Transcript Hydrogen Bonds

Chapter 2
Essential Chemistry for Biology
PowerPoint® Lectures for
Campbell Essential Biology, Fourth Edition
– Eric Simon, Jane Reece, and Jean Dickey
Campbell Essential Biology with Physiology, Third Edition
– Eric Simon, Jane Reece, and Jean Dickey
Lectures by Chris C. Romero, updated by Edward J. Zalisko
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SOME BASIC CHEMISTRY
• Take any biological system apart, and you eventually end up at
the chemical level.
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Matter: Elements and Compounds
• Matter is anything that occupies space and has mass.
• Matter is found on the Earth in three physical states:
– Solid
– Liquid
– Gas
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• Matter is composed of chemical elements.
– Elements are substances that cannot be broken down into other
substances.
– There are 92 naturally occurring elements on Earth.
• All of the elements are listed in the periodic table.
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6
C
12
H
He
Li Be
B
Na Mg
Al Si P
K Ca Sc Ti
C
N
O
F Ne
S Cl Ar
V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te
I
Xe
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac Rf Db Sg Bh Hs Mt Uun Uuu Uub
Uuq
Uuh
Uuo
Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
Figure 2.1
• Twenty-five elements are essential to life.
• Four elements make up about 96% of the weight of the human
body:
– Oxygen
– Carbon
– Hydrogen
– Nitrogen
CHON
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Carbon C: 18.5%
Oxygen O:
65.0%
Calcium Ca: 1.5%
Hydrogen H:
9.5%
Nitrogen N:
3.3%
Phosphorus P: 1.0%
Potassium K: 0.4%
Sulfur S: 0.3%
Sodium Na: 0.2%
Chlorine Cl: 0.2%
Magnesium Mg: 0.1%
Trace elements: less than 0.01%
Manganese Mn
Boron B
Chromium Cr Molybdenum Mo
Cobalt Co
Selenium Se
Silicon Si
Copper Cu
Tin Sn
Fluorine F
Vanadium V
Iodine I
Zinc Zn
Iron Fe
Figure 2.2
• Trace elements
– Occur in smaller amounts
– Are essential for life
• An iodine deficiency causes goiter.
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• Elements can combine to form compounds.
– Compounds are substances that contain two or more elements in a
fixed ratio.
– Common compounds include
–
NaCl (table salt)
–
H2O (water)
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Atoms
• Each element consists of one kind of atom.
– An atom is the smallest unit of matter that still retains the
properties of an element.
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The Structure of Atoms
• Atoms are composed of subatomic particles.
– A proton is positively charged.
– An electron is negatively charged.
– A neutron is electrically neutral.
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Helium (He)
2
Protons
Nucleus
2
Neutrons
2
Electrons
Nucleus
Cloud of negative
charge 2 electrons
Figure 2.4
• Most atoms have protons and neutrons packed tightly into the
nucleus.
– The nucleus is the atom’s central core.
– Electrons orbit the nucleus.
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• Elements differ in the number of subatomic particles in their
atoms.
– The number of protons, the atomic number, determines which
element it is.
– An atom’s mass number is the sum of the number of protons and
neutrons.
– Mass is a measure of the amount of matter in an object.
(This = protons + neutrons or = atomic mass)
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How to read the periodic table:
Every table has:
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Drawing an Atom of Carbon
6
C
12.011
Atomic #
= # of p+ and # of e-
Carbon has 6 p+ and 6 e-
Atomic Mass minus Atomic # = # of n
Carbon has 6 n
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Isotopes
• Isotopes are alternate mass forms of an element.
• Isotopes have the same number of protons and electrons, but they
have a different number of neutrons.
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Table 2.1
Electron Arrangement and the Chemical Properties
of Atoms
• Electrons determine how an atom behaves when it encounters
other atoms.
• Electrons orbit the nucleus of an atom in specific electron shells.
• The farther an electron is from the nucleus, the greater its energy.
• The number of electrons in the outermost shell determines the
chemical properties of an atom.
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First electron shell
can hold 2 electrons
Outer 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
Figure 2.5
Draw the following:
Be
B
Al
O
Na
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Be
B
Al
4 p+
5 n°
O
8 p+ 2e– 6e–
8 n°
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5 p+
6 n°
13 p+
14 n°
Na
11 p+ 2e– 8e– 1e–
12 n°
Chemical Bonding and Molecules
• Chemical reactions enable atoms to give up or acquire electrons
to complete their outer shells.
• Chemical reactions usually result in atoms
– Staying close together
– Being held together by chemical bonds
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Ionic Bonds
• When an atom loses or gains electrons, it becomes electrically
charged.
– Charged atoms are called ions.
– Ionic bonds are formed between oppositely charged ions.
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Outer shell
has 1 electron
The outer electron is stripped
from sodium and completes
the chlorine atom’s outer shell
Outer shell
has 7 electrons
Na
Sodium atom
Cl
Chlorine atom
Figure 2.6-1
Outer shell
has 1 electron
The outer electron is stripped
from sodium and completes
the chlorine atom’s outer shell
Complete
outer shells
Outer shell
has 7 electrons
Na
Sodium atom
Cl
Chlorine atom
Na
Sodium ion
Cl
Chlorine ion
The attraction
between the
ions—an ionic
bond—holds
them together
Sodium chloride (NaCl)
Figure 2.6-2
Covalent Bonds
• A covalent bond forms when two atoms share one or more pairs
of outer-shell electrons.
• Atoms held together by covalent bonds form a molecule.
• The number of covalent bonds an atom can form is equal to the
number of additional electrons needed to fill its outer shell.
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Electron sharing
Atoms joined into a molecule
via covalent bonds
Figure UN2-7
Name
Electron configuration
molecular formula
Hydrogen gas H2
Structural formula
Space-filling model
Ball-and-stick model
Single bond
a pair of shared electrons
Oxygen gas O2
Double bond
two pairs of shared electrons
Methane CH4
Figure 2.7
Hydrogen Bonds
• Water is a compound in which the electrons in its covalent bonds
are shared unequally.
– This causes water to be a polar molecule, one with opposite
charges on opposite ends.
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slightly 
slightly 
H
H
O
slightly –
Figure UN2-2
Hydrogen bond
Figure 2.8
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.
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• Chemical reactions include
– Reactants, the starting materials
– Products, the end materials
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
2 H2
O2
2 H2O

Hydrogen
gas
Oxygen
gas
Reactants
Water
Products
Figure UN2-3
• Chemical reactions can rearrange matter but cannot create or
destroy matter.
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WATER AND LIFE
• Life on Earth began in water and evolved there for 3 billion years.
– Modern life remains tied to water.
– Your cells are composed of 70%–95% water.
• The abundance of water is a major reason Earth is habitable.
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Figure 2.9
Water’s Life-Supporting Properties
• The polarity of water molecules and the hydrogen bonding that
results explain most of water’s life-supporting properties.
– Water molecules stick together.
– Water has a strong resistance to change in temperature.
– Frozen water floats.
– Water is a common solvent for life.
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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.
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Evaporation from the leaves
Microscopic tubes
SEM
Cohesion due to
hydrogen bonds
between water
molecules
Figure 2.10
• 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.
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Figure 2.11
How Water Moderates Temperature
• Because of hydrogen bonding, water has a strong resistance to
temperature change.
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• Heat and temperature are related, but different.
– Heat is the amount of energy associated with the movement of the
atoms and molecules in a body of matter.
– Temperature measures the intensity of heat.
• Water can absorb and store large amounts of heat while only
changing a few degrees in temperature.
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• Water can moderate temperatures.
– Earth’s giant water supply causes temperatures to stay within
limits that permit life.
– Evaporative cooling removes heat from the Earth and from
organisms.
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The Biological Significance of Ice Floating
• When water molecules get cold enough, they move apart, forming
ice.
• A chunk of ice has fewer molecules than an equal volume of
liquid water.
• Ice floats because it is less dense than the liquid water around it.
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Hydrogen bond
Liquid water
Ice
Figure 2.13
• If ice did not float, ponds, lakes, and even the oceans would
freeze solid.
• Life in water could not survive if bodies of water froze solid.
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Water as the Solvent of Life
• A solution is a liquid consisting of a homogeneous mixture of
two or more substances.
– The dissolving agent is the solvent.
– The dissolved substance is the solute.
• When water is the solvent, the result is an aqueous solution.
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Acids, Bases, and pH
• A chemical compound that releases H+ to solution is an acid.
• A compound that accepts H+ and removes it from solution is a
base.
• To describe the acidity of a solution, chemists use the pH scale.
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14
Oven cleaner
Increasingly basic
lower H concentration
Basic
solution
13
12
Household ammonia
11
Milk of magnesia
10
9
Seawater
8
Acidic
solution
Increasingly acidic
greater H concentration
Neutral
[H+]  [OH–]
Neutral
solution
Household
bleach
Human blood
7 Pure water
6 Urine
5
4 Tomato juice
3 Grapefruit juice,
soft drink
2 Lemon juice,
gastric juice
1
0
pH scale
Figure 2.16
• Buffers are substances that resist pH change.
• Buffers
– Accept H+ ions when they are in excess
– Donate H+ ions when they are depleted
• Increases in global CO2 concentrations may lead to the
acidification of the oceans.
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