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The Chemistry of Life
Chemical Elements and Water
Biochemistry – the study of the chemical reactions that take place in living systems

The basic unit of matter = the atom

4 types of atoms make up 97% of all living systems:
-carbon – 19%
-nitrogen – 3%
-hydrogen – 10%
-oxygen – 65%

atoms bond with one another to form compounds by intramolecular bonding

types of compounds = ionic or covalent
INTRAMOLECULAR BONDING

Intramolecular bonding- bonds within a molecule
Ionic compounds:


-made of metal + non-metal
-held together by ionic bond
-ionic bond = electrostatic force of attraction formed by the
gaining and losing of electrons
cations = atoms that lose electrons to become positively charged
anions = atoms that gain electrons to become negatively charged
Covalent (molecular) compounds


-made of non-metal + non-metal
-held together by covalent bond
-also called covalent compounds
-covalent bond = bond formed by the sharing of
electrons between atoms
-can be single, double, or triple
-ex. F2, O2
most biological molecules contain covalent bonds
There are several other elements need by living organisms
INTERMOLECULAR BONDING
-
Chemical bonds between molecules
Weaker than intramolecular bonds
There are three types of intermolecular bonding and collectively they are called
Van der Waals forces.
1. London dispersion forces –attractive force formed by temporary charges that
occur as electrons move around the nucleus.
2. Dipole-dipole- attractive force between molecules resulting from interactions due
to polarity
3. Hydrogen Bonds-Form between an electropositive atom like hydrogen, and an
electronegative atom like oxygen (occurs between water molecules).
TYPES OF REACTIONS
Metabolism: is the sum of all enzyme catalyzed reactions that occur in the body
Catabolism: is the breakdown of complex molecules into simpler molecules including
the hydrolysis of macromolecules into monomers.
Anabolism: is the synthesis of complex molecules including the formation of
macromolecules from monomers by condensation reactions.
Redox Reaction- chemical reaction involving the transfer of one or more electrons
from one atom to another (LEO says GER).
Dehydration Synthesis/ Condensation Reaction- a type of anabolic reaction
(joins molecules) where water is formed. The water is removed in order to create a
polymer. One monomer gives up an H and the other gives up OH.
Example: synthesis of Urea
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Urea is a nitrogen containing compound that is produced by living organisms,
but can also be artificially synthesized.
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Produced when there is an excess of amino acids in the body, in order to excrete
the excess nitrogen.
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Synthesis occurs in the liver
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Urea is transported in the blood stream to the kidneys where it is filtered and
passed out into the urine.
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In 1892, Friedrich Wohler synthesized urea artificially. Disproving the theory of
vitalism; that organic compounds could only be synthesized by living organisms
Liver Synthesis:
Artificial Synthesis:
Ammonia + carbon
dioxide  ammonium
carbamate urea +
water
Hydrolysis Reaction- a type of catabolic reaction (breaks molecules) in which water is
added to break up a polymer into monomers.
ORGANIC MOLECULES
CARBON
– A small relatively light element with four single valence electrons
– It can form up to four stable bonds with other atoms
– Carbon atoms attach to each other to form straight chain or branched chains and
ring structures
– These structures form the backbone of many organic molecules (An organic
molecule is made of C, H, S, O, N, P)
Example: Methane, CH4
SULFUR
- found in certain amino acids (the building blocks of proteins), therefore, are
required for protein and enzyme production.
- The sulfur in amino acids can lead to connections called “disulfide bridges” which
causes a protein chain to fold.
- Is a source of energy for some prokaryotes (chemo-autotrophs)
- Can make TWO bonds
PHOSPHORUS
- a key component of ATP (chemical energy made in cellular respiration) and DNA
– both of which are found in prokaryotes, plants, and animals
- ATP – Adenosine Triphosphate
- Can make up to FIVE bonds in covalent compounds
CALCIUM
- Required to form bone tissue (lack of calcium leads to osteoporosis)
- Involved in releasing neurotransmitters for brain cell communication
- Important in cell walls and cell membranes
IRON
- Found in the “heme” group of hemoglobin, which is a protein
in red blood cells.
- Hemoglobin is responsible for oxygen transport
-
Oxygen binds to the iron, and is transported from the lungs to the body cells.
used by some bacteria to as a source of energy
needed to form chlorophyll
SODIUM
- helps move the flagellum
- sodium-potassium pump (see cell membrane notes)
- involved in transporting glucose across the cell membrane
FUNCTIONAL GROUPS:
–
–
–
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Molecules containing only carbon and hydrogen are called Hydrocarbons.
Hydrocarbons are non-polar because of their symmetrical shape
Other elements may attach to hydrocarbons to form reactive clusters called
functional groups.
Most reactions occur as a result of interactions between functional groups.
Functional Group
Chemical Formula Structural Formula
Compounds
Hydroxyl
Carboxyl
Carbonyl
Amine
Sulfhydryl
Phosphate
Methyl
POLAR MOLECULES – ex: WATER

electrons shared in covalent bonds may be shared unequally - they may spend
more time around one particular atom over another

this is called a polar molecule = molecule in which electrons are not shared
equally thus giving one end of the molecule a partially negative charge and the
other end a partially positive charge

electronegativity= relative ability of an atom to attract electrons
Water (H2O)
 water is covalent but the electrons are not shared equally

O is more electronegative than H and thus electrons spend more time around O,
making it more negative (relative to H) and H is more positive (relative to O)

water is therefore polar
O ∂-
H ∂+
H ∂+

electrons in the intramolecular bonds of water are not shared equally and thus
water is polar

the intermolecular bonds in water are called hydrogen bonds

hydrogen bond (H-bond) = forces of
attraction between a hydrogen of
one molecule and a highly
electronegative element of another
molecule (usually F, O, N)

these H-bonds hold water
molecules together
Properties of Water
 because of water’s polarity and it’s H-bonds, it tends to posses extraordinary
properties
1) high surface tension- the H-bonds hold water molecules together,
giving it a surface like a trampoline
-ex. water strider can walk on water due to surface tension
2) cohesive – water molecules stick together
-if you pull on one molecule it brings another with it because of Hbonding between water molecules
-ex. transport of water up plant stems (against gravity)
3) adhesive – water molecules stick to other substances
-its polarity allows it to attract other polar substances
-ex. drops of water on glass
4) high specific heat capacity
– water can absorb a lot of energy before its temperature
changes (heat absorbed = bonds broken)
- water can release a lot of energy before its temperature
changes (heat released = bonds formed)
-(much of E is used in the disruption or formation of Hbonds and thus E does not affect molecular motion as
quickly/dramatically)
specific heat capacity = -the amount of E required to raise the
temperature of 1 g of a substance by 1 °C
-it’s a measure of how well a substance resists
changes in temperature
-the specific heat capacity of water is 4 J/g
5) denser as a liquid than as a solid
– when water is a solid it expands since it possess a maximum # of Hbonds which hold water molecules further apart making it less dense
-ex. water bottle expands when frozen
-as it warms, H-bonds break and water molecules move closer together
making it more dense
-ex. ice remains on the top of frozen lakes during the winter (liquid is
below because it is more dense – allows aquatic organisms to survive
winter)
6) excellent solvent
– polar solvents dissolve in water because of it’s polarity
– acts as a medium for reactions and transport of materials through the body.