Download week 3_biomolecules

Mdm Khadijah Hanim bt Abdul Rahman
Sem I: 2013/2014
[email protected]
CO 1:
 Ability to differentiate basic structure,
properties, functions and classification of
important biomolecules.
- Demonstrate types of biomolecules, chemical
nature and biological roles of water, buffer and
its importance.
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Living organisms: organic and inorganic
molecules.
Composed of water- inorganic molecules. 5095% of cell’s content.
Other ions: Na+, K+, Mg2+ and Ca2+ = 1%
Other molecules are organic: composed of 6
elements: C, H, N, P and S.
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Simplest type of biomolecules are derived from
hydrocarbons
Hydrocarbon: H and C containing molecules
that are hydrophobic.
Eg: CH4, C2H6, C6H12
The chemical properties are determined by
their functional groups. (alcohol, aldehyde,
ketone, acids, amines etc).
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Organic compounds are relatively small found in
the cells.
4 families of small molecules: amino acids, sugars,
fatty acids and nucleotides.
Several functions:
Used to synthesis larger molecules; polymersproteins, carbohydrates and nucleic acids.
Special biological functions; nucleotide adenosine
triphosphate (ATP) serve as cellular reservoir of
chemical energy
Involved in complex reaction pathways.
Small molecule
Polymer
General functions
Amino acids
Proteins
Catalysts and structural
elements
Sugars
Carbohydrates
Energy sources and
structural elements
Fatty acids
N.A
Energy sources and
structural elements of
complex lipid molecules
Nucleotides
DNA, RNA
Genetic information,
protein synthesis
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Hundreds of naturally occurring amino acids.
Each contain amino and hydroxyl group.
Most common type: α-amino group
R group: side chain- determined the chemical
properties of amino acid.
Hydrophobic/hydrophilic.
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20 standard a-amino acids that occur in
proteins.
Some like glycine and glutamic acid:
neurotransmitters in animal
Amino acids are used primarily in the
synthesis of long, complex polymers:
polypeptides.
Molecules that composed of polypeptides:
enzymes, structural proteins and transport
proteins.
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Individual amino acids are connected in
peptides by peptide bond involving a carbonyl
group which occurs between amino group and
carboxyl group of another molecule. NH-CO
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Sugars: alcohol and carbonyl groups.
Sugars with aldehyde group: aldoses
Sugars with ketone group: ketoses
Eg: 6 carbons sugar glucose: aldohexose
Fructose: ketohexose
Sugars are basic units for carbohydrates:
monosaccharides (glucose and fructose);
polysaccharides (starch and cellulose)
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Functions:
glucose: principle energy source in animals and
plants
Sucrose: use by plants as efficient means to
transport energy
Cellulose: structural component of wood
Chitin: protective outer coatings of insects
Some biomolecules contain carbohydrate
components: nucleotides contain sugar ribose
or deoxyribose.
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Monocarboxylic acids that contain an even no
of carbon atoms.
They serve as energy sources.
Fatty acids chemical formula R-COOH; R is
alkyl group that contain Cand H atoms.
2 types: saturated (no double bond) and
unsaturated F.A (contain double bond; 1 or
more)
F.A occur as independent molecules and only
in trace amounts in living organisms
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Most often they are components of lipid
molecules.
Lipids are diverse groups that are soluble in
organic solvents but are insoluble in water.
Eg: triacylglycerols are esters containing
glycerol.
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Each nucleotides contain 3 components: a 5carbon sugar (ribose or deoxyribose),
nitrogenous base and 1 or more phosphate
groups
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Functions:
Energy generating reactions: energy obtained from
food is used to form a high-energy ATP
Building block molecules of nucleic acids: 2 types
of nucleic acids.
DNA- genetic infromation.
Structure: 2 polynucleotide strands wound around
each other to form a right-handed double helix.
4 types of base: purines adenine and guanine.
Pyrimidines thymine and cytosine.
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RNA: different from DNA. Contain ribose
sugar and base uracil instead of thymine.
RNA is single stranded.
3 major types of RNA: rRNA, tRNA and
mRNA.
More than 70% of the earth’s surface is covered
with the molecule of water.
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Cell components and molecules (protein,
poly sacharides, nucleic acid, membranes)
assume their shape in response to water
 Water acts as a solvent & substrate for
many cellular reactions
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Water is a common chemical substance that is
essential for the survival of all known forms of life.
(In typical usage, water refers only to its liquid form or state, but the substance also has
a solid state, ice, and a gaseous state, water vapor.
)
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Water is the chemical substance with chemical formula
H2O: one molecule of water has two hydrogen atoms
covalently bonded to a single oxygen atom.
Water is a tasteless, odorless liquid at ambient
temperature and pressure, and appears colorless in
small quantities, although it has its own intrinsic very
light blue hue.
Oxygen attracts electrons much more strongly than
hydrogen, resulting in a net positive charge on the
hydrogen atoms, and a net negative charge on the
oxygen atom.
The presence of a charge on each of these atoms gives
each water molecule a net dipole moment.
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Electrical attraction (hydrogen bonding) between water
molecules due to this dipole pulls individual molecules
closer together, making it more difficult to separate the
molecules and therefore raising the boiling point.
Water can be described as a polar liquid that
dissociates disproportionately into the hydronium ion
(H3O+(aq)) and an associated hydroxide ion (OH−(aq))
Water is in dynamic equilibrium between the liquid,
gas and solid states at standard temperature and
pressure (0°C, 100.000 kPa) , and is the only pure
substance found naturally on Earth.
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Exist in all three physical states of matter:
solid, liquid, and gas.
Has high specific heat
Water conducts more easily than any liquid
except mercury
Water has a high surface tension
Water is a universal solvent
Water in a pure state has a neutral pH.
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The oxygen in
water is sp3
hybridized.
Therefore water
has tetrahedral
geometry.
Consequently the
water molecule is
bent. The H-O-H
angle is 104.5o.
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The bent structure indicate water is polar
coz linear structure is nonpolar.
Phenomenon where charge is separated to
partial –ve charge and partial +ve charge
is called dipoles.
Becoz of the large difference in
electronegativity of H and O, the electrondeficient H are attracted to the unshared
pairs of electrons of another H2O
molecule.
Interaction- hydrogen bonding
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Ionic interactions
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Hydrogen bonding
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Van der Waals forces
 Dipole-dipole
 Dipole-induced dipole
 Induced dipole-induced dipole
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Ionic interactions occur between charged atoms or
groups.
Oppositely charged ions are attracted to each other.
In proteins, the attraction of positively and negatively
charged amino acid side chains sometimes form ionic salt
bridges.
Salt bridge
-
CH2CH2COO
+
H3N CH2CH2
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Repulsive forces created when similarly
charged species come into close
proximity
Important features in protein folding
and enzyme catalysis
Most salt bridges rarely form in the
presence of water- attraction between
biomolecules decreases.
Salt bridges normally occur in free
water or at molecular interfaces where
water is excluded.
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Water molecules can perform hydrogen bond
with one another. Four hydrogen bonding
attractions are possible per molecule:
2 through the
hydrogens and
H
H
2 through the
O
O
nonbonding
H
H
electron pairs.
H
O
H
H
O
H
H
O
H
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hydrogen attached to an O
becomes very polarized and
highly partial plus (δ+). This
partial positive charge interacts
with the nonbonding electrons on
another O giving rise to the very
powerful hydrogen bond.
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Water has an abnormally high boiling point
due to intermolecular hydrogen bonding.
H 

O
H

H 
O
H

H

O

H

H bonding is a
weak attraction
between an
electronegative
atom in one
molecule and an H
(on an O) in
another.
Van der Waal’s forces
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These forces are electrostatic interactions.
Relatively weak.
These interactions occur among permanent and/or
induced dipoles
The magnitude of Van der Waals forces depends on how
easily an atom is polarized.
Electronegative atoms with unshared pairs of electrons
are easily polarized.
Interactions among permanent dipoles such as carbonyl
groups are much weaker than ionic interactions
a. Dipole-dipole: occur between molecules
containing electronegative atoms, cause
molecules to orient themselves (positive end is
directed toward negative end of another
molecule)
+ C
O
+ C
O
b. Dipole-induced dipole: permanent dipole induces
transient dipole in a nearby molecule by
distorting its electron distribution.
+ C
-
O
H
+
H
H
H -
c. Induced dipole-induced dipole: the electron
motion in nearby non polar molecules result in
charge imbalance in adjacent molecules.
H
H
+
+
H
H
H - H
H
H -
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Hydrogen bonding keeps water in the liquid phase
between 0oC and 100oC.
Liquid water has a high:
Heat of vaporization - energy to vaporize one mole
of liquid at 1 atm
Heat capacity - energy to change the
temperature by 1oC
Water plays an important role in thermal regulation
in living organisms.
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Max number of hydrogen bonds form when water has
frozen into ice.
Hydrogen bonds is approximately 15% break when
ice is warmed.
Liquid water consists of continuously breaking and
forming hydrogen bonds.
The rising tempt. The broken of hydrogen bonds are
accelerating.
When boiling point is reached, the water molecules
break free from one another and vaporize.
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Water easily dissolves a wide variety of the
constituents of living organisms.
Water also unable to dissolve some substances:
lipids and certain amino acid- lead to
formation of membrane and protein folding.
This behavior is called hydrophilic and
hydrophobic properties of water.
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The polar nature of water makes it an excellent solvent
for polar and ionic materials that are water loving
(hydophillic)
Salts such as NaCl are held together by ionic forces>
Ionic interactions in aqueous solution- hydration of
ions.
Water molecules are polar, therefore attracted to
charged ions. Shells of water molecules refered to as
solvation spheres cluster around these ions.
Ions become hydrated and the attractive force between
them is reduced- dissolved in water.
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Nonpolar molecules tend to coalesce
into droplets in water. The repulsions
between the water molecules and the
nonpolar molecules cause this
phenomenon.
The water molecules form a “cage”
around the small hydrophobic droplets.
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Water forms hydrogen-bonded cage like
structures around hydrophobic molecules,
forcing them out of solution.
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Amphipathic molecules contain both polar and
nonpolar groups.
Ionized fatty acids are amphipathic. The
carboxylate group is water soluble and the long
carbon chain is not.
Amphipathic molecules tend to form micelles,
colloidal aggregates with the charged “head”
facing outward to the water and the nonpolar
“tail” part inside.
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Osmosis is a spontaneous process in which solvent
(e.g. water) molecules pass through a semi permeable
membrane from a solution of lower solute (e.g.
chemical) concentration to a solution of higher solute
concentration.
Osmosis is the movement of solvent from a region of
high concentration (here, pure water) to a region of
relatively low concentration (water containing
dissolved solute).
Water moves by osmosis and solutes by diffusion.
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Osmotic pressure is the pressure required to
stop osmosis or the influx of water (22.4 atm
for 1M solution).
Because cells have a higher ion concentration
than the surrounding fluids, they tend to pick
up water through the semi permeable cell
membrane.
The cell is said to be hypertonic relative to the
surrounding fluid and will burst (hemolyze) if
osmotic control is not effected.
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Cells placed in a hypotonic
solution will lose water and
shrink (crenate).
If cells are placed in an
isotonic solution (conc. same
on both sides of membrane)
there is no net passage of
water.
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Hypotonic solution: A solution with a lower
salt concentration than in normal cells of the
body and the blood.
Hypertonic solution: A solution with a higher
salt concentration than in normal cells of the
body and the blood.
Isotonic solution: A solution that has the
same salt concentration as the normal cells of
the body and the blood. An isotonic beverage
may be drunk to replace the fluid and
minerals which the body uses during physical
activity.
Liquids move from high osmotic pressure
(high conc. solvent and low conc. solute) to
low osmotic pressure (high conc. solute and
low conc. of solvent)
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The self-ionization of water is the chemical reaction in
which two water molecules react to produce a
hydronium (H3O+) and a hydroxide ion (OH−).
Water ionization occurs endothermically due to electric
field fluctuations between molecules caused by nearby
dipole librations resulting from thermal effects, and
favorable localized hydrogen bonding.
Ions may separate but normally recombine within a
few min. to seconds. Rarely (about once every eleven
hours per molecule at 25°C, or less than once a week at
0°C) the localized hydrogen bonding arrangement
breaks before allowing the separated ions to return,
and the pair of ions (H+, OH-) hydrate independently
and continue their separate existence.
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Water dissociates. (self-ionizes)
H2O = H+ + OHKa=[H+][OH-]/[H2O]
Ka: equilibrium constant for the
reaction
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The conditions for the water dissociation equilibrium
must hold under all situations at 25o C. equib.
constant for ionization of water is, Ka =1.8 x10-16 M
and conc of pure water is 55. 5 M
Kw= [H+][OH-]=1 x 10-14
Kw= ion product of water. This means that the product
of [H+] and [OH-] in any water solution is always
1x10-14.
Since [H+] is equal to [OH-] when pure water
dissociates:
[H+ ] = [OH-] = 1 x 10-7 M
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When solution contains equal amount of [H+]
and [OH-] : neutral
 Sol with excess [H+] : acidic
 Sol with excess [OH-] : basic
 H+ ion conc varies over a wide range :
provides the basis of pH scale :
pH = - log [H+]
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An acid is a substance that can donate a proton
A base is a substance that can accept a proton
H+ ions (called a protons, since a H+ ion has neither
electrons nor neutrons).
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Weak acids do not completely dissociates in
water
The dissociation of organic acid is decribed
below
HA ↔ H+ + A- (conjugate base of HA)
Deprotonated product of the dissociation
reaction : conjugate base
The strength of a weak acid (capacity to release
H ions):
Ka = [H+][A-]/[HA]
Ka is the acid dissociation constant, the larger
value of Ka, the stronger the acid.
pKa = - log Ka
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Added acids increase the concentration of
hydronium ion and bases the concentration of
hydroxide ion.
+
-7
In acid solutions [H ] > 1 x 10 M
-7
[OH ] < 1 x 10 M
-
> 1 x 10-7 M
[H+] < 1 x 10-7 M
In basic solutions [OH ]
pH scale measures acidity without using
exponential numbers.
Ka
pKa
CH3COCOOH
3.2x10-3
CH3CHOHCOOH 1.4x10-4
2.5
3.9
CH3COOH
4.8
1.8x10-5
Larger Ka and smaller pKa values indicate stronger acids.
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Buffer : a solution that resists change in pH
when small amounts of strong acid or base
are added. Help maintain a relatively
constant H ion conc.
A buffer consists of:
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a weak acid and its conjugate base or
a weak base and its conjugate acid
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The capacity of a buffer to maintain a specific
pH depends on 2 factors:
The molar conc of the acid-conjugate base pair
The ratio of their conc.
The more molecules of buffer present, the more
H+ and OH- can be absorbed without changing
the pH.
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The Henderson-Hasselbalch (HH)
equation is derived from the
equilibrium expression for a
weak acid.
[A ]
pH = pKa + log
[HA]
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The HH equation enables us to calculate
the pH during a titration and to make
predictions regarding buffer solutions.
What is a titration?
It is a process in which carefully measured
volumes of a base are added to a solution
of an acid in order to determine the acid
concentration.
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When chemically equal (equivalent)
amounts of acid and base are present
during a titration, the equivalence point is
reached.
The equivalence point is detected by using
an indicator chemical that changes color or
by following the pH of the reaction versus
added base, ie. a titration curve.
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Water is essential for all living things.
Water molecules can form hydrogen
bonds with other molecules because
they have 2 H atoms that can be
donated ans 2 unshared electron pairs
that can act as acceptors.
Liquid water is an irregular network of
water molecules that each form 4
hydrogen bonds with neighbouring
water molecules.
Summary contd.
 Hydophilic substances such as ions
and polar molecules dissolve readily in
water.
 The hydrophobic effect is the tendency
of water to minimizeits contact with
nonpolar substances.
 Water molecules move from regions of
high concentration to regions of low
concentration by osmosis.
 Solutes move from regions of high
conc. to regions of low conc. by
diffusion.
Summary contd.
 Water ionizes to H+ (which represents the
hydronium ion H3O) and OH-.
 The concentration of H+ ions in solutions is
expressed as a pH value.
 Acids can donate protons and bases accept
protons.
 The strength of an acis is expressed as its pK.
 Henderson-Hasselbalch equation relates the
pH of a solution to the pK and concentration
of an acid to its conjugate base.
 Buffered solutions resist changes in pH within
about one pH unit of the pK of the buffering
species.
Noncovalent bonding of water has play a
vital role in determining the properties of
water. Describe types of those bonding and
water properties they determined.
2. Differentiate polar and nonpolar
molecule.Explain how polar nature of
water makes it an excellent solvent for
polar and ionic materials.
1.