Chemistry 101 PDF

28/08/2019
A Chemical Connection to Biology

• Organisms and their
environments are subject
to basic laws of physics
and chemistry
• One example is the use of
formic acid by ants to
protect themselves
against predators and
microbial parasites
© 2018 Pearson Education Ltd.
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“ Studying biochemistry in
a holistic way is going to be
the key to the answers we
need.”
- Dr. Lovell Jones
Concept 2.1: Matter consists of chemical

elements in pure form and in combinations
called compounds
• Organisms are composed of matter
Sodium
An element is a
substance that cannot
be broken down to
other substances by A compound is a substance
chemical reactions consisting of two or more Sodium
elements in a fixed ratio chloride
Chlorine
A compound has characteristics different from those

of its elements
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The Elements of Life

• About 20–25% of the 92 natural
elements are required for life
(essential elements)
• Carbon, hydrogen, oxygen, and
nitrogen make up 96% of living
matter
• Most of the remaining 4% consists of
calcium, phosphorus, potassium, and
sulfur
• Trace elements are required by an
organism in only minute quantities
Table 2.1
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Concept 2.2: An element’s properties

depend on the structure of its atoms
• Each element consists of unique atoms
• An atom is the smallest unit of matter that still retains
the properties of an element
Cloud of negative Electrons
charge (2 electrons)
Nucleus
− −
+ +
+ +
(a) (b)
Isotopes
• Isotopes are two atoms of an
element that differ in number of
neutrons
• Radioactive isotopes decay
spontaneously, giving off particles
and energy
• Radioactive isotopes are often
used as diagnostic tools in
medicine
 A “parent” isotope decays into its “daughter” isotope

at a fixed rate, expressed as the half-life
 In radiometric dating, scientists measure the ratio of
different isotopes and calculate how many half-lives
have passed since the fossil or rock was formed
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Some Fundamental Concepts

• An electron’s state of potential energy is called its energy
level, or electron shell
• The chemical behavior of an atom is determined by the
distribution of electrons in electron shells
2 Atomic number Helium

He 2He
4.003
Element symbol
Atomic mass Electron

distribution
diagram
Hydrogen 2 Atomic number Helium

1H He 2He
Atomic mass 4.003 Element symbol
First
shell Electron
distribution
diagram
Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon

3Li 4Be 5B 6C 7N 8O 9F 10Ne
Second
shell
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

11Na 12Mg 13AI 14SI 15P 16S 17CI 18Ar
Third
shell
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Some Fundamental Concepts

• An orbital is the three-dimensional space where an
electron is found 90% of the time
• Each electron shell consists of a specific number of orbitals
Concept 2.3: The formation and function of

molecules depend on chemical bonding
between atoms
A covalent bond is
the sharing of a pair
of valence electrons An ionic bond is an
by two atoms attraction between an
anion and a cation
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Name and Electron Lewis Dot Space-

Molecular Distribution Structure and Filling
Figure 2.10
Formula Diagram Structural
Formula
Model
(a) Hydrogen (H2)
H H
(b) Oxygen (O2)

O O
(c) Water (H2O)

O H
(d) Methane (CH4)

H
H C H
Figure 2.12_2
+ −
Na Cl Na Cl
Na Cl Na+ Cl−
Sodium atom Chlorine atom Sodium ion Chloride ion
(a cation) (an anion)
Sodium chloride (NaCl)
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Figure 2.13
Na+
Cl−
Weak Chemical Interactions

A hydrogen bond forms when a
hydrogen atom covalently bonded to
one electronegative atom is also
attracted to another electronegative
atom
Van der Waals interactions are

attractions between molecules that
are close together as a result of
charges being unevenly distributed
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δ– δ+
Figure
Water (H2.14
O) 2
δ–
δ+
Hydrogen bond
δ–
Ammonia (NH3)
δ+ δ+
δ+
Molecular Shape & FunctionCarbon Nitrogen
• Molecular
Hydrogen Sulfur
Natural
Oxygen
endorphin
shape
determines how Morphine
biological
molecules
recognize and
respond to one (a) Structures of endorphin and morphine
another
Natural
endorphin
Morphine
Endorphin
Brain cell receptors
© 2018 Pearson Education Ltd. (b) Binding to endorphin receptors
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The Molecule That Supports All of Life

• Water makes life possible on
Earth
• Water is the only common
substance to exist in the natural
environment in all three
physical states of matter
• The structure of the water
molecule allows it to interact
with other molecules
Black guillemots, threatened

by climate change
Concept 3.1: Polar covalent bonds in water

molecules result in hydrogen bonding
• In the water molecule, the
electrons of the polar covalent
bonds spend more time near the
oxygen than the hydrogen
• The water molecule is thus a polar
molecule:
The overall charge is unevenly
distributed
• Polarity allows water molecules to
form hydrogen bonds with each
other
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δ+
Figure 3.2 δ+
Polar covalent bond

δ–
δ–
Region of partial δ+
Hydrogen bond
negative charge
δ–
δ+
δ– δ+
δ–
δ+
Concept 3.2: Four emergent properties of water

contribute to Earth’s suitability for life
• Four of water’s properties
that facilitate an
environment for life are:
Ability to
Cohesive
moderate
behavior
temperature
Expansion
Versatility as
upon
a solvent
freezing
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Evaporation pulls water upward.

attraction between different
Figure
H O3.3 2 substances
Adhesion
Two types of
water-conducting
cells
Cohesion helps the

transport of water
against gravity in
plants Direction Cohesion
of water 300 µm hydrogen bonds hold
movement water molecules
together
H2O
H2O
Animation: Water Transport in Plants

(Cohesion & Adhesion)
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• Surface tension is a measure of how difficult it is

to break the surface of a liquid
• Water can absorb or release a large amount of

heat with only a slight change in its own
temperature
Moderation of Temperature by Water

Water’s High Specific Heat Evaporative Cooling
• The specific heat of a substance • Evaporation (or vaporization) is

is the amount of heat that must transformation of a substance
be absorbed or lost for 1 g of from liquid to gas
that substance to change its • Heat of vaporization is the heat
temperature by 1ºC a liquid must absorb for 1 g to
• The specific heat of water is 1 be converted to gas
cal/(g  ºC) • As a liquid evaporates, its
• Water resists changing its remaining surface cools, a
temperature because of its high process called evaporative
specific heat cooling
• Evaporative cooling of water
helps stabilize temperatures in
organisms and bodies of water
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Floating of Ice on Liquid Water

• Ice floats in liquid water because hydrogen bonds in ice
are more “ordered,” making ice less dense than water
• Water reaches its greatest density at 4ºC
Hydrogen bond Liquid water:

Hydrogen bonds
break and re-form
Ice:
Hydrogen bonds
are stable
Benefiting from loss of ice:
Figure 3.7 Phyto-

plankton
Bowhead
whales Capelin
Harmed by
loss of ice:
Russia
Arctic
ocean
Extent of sea ice in Sept. 2014
Extent of sea ice in Sept. 1979
Polar bears Bering
Strait
North Pole
Greenland
Pacific walrus
Alaska
Black Canada
guillemots
Sea ice in Sept. 2014
Ice lost from Sept. 1979 to Sept. 2014
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Water: The Solvent of Life

• A solution is a liquid that
is a completely
homogeneous mixture of
substances
• An aqueous solution is
one in which water is the
solvent
hydrophilic VS
hydrophobic
Possible Evolution of Life on Other Planets

• More than 800 planets have been found outside
our solar system; there is evidence that a few of
them have water vapor
• In our solar system, Mars has been found to
have water
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Concept 3.3: Acidic and basic conditions

affect living organisms
• A hydrogen atom in a hydrogen bond between two water
molecules can shift from one to the other
• The hydrogen atom leaves its electron behind and is transferred
as a proton, or hydrogen ion (H+)
• The molecule that lost the proton is now a hydroxide ion (OH–)
• The molecule with the extra proton is now a hydronium ion
(H3O+), though it is often represented as H+
+ –
H H
O H O O H O
H H H H
2 H2O Hydronium Hydroxide
ion (H3O+) ion (OH–)
Acids and Bases
An acid is a substance
that increases the H+
concentration of a A base is a substance that
solution reduces the H+
concentration of a
solution
• Strong acids and bases dissociate completely

in water
• Weak acids and bases reversibly release and accept back
hydrogen ions, but can still shift the balance of H+ and OH–
away from neutrality
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pH Scale
The pH Scale 0
1
Battery acid
Increasingly Acidic
2 Gastric juice (in stomach),
• Acidic solutions lemon juice
[H+] > [OH–]

have pH values 3 Vinegar, wine,
cola
less than 7 Acidic

solution
4 Tomato juice
Beer
5 Black coffee
• Basic solutions Rainwater
have pH values 6 Urine

Saliva
Neutral
greater than 7 [H+] = [OH–]
7 Pure water
Human blood, tears
• Most biological solution

Neutral 8 Seawater
Inside small intestine
Increasingly Basic
fluids have pH 9
[H+] < [OH–]

values in the 10
Milk of magnesia
range of 6 to 8 11
Household ammonia
12
Basic
solution Household
13 bleach
Oven cleaner
14
• Buffers are 0
substances that
Acidic
minimize + –
[H ] > [OH ]
changes in +
Acids donate H in
concentrations aqueous solutions.
of H+ and OH– in
a solution
• Most buffer solutions Neutral
+ –
contain a weak acid and [H ] = [OH ] 7
its corresponding base,
which combine
reversibly with H+ ions
–
Bases donate OH
+
or accept H in
aqueous solutions.
Basic
+ –
[H ] < [OH ]
14
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Acidification: A Threat to Our Oceans

• CO2 dissolved in seawater forms
carbonic acid; this process is CO2
called ocean acidification
• As seawater acidifies, H+ ions
combine with carbonate ions to
CO2 + H2O H2CO3
produce bicarbonate
• Carbonate is required for H2CO3 H+ + HCO3–
calcification (production of H+ + CO32– HCO3–

calcium carbonate) by many
marine organisms, including CO32– + Ca2+ CaCO3
reef-building corals
Figure 3.UN02a
[mmol CaCO3/(m2  day)]
20
Calcification rate
10
0
220 240 260 280
[CO32–] (µmol/kg of seawater)

Data from C. Langdon et al., Effect of calcium carbonate saturation state on the calcification
rate of an experimental coral reef, Global Biogeochemical Cycles 14:639–654 (2000).
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SUMMARY
a. BIOLOGICAL SOLVENT
- ability to dissolve many substances
b. HIGH HEAT CAPACITY
- prevents the abrupt temperature changes
in the organisms, maintaining constant
body temperature
c. HIGH HEAT OF VAPORIZATION
- prevent organisms from dehydration
SUMMARY
d. HIGH HEAT OF FUSION
- protects organisms from freezing at low
temperatures
e. MEDIUM where chemical and physical
processes take place
- formation of food, absorption, secretion, and
excretion ; dynamic structure
f. MOISTURIZER OF SURFACES
- gas exchange, outer surface of the eye
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SUMMARY
g. MEANS OF TRANSPORT
- serves as vehicle for the distribution of
nutrients, gases, etc.
h. LUBRICANT
- prevents friction in joints during movement, in
the heart during contraction, intestines during
digestion
i. GOOD CUSHION
- cerebrospinal fluid in the brain & spinal cord
Water doesn’t make me week

(to the tune of Weak)
Bio-lo-gical Sol-vent, High heat capa-city

High heat of fu-sion at vapori-zation
Medium na, mois-turizer pa
Means of trans-port din
Cushion sa u-tak
Po-lar mo-lecule, may sur-face ten-sion
Lubri-cant ng joint, ng heart, at mg-a in-tes-tines
I can explain why it doesn’t make me weak.
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Carbon: The Backbone of Life

• Living organisms consist mostly of
carbon-based compounds
• Carbon is unparalleled in its
ability to form large, complex,
and varied molecules
• Proteins, DNA, carbohydrates, and
other molecules that distinguish
living matter are all composed of
carbon compounds
Concept 4.1: Organic chemistry is the study

of carbon compounds
• Organic chemistry is
the study of
compounds that
contain carbon,
regardless of origin
• Stanley Miller ’ s
classic experiment
demonstrated the
abiotic synthesis of
organic compounds
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Concept 4.2: Carbon atoms can form diverse

molecules by bonding to four other atoms
• With four valence electrons, carbon can form four
covalent bonds with a variety of atoms
• This makes large, complex molecules possible!
• The number of unpaired electrons in the valence shell of
an atom is generally equal to its valence, the number of
covalent bonds it can form
Hydrogen Oxygen Nitrogen Carbon

(valence = 1) (valence = 2) (valence = 3) (valence = 4)
H O N C
Figure 4.3
Molecule Molecular Structural Ball-and-Stick Model Space-Filling
Formula Formula Model
(a) Methane
CH4
(b) Ethane
C2H6
(c) Ethene (ethylene)

C2H4
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• The valences of carbon and its most frequent partners

(hydrogen, oxygen, and nitrogen) are the building code
for the architecture of living molecules
• Carbon atoms can partner with atoms other than
hydrogen, such as the following:
• Carbon dioxide: CO2
Molecular Diversity Arising from Variation in

Carbon Skeletons
• Carbon chains vary in length and shape
(a) Length (c) Double bond position
Ethane Propane 1-Butene 2-Butene
(b) Branching (d) Presence of rings
Butane 2-Methylpropane Cyclohexane Benzene

(isobutane)
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Hydrocarbons
• Hydrocarbons are organic molecules consisting of only
carbon and hydrogen
• Many organic molecules, such as fats, have hydrocarbon
components
Nucleus
Fat droplets
10 µm
(a) Part of a human adipose cell (b) A fat molecule

Isomers
• Isomers are compounds with the same molecular formula
but different structures and properties
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Structural isomers have different covalent

arrangements of their atoms
(a) Structural isomers
Pentane 2-Methylbutane
Cis-trans isomers have the same covalent bonds

but differ in their spatial arrangements
(b) Cis-trans isomers
cis isomer: The two Xs trans isomer: The two Xs

are on the same side. are on opposite sides.
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Enantiomers are isomers that are mirror

images of each other
(c) Enantiomers
CO2H CO2H
C C
H NH2 NH2 H
CH3 CH3
L isomer D isomer
• Enantiomers are important in the pharmaceutical industry

• Two enantiomers of a drug may have different effects
Effective Ineffective
Drug Effects Enantiomer Enantiomer
Reduces
Ibuprofen inflammation
and pain
S-Ibuprofen R-Ibuprofen
Relaxes bronchial
(airway) muscles,
Albuterol improving airflow
in asthma
patients R-Albuterol S-Albuterol
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Animation: L-Dopa
Concept 4.3: A few chemical groups are key

to molecular function
• Estradiol and testosterone are both steroids with

a common carbon skeleton, in the form of four
fused rings
• These sex hormones differ only in the chemical
groups attached to the rings of the carbon skeleton
Estradiol Testosterone
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• Functional groups are the components of organic

molecules that are most commonly involved in chemical
reactions
• The seven functional groups that are most important in
the chemistry of life are the following:
• Hydroxyl group
• Carbonyl group
• Carboxyl group Are you familiar
• Amino group
• Sulfhydryl group with these
• Phosphate group
• Methyl group functional
groups!
Hydroxyl group (—OH)

Ethanol, the alcohol
present in
alcoholic beverages
(may be written HO—)
Polar due to electronegative oxygen. Forms hydrogen bonds with water.

Compound name: Alcohol
Carbonyl group ( C ═ O)
Acetone, Propanal,
the simplest ketone an aldehyde
Sugars with ketone groups are called ketoses; those with aldehydes
are called aldoses.
Compound name: Ketone or aldehyde
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Carboxyl group (—COOH)
Acetic acid, which Ionized form of —COOH

gives vinegar its (carboxylate ion),
sour taste found in cells
Acts as an acid.
Compound name: Carboxylic acid, or organic acid
Amino group (—NH2)
Glycine, an amino acid Ionized form

(note its carboxyl group) of —NH2,
found in cells
Acts as a base.
Compound name: Amine
Sulfhydryl group (—SH)
Cysteine, a sulfur-
containing amino acid
(may be written HS—)
Two —SH groups can react, forming a “cross-link” that helps stabilize
protein structure.
Compound name: Thiol
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Phosphate group (—OPO32−)

Glycerol phosphate,
which takes part in
many important
chemical reactions
in cells
Contributes negative charge. When attached, confers on a molecule the

ability to react with water, releasing energy.
Compound name: Organic phosphate
Methyl group (—CH3)

5-Methylcytosine, a
component of DNA
that has been modified
by addition of a methyl
group
Affects the expression of genes. Affects the shape and function of

sex hormones.
Compound name: Methylated compound
ATP: An Important Source of Energy for Cellular

Processes
• An important organic phosphate is
adenosine triphosphate (ATP)
• ATP consists of an organic molecule called
adenosine attached to a string of three
phosphate groups
• ATP’s reaction with water releases energy
Adenosine
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Figure 4.UN06
Reacts with H2O

P P P Adenosine P P Adenosine Pi Energy
ATP ADP Inorganic

phosphate
31

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28/08/2019

A Chemical Connection to Biology

© 2018 Pearson Education Ltd.

Concept 2.1: Matter consists of chemical

A compound has characteristics different from those

The Elements of Life

© 2018 Pearson Education Ltd.

Concept 2.2: An element’s properties

 A “parent” isotope decays into its “daughter” isotope

Some Fundamental Concepts

2 Atomic number Helium

Atomic mass Electron

© 2018 Pearson Education Ltd.

Hydrogen 2 Atomic number Helium

Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

Some Fundamental Concepts

© 2018 Pearson Education Ltd.

Concept 2.3: The formation and function of

Name and Electron Lewis Dot Space-

(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

(d) Methane (CH4)

Sodium chloride (NaCl)

Weak Chemical Interactions

Van der Waals interactions are

© 2018 Pearson Education Ltd.

Molecular Shape & FunctionCarbon Nitrogen

The Molecule That Supports All of Life

Black guillemots, threatened

Concept 3.1: Polar covalent bonds in water

© 2018 Pearson Education Ltd.

Polar covalent bond

Concept 3.2: Four emergent properties of water

© 2018 Pearson Education Ltd.

Evaporation pulls water upward.

Cohesion helps the

Animation: Water Transport in Plants

© 2018 Pearson Education Ltd.

• Surface tension is a measure of how difficult it is

• Water can absorb or release a large amount of

© 2018 Pearson Education Ltd.

Moderation of Temperature by Water

• The specific heat of a substance • Evaporation (or vaporization) is

Floating of Ice on Liquid Water

Hydrogen bond Liquid water:

Benefiting from loss of ice:

Figure 3.7 Phyto-

Water: The Solvent of Life

Possible Evolution of Life on Other Planets

© 2018 Pearson Education Ltd.

Concept 3.3: Acidic and basic conditions

Acids and Bases

• Strong acids and bases dissociate completely

© 2018 Pearson Education Ltd.

[H+] > [OH–]

less than 7 Acidic

have pH values 6 Urine

• Most biological solution

[H+] < [OH–]

Acidification: A Threat to Our Oceans

calcification (production of H+ + CO32– HCO3–