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The Chemical Basis of Life

The building blocks

Basic Chemistry
Matter is anything that takes up space and
has mass.
3 states solid, liquid, and gas

All matter, living or non-living, is made up


of elements.
Elements are substances that cannot be
broken down to simpler substances with
different properties.

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Percent by Weight

60

Earths crust
organisms

40

20

0
Fe

Ca

Si Al Mg Na
Element

Gunter Ziesler/Peter Arnold

Only 92 naturally occurring elements serve as the building blocks of all matter.
Other elements have been human-made and are not biologically important.

Elements that make up 95%


of living organisms (by
weight)
C
H
N
O
P
S

Carbon
Hydrogen
Nitrogen
Oxygen
Phosphorus
Sulfur

Atomic Structure
An atom is the smallest part of an element
that displays the properties of the element.
Atoms are made up of subatomic particles.
Protons - positively charged, found in nucleus
Neutrons - uncharged, found in nucleus
Electrons - negatively charged, move around
nucleus

Helium (He)
= proton
= neutron
= electron
a.

b.
Subatomic Particles

Particle

Atomic Mass

Location

+1

Nucleus

Neutron

Nucleus

Electron

~0

Proton

c.

Electric
Charge

Electron orbital

Atomic Mass = Number of Protons +


Number of Neutrons
Atomic Number =
in the Nucleus

The Number of Protons

The Periodic Table


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VIII

He

1.008

II

III

IV

VI

VII

4.003

10

Li

Be

Ne

12.01

14.01

16.00

19.00

20.18

6.941

Periods

9.012 10.81

11

12

13

14

15

16

17

18

Na

Mg

Al

Si

Cl

Ar

22.99

24.31

26.98

28.09

30.97

32.07

35.45

39.95

19

20

31

32

33

34

35

36

Ca

Ga

Ge

As

Se

Br

Kr

39.10

40.08

69.72

72.59

74.92

78.96

79.90

83.60

Groups

Isotopes
Atoms of the same element with a differing
numbers of neutrons
Radioactive isotopes emit various types of
energy as they decay.

12

13

14

*radioactive

Uses of low level radiation


a. The missing area in this thyroid scan indicates the
presence of a tumor that does not take up the
radioactive iodine.

b. A PET (positron emission tomography) scan reveals


which portions of the brain are most active (yellow and
red colors).

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larynx
thyroid gland
trachea
a.

b.
a: Biomed Commun./Custom Medical Stock Photo; b(left): Mazzlota et al./Photo Researchers, Inc; b(right): Hank Morgan/Rainbow

Uses of high level radiation


a. Radiation kills bacteria and fungi. Irradiated
peaches spoil less quickly and can be kept
for a longer length of time.
b. Physicians use radiation therapy to kill
cancer cells.

Electrons
In an electrically neutral atom, the positive
charges of the protons in the nucleus are
balanced by the negative charges of electrons
moving about the nucleus.
Energy levels (electron orbitals)
*1st contains 2 electrons
*Every one after that can contain 8 electrons
- Octet rule

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hydrogen
1
H
1

electron
electron orbital
nucleus

carbon
12
C
6

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nitrogen
14
N
7

Oxygen
16
O
8

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Phosphorus
31
P
15

Sulfur
32
S
16

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hydrogen
1
H
1

electron
electron orbital
nucleus

carbon
12
C
6

nitrogen
14
N
7

Phosphorus
31
P
15

Sulfur
32
S
16

Oxygen
16
O
8

Molecules and Compounds


Molecules form when two or more atoms
bond together (example: O2)
Compounds form when two or more
different elements bond together (H 2O)
When a chemical reaction occurs, energy
may be given off or absorbed.

Ionic Bonding
Ions form when electrons are
transferred from one atom to
another.
Ionic compounds are held together
by an attraction between oppositely
charged ions called an ionic bond.

Both atoms now


have 8 electrons
in their outermost
orbital

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Cl

Na

sodium atom (Na)

Electron transfer
creates charge
imbalance
Ionic bond held
together by
attraction of ions

chlorine atom (Cl)

+
Na

Cl

sodiumion (Na+)

chlorideion (Cl+)

sodium chloride (NaCl)


a.

Covalent Bonding
A covalent bond results when two atoms
share electrons in such a way that each
atom has an octet of electrons in the outer
orbit.
{An atom may share electrons with one or more
atoms}

Covalent Bonding
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Electron Model

Structural
Formula

Molecular
Formula

H2

a. Hydrogengas

A single covalent bond results from


sharing one pair of electrons.

Covalent Bonding
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O2

b. Oxygen gas

A double covalent bond results from


sharing two pairs of electrons.

Shape of Molecules
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H
H
H

C H
H

c. Methane

CH4

Shape of Molecules
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Space-filling Model

Ball-and-stick Model
H

hydrogen

carbon

covalent bond
H

109

d. Methanecontinued

Nonpolar Covalent Bonds

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Structural
Formula

Electron Model

If the sharing
between two
atoms is fairly
equal, the
covalent
bond is
described as
nonpolar.

Molecular
Formula

H2

C H

CH4

a. Hydrogen gas

H
H
H

H
H

c. Methane

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Structural
Formula

Electron Model

Molecular
Formula

H2

O2

a. Hydrogen gas

b. Oxygen gas

H
C

CH4

c. Methane

Ball-and-stick Model

hydrogen

Space-filling Model

carbon

covalent bond
H
d. Methanecontinued

109

Polar Covalent Bonds


If the sharing between two atoms is
unequal, the covalent bond is described
as polar.
Oxygen is more electronegative than
hydrogen.
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Electron Model

Ball-and-stick Model

Space-filling Model
Oxygen attracts the shared
electrons and is partially negative.

O
O

O
H

104.5

H
+

H
+

Hydrogens are partially positive.


a. W ater (H2O)

Hydrogen Bonding

Polarity
within a
water
molecule
causes the
hydrogen
atoms in one
molecule to
be attracted
to the oxygen
atoms in
other water
molecules.
Weak
individually
but quite
strong
collectively.

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H
O

hydrogen
bond

b. Hydrogen bonding between water molecules

Chemistry of Water
The first cell(s) evolved in water
All living things are 7090% water
Water is a polar molecule
Water molecules are hydrogen-bonded to one
another
Water is liquid at temperatures typical of the Earths
surface due to hydrogen bonding.

Properties of Water
Water has a high heat capacity.
A calorie is the amount of heat energy needed
to raise the temperature of 1g of water 1C.
The many hydrogen bonds that link water
molecules help water absorb heat without a
great change in temperature.
Because the temperature of water rises and
falls slowly, organisms are better able to
maintain their normal internal temperatures
and are protected from rapid temperature
changes.

Properties of Water
Water has a high heat of vaporization.
Converting 1 g of the hottest water to a gas
requires an input of 540 calories of heat energy.
Gives animals in a hot environment an efficient
way to release excess body heat.
Also helps moderate temperatures along coasts.

Properties of Water
Water is a solvent
Due to its polarity, water facilitates chemical
reactions, both outside and within living systems.
A solution contains dissolved substances, which
are then called solutes.
Hydrophilic molecules attract water.
Hydrophobic molecules do not attract water.

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+ H

O
H

Na+
H

Cl
O
H

H
O H

H
H

Properties of Water
Water molecules are cohesive and adhesive.
Water molecules cling together because of
hydrogen bonding (cohesion).
Waters positive and negative poles allow it to
adhere to polar surfaces (adhesion).
Water is an excellent transport system, both
outside and within living organisms.

Properties of Water
Water has a high surface tension
The stronger the force between molecules in
a liquid, the greater the surface tension.
This allows some insects to walk on the
surface of a pond or lake.

Properties of Water
Frozen water (ice) is less dense than liquid
water.
As liquid water cools, the molecules come closer
together.
Water expands as it freezes.
Ice floats.
Bodies of water freeze from the top down.

ice lattice

liquid water

Acids and Bases

water

hydrogen
ion

hydroxide
ion

When water ionizes, it releases an equal number


of hydrogen ions (H+) and hydroxide ions (OH-).

Acids and Bases


Acidic Solutions (High H+ Concentrations)
Acids are substances that that release
hydrogen ions (H+) when they dissociate in
water.
An example:

HCl

H+ + Cl-

Acids and Bases


Basic Solutions (Low H+ Concentrations)
Acids are substances that dissociate in water,
releasing hydroxide ions (OH-) or take up
hydrogen ions (H+).
An example:

NaOH

Na+ + OH-

Acids and Bases


The pH Scale
Ranges from 0 - 14
A pH below 7 is acidic

[H+] > [OH-]

A pH above 7 is alkaline [OH-] > [H+]


A pH of 7 is neutral [H+] = [OH-]

h uma n b
l ood
egg w
hi tes ,
se aw a
ter
st o bakin
ma g s
ch
o
an da,
ta c
ids

pure water, tears

ric
hydrochlo
acid

milk

stomach
aci d

e
urin

l em
on
juic
e

,
beer
r
root
ate
inw

l ra
ee
ma
off
nor
kc
l ac
,b
ad
bre

s
oe
at
m
to

be so
e r da
,v ,
ine
ga
r

ke
a
L
lt
a
S
nia
t
o
a
m
re
m
a
G
old
h
se
u
ho

oven
cleaner

sodium
hydroxide
(NaOH)

Buffers and pH
A buffer is a chemical or combination of
chemicals that keep pH within normal
limits.
Bicarbonate ions (HCO3-) and carbonic
acid (H2CO3) found in human blood buffers
the pH to 7.4

Buffers and pH
If hydrogen ions (H+) are added to the blood, this reaction occurs:

H+ + HCO3-

H2CO3

If hydroxide ions (OH-) are added to the blood, this reaction occurs:

OH- + H2CO3HCO3- + H2O

Organic Molecules
Always contain:
Carbon (C) and Hydrogen (H)
A carbon atom may share electrons with
another carbon atom or other atoms.
H

Organic Molecules
Macromolecules contain many molecules joined
together
Monomers: Simple organic molecules that
individually
Dimers, Trimers, Oligomers:.
Polymers: Large organic molecules form by
combining monomers

exist

Organic Molecules

Polymer

Monomer

carbohydrate (e.g., starch)


protein
nucleic acid

monosaccharide
amino acid
nucleotide

A meal containing carbohydrates, lipids, and proteins.

Organic Molecules
Cells have common mechanisms
Dehydration Reaction: an -OH and -H are
removed as a water molecule
Hydrolysis Reaction: the components of
water are added

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monomer

OH

dehydration
reaction

monomer

H2O

monomer

monomer

monomer

monomer

a.

H2O

hydrolysis
reaction

monomer
b.

OH

monomer

Carbohydrates
Simple Carbohydrates
Monosaccharides are sugars with 3 - 7
carbon atoms
Pentose refers to a 5-carbon sugar
Hexose refers to a 6-carbon sugar
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6 CH2OH
O
5C

CH2OH
H

C
4

H
OH

HO

C OH

C1

OH

H
OH

HO

OH

C6H12O6

OH

Carbohydrates
Disaccharides contain two monosaccharides.
Examples maltose, sucrose, lactose
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CH2OH

CH2OH

O H

+
OH

hydrolysis reaction

HO

dehydration reaction

CH2OH

O
O

glucose C6H12O6
monosaccharide

CH2OH

glucose C6H12O6
monosaccharide

maltose C12H22O11
disaccharide

H2O

water

water

Carbohydrates
Polysaccharides are long polymers that contain
many glucose subunits.
Starch is the storage form of glucose in plants.
Glycogen is the storage form of glucose in animals.
Cellulose can be found in the cell walls of plants.

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CH2OH
CH2OH
CH2OH
CH2OH
O
O
O
O H
H
H H
H H
H H
H
H
H
H
OH
H
OH
H
OH
H
OH
H
O
O
O
O
O
H

OH

OH

OH

OH

branched
nonbranched

starch
granule
cell wall

potato cells
Jeremy Burgess/SPL/Photo Researchers, Inc.

CH2OH

CH2OH
O

H
O

H
OH

OH

H
O

CH2OH
O

H
OH

OH

H
O

CH2OH
O

H
OH

OH

H
O

H
OH

OH

H
O

glycogen
granule

liver cells
Don W. Fawcett/Photo Researchers, Inc.

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plant
cell wall

cellulose
fiber
cellulose fibers
microfibrils

CH2OH
H
H
OH

CH2OH
H
H
OH

H
CH2OH
H
H
OH

CH2OH

OH
H

H
O

O
H

H
OH

O
H
H

O
O

OH

OH
H

CH2OH

OH

O
CH2OH

OH
H

CH2OH

OH

OH

CH2OH

H
H

OH

H
OH

CH2OH

OH

OH

O
H
H

OH

OH
H

H
OH

CH2OH

OH

H
H

OH
H
H

CH2OH

OH
H

H
H

OH

O
O

OH

OH
H

glucose
molecules
O

O
CH2OH

Science Source/J.D. Litvay/Visuals Unlimited

Lipids
Lipids are diverse in structure and function.
One common characteristic they do not
dissolve in water (hydrophobic)

Types
Fats and oils
Phospholipds
Steroids

Lipids
Fats
Usually of animal origin
Solid at room temperature

Oils
Usually of plant origin
Liquid at room temperature

Triglycerides
One glycerol and 3 fatty acid molecules

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H C OH

H C OH

HO

O
HO

O
H C OH
H
glycerol

HO

3 fatty acids

dehydration reaction
H

hydrolysis reaction

H C
H

H
fat molecule

3 H2O

3 water
molecules

A fatty acid is a hydrocarbon chain that ends with the acidic


group COOH
Saturated fatty acids have no double covalent bonds between
carbon atoms.
Unsaturated fatty acids have 1 or more double bonds between
carbon atoms.

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polar end

+
nonpolar end
emulsifier

fat

emulsification

Emulsification
Fat droplets disperses in water.
Emulsifiers contain molecules with a polar
and nonpolar end.

Polar Head

inside cell

CH2

Primary components of
cellular membranes
They spontaneously
form a bilayer in which
the hydrophilic heads
face outward toward
watery solutions and the
tails form the
hydrophobic interior.

CH2

CH2
CH2
CH2

outside cell
a. Plasma membrane of a cell

C
CH2
CH2
CH2
CH2
CH2
CH2
CH2

CH

CH

CH

CH

CH2
CH2

CH2

Fatty acids

CH2

CH O

glycerol

CH2 O

Comprised of 2 fatty
acids + a phosphate
group

Phospholipids

phosphate

R O P O 3CH2

Lipids

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CH2
CH2
CH2

CH2
CH2
CH2

CH2

Nonpolar Tails

CH2
CH2
CH2
CH3

b. Phospholipid structure

CH2
CH2
CH2
CH2
CH3

Lipids
Steroids
All have a backbone of four fused carbon
rings.
Examples: Cholesterol, Testosterone, Estrogen
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OH

OH
CH3

CH3
CH3

HO

a. Testosterone

b. Estrogen

Proteins
Proteins are polymers composed of amino
acid monomers.
Amino acids
Amino group (-NH2)
Acidic group (-COOH)
R group varies
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amino group

acidic group

C
R

O
C
OH
amino acid

OH
C

H
amino acid

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H
H3N+

H3N+

O
C

CH3

C
O

CH

CH3

H3C
H
H3N+

O
C
O

CH2
SH
H
H3N+

C
CH2

O
C
O

Proteins

Peptides

A polypeptide is a single chain of amino acids.


A peptide bond joins two amino acids.
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amino group

C
R

peptide bond

acidic group
O
C
OH
amino acid

OH
C

H
amino acid

dehydration reaction
hydrolysis reaction

R
N

dipeptide

OH
C

H2O
O
water

Proteins
Levels of Protein Organization
The structure of a protein has at least 3 levels of
organization.
Some can have four.

The final shape of a protein is very important to


its function.
Denatured A protein loses structure and function
due to heat or pH.

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H3N+

amino acid

COO

peptide bond

C
CH
C N
R
CH

CH

C N
R

hydrogen bond

C
CH

C N

hydrogen bond

CH

C
C

CH
C N
R
CH

CH
N R

(alpha) helix

(beta) pleated sheet

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(alpha) helix

(beta) pleated sheet

disulfide bond

Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H3N+

amino acid

COO

peptide bond

C
C
C
CH

CH
N

CH

CH
N

C
C

CH

CH
N

hydrogen bond

R
hydrogen bond

C
C

CH

CH
N

(alpha) helix

(beta) pleated sheet

disulfide bond

Nucleic Acids
DNA (deoxyribonucleic acid)
DNA stores genetic information in the cell and in the
organism.

RNA (ribonucleic acid)


Both are polymers of nucleotides
Components of a nucleotide
Phosphate
Pentose sugar (ribose or deoxyribose)
Nitrogen-containing base (1 of 5)

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O
O

phosphate

C
O

5'
4'

1'

2'
3'
pentose sugar
Nucleotide structure

nitrogencontaining
base

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G
C

A
T

G
T

T
C

one nucleotide

S
P

S
P

A
P

a.

c.

b.
a: Radius Images/Alamy RF

DNA is a double helix


2 strands held together by hydrogen
bonding
Complementary base pairing
Adenine (A) always pairs with thymine (T)
Cytosine (C) always pairs with guanine
(G)

Nucleic Acids
RNA is single stranded
Several types involved in carrying information
in DNA to make proteins

ATP (Adenosine Triphosphate)


A high energy molecule
ATP undergoes hydrolysis and energy is
released
Energy currency of the cell.

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H2O
P

ATP is the high energy form


Last phosphate bond broken to release
energy
Forms ADP (adenosine diphosphate)
ATP can be rebuilt
Add P to ADP to make ATP

+ energy

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