Chapter Two:
Chemistry Comes Alive
M.C. Shamier, MD
Shenzhou University
Subjects

Matter and Energy
The Composition of Matter
Chemical Bonds
Chemical Reactions

Biochemistry: organic and inorganic compounds
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Matter

Anything that has mass and occupies space

Matter exists in one of three states:
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Solid:
Liquid:
Gas:
definite shape and volume
definite volume, changeable shape
changeable shape and volume
Energy
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The capacity to do work
Energy exists in different forms and the one is easily
converted to another
Question
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What forms of energy can you think of?
Forms of energy explained
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Kinetic energy is the energy of motion.
Potential energy is stored energy.
Chemical energy is energy stored in chemical bonds.
Electrical energy results from the movement of charged
particles.
Mechanical energy is energy directly involved with moving
matter.
Radiant energy is energy that travels in waves.
The composition of matter

“All matter is composed of elements, unique substances
that cannot be broken down into simpler substances by
ordinary chemical methods”
Elements…
The Human Body
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About 96% of human body mass is composed of:
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Oxygen (O)
Carbon (C)
Hydrogen (H)
Nitrogen (N)
Atom
Different atoms
Atom mass
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Proton:
mass of 1u, positively charged
Neutron: mass of 1u, neutrally (not) charged
Electron: mass of 0u, negatively charged
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The number of protons is equal to the number of electrons to
keep the electric charge 0.
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1u = 1.67262158 × 10-27kilograms
Atoms vs Elements
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The classification in elements depends on the number of
protons in the nucleus (the atomic number).
Atoms belonging to one element can have a different
number of neutrons, thus a different mass. These different
atoms are called isotopes.
Planetary model vs Orbital model


The planetary model is outdated and oversimplified, 2
dimensional, incorrectly depicting fixed circular paths of
electrons.
The orbital model depicts electrons as a cloud with
probable regions of greatest electron density.
Molecule: Atoms Combined
Chemical Bonds
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Now how do these atoms stick together?
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The octet rule states that except for the first energy
shell (stable with two electrons), atoms are stable with
eight electrons in their outermost shell.
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Unstable atoms tend to gain, lose or share electrons with
other atoms to achieve stability.
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This is essentially the forming of bonds
Stable atoms
Unstable atoms
Three types of bonds
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Ionic Bonds
Covalent Bonds
Hydrogen Bonds
Ionic Bonds
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Ionic bonds are chemical bonds that form between two
atoms that transfer one or more electrons from one atom to
the other.
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Anions (– charge) have gained one or more electrons
Cations (+ charge) have lost one or more electrons
Postively and negatively charged atoms attract eachother
Ionic Bonds
Covalent Bonds
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When electrons are shared between two atoms
Example: Methane (CH4)
Double Covalent Bond: Oxygen
Triple Covalent Bond: Nitrogen
Polarity
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The sharing of electrons may be equal or unequal
Polar molecules
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In polar molecules, electrons spend more time around
one atom, providing that atom with a partial negative
charge, while the other atom takes on a partial positive
charge.
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These are the symbols used for partial charge
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δ+
δ-
You can look at it as a spectrum:
Hydrogen bonds
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Weak attractions that form between partially charged
atoms found in polar molecules.
Bonding atoms within different molecules!
Hydrogen bonds are responsible for water
surface tension
Concluded
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Matter is anything with mass that occupies space.
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All matter is composed of elements, this classification is based
on the number of protons in the nucleus
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Atoms belong to elements, but vary in numbers of neutrons
(and in mass).
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Atoms are bound together by bonds to form molecules
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Ionic bonds, covalent bonds (polar or nonpolar)
Hydrogen bonds are bonds between atoms in different
molecules
Chemical reactions
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Occur whenever chemical bonds are formed, rearranged
or broken.
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The chemical equation:
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H + H  H2 (hydrogen gas)
4H + C  CH4 (methane)
Left: reactants, right: products, notated in molecular
formula
What’s left of the arrow should balance with what’s right
of the arrow
Three types of reactions
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Synthesis (combination) reactions
Decomposition reactions
Exchange reactions
Synthesis Reactions (bond formation)
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Smaller molecules form larger molecules
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A + B  AB
Decomposition Reactions (bond breaking)
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Larger molecules are split into smaller molecules
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AB  A + B
Exchange Reactions
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Bonds are broken and made
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AB + C  AC + B
Some facts
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All chemical reactions are theoretically reversible
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A+B  AB
When neither forward nor backward reaction is
dominant a chemical equilibrium occurs. The balance is
dynamic, not static.
The forward and backward reaction take place at equal
rates with no net effect.
Dominance of one direction:
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Energy requirement
Removal of products
Energy in chemical reactions
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Endergonic reactions
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Require energy (heat), the products contain more potential
energy than the reactants
Exergonic reactions
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The (potential) energy is released
Think of the chemical experience ending in an explosion
Rate of the chemical reaction
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A chemical reaction happens at the collision of particles.
The amount of collisions in a certain amount of time is
dependent on:
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Temperature:
faster movement of particles
Concentration: more particles to collide
Particle size:
less free space for particles to pass
eachother
Biochemistry
Biochemistry
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Biochemistry is the study of chemical processes in living
organisms. Including:
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Genetics (DNA)
Cell metabolism
Protein synthesis
pH (acids and bases)
Classes of Compounds
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Compounds consist of molecules containing atoms of
different elements.
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Inorganic compounds
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Water, salts, many acids and bases
Do not contain carbon (C)
Organic compounds
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Carbohydrates, fats, proteins, and nucleic acids
Contain carbon, usually large, and are covalently bonded
Water (H2O)
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60-80% of the volume of living cells
Most important inorganic compound:
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High heat capacity
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High heat of vaporization
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Temperature buffer: absorbs and releases heat with little temperature
change
Much energy is required to break molecule bonds
Useful cooling system (transpiration!)
Protective cushion around organs
Important chemical reactant
Universal solvent
Salts
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Ionic compounds (containing anions and cations), that dissociate in
water
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NaCl(s)
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Important ions: sodium (Na+), potassium (K+), calcium (Ca2+), iron
(Fe2+/3+).

Na+(aq) + Cl-(aq)
pH, acids and bases
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pH (0-14) is the measure of acidity or basicity in a
solution.
Measured by the relative concentration of hydrogen ions
Neutral pH (pure water) is 7
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Below 7 is acid
Above 7 is basic/alkaline
pH
Acids and Bases
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Acids are proton donors (release H+)
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Example: Hydrochloric acid donates a proton (H) to a water
molecule when dissolved in water.
HCl(s) + H2O(l) 
H3O +(aq) + Cl-(aq)
Bases are proton acceptors (take up H+)
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Example: Hydroxide accepts a proton from an acid ion.
NaOH(s)

Na +(aq) + OH-(aq)
OH-(aq) + H +(aq) 
H2O(l)
Buffers
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Buffers, such as bicarbonate (HCO3-), prevent large
fluctuations in pH of body fluids.
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Acidosis: increased blood acidity (below 7,35) can lead to
coma.
Alkalosis: increased blood basicity (above 7,45) can cause
tetany.
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So blood pH must be maintained between the values of
7,35 and 7,45. Homeostasis!
Organic Compounds
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Contain carbon and are unique to living systems
Carbohydrates
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Major source of cellular fuel
Contain Carbon (C), Hydrogen (H) and Oxygen (O)
Three classes
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Monosaccharides
Disaccharides
Polysaccharides
Larger molecules, less
soluble
Lipids
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Contain C, H, O (less than in carbohydrates), and
sometimes P
Insoluble in water
Main types:
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Neutral fats or triglycerides (fats and oils)
Phospholipids (cell membrane)
Steroids (sex hormones)
Proteins
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10-30% of cell mass
The basic structural material of the body
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Contain C, H, O, N, and sometimes S(ulfur) and P(hosphor)
Polymers (long chains) of amino acids (20)
Protein Structure
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Denaturation means loss of
the 3D shape/structure of a
protein.

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Due to environmental
changes such as pH or
temperature.
Again the importance of
homeostasis!
Enzymes
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Are (mostly) proteins with the function of biological
catalyst
Concluded
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Thus: there are organic and inorganic compounds
Inorganic compounds include water, salts, acids (H+-donors)
and bases (H+-acceptors).
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pH is the measure for acidity
Organic compounds include carbohydrates, lipids, proteins
and enzymes, contain carbon (C) and are unique to living
organisms.
End of Chapter Two