Download Chapter 2 – Fundamental Building Blocks: Chemistry, Water, and pH

Chapter 2 – Fundamental Building Blocks: Chemistry, Water, and pH
2.1 Chemistry’s Building Block: The Atom
 Everything that exists can be viewed as falling into one of two categories: matter
or energy
 Matter and its transformations is the subject of chemistry
 Matter can be defined as anything that takes up space and has mass
 Mass is a measure of quantity of matter in any given object – how much space
does an object occupy and how dense is the matter
o Think of mass as equivalent to weight
 Matter is composed of tiny pieces of matter, which we call atoms, but these atoms
are not indivisible
 They are themselves composed of constituent parts
 Protons, Neutrons and Electrons:
o There are three important constituent parts of an atom: protons, neutrons
and electrons
o These three parts exist in a spatial arrangement that is uniform in all
matter
o Protons and neutrons are packed tightly together in a core (the atoms
nucleus) and the electrons move around this core some distance away
o One variation on this is hydrogen – hydrogen has no neutrons but rather
only one proton in its nucleus and one electron in motion around it
o The whole atom, with electrons at its edge, is 100,000 times bigger than
the nucleus
o The nucleus accounts for little of the space an atom takes up but it
accounts for almost all of the mass an atom has – all of the mass (or
weight) of an atom is considered to reside with the protons and neutrons of
the nucleus
o Protons are positively charged and electrons are negatively charged –
neutrons are electrically neutral
o All these particles do not exist separately but combine to form an atom, as
a whole atom may be electrically neutral as well
o In this state the number of protons an atom has is exactly equal to the
number of electrons it has
o The number of neutrons an atom has can vary in relation to the other two
particles
o Matter is any substance that exists in our everyday experience
 The Fundamental Forms of Matter: The Element
o Element – a substance that is pure in that it cannot be reduced to any
simple set of component substances through chemical processes – Gold is
an example of an element
o The thing that defines each element is the number of protons it has in its
nucleus
o Protons and neutrons are components of atoms but they are not component
substances because they cannot exist by themselves as matter – protons
and neutrons must combine with each other to make up atoms
o Assigning Numbers to the Elements:
 Elements, which are defined by protons in their nuclei, have an
atomic number assigned to them
 Atom numbering system goes from smallest number of protons to
largest
 Thus hydrogen which only has one proton in its nucleus has the
atomic number 1
o Isotopes:
 Atoms also have neutrons in their nuclei and these neutrons add
weight to the atom and the number of neutrons can vary
independently to the number of protons
 Because the number of neutrons in an element’s nucleus may vary,
we can have various forms of elements, called isotopes.
 Example: The element carbon has six protons giving it an atomic
number of 6. In its most common form, it also has six neutrons.
However, small amounts of carbon exist in a form that has eight
neutrons. The element is still carbon and in this form the number
of its protons and neutrons equals 14, so the isotope is carbon-14
 Most elements have several isotopes
o The Importance of Electrons
 What’s most important in biology is the way elements combine
with other elements
 It is the outermost electrons that play a critical role in this
combining
 Atoms link with one another through what lies at their outer edges
2.2 Matter is transformed through Chemical Bonding
 The process of chemical combination and rearrangement is called chemical
bonding
 When the outermost electrons of two atoms come into contact, it becomes
possible for these electrons to reshuffle themselves in a way that allows the atoms
to become attached to one another
 This can take place in two ways: one atom can give up one or more electrons to
another, or one atom can share one or more electrons with another atom
 Giving up electrons is called ionic bonding, sharing electrons is called covalent
bonding
 There is a third type of bond – the hydrogen bond
 Energy Always Seeks Its Lowest State
o Atoms take undertake bonding with one another do so because they are in
a more stable state after the bonding than before it
o Energy always seeks its lowest state
o Atoms bond with one another to the extent that doing so moves them to a
lower, more stable energy state
o Atoms more to this more stable state by filling what is known as their
outer shells
 Seeking A Full Outer Shell: Covalent Bonding
o Electrons reside in certain well defined “energy levels” outside the nuclei
of atoms
o The number of these energy levels varies depending on the element in
question
o Two electrons are required to fill the first energy level (or shell) or any
given atom, but eight are usually required to fill all the levels thereafter
o This means that hydrogen and helium each require only two electrons in
orbit around their nuclei to have filled outer shells but that other elements
require eight electrons to complete their outer electron shells
o How Chemical Bonding Works in One Instance: Water
 The chemical symbol for water is H20 – this means that two atoms
of hydrogen H2 have combined with one atom of oxygen O to form
water
 Hydrogen has only one electron running around in its single energy
level
 This first level is not completed until it has two electrons in it
 The oxygen atom has eight electrons, this means: two electrons fill
oxygen’s first energy level, which leaves six for its second.
 The second shells of most atoms are not completed until they hold
eight electrons – thus oxygen, like hydrogen, would welcome a
partner
 It needs two electrons to fill its outer shell – something that two
atoms of hydrogen could provide
 The outcome is a bonding of two hydrogen atoms with one atom of
oxygen
 Each of the hydrogen atoms is linked to the oxygen in a covalent
bond – a chemical bond in which atoms share a pair of electrons
 Three atoms covalently bonded together, and all of them
“satisfied” in that condition
o Matter is Not Gained or Lost in Chemical Reactions
 When this pairing of electrons happens, no matter has been gained
or lost
 This points up an important principle known as the law of
conservation of mass which states that matter is neither created
nor destroyed in a chemical reaction
o What is a Molecule?
 When two or more atoms combine in this kind of covalent
reaction, the result is a molecule: a compound of a defined number
of atoms in a defined spatial relationship
 With water – one atom of oxygen has combined with two atoms of
hydrogen to create one water molecule
 A molecule need not be made of two different elements – two
hydrogen atoms can covalently bond to form one hydrogen
molecule
 Conversely, a molecule can contain many different elements
bonded together
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Reactive and Unreactive Elements
o The helium atom has two electrons – it thus comes equipped with a filled
outer shell
o Therefore it is extremely stable, it is unreactive with other elements
o At the opposite end of the spectrum are elements that are extremely
reactive
o For example – the sodium atom – it has 11 electrons, two in the first shell,
eight in the second, leaving only one electron in the third – a very unstable
state
o Thus there is a spectrum of stability in the chemical elements, based on the
number of outer shell electrons each element has – from 1 to 8, with 1
being the most reactive and 8 being the least reactive
Polar and Nonpolar Bonding
o When two hydrogen atoms come together, the result is a hydrogen
molecule (H2)
o In the hydrogen molecule, the electrons are shared equally
 The two electrons the hydrogen atoms share are equally attracted
to each hydrogen atoms
o The oxygen atom has greater power to attract electrons to itself than do the
hydrogen atoms
o The term for measuring this kind of pull is electronegativity
o The oxygen atom has more electronegativity than do the hydrogen atoms
so it tends to pull the shared electrons away from the hydrogen and toward
itself
o When this happens the molecule takes on a polarity – or a difference in
electrical charge at one end as opposed to the other
o Electrons are negatively charged and because they can be found closer to
the oxygen nucleus, the oxygen end of the molecule becomes slightly
negatively charged while the hydrogen regions become slightly positively
charged – this is a polar covalent bond
o With the hydrogen molecule – where the electrons are shared equally – we
have a nonpolar covalent bond
o Consider the water molecule with its positive and negative regions –
what’s going to happen when it comes into contact with other polar
molecules? – The oppositely charged parts of the molecule will attract and
the similarly charged parts will repel
o Molecules flip around in relation to their polarity
o It is possible for atoms with different electronegativity to link and still
have the resulting molecule be nonpolar
o Water is polar because the atom with more electronegativity (the oxygen)
lies to one side of the two hydrogen
o In a molecule such as methane, four hydrogen atoms are arranged in a
symmetrical way around a central, and more electronegative end –
meaning it is nonpolar
o Some molecules are polar while others are nonpolar, and this difference
has significant consequences for chemical bonding
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Ionic Bonding: When Electrons Are Lost of Gained
o Electronegativity differences between two atoms are sometimes so
extreme that electrons are pulled off one atom, only to latch on to the atom
that was attracting them – this is called ionic bonding
o Example: sodium has 11 electrons, meaning that there is a lone electron in
its third shell. Chlorine has 17 electrons meaning it has 7 electrons in the
third shell. Sodium could get to this number by losing one electron while
chlorine could get to it by gaining one electron – both parties would
become stable in the process
o What is an Ion?
 Having lost an electron (with a negative charge) Sodium (Na) then
takes on an overall positive charge. Having gained an electron,
chlorine (Cl) takes on an negative charge
 Ion – a charged atom or an atom with an electron number that
differs from its number of protons
 We denote the ionized forms of these atoms like this, NA+ and CL Were an atom to gain or lose more electrons, a number would be
put before the charge sign
 Note that we now have two ions, NA+ and CL- with differing
charges in proximity to one another they are thus attracted to one
another through an electrostatic attraction and have thus become
bonded – through an ionic bond
 Many billions of atoms are bonded in this way, up, down and
sideways from each other
 If two or more elements are mixed together this way its an ionic
compound
 In an ionic compound there is no fixed number of atoms linked in a
defined spatial relationship, as in H20.
 Rather an undefined number of charged atoms are bonded together
as in NaCl
 There is a spectrum of polarity, and within it, some bonds are
almost completely ionic while others are completely nonpolar
A Third Form of Bonding: Hydrogen Bonding
o What happens when you place several water molecules together? A
positive hydrogen atom of one molecule is weakly attracted to the
negative, unshared electrons of its oxygen neighbour
o Thus a hydrogen bond is created – which links an already covalently
bonded hydrogen atom with electronegative atom
o Hydrogen bonding is a linkage that nearly always pairs relatively weak
bonds, indicated by a dotted line in illustrations are important in many of
the molecules of life
2.3 Some Qualities of Chemical Compounds
 Molecules Have a Three Dimensional Shape
o Molecules and ionic compounds have a three dimensional shape
 Molecular Shape is Very Important in Biology
o Molecular shape is critical in enabling biological molecules to carry out
their activities
o Molecular shape determines the capacity of molecules to latch on to or
bind with one another
2.4 Water and Life
 Life got started in water and then existed almost nowhere but water for eons
 Human bodies are about 66% water by weight
 Almost all organisms must have a regular supply of water to survive
 No living thing can be fully functional without water
 Water Is a Major Player in Many of Life’s Processes
o Life is at one level a series of chemical reactions
o It makes sense that these reactions would best take place in some liquid
medium
 That medium is water
o Water is not just a passive medium, it facilitates many of these reactions
o If you pour salt into a container of water – you have a solution which is a
mixture of two or more kinds of molecules, atoms or ions that is
homogeneous throughout
o Salt is what’s being dissolved so it is the solute
o The water is doing the dissolving so it is the solvent
o Water is a terrific solvent – it has a great ability to dissolve other
substances
o Water is a polar molecule – it has differing electric charges at one end as
opposed to the other
o Attracted by the polar nature of the water molecule, the sodium and
chloride ions that make up a salt crystal separate from the crystal – and
from each other
o Each ion is then surrounded by several water molecules
o These units keep the sodium and chloride ions from getting back together
 They keep the ions evenly dispersed throughout the water
o Water works as a solvent here because the ionic compound sodium
chloride carries an electrical charge
o What generally makes water work as a solvent, however, is its ability to
form, with other molecules, the hydrogen bonds
 Water’s Structure Gives It Many Unusual Properties
o Water is not just a solvent: over the range of substances, nothing can
match it as a solvent
o It can dissolve more compounds in greater amounts than can any other
liquid
o Ice Floats Because It Is Less Dense than Water
 Water is a multitalented performer
 Ice floats on water – this is so because the solid form of H20 is less
dense than the liquid form – a strange reversal of nature’s normal
pattern
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When water molecules slow their motion in cooling they are able
to form the maximum number of hydrogen bonds with each other
 The result is that water molecules are spaced farther apart when
frozen
 Has the effect of making possible life as we know it – ice on the
surface of water acts to insulate the water beneath it from the
freezing surface temperatures and wind above creating a warmer
environment for organisms such as fish
o Water Has a Great Capacity to Absorb and Store Heat
 Water serves as an insulator not only when it is frozen but also
when it is a liquid or gas
 Specific heat: the amount of energy required to raise the
temperature of a substance by 1o Celsius
 Water has a high specific heat
 It will talk almost twice as much energy to raise the temperature of
the water 1oC as it will alcohol
 Having absorbed this much heat, however, water then has the
capacity to release it when the environment around it is colder than
the water itself
 Water acts as a great heat buffer for Earth
 Without this buffering, temperature on Earth would be less stable
 Our internal temperature can remain much more stable because the
water that makes up so much of us is first able to absorb and then
release great amounts of heat
 The sweat created in exercise has considerable cooling power
because each drop of perspiration carries with it a great deal of
heat
 Water derives these powers from its chemical structure, in
particular from the hydrogen bonding described earlier
 Collectively hydrogen bonds have great strength
 To get molecules moving chemical bonds must first be broken
 Because water has a formidable set of hydrogen bonds it takes a lot
of energy to break the bonds and get its molecules moving
 This same set of bonds gives water molecules another notable
characteristic – cohesion, meaning a tendency to stay together
o What Water Cannot Do
 Life requires molecules that cannot be dissolved by water
 Such is the case with nonpolar covalent molecules – such as the
methane molecule
 Compounds such as methane are known as hydrocarbons because
they are made up solely of hydrogen and carbon atoms
 Oil doesn’t dissolve in water because the oil carries almost no
electrical charge that water can bond with, thus, water has no way
to separate one oil molecule from another
Two Important Terms: Hydrophobic and Hydrophilic
o Compounds that will interact with water are known as hydrophilic (water
loving)
o Compounds that do not interact with water are known as hydrophobic
(water fearing)
o The strong bonding that water molecules do with each other causes them
to form circles around concentrations of hydrophobic molecules, as if they
had lassoed them
o We living organisms need some kind of carton that can separate the world
outside of us from ourselves
o Organisms have great use within themselves for compartments that can be
sealed off to one degree or another
o A number of important molecules have both hydrophilic and hydrophobic
portions
2.5 Acids and Bases are Important to Life
 An important concept it that of acids, bases and the pH scale used to measure their
levels
 The safe zone for living tissue in general lies with substances that are neither
strongly basic nor strongly acidic
 A way of measuring the degree to which something is acidic or basic is the pH
scale
 Acids Yield Hydrogen Ions in Solution, Bases Accept Them
o The H in pH stands for hydrogen, while the p can be thought of as
standing for power
o An acid is any substance that yields hydrogen ions when put in aqueous
solution
o A base is any substance that accepts hydrogen ions in aqueous solution
o Hydrogen atom amounts to one central proton and one electron that circles
around it
o A hydrogen ion, then, is a long proton that has lots its electron, a
positively charged ion whose symbol is H+
o Acid – hydrochloric acid (HCl) – is put into water – the HCL dissociates
or breaks apart into H+ and CL- - the HCL has therefore yielded a
hydrogen ion (H+)
o With a greater concentration of hydrogen ions in it, the water is more
acidic than it was
o There is a compound called sodium hydroxide (NaOH) – lye – that when
poured into water dissociates into Na+ and OH- ions. The place to look
here is the OHo Negatively charged as they are they would readily bond with positively
charged H+ ions in a solution, which is the definition of a base
o This accepting of the H+ ion makes the solution more basic
o Acids and bases are something like the two ends of a teeter-totter – when
one goes up, the other comes down
o Mixing them, the collection of H+ and OH- ions now comes together in
water and for each part of ions that interacts the result is: H+ + OH- = H2O
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o Water is neutral on the pH scale
o The OH- ion is generally referred to as the hydroxide ion
o It is important because compounds that yield them in quantity are strongly
basic and can be used to move solutions from the acidic toward the basic
Many Common Substances Can Be Ranked According to How Acidic of
Basic They Are
o As you move to lemon juice the acids are weaker – which is to say they
are substances that yield fewer H+ ions in a solution
The pH Scale Allows us to Quantify How Acidic of Basic Compounds Are
o The net effect of all this yielding and accepting of hydrogen ions is the
concentration of H+ ions in a solution
o The notion of pH can be quantified on a pH scale – a scale used in
measuring the relative acidity of a substance
o 0 on the scale is the most acidic, 14 is the most basic
o pH scale is logarithmic: a substance with a pH of 9 is 10 times more basic
as a substance with a pH of 8 and 100 times more basic as a substance
with a pH of 7
Some Terms Used When Dealing with pH
o As a solution becomes more basic, the pH rises
o A hydrogen ion amounts to a single proton, it is also correct to say that an
acid is something that yields protons in a solution while a base is
something that accepts protons
o A solution that is basic is also referred to as an alkaline solution
Why does pH Matter?
o Living things are sensitive to its levels in many ways
o Enzymes are chemical tools that must retain a specific shape to function
o However, if you put an enzyme in a solution with a pH that is too acidic
the enzyme loses its shape
o The charged nature of the acidic solution starts breaking down the
enzyme’s hydrogen bonds
o Cell membranes can start to break down if the pH levels start to go outside
normal limits
o Many organisms have developed so called acid-base buffering systems,
meaning physiological systems that function to keep pH within normal
limits
o The usual range for living things is about 6-8
o Some parts of the body have special pH requirements – the stomach has a
pH of 1 – very acidic
o Even a stomach can become too acidic however in which case people turn
to pharmaceutical pH buffers commonly known as antacids – they raise
the pH levels in the stomach, thus helping to alleviate heartburn
o pH can affect entire communities of living things
o Acid rain is just what it sounds like: rain whose pH level has been skewed
toward the acidic side of the pH scale, with air pollution being the cause of
this shift
o Air pollution regulations have lessened the severity of acid rain in recent
years, but it remains a long term problem that requires constant monitoring
On to Biological Matters
 These building blocks fit together to create some of the larger scale component
parts of life
 These component parts usually are referred to as biological molecules
 Carbohydrates are one variety of them
