Download Chemistry

Chemistry of
Life
Keri Muma
Biology 6
Copyright © 2004 Pearson Education, Inc. publishing as Benjamin Cummings
Matter
• Matter is anything that occupies space and has mass
• Matter is composed of chemical elements
– Elements are substances that cannot be broken down
into other substances
Periodic Table
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• Twenty-five elements are essential to life
– Four of these make up about 96% of the
weight of the human body
– Trace elements occur in smaller amounts
Figure 2.3
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The Structure of Atoms
• Each element consists of one kind of atom
– An atom is the smallest unit of matter that still retains
the properties
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Electron Arrangement
• Maximum number of electrons per shell
– 2 in the first shell; 8 in the other shells
• Number of electrons on the outer shell – determines the
atoms chemical behavior and the bonds it will form
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Ionic Bonds
• When an atom loses or gains electrons, it becomes
electrically charged
– Ions are charged atoms
– Ionic bonds are formed between oppositely charged
ions
Cation
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Anion
Electrolytes – conduct electric currents
• Some very important ions in humans:
• Calcium (Ca 2+ ) – muscle contraction, blood
clotting, bones
• Sodium (Na+) – nerve impulses, muscle
contraction, water balance
• Potassium (K+) – nerve impulses and muscle
contraction
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Covalent Bonds
• Covalent bonds form when electrons are shared
between atoms.
Non-polar
Polar
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Hydrogen bonds
• The polarity of water
results in weak attractions
between neighboring water
molecules
– These interactions
are called
hydrogen bonds
()
()
()
Hydrogen bond
()
()
()
()
()
(b)
Figure 2.11b
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Vital Properties of Water
• High heat capacity
– Requires a lot of energy to increase in temperature,
and releases a lot of energy when it cools
– Important in maintaining a constant body
temperature
• High heat of vaporization
– As water evaporates it takes large amounts of heat
with it
– Good cooling mechanism
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Vital Properties of Water
Solvent properties
– Dissolves chemicals, making it a good medium for
transporting biological molecules
• A solution is a liquid consisting of two or more
substances evenly mixed
– Solvent: is the
dissolving agent
Ion in solution
Salt crystal
– Solute: is the
substance being
dissolved
Figure 2.16
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Water is a Good Solvent
• Hydrophilic – water soluble (likes water)
– Polar molecules
• Hydrophobic – does not dissolve in water (water
fearing)
– Non – polar molecules
• Amphiphilic – molecules that is both hydrophilic and
phobic
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Vital Properties of Water
• Chemical reactivity
– Hydrolysis – water breaks bond apart
– Dehydration – removing water to form bonds
Dehydration
• Cohesion
• Cushioning
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Hydrolysis
Acids, Bases, and pH
• Acid
– A chemical compound that donates
H+ ions to solutions
HCl
H+ + Cl-
• Base
– A compound that accepts H+ ions
and removes them from solution
NaOH
Na+ + OH-
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Concept of pH
• Measures concentration of
hydrogen ions
• Logarithmic scale – each pH
unit is a tenfold change in
H+ concentration
– pH 7 = neutral
– pH below 7 = acidic
– pH above 7 = basic
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Copyright © 2004 Pearson Education, Inc. publishing as Benjamin Cummings
Concept of pH
• Buffers are substances that resist pH change
– They accept H+ ions when they are in excess
– They donate H+ ions when they are depleted
Bicarbonate ions as a buffer:
CO2 + H2O
H2CO3
HCO3- + H+
Figure 2.18
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ORGANIC MOLECULES
• A cell is mostly water but the rest of the cell consists
mostly of organic molecules
– Organic molecules are large molecules containing
carbon (macromolecules)
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ORGANIC MOLECULES
• Each type of organic molecule has a unique threedimensional shape that defines its function in an
organism
– The molecules
of your body
recognize one
another based
on their shapes
Receptor
molecule
Transmitting
cell
Receiving
cell
Signal
molecule
Figure 3.5
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BIOLOGICAL MOLECULES
• There are four categories of macromolecules in cells
– Carbohydrates
– Lipids
– Proteins
– Nucleic acids
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• Most macromolecules are polymers
– Polymers are made by stringing together many
smaller molecules called monomers
– Cells link monomers together to produce polymers
– Organisms also have to break down macromolecules
Short polymer
Monomer
Longer polymer
(a) Dehydration synthesis of a polymer
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(b) Hydrolysis of a polymer
• Carbohydrates
– Includes sugars and starches
– Contain carbon, hydrogen, and oxygen (1:2:1 ratio)
•Glucose C6H12O6
•Ribose
C5H10O5
– Function: quick source of energy,
biological markers
Fructose
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Carbohydrates
– Classified according to size
• Monosaccharides – one sugar, referred to as
simple sugars
Examples: glucose, fructose
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Disaccharides
• A disaccharide is a double sugar
– It is constructed from two monosaccharides joined
together
Examples: maltose, sucrose
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Polysaccharides
• Polysaccharides are complex carbohydrates formed
by long chains of monosaccharides
– Starch, cellulose (plants), glycogen (animals)
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Lipids
– Carbon and hydrogen outnumber oxygen
C57H110O6
– Lipids are hydrophobic
– Functions:
• Energy storage
• Cushioning
• Insulation
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Lipids
• Neutral fats – mostly triglycerides
– A combination of glycerol and three fatty acids
– Found in fat deposits (adipose tissue)
– Source of stored energy and insulation
– Cushions organs
Glycerol
Fatty acid
(a) Dehydration synthesis linking a fatty acid to glycerol
Figure 3.15a
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• Unsaturated fatty acids - have less than the
maximum number of hydrogens bonded to
the carbons
– Examples: Most plant oils;
vegetable or corn oil
• Saturated fatty acids - have the
maximum number of hydrogens
bonded to the carbons
– Example: Most animal fats
What is a trans fat then???
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Lipids
• Phospholipids
– Forms cell membranes and the myelin sheaths of
neurons
– Phosphate head (hydrophilic) and lipid tail
(hydrophobic)
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Lipids
• Eicosanoids
– A 20 carbon fatty acid with a 5 or 6 carbon ring
– Regulators of various physiological functions
– Examples: prostaglandins, leukotrienes,
thromboxanes
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Lipids
• Steroids are very different from other fats in structure
and function
– The carbon skeleton is bent to form four fused rings
• Cholesterol is the “base steroid” from which your body
produces other steroids
– Example: testosterone, estrogen, cortisol, bile salts
Cholesterol
Figure 3.16
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Proteins
• A protein is a polymer constructed from chains of
amino acid monomers
• Contains C, H, O, N, and sometimes S
• There are 20 different amino acids
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Amino Acids
• The arrangement of amino
acids makes each protein
different
• Amino acids are held
together by peptide bonds
• Humans have an estimated 2
million different proteins, 1
million have been identified
as of 2007
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Types of Proteins
• Fibrous proteins
– Provides for construction materials for body tissues
– Important role in structure
– Examples: collagen, elastic fibers, myosin and actin
Structural proteins
Contractile proteins
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Types of Proteins
• Globular Proteins
– Complex folded structure
– Plays a vital role in cell
function
– Act as enzymes, hormones,
transport proteins or
antibodies
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Protein Shape
5
1
• Primary structure
– The specific
sequence of amino
acids in a protein
15
10
30
35
20
25
45
40
50
55
65
60
70
– Genetically
determined
85
80
75
95
90
100
110
105
115
120
125
129
Figure 3.21
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Amino acid
Protein Shape
• Secondary structure -polypeptide folded into a helix or a sheet
• Tertiary structure- sheets and helices folded into a 3-D globule
• Quaternary structure - several tertiary units put together
Figure 3.23
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Protein Shape
• A slight change in the primary structure of a protein
affects its ability to function
– The substitution of one amino acid for another in
hemoglobin causes sickle-cell anemia
1
2
(b) Sickled red blood cell
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6
7. . . 146
4
5
Normal hemoglobin
(a) Normal red blood cell
1
3
2
3
6
7. . . 146
4
5
Sickle-cell hemoglobin
Figure 3.22
What Determines Protein Structure?
• A protein’s shape is sensitive to the surrounding
environment
– Unfavorable temperature and pH changes can cause a
protein to unravel and lose its shape
– This is called denaturation
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Nucleic Acids
• Nucleic acids are information storage molecules
– They provide the directions for building proteins
– Two types: DNA and RNA
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Nucleic Acids
• Nucleotides are the monomers of nucleic acids
Each nucleotide consists of a:
5 carbon sugar
Phosphate group
Nucleic base
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Deoxyribonucleic acid
• DNA is composed of 4
types of nucleotides
• Purines
– Adenine (A)
Thymine (T)
Cytosine (C)
– Guanine (G)
• Pyrimidines
– Thymine (T)
– Cytosine (C)
Figure 3.25
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Deoxyribonucleic Acid (DNA)
• Organized by complimentary base pairing to form a
double stranded helix
• The nucleotides of the two stands are joined by
hydrogen bonds
–A=T
–G=C
• Contains a
sugar-phosphate
backbone
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Ribonucleic acid
• RNA is different from
DNA in that:
Nitrogenous base
(A,G,C, or U)
– Its sugar is ribose
– It has the base
uracil (U) instead
of thymine (T)
– It’s single
stranded
Uracil (U)
Phosphate
group
Sugar (ribose)
Figure 3.27
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Nucleotides
• Some other nucleotides are used to transfer and
store energy or are used in chemical signaling
– ATP used for cellular work
– NAD and FAD, used as electron carriers in cellular respiration
– GTP, cyclic AMP, ADP
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Summary
Copyright © 2004 Pearson Education, Inc. publishing as Benjamin Cummings