BCH1002 Biochemical Aspects of Health and Disease

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BCH1002Biochemical Aspects of Health and Disease
1. BASIC CHEMISTRY OF LIFE

• Prof. K. M. Chan
• Dept. of Biochemistry
• Chinese University
• Room 513B, Basic Medical Sciences Building
• Tel [phone]
• Email kingchan_at_cuhk.edu.hk chankingming_at_gmail.co
  m

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Chemical Context of Life

1. Units Concentrations (units), molarities,
   normality, ion concentration, dilution, valence
2. Chemical Bonds
3. Energy Laws
4. Water as an reactant
5. Oxidation and Reduction
6. Ionization (pH scale), acid-base balance and
   physiological buffers
7. Functional Groups
8. Self learning questions

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1.1 Units

• Concentration A measure of the number of
  particles of a substance, or the mass of those
  particles, that are contained in a specified
  volumn (L, mL, µL)
• Amount of drug in blood to indicate certain
  extent of intoxication
• Proper use of drug, based on a patients weight
  is a relevant dosage measure.

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• Mole the amount of substance containing
  Avogadros number of particles
• Molarity (M) the number of moles of solute per
  liter (L) of solution or per kilogram (m,
  molality) of solvent
• M moles solute/ L solution m moles/ kg
• Normality one equivalent of an ion is the number
  of grams of the ion corresponding to Avogadros
  number of electrical charges. Meq
  (milliequivalent) per liter is commonly used in
  blood, plasma and urine samples.
• Concentrations ppm, ppb, ppt(w/w mg/kg, ug/kg,
  ng/kg, pg/kg, fg/kgor w/v mg/L as ppm ppb
  ppt. )

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Serial Dilution

• This technique involves the removal of a small
  amount of an original solution to another
  container which is then brought up to the
  original volume using the required buffer or
  water.
• Serial dilutions are usually made in increments
  of 1000, 100 or 10. The concentration of the
  original solution and the desired concentration
  will determine how great the dilutions need to be
  and how many dilutions are required.
• The idea is to avoid a huge jump of dilution
  which would create error when pipetting.

Mix and vortex well on each dilution before
removing the solution into the next
1ml
1ml
1ml
Remove 1 ml
9 ml buffer
10 ml buffer
9 ml buffer
9 ml buffer
1M
0.1M
0.01 M
0.001 M
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mole Avogadro's number (6.02 X 1023 atoms) of a
substance. molecules  Units of two or more atoms
held together by chemical bonds. The combination
of atoms by chemical bonds with the component
atoms in definite proportions, such as water (two
H to one O).
C6H12O6
H2O
Can you write the formulae of Alanine?
atom  The smallest indivisible particle of matter
that can have an independent existence. atomic
number  The number of protons in the nucleus of
an atom. atomic weight  The sum of the weights of
an atom's protons and neutrons, the atomic weight
differs between isotopes of the same element.
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Valence

• Octet rule (Lewis) in covalent bond formation,
  atoms go as far as possible toward completing
  their octets by sharing electron pairs.
• The valence of an element is the number of
  covalent bonds an atom of the element forms.
• The number of valence is found by the Lewis
  structure or symbol, according to the valence
  electron number. E.g. K is 1, Mg is 2.
• Some ions would have multiple valences with
  different toxicities. Cr (V, VI) are more toxic
  than Cr (III) As III behaves differently from As
  V. Q Why arsenic (III) is more toxic than
  arsenic (V)?? (Google your answer please.)

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1.2 Chemical Bonds

• Covalent bond
• Hydrogen bond
• Ionic bond
• Electrostatic Interaction
• Hydrophobic Interaction
• Van der Waals Interaction (Force)

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1.2.1 Covalent bond

• A pair of electrons shared between two atoms
• H2 , O2 , H2O, N2
• Strong bonding (stronger than non-covalent bonds)
• The compounds are electrically neutral

Covalently bonded hydrogen and carbon in a
molecule of methane. One way of representing
covalent bonding in a molecule is with a dot and
cross diagram. (Adapted from Wikipedia).
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1.2.2 Hydrogen Bond

• weak attraction between an electronegative atom
  in one molecule and another electropositive atom
  in another molecule.

Bond distances differ in different pairs, e.g.
O-H N- distance between N and O is 2.88 Å
-N-H O- distance between N and O is 3.04 Å.
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Ice crystal frozen water molecules linked with
hydrogen bonds among each others. Density of ice
is lighter than water because of the increased
volumn in the ice crystal fixed by the hydrogen
bonds.
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1.2.3 Ionic Bond
(Adapted from Wikipedia).

• Ion an electrically charged particle formed by
  the gain or loss of electrons
• Positive charged ( e.g. Na )or negatively
  charged (Cl -)
• Ionic bonding an electrostatic attractive force
  between a positive and negative ion
• Strong interaction F is strong and proportional
  to the q values of two charged atoms, when water
  is diminishing.

Electron configurations of lithium and
fluorine. Lithium has one electron in its outer
shell, held rather loosely because the ionization
energy is low. Fluorine carries 7 electrons in
its outer shell. The bonding energy from the
electrostatic attraction of the two
oppositely-charged ions has a large enough
negative value that the overall bonded state
energy is lower than the unbonded state
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1.2.4 Electrostatic Interactions

• These interactions occur between oppositely
  charged atoms or groups.
• Electrostatic interactions are responsible for
  the hydration of ions.
• The polar water molecules form shell of water
  molecules when attracted to charged ions.
• As ions become hydrated, the attractive force
  between them is reduced and the charged species
  dissolve in the water.
• The force of electrostatic attraction is given by
  Coulombs law F q1 q2 /r2 D, where q1 and q2
  are the charges of the two groups, r is distance,
  D is dielectric constant of the medium (D1 at
  vacuum, D80 in water)

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Have ionic attractions among molecules
Show hydrophobic interactions
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1.2.5 Hydrophobic Interactions

• Very important in biomolecules.
• Water is a poor solvent for non-polar substances.
• Responsible for maintaining membrane structure
  and protein folding.
• As small amount of non-polar substances are
  observed to coalesce into droplets when mixed
  with water. So as membrane forms boundaries to
  create compartments, and thus establish cellular
  nature. Life began to emerge.
• Counteracts with hydrophilic interactions.

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• Amphipathic compounds in aqueous solution.
• Hydrophobic alkyl chains in long chain fatty
  acids,
• Clustering in micelles, fatty acids expose the
  smallest possible hydrophobic surface area to
  water.

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Release of ordered water favours formation of an
enzyme-substrate complex.
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1.2.6 Van der Waals Interactions

• As two molecules come in contact, weak and
  transient electrostatic interactions occur
  between them as attractive and/or repulsive
  forces.

Van der Waals contact distance
Repulsion
distance
Energy
0
Attraction
Energy of a van der Waals interaction as a
function of the distance between two atoms
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1.3 Energy measurement units

• Energy, heat and enthalpy
• Law of the conservation of energy energy can
  neither be created or destroyed.
• Energy is the capacity to do work or release heat
  (thermal motion)
• The unit of energy and heat is joule, J, or
  calorie.
• One calorie is the energy needed to raise the
  temperature of 1 g of water by 1 C. 1 cal
  4.184 J or 1 J 0.24 cal.
• One kJ of heat can raise the temperature of 240 g
  of water, around a cup of coffee, by 1 C.

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1.3.1 Heat capacity

• Heat capacity heat supplied/ temp rise unit
  kJ per C.
• Heat capacity mass X specific heat capacity of
  a substance
• Specific heat capacity of water 1, copper
  0.38, ethanol 2.42, polyethylene 2.3, all in
  J/ C/g.

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1.3.2 First Law of Thermodynamics

• The law of energy conservation
• Energy cannot be created or destroyed.
• Energy is conserved in any closed system ( a
  system without any transfer of energy and matter
  in and out).
• E.g. The food pyramid photosynthetic organisms
  at the base capture light energy as primary
  producers, herbivores and carnivores derive their
  energy ultimately from the primary producers. The
  energy further transferred to the tertiary
  consumers who eat the secondary consumers
  (herbivores).

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However, first law alone cannot explain living
processes.

• Why place an ice cube in a glass of water at room
  temperature and the ice melts instead of freezing
  the whole glass of water? (directional control)
• Why cant we mix carbon dioxide and water to make
  paper?
• Why some reactions are reversible and some are
  irreversible?
• We thus need the second Law of thermodynamics, as
  biochemical processes always have tight control
  of their directions and rates of reactions by
  enzymes.

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1.3.3 Second Law of Thermodynamics

• Any system tends to become increasingly
  disorganized (free).
• In any spontaneous process, there is always an
  increase in entropy (S) ?.
• Entropy describes the number of the possible
  microscopic configurations of the system.
• The total entropy change in any reaction that
  occurs spontaneously must be greater than zero.

• Considering work, heat and energy together,
  entropy is a state function of a thermodynamic
  system defined by the differential quantity dS
  dQ / T, where dQ is the amount of heat absorbed
  in a reversible process in which the system goes
  from the one state to another, and T is the
  absolute temperature.

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1.3.4 Free Energy Concept

• Considering the second law in open systems, as
  biological systems are always opened to exchange
  energy and matter with its environment.
• Using concepts of entropy (?) and enthalpy (?)
  (heat content) and the concept of Gibbs free
  energy to include both heat energy and entropy G
  H - TS.
• Change of free energy ?G ?H - T?S
• A thermodynamically favored process tends in the
  direction that minimizes free energy, results in
  a negative ?G, (?H - T?S) lt 0, this is also one
  way of stating the second law.

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The variation of reaction spontaneity (sign of
?G) with the signs of ?H and?S.

The reaction is both enthalipically favoured (exothermic) and entropically favoured. It is spontaneous (exergonic at all temperatures).
The reaction is enthalpically favoured but not entropically, it is spontaneous only when temperatures below T ?H/ ?S
The reaction is endothermic and enthalpically opposed but entropically favoured. It is spontaneous at temperature above T ?H/ ?S
Both enthalpically and entropically opposed, endergonic at all temperatures
?H
?S
?G ?H - T?S
-

-
-


-

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Chemical potential and chemical equilibrium

• GA GA RT InA
• G Gibbs free energy, GA is standard-state
  value of the chemical potential for compound A,
  and GA also consider the concentration of A and
  temperature.
• For the reaction aA bB cC dD
• ?G G products G reactants
• ?G ?G RT In Cc Dd/ Aa Bb
• ?G 0, ?G - RT In Keq

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The rate of a reaction

• However, the ?G values dictate the direction NOT
  the rate of the reaction
• The rate of a reaction is determined by kinetic
  parameters and is restricted by activation
  energy.
• Many biochemical reactions with a negative ?G
  value, however could not have happened without
  lowering their activation energy. Appropriate
  enzyme is needed to make the reaction become
  kinetically feasible and proceed at a much faster
  rate.

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1.3.5 Steady-state thermodynamics

1. The above laws state that the reversible
   reactions tend to operate to approach
   equilibrium, but living processes seem to
   contradict this ever increasing entropy scenario.
2. Living things are however never at equilibrium,
   the cells maintains itself at a stage far from
   equilibrium with its surrounding. Otherwise, no
   useful work can be done when at equilibrium,
   entropy is at maximum, and ?G 0.
3. At steady state, output of energy and matters is
   continuously replaced by the input of an exactly
   the same amount of matters and energy. A steady
   state is also very responsive to its surrounding
   environment (or system). We need energy to
   sustain all living processes.
4. Solar energy is captured in plants as sugars
   (glucose) to be converted into high energy
   compounds like ATP for living processes. For
   human, we need to eat to obtain energy for
   biological processes and our normal activities.

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1.4. Water as a reactant

• Hydrolysis reactions are common reaction using
  water as an reactant.
• Condensation reactions, however, involve water
  elimination.
• We may get water from metabolic sources, e.g.
  oxidation of glucose into carbon dioxide and
  water. Using photosynthesis, sunlight can
  breakdown water into oxygen and an electron
  accepting species.
• But why water is so important anyway??

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• Properties of water dipoles, bent geometry,
  hydrogen bonding.
• Biochemical reactions take place in a water
  medium.
• Non-covalent interactions (bonding) control the
  shape, property and function of all biomolecules,
  and thus all biochemical reactions.

On earth 70 seawater, lt 10 freshwater
hydrological cycle create niches all life forms
need water and adapt how to deal with water.
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1.4.1 Properties of Water
Dipoles, Bent Geometry and H Bond
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1.4.2 Water is an excellent solvent
Water dissolves many crystalline salts by
hydrating their component ions, e.g. NaCl. The
ionic charges are partially neutralized, and the
electrostatic attractions necessary for lattice
formation are weakened.
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• Water is a remarkable solvent due to its ability
  to dissolve a large variety of ionic and polar
  substances as contributed by its dipolar
  structure and capacity of forming hydrogen bonds.
• In addition, its ionization and amphipathic
  properties also helpful in making water as an
  ideal solvent and reactant.
• Colligative properties stem from the reduction of
  the chemical potential of the liquid solvent as a
  result of the presence of solute.

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1.4.3 Osmosis and osmotic pressure

• Solutes affect colligative properties of aqueous
  solution its osmotic pressure, vapour pressure,
  boiling point and melting point.
• Water tends to move from high water concentration
  to a lower water concentration
• Osmosis, water movement across a semi-permeable
  membrane driven by differences in osmotic
  pressure
• The number of solute (concentration) in a given
  amount of water affects the colligative
  properties of the water.

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Osmotic pressure is the force of osmosis
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DISCUSSION We use sea salt to preserve fish to
make salted-fish. Both eastern and western
cultures use the same principles, but of course
they use different methods to cook them. Explain
the principles of using salt for food
preservation. Why do we eat fish any way?
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1.4.4 Dialysis

• Biomolecules (e.g. DNA and proteins) are
  routinely separated from low molecular weight
  impurities or salts by dialysis.
• Using dialysis tubing or bags with known
  molecular weight cut-off or pore sizes, salts and
  the impurities with smaller sizes could go away
  with water through the pores of the membrane of
  the dialysis bag or tubing.
• In medicine, dialysis is the process to use a
  machine to filter blood when kidney function
  fails. Kidney normally removes waste (e.g. urea)
  from blood and excessive fluid in the form of
  urine.

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Take home exercise 1 Hemolysis
(Haemolysis)Study the following terms by using
google and Wikipedia
Dialysis treatments mimic kidney function as
dialysis (waste removal) and ultra-filtration
(fluid removal)
http//www.schoolscience.co.uk/content/4/biology/a
bpi/kidneys/kid5.html

• What is hemolysis? And What causes hemolysis?
• What is hemodialysis?

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1.4.5 Thermal Properties of Water

• Water has an exceptionally high heat capacity.
• Its boiling and melting points are significantly
  higher than those compounds with similar
  structure and molecular weight.
• Hydrogen bonding is responsible for this
  anomalous behavior and property.
• Water also has the highest surface tension of all
  common liquid, except mercury.

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From Ice to Vapour

• Ice, is less dense than water in its liquid
  state.
• Heat capacity, high enough to take a role in
  thermal regulation in biological organisms.
• We sweat to reduce heat in our body. We drip -
  from the 2 million sweat glands covering our
  body. Most of our sweat glands are in our palms,
  the bottoms of our feet, etc. Our bodies are
  cooled when the sweat evaporates from the surface
  of our skin.
• Vapour pressure, water evaporate into air but as
  non-volatile molecules added (e.g. glucose) the
  vapour pressure could be reduced according to the
  amount added and thus less water evaporate.

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Boiling point elevation, and Freezing point
depression

• Boiling point is 100 C at 1 atm, as adding
  nonvolatile solutes reduce the vapour pressure, a
  higher temperature is required to raise the
  vapour pressure up to boil.
• Because solute molecules lower the vapour
  pressure of water, the solution must be cooled to
  below 0 C to freeze.

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• Full seawater with 35 o salinity (mainly NaCl)
  has a freezing point of 1.86 C. Sera with
  electrolytes have a freezing temperature of 0.6
  C to 0.7 C , but some arctic fish and worms
  produce antifreeze proteins to further reduce
  their blood sera freezing point for winter
  survival.
• These proteins have different structures to block
  the growth of ice crystals.

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1.5 Oxidation and Reduction

• In living organisms, both energy releasing and
  capturing processes consist mainly of redox
  reactions.
• Redox reactions occur when there is a transfer of
  electrons between an electron donor and electron
  acceptor.
• Oxidation refers to a reaction in which oxygen
  combined with an element or compound, e.g., the
  reaction of magnesium with oxygen to form
  magnesium oxide or the combination of carbon
  monoxide with oxygen to form carbon dioxide. In
  the process, the compound gives up electrons to
  the oxygen in forming a chemical bond. Thus,
  electrons released (lost) is oxidation with an
  increase in oxidation number.

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1.5.1 Redox Pairs and energy

• Reduction refers to a decrease in the amount of
  oxygen in a substance, and gain electrons, or a
  decrease in oxidation number, whether or not
  oxygen itself is actually involved in the
  reaction.
• The tendency for a specific conjugate redox pair
  to lose an electron is called redox potential.
• Electrons flow spontaneously from electronegative
  redox pairs to those that are more positive. As
  they flow, electrons lose energy.
• A significant portion of free energy generated as
  electrons move from NADH to oxygen in the
  electron transport system is used to synthesize
  ATP.
• In many metabolic processes, energy is required
  to move electrons from redox pairs with more
  positive reduction potentials to those with more
  negative reduction potentials.

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1.5.2 Redox and Health

• In photosynthetic pathways, light energy is
  needed to drive electrons from electron donors
  (such as water), to electron acceptors with more
  negative reduction potentials.
• The energized electrons eventually flow back to
  acceptors with more positive reduction
  potentials, thus providing energy for ATP
  synthesis and carbon dioxide reduction to form
  carbohydrates.
• Free radicals are formed in many redox reactions,
  antioxidants (e.g. glutathione, GSH) are required
  to remove the peroxidative compounds, which may
  damage cell membranes or biomolecules.
• Free radicals and Health Peroxidation or
  antioxidation.
• Take Home Exercise 2
• Search for the importance of antioxidation in
  health and diseases)

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1.6 Ionization, acid-base balance and
physiological buffer

• Pure water is slightly ionized
• Formation of hydronium ions, H3O OH-
• Water ionization can be measured by its
  electrical conductivity.
• The position of equilibrium of any chemical
  reaction is given by its equilibrium constant,
  Keq.
• AB CD, Keq CD/AB, for water, KeqH
  OH-/H2O
• pH log 1/ H

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1.6.1 Proton Hopping
OH-
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1.6.2 The pH scale
Increasingly Acidic
pH
- 1M HCl
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
- Gastric juice
- Lemon juice
- Coke, vinegar
- Tomato juice
- Black coffee
- Milk, saliva
Neutral
- Blood, tears
- Seawater
- Baking soda (Sol)
- Household Ammonia
- Household Bleach
- 1M NaOH
Increasingly basic (alkaline)
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1.6.3 Ionization of Acetic Acid (HAc)
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1.6.4 The Henderson-Hasselbalch Equation
It combines the equilibrium constant expression
and the pH resulted.
In other words, the dissociation of an ion is
related to the pH and the concentrations of
cations and anions in the solution.
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1.6.5 Physiological Buffers

• Buffers are mixture of weak acids and their
  conjugate bases.
• An acid-base conjugate pair (such as acetic acid
  and acetate ion) has an important property to
  resist change in the pH of a solution act as
  buffer.
• We use Bicarbonate buffer system mainly in our
  circulatory system (blood and lungs). A pH of 7.4
  is maintained in blood partly by a carbonic
  acid-bicarbonate buffer system. The CO2 in the
  blood contributes bicarbonate.
• Phosphate buffer and protein/amino acids as
  buffer systems are useful in plasma (blood), body
  fluids and inside the cells as well.

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Histidine
Terminal COOH
Terminal NH2
Red cell pH
Side chain COOH
Arginine
Cysteine
Tyrosine, Lysine
2
4
6
8
10
12
pK of some functional groups in proteins
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1.6.6 Effects of pH, e.g. Bohr Effects

• Binding of CO2lowers the affinity of oxygen to
  hemoglobin, a protein with heme to carry oxygen
  to tissues.
• CO2 binds to the terminal amino groups of
  hemoglobin to lower its oxygen affinity.
• About 0.8 equivalents of CO2 are produced per O2
  consumed, the CO2 is transported as bicarbonate
  by carbonic anhydrase. H generated from the
  reaction is taken up by deoxyhemoglobin as part
  of the Bohr effect.
• Lowering of pH in the physiological range,
  decreased the oxygen affinity and CO2 is carried
  by hemoglobin with NH2 as carbamate (NHCOO-) and
  H.
• The carbamates form salt bridges to stabilized a
  special form (structure) of hemoglobin that binds
  oxygen with a lower affinity.
• In other words, CO2 and H promote the release of
  O2 , this is known as Bohr Effect.

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Schematic diagram of Bohr effect
O2Hb H CO2
In actively metabolizing tissues (e.g. muscle)
with higher CO2 concentrations
In the alveoli of the lungs with higher oxygen
content
H
Hb

O2
CO2

• The reciprocal effect occurs in the alveolar
  capillaries of the lung with high concentrations
  of oxygen there to unload CO2 and H from
  hemoglobin (Hb). Hb binds with oxygen with heme.
  Without Bohr effect, gas exchanges cannot happen
  that efficient.

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Effect of pH on the oxygen affinity of
hemoglobin lowering the pH from 7.6 to 7.2 from
carbon dioxide leads to the release of oxygen
from oxyhemoglobin
1.0
pH 7.6
pH 7.2
Saturation
0.5
Bohr effect H releases O2 (saturation drops at
the same partial pressure of oxygen)
20
40
60
80
pO2 (torrs, O2 pressure)
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Effects of pH on enzymatic activities
Q1 Deposition of HCl into the stomach lumen to
make gastric juice more acidic for digestion of
protein. What chemicals can be used as drug to
control over production of acid in our stomach?
Importance of pH Different enzymes have their
own optimal pH values, e.g. pepsin works well at
pH 2 in the stomach, trypsin in pancreatic juice
at 6.4, etc.
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1.7. Organic molecules and functional groups
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Organic Molecules by Functional
Groups Rhydrocarbon group
Hydrocarbons Alcohols Ethers Halides Aldehyde
s Keytones Carboxylic acids Esters
Amides Amines Nitro compounds Nitriles Thiols


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Functional groups in Life
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Functional groups in Life
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1.8 Self-learning Questions(Go search the web
and answer the following questions on your own,
using three to four simple sentences)

• 3. Illustrate the properties of water to explain
  why water is an ideal solvent and reactant for
  biological processes.
• 4. Water is so important in health, how our
  bodies adjust water balance?
• 5. Bicarbonate is one of the main buffers of the
  blood, and phosphate is the main buffer of the
  cells. Explain why this observation is true and
  the chemical properties of these two chemicals.

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• 6. What is acidosis? Explain this symptom and
  acid-base balance in our bodies.
• 7. Explain the colligate properties of aqueous
  solution. Explain the effect of hypertonic and
  hypotonic solution on animal cells using red
  blood cell as an example.
• 8. What is reverse osmosis??

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Multiple choice questions

• Which ONE of the following properties of water
  molecule does NOT contribute to its colligative
  properties?
• Amphipathic properties
• Hydrogen bonding
• Ionization property
• Dipole moment
• Heat capacity
• Which ONE of the following statements on thermal
  dynamic laws is INCORRECT?
• First law of thermodynamics is the law of energy
  conservation, because energy cannot be created or
  destroyed.
• The second law of thermodynamics states that any
  system tends to become increasingly disorganized
  with a spontaneous process to increase in entropy
  and degree of randomness.
• A thermodynamically favored process tends in the
  direction to minimize free energy.
• At steady state, output of energy and matters is
  continuously replaced by the input of an exactly
  the same amount of matters and energy.
• Living things are all aimed at approaching
  equilibrium the cells maintain itself at a stage
  of equilibrium with its surrounding.
• Which ONE of the following statements on the
  properties of buffers is INCORRECT?
• Buffers are mixture of weak acids and their
  conjugate bases.
• Bicarbonate buffer system occurs in our
  circulatory system to maintain a blood pH of 7.4.
• Carbon dioxides and carbonic acid-bicarbonate
  buffer system maintain the blood pH in our body.
• Phosphate buffer and protein (amino acids) buffer
  systems are useful in plasma, body fluid and
  intracellular pH maintenance.
• All enzymes have their optimal pH at 7.4 as well.