Download The Chemistry of Biology

The Chemistry of
Biology
Chapter 2
Adapted from McGraw Hill
by Dr. G Cornwall
1
What is Matter?
• Matter is anything
that occupies space
and has mass
• Matter can exist in
three states:
• Solid (like ice)
• Liquid (like water)
• Gas (like steam)
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
© Kathy Park Talaro
2
2.1 Atoms, Bonds, and Molecules:
Fundamental Building Blocks
• Atom- smallest particle of
an element that retains
properties of the element
• Subatomic particles of
atoms- protons (p+),
neutrons (n0), and
electrons (e-)
• Protons and neutrons make
up the nucleus, electrons
surround the nucleus
• Held together by the
attraction of positive protons
to negative electrons
3
Different Types of Atoms: Elements and
Their Properties
• Different numbers of protons, neutrons, and electrons
in atoms create different elements
• Each element has a characteristic atomic structure
and predictable chemical behavior
• Each assigned a distinctive name with an abbreviated
shorthand symbol
4
The Major Elements of Life and Their
Primary Characteristics
• Isotopes- variant forms of the same element that
differ in the number of neutrons
• Radioactive isotopes used in research and
medical applications and in dating fossils and
ancient materials
• Electron orbitals and shells
5
Biologically Important Atoms
Electron Orbitals and Shells
• An atom can be envisioned as a central nucleus
surrounded by a “cloud” of electrons
• Electrons rotate about the nucleus in pathways called
orbitals- volumes of space in which an electron is likely to
be found
• Electrons occupy energy shells, from lower-energy to
higher-energy as they move away from the nucleus
7
Electron orbitals (cont.)
• Electrons fill the orbitals and shells in pairs starting
with the shell nearest the nucleus
• Each element, then, has a unique pattern of
orbitals and shells
8
Bonds and Molecules
• Most elements do not exist naturally in pure form
• A combination of two or more atoms is called a
molecule (like N2)
• Molecules formed from two or more different
elements are called compounds (like C6H12O6)
• Molecules and compound are held together with
chemical bonds
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Concept Check
If an extra neutron were added to a carbon atom,
what would be the result?
A. It would be a new element
B. It would be an ion
C. It would be radioactive
D. It would be an isotope
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0
Types of Chemical Bonds
• There are a variety of
bonds
• These vary in strength,
but all are important
• Covalent bonds
• Ionic bonds
• Hydrogen bonds
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1
Covalent Bonds
• Formed by the sharing of
electrons between atoms
• Strongest bonds
• The most common bonds
in living cells
• Form between C, H, O, N,
S, and P.
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2
Polar Molecules
• Some atoms do not share electrons equally
(Oxygen binds tightly; Hydrogen binds weakly)
• Unequal distribution of electrons forms a polar
molecule
• True of most large biological molecules
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Non-Polar Molecules
• An electrically neutral molecule is nonpolar
• Electrons are shared equally
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4
Ionic Bonds
• Complete transfer of
electrons (ex. NaCl)
• Can separate into
charged particles
called ions
• Cations are
positively charged
• Anions are
negatively charged
• Electrolytes are ionic
molecules that dissolve
to form ions
1
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Hydrogen Bonds
• Weak bond between a
H covalently bonded to
one molecule and an O
or N atom on the same
or different molecule
+
• Important in many
biological molecules
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Chemical Shorthand: Formulas, Models,
and Equations
• Molecular formula- gives
atomic symbols and the
number of elements involved in
subscript (H2O, C6H12O6).
• Molecular formulas might not
be unique (glucose, galactose,
and fructose, for example)
• Structural formulas illustrate
the relationships of the atoms
and the number and types of
bonds
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Chemical Equations
• Equations are used to illustrate chemical reactions
• Reactants- Molecules entering the reaction
• Products- the substances left by a reaction
6H2O + 6CO2  C6H12O6 + 6O2
Reactants
products
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Types of Reactions
• Synthesis: reactants bond together to form an entirely new
molecule
• A + B  AB
• S + O2  SO2
• 2H2 + O2  2H2O (note that equations must be balanced)
• Decomposition: bonds on a single reactant molecule are
permanently broken to release two or more product molecules
• AB  A + B
• 2H2O2  2H2O + O2
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Types of Reactions (cont.)
• Exchange: The reactants trade places between
each other and release products that are
combinations of the two
• AB + XY ---> AX + BY (reversible reaction)
2
0
Solutions: Homogenous Mixtures
• Solutions a mixture of
one or more solutes
uniformly dispersed in
a solvent
• Cannot be separated
by filtration or settling
• “like dissolves like”
• Water is the most
common solvent in
biological settings
2
1
Solutions (cont.)
• Water- the most common solvent in natural systems
because of its special characteristics
• Hydrophilic molecules- attract water to their surface
(polar)
• Hydrophobic molecules- repel water (nonpolar)
• Amphipathic molecules- have both hydrophilic and
hydrophobic properties
2
2
Concentration of Solutions
• Concentration- the amount of solute dissolved in
a certain amount of solvent
• In biological solutions, commonly expressed as
molar concentration or molarity (M)
• One mole dissolved in 1 L
• One mole is the molecular weight of the
compound in grams
2
3
Acidity, Alkalinity, and the pH Scale
• Acidic solutions- when a component dissolved in water (acid)
releases excess hydrogen ions (H+)
• Basic solutions- when a component releases excess
hydroxide ions (OH-)
• pH scale- measures the acid and base concentrations of
solutions
• Ranges from 0 (most acidic) to 14 (most basic); 7 is neutral
• pH = -log[H+]
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4
2
5
Concept Check
What type of bond is formed when an
electron is completely transferred from
one atom to another?
A. Ionic
B. Hydrogen
C. Covalent
D. Van der Waals
2
6
The Chemistry of Carbon and Organic
Compounds
• Inorganic chemicals- usually does not contain
both C and H (ex. NaCl, CaCO3)
• Organic chemicals- Carbon compounds with a
basic framework of the element carbon bonded to
other atoms
• Most of the chemical reactions and structures of
living things involve organic chemicals
2
7
The Importance of Carbon
• Valence (electron
arrangement) allows four
bonds to be made
• Can form linear, branched, or
ringed structures
• Can form single, double, or
triple bonds
• Most often associates with H,
O, N, S, and P
Functional Groups
• Special molecular
groups of organic
compounds
• Give organic
compounds unique
reactive properties
2
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Concept Check
What kind of reaction is illustrated here?
2 H2 + O2 
2 H2O
A. Decomposition
B. Synthesis
C. Exchange
D. Spontaneous
3
0
2.2 Biological Macromolecules
• Biochemistry is the study of the compounds and
reactions of living systems
• Four kinds of macromolecules (large molecules)
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
• All macromolecules except for lipids are formed by
polymerization (monomers linked into polymers)
3
1
Carbohydrates
• Carbohydrates include sugars and polysaccharides
• Represented by the general formula (CH2O)n,
n = the number of repeats
• Polysaccharides are built from repeats of
monosaccharides
• Used for structure (e.g. cellulose) or energy
storage (e.g. starch)
3
2
Carbohydrates
• Exist in a variety of configurations
• Sugar (saccharide)- a simple carbohydrate with a
sweet taste
• Monosaccharide contains 3-7 carbons
• Disaccharide contains two monosaccharides
• Polysaccharide contains five or more
monosaccharides
3
3
• Monosaccharides and disaccharides are specified by
combining a prefix that describes a characteristic of the
sugar with the suffix –ose
• Hexoses- six carbons
• Pentoses- five carbons
• Fructose- for fruit
34
The Functions of Polysacharides
• Structural support and protection
• Serve as nutrient and energy stores
• Cell walls in plants and many microscopic
algae from cellulose
3
5
Important Polysaccharides
• Include agar, chitin,
lipopolysaccharide,
glycocalyx, and
glycogen, strarch
3
6
Lipids: Fats, Phospholipids, and Waxes
• Lipids- a variety of substances that are not
soluble in polar substances
• Will dissolve in nonpolar solvents
• Biologically important kinds of lipids
• Triglycerides
• Phospholipids
• Sterols
3
7
Triglyceride
• Fats & Oils
• Primarily energy
storage
3
8
Phospholipids
• Amphipathic
• 2 fatty acids (hydrophobic)
• Phosphate (hydrophilic)
• Important membrane
molecules
Sterols
• Multi-ring structure
• Used in membranes
cholesterol, ergosterol
• Bile acids
• Hormones
• Steroids- complex ringed compounds commonly found
in cell membranes and animal hormones
• Best known- cholesterol
• Waxes- esters formed between a long-chain alcohol
and a saturated fatty acid
4
0
Concept Check
What is the main function of a triglyceride?
A. Cell structure
B. Membrane structure
C. Energy storage
D. Enzyme activity
4
1
Proteins: Shapers of Life
• Predominant organic molecules
• Building blocks- amino acids
• 20 different naturally occurring
forms
• Basic skeleton- a carbon (the α
carbon) linked to an amino group
(NH2), a carboxyl group (COOH), a
hydrogen atom (H), and a variable
R group
• Peptide bond forms between the
amino group on one amino acid
and the carboxyl group on another.
4
2
4
3
Proteins
• Can be structural
(cytoskeleton)
• Mechanical (dynein)
• Enzymatic (biological
catalysts)
4
4
Protein Structure and Diversity
• Primary structure is
the order of amino acids
• Secondary structure is
localized modular
structure
• Tertiary structure is the
three-dimensional
shape of the protein
• Quaternary structure
is the association of
more than one peptide
4
5
Protein Shape
• Each different type of protein
develops a unique shape, so it can
only react with molecules that fit its
particular surface features
• Ex. enzymes and antibodies
• Native state- the functional threedimensional form of a protein
• Denatured- when the protein’s
native state has been disrupted
4
6
The Nucleic Acids: A Cell Computer and
Its Programs
• DNA- specially coded genetic
program
• DNA transfers its program to RNA
• Both are polymers of repeating
units called nucleotides
• Nucleotides- composed of three
smaller units: a nitrogen base, a
pentose sugar, and a phosphate.
4
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The Nucleic Acids: A Cell Computer and
Its Programs
• The nitrogen base can be one of two
forms- a purine (two rings) or a
pyrimidine (one ring)
• Two types of purines: adenine
(A) and guanine (G)
• Three types of pyrimidines:
thymine (T), cytosine (C), and
uracil (U)
• DNA contains no uracil
• RNA contains no thymine
• The nitrogen base is covalently bonded
to ribose in RNA and deoxyribose in
DNA
• Phosphate (PO43-) covalently bonds
the sugars in series
4
8
Nucleotides
• Purines: A and G
• Pyrimidines: C and T
• U in RNA
• Chargaff’s Rules
• A=T
•C=G
49
DNA
• The genetic material of
all cells
• Encodes all information
for the cell
• Four monomers:
A,C,G,T
• Double-stranded helix
5
0
RNA: Organizers of Protein Synthesis
• Also consists of a long chain of nucleotides
• It is single stranded and contains ribose instead of
deoxyribose and uracil instead of thymine
• Several functional types of RNA formed using the
DNA template
• Messenger RNA (mRNA)- a copy of a gene that
provides the order and type of amino acids in a protein
• Transfer RNA (tRNA)- a carrier that delivers the correct
amino acids for protein assembly
• Ribosomal RNA (rRNA)- a major component of
ribosomes
5
1
RNA
• Involved in translation
• Several kinds
• mRNA
• rRNA
• tRNA
• snRNA
• Ribose not deoxyribose
• U not T
ATP: The Energy Molecule of Cells
• Adenosine triphosphate (ATP)- a
nucleotide containing adenine, ribose,
and three phosphates
• High-energy compound that gives off
energy when the bond is broken
between the outermost phosphates
• Releases and stores energy for
cellular chemical reactions
• When the terminal phosphate bond is
broken to release energy, adenosine
diphosphate (ADP) is formed
• ADP can be converted back to ATP
when the third phosphate is restored.
5
3
Adenosine Triphosphate
• Chemical energy
storage for the cell
• High-energy bonds
• ATP  ADP + P
releases 32 kJ energy
5
4
2.3 Cells: Chemicals Come to Life
• The fundamental unit of life- cell
• Fundamental characteristics of cells
• Tend to be spherical, polygonal, cubical, or cylindrical
• Have a cytoplasmic membrane
• Have chromosomes made of DNA
• Have ribosomes for protein synthesis
• Reproduce to form progeny cells
• Obtain energy from their environment
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Eukaryotic and Prokaryotic Cells
• Eukaryotic cells
• Animals, plants, fungi, and protists
• Have a nucleus and cellular organelles
• Tend to be larger
• Prokaryotic cells
• Bacteria and archae
• No nucleus or other organelles
• Tend to be smaller
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Concept Check
At what level of protein structure are alpha helices
and beta sheets formed?
A. Primary
B. Secondary
C. Tertiary
D. Quaternary
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