with hydrogens”; contain all
single bonds. Typically from
animal source, solid at room
temp. Associated with
greater health risk.
 Unsaturated fats – Contain
double bonds, fewer Hatoms. Results in “kinked”
hydrocarbon chain.
Typically from plant source,
liquid at room temp.
Fats, cont.
• Saturated fat
• Unsaturated fat
VI. LIPIDS, cont
• Phospholipids
 2 fatty acids
attached first 2carboxyl groups of
glycerol.
 Negatively-charged
phosphate group is
attached to 3rd
carboxyl
 Partially polar and
partially non-polar
 Found in all cell
membranes.
Phospholipid, cont.
VI. LIPIDS, cont
• Waxes – One fatty acid attached to an alcohol. Very
hydrophobic. Used as coating, lubricant
• Steroids – Consist of 4-rings with different functional
groups attached.
o Cholesterol – steroid found in animal cell membranes;
precursor for sex hormones
Steroids, cont.
VII. PROTEINS
• Important part of virtually all cell structures, processes,
reactions
• Amino Acids – Proteins are large polymers made up of amino
acid monomers. All amino acids have the same basic
structure:
o
o
o
o
Amino group
Carboxyl group
Carbon, known as alpha carbon
R group → variable component; gives each amino acid its unique
properties. Determines whether amino acid is classified as polar, nonpolar, acidic, or basic.
VII. PROTEINS, cont
VII. PROTEINS, cont
VII. PROTEINS, cont
VII. PROTEINS, cont
• Amino Acid → Protein
o Dehydration synthesis results in formation of a peptide bond
o Polypeptide – many amino acids covalently bonded together
VII. PROTEINS, cont
• Protein Conformation
o Protein’s shape is related to its function. Generally, a
protein must recognize/bind to another molecule to carry
out its function.
o Denaturation - A change in a protein’s shape. Results in a
loss of protein’s ability to carry out function.
o Four levels of protein structure
 Primary
 Secondary
 Tertiary
 Quaternary
VII. PROTEINS, cont
 Primary – Sequence
of amino acids
VII. PROTEINS, cont
 Secondary – Coiling of polypeptide chain due to formation of H-bonds
between H of amino end of one aa and OH of carboxyl end of another
aa
 Alpha helix – created from H-bonds forming within one pp chain
 Beta pleated sheet – H-bonds form between aa in parallel pp chains
VII. PROTEINS, cont
 Tertiary - Involves
interactions
between R groups
of amino acids.
Helps to give each
protein its unique
shape.
VII. PROTEINS, cont
 Quaternary – Proteins
that are formed from
interactions between 2
or more polypeptide
chains folded together.
Examples include
hemoglobin, collagen,
chlorophyll
VII. PROTEINS, cont
• Enzymes
o Biological catalysts that act by lowering activation energy; that is, the
amount of energy needed to get the reaction going
o Only catalyze reactions that would normally occur
o Recycled – not used up or changed by the reaction
o Temperature and pH sensitive
o Substrate specific
VII. PROTEINS, cont
o Induced fit – As enzyme
envelops substrate, a slight
change takes place in bond
angles, orientation of atoms.
Allows chemical rxns to occur
more readily
o Inhibition of Enzyme Function
 Competitive inhibitor – mimics
normal substrate
 Non-competitive inhibitor –
attaches to another part of
enzyme; changes shape of active
site
VII. PROTEINS, cont
o Regulation of enzyme
function
 Allosteric Regulation –
binding of a molecule to
enzyme that affects
function of protein at
another site
 Feedback Inhibition – as
end product is
synthesized and
accumulates, enzyme is
inactivated → switches
off metabolic pathway
VIII. NUCLEIC ACIDS
• Nucleic acid group includes
DNA, RNA, ATP
• Monomers = _NUCLEOTIDES_
 Composed of
 Pentose
 deoxyribose (DNA)
 ribose (RNA)
 Phosphate group
 Nitrogen base
• Polymers formed through
_dehydration synthesis__
 Phosphate group of one
nucleotide covalently binds
to sugar of next
VIII. NUCLEIC ACIDS, cont
 Nitrogen Bases
Pyrimidines –
Single-ringed
structure
 Thymine
 Cytosine
 Uracil
Purines – Doubleringed structure
 Adenine
 Guanine
VIII. NUCLEIC ACIDS, cont
• DNA