Biology Biochemistry for Biology

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Biology                                                         Biochemistry for Biology
How to learn this material:

Because so much of this material can't be seen or touched, many
students find learning the vocabulary and concepts of chemistry
challenging. Overcoming this is mostly a matter of using your
imagination, and working with these new concepts as much as you
can. Repetition will help make these new ideas familiar to you.

Try making flash cards with important vocabulary words (in bold on this sheet) and their
definitions. Quiz yourself on the bus, waiting in lines, or before you go to bed. Breaking learning
up into short sessions will help you learn a few new concepts at every session. Be sure to
review this material at least once a day until you've achieved mastery, and then at least one a
week until the end of your class.

If you've been away from science for a few years, you may have forgotten what you learned in
high school. Firm up your foundation by browsing through a grade 10 science textbook. It will
remind you of some of the fundamental concepts you will use in Biology.


                                           THE BASICS
All matter on earth is made up of elements. There are 116 elements in the periodic table. For
biology, you need to know the names and symbols of the first twenty:




A sample of any element can be divided up into smaller and smaller parts until you reach the
atom, the smallest piece of matter that still has the physical properties of the element.
                       Atoms are made up of three major components: protons, neutrons, and
                       electrons.
                       The nucleus is the centre of the atom and contains the atom's protons
                       and neutrons.
                       Electrons form a cloud around the nucleus.
                       Protons have a positive electrical charge. Electrons have a negative
                       charge equal to that of protons. Neutrons have no electrical charge.



                  2007 Vancouver Community College Learning Centre.
                 Student review only. May not be reproduced for classes.
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                  An atom is one particle of an element. It is made up of a nucleus (protons and
                  neutrons) and an electron cloud. An atom has equal numbers of protons and
                  electrons, and so has no electrical charge. H and Na are both examples of
                  atoms.

                 An ion is an atom or molecule that has either gained or lost electrons and
therefore has an electrical charge. The charge can be either positive or negative. NH4+
(ammonium) and Cl (chloride) are both ions.

A compound is a group of elements combined in a fixed ratio. There are two kinds of
compounds. Molecules and ionic solids differ in the type of bone holding the atoms together
         (you'll learn about these types of bonds later on).

            A molecule is two or more atoms bonded to each other covalently. CH4 (methane)
            is an example of a molecule.

An ionic solid is a group of atoms held together by ionic bonds, forming a
crystal. NaCl (table salt) is one example of an ionic compound.
The number of protons determines the identity of the element. An element's atomic number is
equal to its number of protons.

For example, if an atom has six protons in its nucleus, then its atomic number will be 6. From
the periodic table, we see that atomic number 6 corresponds to carbon. Therefore, any atom
with six protons is carbon.
Unlike protons, the number of neutrons in an atom can vary without changing
the identity of the element. Atoms of the same element that don't have the same
number of neutrons are isotopes.

Some isotopes are stable, and others are unstable. Those that are unstable are
radioactive.
The weight of an atom is determined by adding the number of protons plus the number of
neutrons. (The weight of electrons is so small that they aren't included)

Protons + neutrons = the mass of the atom, in atomic mass units.

For example, an atom with six protons and seven neutrons has a mass of 13 atomic mass units.
The number of electrons determines the electrical charge of the atom.

An atom with an equal number of electrons and protons has a neutral charge.
An atom with more electrons than protons has a negative charge. (it is a negative ion or anion)
An atom with fewer electrons than protons has a positive charge. (it is a positive ion or cation)

For example, an atom with six protons and eight electrons has a charge of -2.
Electrons arrange themselves in energy levels around the nucleus of the atom.
The innermost shell is filled first. Once an inner shell is full, electrons fill the next shell, moving
further away from the nucleus.


                   2007 Vancouver Community College Learning Centre.
                  Student review only. May not be reproduced for classes.
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The electrons in the outermost shell are called valence electrons. Valence electrons
participate in bonding.
To determine how many valence electrons an element has, count backwards from the element
(to the left) until you reach the end of it's row.
Using this method, we find that oxygen has 6 valence electrons:




                6         5                    4        3       2          1




                                       CHEMICAL BONDING
Atoms can bond to each other in two different ways:

In an ionic bond, an atom donates one or more electrons to another atom, and the resulting
ions are held together by electrical attractions between their different charges.

              Na + Cl  [Na]+ [Cl]-

The other type of bond is a covalent bond, the most common bond in biology.

In a covalent bond, atoms overlap their electron clouds and share two electrons.

Covalently bonded atoms arrange themselves so that all the bonding atoms have eight valence
electrons. Having a complete octet (8 valence electrons) allows the atom to mimic the electron
structure of a noble gas (elements in the last row of the periodic table), which is the most stable
configuration. Hydrogen is an exception to the octet rule, and achieves its noble gas
configuration by having two electrons.
Here is an example of covalent bond formation. Valence electrons are represented by dots
around the atomic symbol.

                      2            +              
The bonds have formed in such a way that both the chlorines and oxygen now have access to
eight electrons, and both elements have now achieved the electron structure of a noble gas (8
valence electrons).

                  2007 Vancouver Community College Learning Centre.
                 Student review only. May not be reproduced for classes.
J:\LLR\LearningCentre\WORKSHEETS\Source files\biology-biochemistry_for_biology-2007.doc

In covalent bonds, elements differ in their tendencies to draw the shared (bonding) electrons
towards their nuclei. This results in unequally shared electrons in the covalent bond. An
element's tendency to draw bonding electrons to its nucleus is its electronegativity.
When the electronegativities of two covalently bonded electrons differ significantly, the more
electronegative atom will pull the bonding electrons into its electron cloud. This unequal sharing
of electrons is called a polar covalent bond.

The different types of chemical bonds form a continuum in their electromagnetic characteristics:

non-polar                                                                                      polar
 no separation of charge        partial separation of charge            complete separation of charge

covalent bonds                     polar covalent bonds                                   ionic bonds
CH4, O2                                  NH3, H2O                                           NaCl, KF



                                               WATER
The chemistry of water is very important to biology because so many physiological processes
depend on water.

Because oxygen is more electronegative than hydrogen, water's bonds
are polar covalent bonds. Because of these polar bonds, water is a polar
molecule.

The Greek letter delta () is used to mark a partial charge on an atom
caused by a polar bond.
                                          Water's polarity causes the oxygen of a water molecule
                                          to be electrically attracted to the hydrogen end of other
                                          water molecules. These attractions result in hydrogen
                                          bonds. These are partial bonds that are longer and
                                          weaker than other types of bonds.

                                      The network of hydrogen bonds between water
molecules draws the molecules into a rough lattice. These bonds are constantly being formed
and broken.

This network of hydrogen bonds gives water some unique characteristics:
Density
Recall that the molecules in solids vibrate less than those in liquids. Since ice molecules aren't
moving around as much as those in liquid water, ice's network of hydrogen bonds is more
stable than water's.

The hydrogen bonds in ice keep the molecules evenly spaced and further apart than those in
liquid water. This increased space between molecules means that ice is less dense than liquid
water.

Since ice is less dense than liquid water, water expands as it freezes. This makes ice cubes

                   2007 Vancouver Community College Learning Centre.
                  Student review only. May not be reproduced for classes.
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float on top of a drink, icebergs dangerous to ships, and pipes burst when water freezes in
them.
Adhesion
Because water is a polar molecule, it can be electrically attracted to any object with a charge on
it. Adhesion is the attraction between water molecules and some other material, like wood or
glass.

This phenomenon allows water to travel against gravity up narrow capillary tubes in the lab and
up the insides of trees, bringing water from the roots to the leaves.
Cohesion
                 The attraction between water molecules is cohesion. Hydrogen bonding and
                 other intermolecular forces (forces acting between molecules) cause cohesion.

                 The cohesion of water molecules leads to surface tension, water's resistance
                 to an increase in its surface area. Surface tension allows water to hold small
                 objects on its surface, like hairs, leaves, or water-walking bugs.


You can observe cohesion and adhesion working together in a still glass of water. Water pulls
up the sides of a glass of water, forming a meniscus. Water forms a meniscus because of the
attraction between its molecules, and the attraction between the water and the glass.

Liquids that don't have strong attraction between their molecules, like oil, don't form a
meniscus.
                                     Two Reactions of Water
Hydrolysis                                     Dehydration
Hydrolysis is a reaction that breaks up a      Dehydration is a reaction that creates water as
water molecule.                                one of its products.

When a molecule joined by covalent bonds       Dehydration is a hydrolysis reaction in reverse. It
dissolves in water, it has reacted with a      creates water and a larger molecule from smaller
awter molecule in the solvent. A water         components.
molecule attaches across the broken bond,
putting an H atom onto one end of the          For example, creating a molecule of table sugar
break and an OH molecule on the other          from glucose and fructose also creates a water
end.                                           molecule as a product.

For example, when sugar dissolves in        Monomers are the two smaller molecules that are
water, a water molecule attaches across the brought together in a dehydration reaction. A
broken bond.                                polymer is the long molecule formed by joining
                                            monomers together by a series of dehydration
                                            reactions.




                  2007 Vancouver Community College Learning Centre.
                 Student review only. May not be reproduced for classes.
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