Transcript BSCS Chapter 01 - HonorsBiology2015-16

Chapter
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Chapter Introduction
General Chemistry
1.1 Atoms, Molecules, and Compounds
1.2 The Structure of Atoms
Reactions in Living Cells
1.3 Chemical Reactions
1.4 Chemical Bonds
1.5 Ions and Living Cells
Biochemistry
1.6
1.7
1.8
1.9
1.10
Organic Compounds and Life
Carbohydrates
Lipids
Proteins
Nucleic Acids
Genetic Coding in Cells
1.11 The Double Helix
1.12 The Functions of DNA
Chapter Highlights
Chapter Animations
Learning Outcomes
By the end of this chapter you will be able to:
A Explain the relationships among atoms,
molecules, elements, and compounds.
B Describe the types of chemical bonds.
C Explain the pH scale and its use.
D Relate the characteristics and functions of the four
classes of macromolecules.
E Recognize the importance of nucleic acids in
inheritance.
The Chemistry of Life
 What roles do chemicals
play in life?
 What evidence do you see
of chemicals in this hot
spring?
The Champagne Pool, a mineral rich hot spring
at Waiotapu Thermal Park in New Zealand
The Chemistry of Life
• A scientist named Lavoisier
founded modern chemistry
by using physical laws and
measurement to understand
how chemicals react.
• Biochemistry—the chemistry
of living organisms—plays a
central role in our
understanding of today’s
biological questions.
The Champagne Pool, a mineral rich hot spring
at Waiotapu Thermal Park in New Zealand
General Chemistry
1.1 Atoms, Molecules, and Compounds
• Water is abundant on Earth today, and it exists in
three physical states depending on temperature—
as a gas, as a liquid, and as a solid.
• Although the forms of water may vary, its chemical
composition remains the same.
General Chemistry
1.1 Atoms, Molecules, and Compounds
(cont.)
• Molecules of water are the smallest units into which
water can be subdivided and still have the essential
chemical properties of water.
• Under certain conditions, water molecules can
break down into two different substances (which
are also molecules), hydrogen and oxygen.
General Chemistry
1.1 Atoms, Molecules, and Compounds
(cont.)
• Hydrogen and oxygen are elements—substances
that cannot be broken down chemically into simpler
substances.
• Atoms are the smallest unit of an element that still
has the chemical properties of that element.
• Molecules are made of atoms that have combined
chemically.
General Chemistry
1.1 Atoms, Molecules, and Compounds
(cont.)
• Molecules may be made from more than one type
of atom or from atoms of the same type.
• Elements can
combine chemically
in many ways to
form the millions of
compounds that
give Earth its variety
of materials.
Molecules of water, hydrogen,
and oxygen are made from
combinations of atoms, as
shown in these models.
General Chemistry
1.1 Atoms, Molecules, and Compounds
(cont.)
• Chemists have given each element a symbol of
letters from the element’s name.
• The number of atoms of each element in a molecule
is shown by the number, called a subscript, following
the symbol for the element (the number 1 is always
understood and not written).
General Chemistry
1.1 Atoms, Molecules, and Compounds
(cont.)
• About 97% of the compounds present in organisms
contain only six elements which are essential to
every organism—carbon (C), hydrogen (H), oxygen
(O), nitrogen (N), phosphorus (P), and sulfur (S).
• The remaining 3% contain small amounts of
other elements.
General Chemistry
1.2 The Structure of Atoms
• Atoms themselves are built of many smaller
subatomic particles.
• The subatomic particles of atoms that are basic to
an understanding of biology are electrons, protons,
and neutrons.
– an electron carries a negative electric charge
– a proton has a positive charge
– a neutron has no charge (it is neutral)
General Chemistry
1.2 The Structure of Atoms (cont.)
• Protons and neutrons remain in the center, or
nucleus, of the atom.
• The rapidly moving electrons form a negatively
charged “cloud” around the nucleus.
• Electrons are distributed throughout the cloud based
on differing levels of energy (or attraction) called
electron shells.
• Electrons in shells near the nucleus are held more
tightly than those in shells farther from the nucleus.
General Chemistry
1.2 The Structure of Atoms (cont.)
• With a single proton, no neutron, and a
single electron that orbits in the energy
shell closest to the nucleus, hydrogen is
the simplest of all atoms.
• An atom of carbon has six
protons and six neutrons in its
nucleus and six electrons orbiting
the nucleus.
General Chemistry
1.2 The Structure of Atoms (cont.)
• Nitrogen has seven protons and
seven electrons (two in the innermost
shell, five in an outer shell which can
hold eight).
• Oxygen has eight protons and
eight electrons (two in the
innermost shell, six in an outer
shell which can hold eight).
General Chemistry
1.2 The Structure of Atoms (cont.)
• Every atom has an equal number of protons
and electrons.
• The atoms of most elements can undergo chemical
change by gaining, losing, or sharing one or more
electrons with other atoms.
• Atoms with unfilled shells have a strong tendency to
lose or gain electrons to complete their outer shells.
General Chemistry
1.2 The Structure of Atoms (cont.)
• Atoms of the same element always have the same
number of protons and electrons, but they may differ
in their number of neutrons.
• Atoms of the same element that differ in their number
of neutrons are called isotopes.
• Some isotopes, called radioisotopes, have
unstable atomic nuclei that break down, releasing
radiation energy.
Reactions in Living Cells
1.3 Chemical Reactions
• Chemical bonds are the attraction, sharing, or
transfer of outer shell electrons from one atom
to another.
• A chemical reaction involves the making and
breaking of chemical bonds which produces new
substances.
Reactions in Living Cells
1.3 Chemical Reactions (cont.)
• For atoms with electrons in more than one energy
shell, only the outermost electrons normally interact
during chemical changes.
• Chemical reactions
occur in the cells—the
basic units of life—of
all living organisms.
Reactions in Living Cells
1.3 Chemical Reactions (cont.)
• Chemical reactions are important to a cell for
two reasons:
1. they are the only way to form new molecules that
the cell requires for such things as growth and
maintenance
2. the making and breaking of bonds involves
changes in energy which allow it to be stored,
used to do work, or released
Reactions in Living Cells
1.3 Chemical Reactions (cont.)
• Chemical reactions can be represented as short
statements called chemical equations.
• The breakdown of water can be represented by
the following equation (note that the arrow points
from the reactants to products):
Models of chemical reactions
Reactions in Living Cells
1.3 Chemical Reactions (cont.)
• Balancing chemical equations illustrates the law of
conservation of matter, which states that matter is
neither created nor destroyed in chemical reactions.
• When molecules collide, they may or may not react,
depending on the energy and orientation of the
molecules.
• Activation energy is the energy needed to get a
chemical reaction started.
Reactions in Living Cells
1.4 Chemical Bonds
• One type of chemical bond forms when electrons
move from one atom to another atom.
• This type of chemical bond occurs in many
substances, including sodium chloride (NaCl).
Reactions in Living Cells
1.4 Chemical Bonds (cont.)
• An ion is an atom or a molecule that has acquired a
positive or negative charge as a result of gaining or
losing electrons.
• An ionic bond is the attraction between oppositely
charged ions, such as the sodium chloride bond.
Reactions in Living Cells
(a) Sodium and (b) chlorine can react to form (c) the salt sodium chloride (NaCl).
By losing one electron, sodium achieves two filled shells (2 + 8) and becomes a
stable positive ion. By gaining one electron, chlorine achieves three filled shells
(2 + 8 + 8) and becomes a stable negative ion, chloride.
Reactions in Living Cells
1.4 Chemical Bonds (cont.)
• In a covalent bond, two atoms share one or more
pairs of electrons.
• Two atoms of hydrogen join to
form a molecule of hydrogen
gas (H2) by sharing a pair of
electrons.
• In a molecule of water, each of
the two hydrogen atoms shares
a pair of electrons with the same
oxygen atom.
Reactions in Living Cells
1.4 Chemical Bonds (cont.)
• If the electrons of a bond are not shared equally,
such as in water, the bond is called a polar
covalent bond.
• When the electrons in a molecule are shared equally,
such as in hydrogen gas, the resulting covalent bond
is said to be nonpolar.
Reactions in Living Cells
1.4 Chemical Bonds (cont.)
• The unequal sharing of electrons in a water molecule
gives the oxygen atom a slight negative charge and
each hydrogen atom a slight positive charge creating
a polar molecule.
• The polar nature of water is biologically significant as
molecules must dissolve in water in order to move
easily in and between living cells.
Reactions in Living Cells
1.4 Chemical Bonds (cont.)
• A hydrogen bond, or weak attraction can occur
between a slightly positive hydrogen atom in a
molecule and a nearby slightly negative atom of
another molecule (or of the same molecule if it is
large enough).
• A large number of hydrogen bonds can be quite
strong, but single hydrogen bonds are much weaker
than covalent bonds.
Reactions in Living Cells
1.5 Ions and Living Cells
• When table salt dissolves in water, the ionic bonds
are broken and Na+ and Cl– ions separate, or
dissociate, but remain as ions in solution.
• Sodium ions are important in regulating water
balance in organisms.
• When a nonionic compound, such as water, is
converted to ions, the process is called ionization.
• Only about one in every 500 million water molecules
ionizes in living cells, yet all life processes depend
on this tiny amount of ionization.
Reactions in Living Cells
1.5 Ions and Living Cells (cont.)
• The level of H+ and OH- ions in solution is described
on a scale from 0 to 14 known as the pH scale.
• A solution (a mixture in water) that has the same
number of H+ and OH- ions is neutral and has a
pH of 7.
Reactions in Living Cells
1.5 Ions and Living Cells (cont.)
• A solution having more H+ than OH- is acidic and
has a pH less than 7 (low pH).
• A solution that has more OH- than H+ ions is basic
(or alkaline) and has a pH greater than 7 (high pH).
Reactions in Living Cells
1.5 Ions and Living Cells (cont.)
• The pH scale is a logarithmic
scale meaning that a change
of one pH unit is equal to a
tenfold change in the level of
H+ ions.
The pH of some common substances.
Note that most biological substances are
slightly acidic (pH 6–7). The greater acidity
of soft drinks (pH 3) is partly responsible
for contributing to tooth decay.
Reactions in Living Cells
1.5 Ions and Living Cells (cont.)
• The pH of a cell’s interior helps regulate the cell’s
chemical reactions.
• Organisms have ways to control pH and to respond
to changes in the pH of their environment.
Biochemistry
1.6 Organic Compounds and Life
• Organic compounds, in which carbon atoms are
combined with hydrogen and usually oxygen, are
needed for life to exist.
• Carbon atoms can combine in long chains that
form the backbone of large complex molecules,
or macromolecules.
Biochemistry
1.6 Organic Compounds and Life (cont.)
• The backbone of carbon atoms, to which other
atoms and molecules can attach, is called the
carbon skeleton.
• The four most important classes of molecules in
living cells are carbohydrates, lipids, proteins,
and nucleic acids.
Biochemistry
1.6 Organic Compounds and Life (cont.)
Carbon atoms (black) make up a carbon skeleton and link with other atoms, such as
hydrogen (white). In each formula, a short line indicates a covalent bond: (a), a
molecule of methane; (b), part of the carbon skeleton of a larger molecule; (c), a
view of (b) that indicates the three-dimensional structure of the molecule.
Biochemistry
1.7 Carbohydrates
• All known types of living cells contain carbohydrates
which contain carbon atoms and hydrogen and
oxygen atoms in the same two-to-one ratio as water.
• The simplest carbohydrates are
single sugars, such as glucose,
called monosaccharides,
which may contain three to
seven carbon atoms in their
carbon skeletons.
Biochemistry
1.7 Carbohydrates (cont.)
• Biologically important sugars often have a phosphate
group composed of an atom of phosphorus and four
atoms of oxygen attached to the carbon skeleton
and are called sugar-phosphates.
Biochemistry
1.7 Carbohydrates (cont.)
• Two simple sugar molecules, or monosaccharides,
may bond to form a double sugar, or disaccharide,
such as sucrose.
Biochemistry
1.7 Carbohydrates (cont.)
• Several glucose molecules may bond to form
complex carbohydrates called polysaccharides,
such as starch and cellulose.
Biochemistry
1.8 Lipids
• Lipids, or fats and oils, are macromolecules that
have two primary functions:
– long-term storage of energy
– carbon and building of structural parts of
cell membranes
Biochemistry
1.8 Lipids (cont.)
• Lipids:
– are nonpolar and generally do not dissolve
in water
– contain carbon, hydrogen, and oxygen, but not
in a fixed ratio
• Building blocks of lipids, called fatty acids and
glycerol, make up the simple fats.
Biochemistry
1.8 Lipids (cont.)
To form a fat, one molecule of glycerol combines with three molecules of fatty
acids. The fatty acids in one fat may be alike or different.
Biochemistry
1.8 Lipids (cont.)
• The biologically important properties of simple fats
depend on their fatty acids.
– Fatty acids in which single bonds join the carbon
atoms are saturated fatty acids.
– Unsaturated fatty acids are fatty acids in which
double bonds join some of the carbon atoms.
Biochemistry
1.8 Lipids (cont.)
• Fats are a more efficient form of energy storage than
are carbohydrates because fats contain a larger
number of hydrogen atoms and less oxygen.
• Two other types of lipids important in cells are
phospholipids and cholesterol.
Biochemistry
1.8 Lipids (cont.)
• Phospholipids form when a molecule of glycerol
combines with two fatty acids and a phosphate
group.
• Together with proteins, phospholipids form cellular
membranes.
Glycerol joins with two fatty acids and a
polar phosphate group to form a
phospholipid (a) and (b). When
phospholipids form membranes (c), the
polar head associates with water on the
membrane surface, and the nonpolar tail
faces the interior of the membrane, away
from water. Membranes prevent the cell
contents from mixing with the external
environment.
Biochemistry
1.8 Lipids (cont.)
• Cholesterol is part of the membrane structure of
animal cells and is important in nutrition.
Cholesterol has a fused four-ring
structure with additional side groups.
Cholesterol is important in membrane
structure, and the sex hormones are
derived from it.
Biochemistry
1.9 Proteins
• Every living cell contains from several hundred to
several thousand different macromolecules known
as proteins.
• Proteins are structural components of cells as well
as messengers and receivers of messages (also
called receptors) between cells.
• The most essential role of proteins is as enzymes,
specialized molecules that assist the many reactions
occurring in cells.
Biochemistry
1.9 Proteins (cont.)
• Cells make proteins by linking building blocks called
amino acids which are small molecules that contain
carbon, hydrogen, oxygen, and nitrogen atoms; two
also contain sulfur atoms.
Amino acids (except for proline) have a central
carbon atom bonded to a hydrogen atom, an
amino group, an acid group, and an R-group.
The R-group is any of 20 arrangements of C, H,
O, N, and S atoms, depending on, and giving
unique structure to, each amino acid.
Biochemistry
1.9 Proteins (cont.)
• Covalent bonds between the acid group of one
amino acid molecule and the amino group of another
are called peptide bonds.
• Additional peptide bonds may form, resulting in a
long chain of amino acids, or polypeptide.
Formation of a polypeptide
Biochemistry
1.9 Proteins (cont.)
• The sequence of amino
acids in a polypeptide
chain forms the primary
structure of a protein.
• In most proteins, the
chain folds or twists to
form local structures
known as secondary
structures.
Biochemistry
1.9 Proteins (cont.)
• More complex folding
creates a tertiary structure,
which usually is globular,
or spherical.
• One of the major forces
controlling how a protein folds
is hydrophobicity, or the
tendency for nonpolar amino
acids to avoid water.
Biochemistry
1.9 Proteins (cont.)
• Each individual protein has a unique shape and,
therefore, a specific function.
• A few proteins become
active only when two or
more tertiary forms
combine to form a complex
quaternary structure.
Biochemistry
1.10 Nucleic Acids
• Nucleic acids are macromolecules that dictate the
amino-acid sequence of proteins, which in turn
control the basic life processes.
• Nucleic acids also are the source of genetic
information in chromosomes, which are passed
from parent to offspring during reproduction.
Biochemistry
1.10 Nucleic Acids (cont.)
• Nucleic acids are made of relatively simple units
called nucleotides connected to form long chains.
• Each nucleotide consists of three parts:
– a 5-carbon sugar (a pentose), which may be
either ribose or deoxyribose
– a nitrogen-containing base, which is a single or
double ringlike structure of carbon, hydrogen,
and nitrogen
– a phosphate group
Biochemistry
1.10 Nucleic Acids (cont.)
Two sugars found in nucleotides. Ribose and deoxyribose form ring
structures with four of their carbon atoms joined by an oxygen atom. The blue
boxes highlight the difference between the two sugars. Ribose has a hydroxyl
group (—OH), whereas deoxyribose has only a hydrogen atom at the same
carbon. Compared to ribose, deoxyribose is missing one oxygen atom.
Biochemistry
1.10 Nucleic Acids (cont.)
Four nitrogen bases that occur in nucleotides. Symbols are used to
represent the nucleotides adenine, guanine, cytosine, and thymine. Note that
cytosine and thymine have a single-ring structure; adenine and guanine have a
double ring.
Biochemistry
1.10 Nucleic Acids (cont.)
• Nucleic acids that contain ribose in their nucleotides
are called ribonucleic acids, or RNA.
• Nucleotides containing deoxyribose form
deoxyribonucleic acids, or DNA.
• In DNA, each of the four different nucleotides
contains a deoxyribose, a phosphate group, and one
of the four bases—adenine, thymine, guanine, or
cytosine—in a double-stranded helix.
Biochemistry
1.10 Nucleic Acids (cont.)
The components of DNA. Each nucleotide contains one of the bases, one
sugar, and one phosphate group. The sugar is deoxyribose, making these the
four nucleotides of DNA.
Biochemistry
1.10 Nucleic Acids (cont.)
• RNA is a nucleic acid much like DNA, except:
– it contains the sugar
ribose instead
of deoxyribose
– the nitrogen base
uracil replaces the
base thymine
– it is single stranded,
although it can fold
into complex shapes
Genetic Coding in Cells
1.11 The Double Helix
• In 1953, James Watson and Francis Crick proposed
a model for the structure of the DNA molecule that is
still accepted today (with some modification).
• Their model was based
on the principle that
hydrogen bonds form
only between the
nucleotide bases of
adenine (A) and thymine
(T) or cytosine (C) and
guanine (G).
Genetic Coding in Cells
A diagram showing the
pairing of two nitrogen bases.
Hydrogen bonds connect
cytosine to guanine and
thymine to adenine.
Genetic Coding in Cells
1.11 The Double Helix (cont.)
• Experiments done by Rosalind Franklin in the
laboratory of Maurice Wilkins suggested to
Watson and Crick that DNA molecules have a
double-helix structure.
Rosalind Franklin
Maurice Wilkins
Genetic Coding in Cells
1.11 The Double Helix (cont.)
• The DNA double helix is composed of two long
chains of nucleotides connected between their
deoxyribose sugars by phosphate groups.
• The two chains are connected by hydrogen bonding
between nitrogen bases to form a long doublestranded molecule.
• Because of the specific pairing between bases, each
strand is the complement of the other.
• The two strands intertwine, forming a double helix
that winds around a central axis.
The structure of DNA
Genetic Coding in Cells
1.11 The Double Helix (cont.)
• The folds in RNA are held together by the same type
of base pairing as in DNA.
Most of the RNA molecule is
single stranded, but the
shaded region shows
hydrogen bonding between
base pairs, which forms a
double-stranded region.
Note the four bases in RNA.
Genetic Coding in Cells
1.12 The Functions of DNA
• DNA forms the genes, units of genetic information,
that pass from parent to offspring.
• The structure of DNA explains how DNA functions as
the molecule of genetic information.
• DNA stores information in a code consisting of units
that are three nucleotides long called triplet codons.
Genetic Coding in Cells
1.12 The Functions of DNA (cont.)
• Certain codons are translated by the cell to mean
certain amino acids allowing the sequence of
nucleotides in DNA to indicate a sequence of amino
acids in protein.
• The sequence of amino acids in a protein determines
its shape, which then determines function.
• The structure of DNA also accounts for its ability to
be copied and passed through inheritance from one
generation to the next.
This concept map
summarizes the major
cellular processes that
involve DNA. Note that
both the information
stored in the structure of
DNA and the copying of
that information during
DNA synthesis have
important effects on the
life of a cell.
Summary
• Cells, the basic units of life, carry out their biological functions
through chemical reactions which occur continuously.
• Elements are the basic chemical form of matter and cannot
break down into substances with new or different properties.
• Atoms contain a characteristic number of positively charged
protons, negatively charged electrons, and neutral neutrons.
• Ions are atoms or molecules that have gained or lost
electrons; ions have a positive or negative charge.
• Chemical bonds hold atoms together to form molecules.
There are two types of chemical bonds, ionic and covalent.
• Weak bonds involving a partially positive hydrogen atom are
called hydrogen bonds.
Summary (cont.)
• In chemical reactions, molecules interact and form different
substances.
• The membranes that surround cells enclose the chemical
reactions of the cells and isolate them from the outside
environment.
• Organisms contain four major types of macromolecules:
Carbohydrates, Lipids, Proteins, and Nucleic Acids.
• Chemical compounds have biological activity because of their
specific chemical structures. Chemical structure dictates
biological function.
Reviewing Key Terms
Match the term on the left with the correct description.
___
lipids
d
___
proteins
b
___
elements
e
___
carbohydrate
a
___
basic
c
a. an organic compound that
contains hydrogen and oxygen
atoms in a 2:1 ratio
b. an organic compound composed
of one or more polypeptide chains
of amino acids
c. pH value reflecting more dissolved
hydroxide ions than hydrogen ions
d. a fatlike compound that usually
has fatty acids in its molecular
structure
e. a substance composed of atoms
that are chemically identical
Reviewing Ideas
1. Why is the polar nature of water biologically
significant?
Most cells and tissues contain large amounts of
water. Molecules must dissolve in water in order
to move easily in and between living cells. Polar
molecules, such as sugar, and ions, such as
Na+, dissolve in water because of the electric
attraction between them and the water
molecules. Nonpolar molecules, such as fats
and oils, do not dissolve in water.
Reviewing Ideas
2. Describe the differences in composition and
structure between RNA and DNA.
RNA is a nucleic acid much like DNA, except that
it contains the sugar ribose instead of
deoxyribose. Also, in RNA the nitrogen base
uracil replaces the base thymine. Structurally,
DNA always occurs in cells as a double-stranded
helix; RNA is single stranded, although it can fold
into complex shapes.
Using Concepts
3. What properties of phospholipids makes them
useful in cellular membranes?
The polar phosphate group of a phospholipid
allows one end of the lipid molecule to associate
with water while the nonpolar end is hydrophobic.
Using Concepts
4. Why is the complimentary structure of a DNA
molecule important in passing genetic
information from parent to offspring?
Complementarity is the basis for copying DNA.
Synthesize
5. What effect could rainfall with a pH of 3.5 have
on a lake ecosystem?
Normal rainwater has a pH of 5.5–6.0. Highly
acidic rainfall could cause the pH level in the
lake to fall causing the decline of organisms that
are adapted to the previous pH level. Organisms
that thrive in lower pH levels could become the
dominant life forms in the ecosystem.
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Chapter Animations
Models of chemical reactions
Formation of a polypeptide
The structure of DNA
Models of chemical reactions
Formation of a polypeptide
The structure of DNA
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