Essential Chemistry in Biology
Mrs. Norris
Topics Discussed in these notes
•
Matter, Elements and Compounds
•
Periodic Table of the Elements: Metals vs. Nonmetals
•
Atomic Structure
•
Chemical Bonding: Ionic vs. Covalent Bonding
•
Chemical Reactions and Chemical Equations
•
The Structure of Water
•
Water as a Solvent
•
The Importance of Water to Living Things
•
Acids, Bases and pH
•
Self-test/Review Questions
BASIC CHEMISTRY
• Organisms and all other things in the universe consist of
matter
Matter: Elements and Compounds
• Matter is anything that occupies space and has mass
– Matter is composed of chemical elements and compounds
– Elements: substances that cannot be broken down into
other substances
– There are 92 naturally occurring elements on Earth
– What are compounds? Examples?
Periodic table of the elements
Location of....
• Metals?
• Nonmetals?
25 Elements are essential to life
• C, H, O, N: 96% of the weight of the human body
Some Elements React to Form Compounds
•
Elements can combine chemically to form
compounds
•
Compounds contain two or more elements
chemically combined in a fixed ratio
Examples of Compounds:
1. Table salt (sodium chloride): NaCl
2. Water: H2O
3. Glucose: C6H12O6
Atom: smallest unit of matter that retains the
properties of an element
• Each element consists of one kind of atom
(a) Hydrogen atom
(b) Carbon atom
Proton
Neutron
(c) Oxygen atom
Electron
First
shell
Second
shell
Atomic nucleus
Fig. 2.02
Atomic Structure
• The subatomic particles of an atom
Electron
Proton
 Positive charge
 Determines element
 Negative charge
• Participates in chemical
reactions
• Outer-shell electrons
determine chemical
behavior
Neutron
 No charge
 Determines isotope
Nucleus
• Consists of neutrons
and protons
• Elements
– differ in the number of subatomic particles in
their atoms
• Atomic Number: number of protons
– determines which element it is
• Mass number
– sum of the number of protons and neutrons
Chemical Properties of Atoms
• Electrons
– Located outside the nucleus of an atom in specific
electron shells (energy levels)
• The number of electrons in the outermost shell
determines the chemical properties of an atom
Atoms of the four elements most abundant in life
First
electron shell:
can hold
2 electrons
Outermost
electron shell:
can hold
8 electrons
Electron
Hydrogen (H)
Atomic number = 1
Carbon (C)
Atomic number = 6
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
Orbital Diagrams of the First 18 Elements
1st
Shell
2
2nd
Shell
8
3rd
Shell
8
Chemical Bonding and Molecules
• Chemical reactions:
– Atoms give up or acquire electrons in order to
complete their outer shells
– Result in atoms staying close together to form
molecules
– Chemical bonds hold molecules together
• Ionic Bonds
• Covalent bonds
Ionic Bonds: form between metals and nonmetals
• When an atom loses or
gains electrons, it
becomes electrically
charged
– Charged atoms are
called ions
– Ionic bonds are
formed between
oppositely charged
ions
Sodium atom (Na)
Chlorine atom (Cl)
Complete
outer shells
Sodium ion (Na)
Chloride ion (Cl)
Sodium chloride (NaCl)
Atoms: electrically neutral
Ions: Electrically charged
(b) Hydrogen ion (H+)
(a) Hydrogen atom (H)
1 electron
No
electron
1 proton
1 proton
No net electrical
charge
(d) Sodium ion (Na+)
(c) Sodium atom (Na)
11
electrons
11 protons
10
electrons
11 protons
No net electrical
charge
Fig. 2.03
Covalent Bonds: form between nonmetallic atoms
• A covalent bond forms when two atoms share one
or more pairs of outer-shell electrons
Covalent bonding in water
Oxygen atom with unfilled
shell
Water molecule (H2O)
Full shell with 8 electrons
– Slightly negative
Covalent
bond
(shared pair
of electron)
+
+ Slightly
positive
Full shells with 2 electrons each
Hydrogen atoms with unfilled shells
Fig. 2.04a
Chemical Reactions
• Cells constantly rearrange molecules by breaking
existing chemical bonds and forming new ones
– Such changes in the chemical composition of matter
are called chemical reactions
Hydrogen gas
Oxygen gas
Reactants
Water
Products
Chemical Equations: symbolize chemical reactions
Reactants: on the left
side of the equation
– the starting materials
Products: on the right side of
the equation
– the ending materials (the stuff
produces)
Law of Conservation of Mass
– Chemical reactions do not create or destroy matter—they only
rearrange it!
WATER AND LIFE
• The abundance of water is a major reason Earth is
habitable
– Modern life still remains tied to water
– Your cells are composed of 70%–95% water
The Structure of Water
• The water molecule:
– two hydrogen atoms joined to one oxygen atom by
single covalent bonds
H
H
O
Water: a polar molecule
• The electrons of the covalent bonds are shared unequally
between oxygen and hydrogen
– unequal sharing of electrons makes water a polar molecule
– hydrogen atoms: partially positive (d ) Why?
– oxygen atom: partially negative (d -) Why?
(d )
(d )
(d )
The Structure of Water
• The polarity of
water results in
weak electrical
attractions between
neighboring water
molecules
()
Hydrogen bond
()
()
()
()
– These interactions
are called
hydrogen bonds
()
(b)
()
()
Water’s Life-Supporting Properties
•
The polarity of water molecules and the hydrogen
bonding that results explain most of water’s lifesupporting properties
1. Versatility of water as a solvent
2. Water’s cohesive nature
3. Water’s ability to moderate temperature
4. Floating ice
Water as the Solvent of Life
• A solution is a liquid consisting of two or more
substances evenly mixed
– The dissolving agent is called the solvent
– The dissolved substance is called the solute
Ion in solution
Salt crystal
Dissolving of
Sodium
Chloride (NaCl)
in Water
Salt
Electrical
attraction
Water molecules dissolve NaCl,
breaking ionic bond
Water
Water
molecules
(H2O)
Hydrogen
bonds
Edge of one
salt crystal
Ionic bond
The Cohesion of Water
• Water molecules
stick together as a
result of hydrogen
bonding
– This is called
cohesion
– Cohesion is vital
for water
transport in
plants
Microscopic tubes
• Surface tension
– is the measure of how difficult it is to stretch or break
the surface of a liquid
– Hydrogen bonds give water an unusually high
surface tension
Figure 2.13
Water Moderates Temperature
• Because of hydrogen bonding, water has a strong
resistance to temperature change
• Water can absorb and store large amounts of heat
while only changing a few degrees in temperature
– Earth’s Oceans cause temperatures to stay within
limits that permit life
• The density of ice is lower than liquid water
– This is why ice floats
Hydrogen bond
Ice
Liquid water
Stable hydrogen bonds
Hydrogen bonds
constantly break and re-form
The Biological Significance of Ice Floating
• When water molecules get cold, they move apart,
forming ice
– A chunk of ice has fewer molecules than an equal
volume of liquid water
• Since ice floats, ponds, lakes, and even the oceans
do not freeze solid
– Marine life could not survive if bodies of water froze
solid
Acids, Bases, and pH
• Acid
– A chemical compound that donates H+ ions to
solutions
• Base
– A compound that accepts H+ ions and removes them
from solution
pH Scale
The pH scale is used to
describe the acidity of a
solution
Oven cleaner
Household bleach
Household ammonia
• Acidic: pH < 7
Basic
solution
Milk of magnesia
-
H+ > OH
Seawater
Human blood
Pure water
• Basic: pH > 7
H+
-
Neutral
solution
< OH
Tomato juice
• Neutral: pH = 7
H+
-
= OH
Urine
Grapefruit juice
Acidic
solution
Lemon juice;
gastric juice
CheckPoint
1. Which of the following are compounds? Elements?:
C6H12O6, CH4, O2, Cl2, HCl, MgCl2, Fe, Ca, Ne, NaI, I
2. What is the difference between an atom and an ion? Give
examples of each to support your response.
3. Which subatomic particle determines the identity of an
atom?
4. Which subatomic particle determines the chemical
properties of an atom?
5. Explain the difference between an ionic and covalent bond
in terms of what happens to the electrons in the outer shell of
the participating atoms.
Chemical Reactions and
Enzymes
PowerPoint® Lecture Slides for
Essential Biology, Second Edition & Essential Biology with Physiology
Neil Campbell, Jane Reece, and Eric Simon
Chemical Reactions
• A chemical reaction is a process that changes one set
of chemicals into another set of chemicals.
• The elements or compounds that enter into a chemical
reaction are known as the reactants.
• The elements or compounds produced by a chemical
reaction are known as products.
Energy in Reactions
• Chemical reactions can either release energy or
absorb energy.
• An exergonic reaction releases energy and will
often occur spontaneously.
• An endogonic reaction absorbs energy and will not
occur spontaneously.
Activation energy is the energy required
to get a chemical reaction started.
Burning glucose (sugar): an exergonic reaction
high
high
activation energy needed
to ignite glucose
energy
content
of
molecules
glucose + O2
energy released
by burning glucose
glucose
energy
content
of
molecules
progress of reaction
net energy
captured by
synthesizing
glucose
CO2 + H2O
CO2 + H2O
low
activation
energy from
light captured
by photosynthesis
low
progress of reaction
Photosynthesis: an endergonic reaction
Enzymes
Enzymes speed up chemical reactions that take place
in cells.
Regulation of Enzyme Activity
Allosteric
inhibition
allosteric
regulator
molecule
Up: Enzyme “off”
Down: Enzyme “on”
Enzyme
structure
substrate
active site
• pH
• Temperature
• “on” or “off”
keys (binding
proteins)
Competitive
inhibition Competitive- key
Fits lock, but wont
Open door
enzyme
allosteric
regulatory site
Up: Enzyme
high
energy
content
of
molecules
A Catalyst is a substance that
speeds of the rate of a
chemical reaction
activation energy
without
catalyst
activation energy
with catalyst
reactants
Enzymes are proteins
that act as biological
catalyst
low
progress of reaction
products
Enzymes provide a site where reactants can
be brought together and aligned properly to
react.
- the reactants
of an enzyme
catalyzed
reaction.
substrates
active site
of enzyme
enzyme
Regulation of Enzyme Activity
Allosteric
inhibition
allosteric
regulator
molecule
Up: Enzyme “off”
Down: Enzyme “on”
Enzyme
structure
substrate
active site
• pH
• Temperature
• “on” or “off”
keys (binding
proteins)
Competitive
inhibition Competitive- key
Fits lock, but wont
Open door
enzyme
allosteric
regulatory site
Up: Enzyme