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Chapter 3
Carbon Molecules in Cells
The Molecules of Life—From Structure to Function
A. General
1. Only living cells can synthesize carbohydrates,
lipids, proteins, and nucleic acids.
2. These molecules are organic compounds consisting
of carbon and one or more additional elements (at
least one hydrogen), covalently bonded to one another
Organic Compounds
1. Carbon atoms nearly always form covalent bonds
2. Carbon atoms can bond to each other to form straight
chains, branched chains and rings
3. since carbon can form up to 4 single bonds, there are a
wide variety of compounds it can form
4. chemists group organic compounds into classes with
similar characteristics to make their study easier
Hydrocarbons - the simplest class of organic compounds contain
only hydrogen and carbon
a. they are broken down into three groups based on the types of
bonding between the carbon atoms
i. the alkanes are composed of only single bonds between
the carbons
- alkanes are also classified as “saturated
hydrocarbons”, this means that they are composed
of all single bonds
ii. the alkenes contain at least one double bond between
carbons
iii. the alkynes contain at least one triple bond between
carbons
-. Alkenes and alkynes “unsaturated compounds”
because their carbons do not have all single bonds
5. Carbon Atoms can Form Rings
a. One class of ring hydrocarbons
i. Aromatic Hydrocarbons
6. Isomers
a. isomers are compounds with the same chemical
formulas but different structures and properties (ex’s. C4H10O is the formula for 2 isomers; 1-butanol
and 2-methyl-1-propanol)
b. different isomers have different properties
C. Naming organic compounds
1. the compound name is chosen from a stem that reflects the
number of carbons present
a. the stems are:
1carbon – Meth, 2carbons – Eth,
3carbons – Prop, 4carbons – But,
5carbons – Pent, 6carbons – Hex,
7carbons – Hept, 8carbons – Oct,
9 carbons – Non, 10carbons – Dec
2. a suffix is then added to indicate how the carbon atoms are
linked to each other
a. the endings can be determined by the class of the
compound
-alkanes – “ane”, alkenes – “ene”,
alkynes – “yne”, alcohols – “anol”, etc.
3. a prefix can then be added to show if the carbon atoms are
arranged in a ring – “cyclo”
4. We name long chain alkenes and alkynes by indicating the
location of the double or triple bond within the molecule
a. number the carbon atoms so the first carbon atom
in the double bond has the lowest number
b. if there is more than one multiple bond, number
the position of each multiple bond and use a prefix to
indicate the number of multiple bonds
5. Naming Branched Hydrocarbons
a. first, determine the number of carbons in the
longest chain and pick the corresponding
stem
b. next, number the carbon atoms on that chain so
that any branches have the lowest number possible
c. name the attached group (CH3 is called methyl – it
is the one we will use)
d. if more than one group is attached, the position of
each group should be given
i. if the same group is attached more than once,
a prefix is used to tell how many
(3,3-dimethylpentane)
6. Names of compounds reflect functional groups
a. Functional groups are atoms or groups of atoms
covalently bonded to a carbon backbone; they convey
distinct properties, such as solubility and chemical
reactivity, to the complete molecule.
b. The common functional groups in biological
molecules are: hydroxyl, methyl, carbonyl, carboxyl,
amino, phosphate, and sulfhydryl
c. see figure 3.5, page 38
d. when necessary, the position of the functional
group is noted by counting the carbon number it is on
7. Many biological molecules have “common” names
CARBOXYL
HYDROXYL
(alcohol)
METHYL
(nonionized;
—COOH)
(ionized;
—COO–)
(nonionized;
—NH2)
(ionized;
—+NH3)
AMINO
CH3
CARBONYL
(aldehyde;
—CHO)
PHOSPHATE
(ketone;
=CO)
Sulfhydryl -SH
(icon for
phosphate
group)
Examples of Functional Groups
Methyl group
- CH3
Hydroxyl group
- OH
Amino group
- NH3+
Carbonyl group
-CHO
Carboxyl group
- COOH
Phosphate group
- PO3-
Sulfhydryl group
- SH
D. Representing Organic Molecules
1. chemical formulas – show numbers of atoms in the molecule,
but does not show the bonds, sizes of atoms or shape of the
molecule
2. structural formulas – shows arrangement of all atoms and
bonds in the molecule, but not the actual shape of the molecule or
sizes of atoms and larger molecules can be difficult to draw
3. skeletal structure – simply shows arrangement of carbon
atoms, does not show actual shape of molecule, or atom sizes and
it does not show all atoms or bonds
4. space filling model – shows three dimensional shape of
molecule and most of the space taken by electrons (relative size),
but uses false colors to differentiate between atoms, bonds are not
clearly shown and parts of large molecules may be hidden
5. A ball-and-stick model depicts bonding of atoms; space-filling
models convey a molecule's size and surfaces.
6. Larger molecules are best visualized using ribbon models, such
as those generated by computer programs.
H
H
C
H
Ball-and-stick model
H
Structural formula
Space-filling model
Chapter 5
Biological Molecules
How Do Cells Build Organic Compounds?
A. Four Families of Building Blocks
1. Simple sugars, fatty acids, amino acids, and
nucleotides are the four major families of small
building blocks (monomers – single units).
2. Monomers can be joined to form larger polymers.
3. simple sugars = carbohydrate monomers
fatty acids = lipid monomers
amino acids = protein monomers
nucleotides = nucleic acid monomers
B. Five Categories of Reactions
1. Enzymes are a special class of proteins that mediate five
categories of reactions:
a. functional-group transfer from one molecule to
another
b. electron transfer —stripped from one molecule
and given to another
c. rearrangement of internal bonds converts one type
of organic molecule to another
d. condensation (also known as dehydration) makes
two molecules into one by removing a water
e. cleavage (or hydrolysis) breaking one molecule into
two by adding a water.
2. In a condensation reaction, one molecule is stripped of its
H+, another is stripped of its OH–; then the two molecule
fragments join to form a new compound and the H+ and OH–
form water.
3. Hydrolysis (a type of cleavage reaction) is the reverse: one
molecule is split by the addition of H+ and OH– (from water)
to the components.
Carbohydrates—The Most Abundant Molecules of Life
-3 main types (mono, oligo, poly)
-Used in cells for structural materials, transportable forms of
energy and energy storage
A. The Simple Sugars (C, H, O usually in a 1:2:1 ratio)
1. Monosaccharides—one sugar unit—are the
simplest carbohydrates.
2. They are characterized by solubility in water, sweet
taste, and several —OH groups.
3. Ribose and deoxyribose (five-carbon backbones)
are building blocks for nucleic acids.
4. Glucose and fructose (six-carbon backbones) are
used in assembling larger carbohydrates.
5. Other important molecules derived from sugar
monomers include glycerol and vitamin C
Structure of glucose
Structure of fructose
Short-Chain Carbohydrates
1. An oligosaccharide is a short chain of two or more
sugar monomers.
2. Disaccharides—two sugar units—are the simplest
oligosaccharides.
a. Lactose (glucose + galactose) is present in
milk.
b. Sucrose (glucose + fructose) is a transport
form of sugar used by plants and harvested by
humans for use in food.
c. Maltose (two glucose units) is present in
germinating seeds.
3. Oligosaccharides with three or more sugar
monomers are attached as short side chains to proteins
where they participate in membrane function.
fructose
glucose
+ H2O
Sucrose - disaccharide
Complex Carbohydrates
1. A polysaccharide is a straight or branched chain of
hundreds or thousands of sugar monomers.
2. Starch is a plant storage form of energy, arranged
as unbranched coiled chains, easily hydrolyzed to
glucose units.
3. Cellulose is a fiberlike structural material—tough,
insoluble—used in plant cell walls.
4. Glycogen is a highly-branched chain used by
animals to store energy in muscles and liver.
5. Chitin is a specialized polysaccharide with nitrogen
attached to the glucose units; it is used as a structural
material in arthropod exoskeletons and fungal cell
walls.
Cellulose chains
Starch chain
Greasy, Oily—Must Be Lipids
-nonpolar, hydrophobic; used in cells for energy storage,
structural materials, signaling molecules
A. Lipids are greasy or oily compounds with little
tendency to dissolve in water.
1. They can be broken down by hydrolysis
reactions.
2. They function in energy storage, membrane
structure, and coatings.
Fats and Fatty Acids
1. A fatty acid is a long chain of mostly carbon and hydrogen
atoms with a —COOH (carboxyl) group at one end.
2. When they are part of complex lipids, the fatty acids
resemble long, flexible tails.
A. Unsaturated fats are liquids (oils) at room
temperature because one or more double bonds
between the carbons in the fatty acids permits
“kinks” in the tails.
B. Saturated fats (triglycerides) have only single
C—C bonds in their fatty acid tails and are
solids at room temperature.
stearic acid
oleic acid
linolenic acid
Fats are formed by the attachment of one (mono-), two (di-),
or three (tri-) fatty acids to a glycerol.
A. They are a rich source of energy, yielding more
than twice the energy per weight basis as
carbohydrates.
B. They are also provide an insulation blanket for
animals that must endure cold, harsh temperatures.
C. ex. Triglycerides (3 f.a. tails)
D. body’s main energy reservoir
glycerol
+ 3H20
three fatty-acid tails
triglyceride
C. Phospholipids
1. These are formed by attachment of two fatty acids plus a
phosphate group to a glycerol.
2. They are the main structural material of membranes where
they arrange in bilayers.
hydrophi
lic
head
two hydrophobic
tails
D. Sterols and Their Derivatives
1. Sterols have a backbone of four carbon rings but no fatty acid
tails.
2. Cholesterol is a component of cell membranes in animals and
can be modified to form sex hormones (testosterone and
estrogen) and vitamin D.
3. steroids, hormones, bile salts
Sterol backbone
Cholesterol
E. Waxes
1. They are formed by attachment of long-chain fatty acids to
long-chain alcohols or carbon rings.
2. They serve as coatings for plant parts and as animal coverings.
A String of Amino Acids: Protein Primary Structure
-most diverse type of biological molecules
A. Proteins function as enzymes, in cell movements, as
storage and transport agents, as hormones, as antibodies,
and as structural material.
B. Amino Acid Structure
1. Amino acids are small organic
molecules with an amino group,
a carboxyl group, and one of
twenty varying R groups.
2. All of the parts of an amino
acid molecule are covalently
Carboxyl
group
bonded to a central carbon atom.
Amino
group
3. see figure 3.17, page 44
R group
Protein Synthesis
• Peptide bond
– Condensation reaction links amino group of
one amino acid with carboxyl group of next
Water forms as a by-product
Polypeptide Chain Formation
1. Primary structure is defined as ordered sequences of amino
acids each linked together by peptide bonds to form polypeptide
chains.
2. There are 20 kinds of amino acids available in nature.
3. The sequence of the amino acids is determined by DNA and is
unique for each kind of protein.
A. shape and function arise from the primary structure
B. Fibrous proteins have polypeptide chains organized as
strands or sheets; they contribute to the shape, internal
organization, and movement of cells.
C. Globular proteins, including most enzymes, have their
chains folded into compact, rounded shapes.
How Does a Protein's Final Structure Emerge?
A. Second and Third Levels of Protein Structure
1. Secondary structure refers to the helical coil (as in
hemoglobin) or sheetlike array (as in silk) that results
from hydrogen bonding of side groups on the amino
acid chains.
2. Tertiary structure is the result of folding due to
interactions among R groups along the polypeptide
chain.
a. adjacent helixes and sheets pack together in
structurally stable units called domains
B. Chaperonins are proteins that help other proteins fold
correctly
Fourth Level of Protein Structure
1. Quaternary structure describes the complexing of two or
more polypeptide chains.
2. Hemoglobin is a good example of four interacting chains
that form a globular proteins; keratin and collagen are
complex fibrous proteins.
3. Glycoproteins consist of oligosaccharides covalently
bonded to proteins; they are abundant on the exterior of
animal cells, as cell products, and in the blood.
4. Lipoproteins have both lipid and protein components; they
transport fats and cholesterol in the blood.
Peptide
group
Tertiary
structure
quaternary structure
Secondary
structure
Denaturation—How to Undo the Structure
1. High temperatures or changes in pH can cause a loss of a
protein’s normal three-dimensional shape (denaturation).
2. Normal functioning is lost upon denaturation, which is
often irreversible (for example, a cooked egg).
Why Is Protein Structure So Important?
A. Just One Wrong Amino Acid...
1. Alteration of a cell's DNA can result in the wrong
amino acid insertion in a polypeptide chain.
2. If valine is substituted for glutamate in hemoglobin,
the result is called HbS.
B. Sickle-Shaped Cells and a Serious Disorder
1. Persons who inherit two mutated genes for the beta
chain of hemoglobin can only make HbS.
2. The altered hemoglobin causes the red blood cells
to be misshapen—sickle-cell anemia, with many
serious body dysfunctions.
Nucleotides and Nucleic Acids
A. The Diverse Roles of Nucleotides
1. Each nucleotide consists of a five-carbon sugar
(ribose or deoxyribose), a nitrogen-containing base,
and a phosphate group.
a. Adenosine phosphates are chemical
messengers (cAMP) or energy carriers (ATP).
b. Nucleotide coenzymes transport hydrogen
atoms and electrons (examples: NAD+ and
FAD).
2. Nucleotides also serve as building blocks for nucleic
acids (DNA & RNA).
Regarding DNA and the RNAs
1. Nucleic acids are polymers of nucleotides.
A. Four different kinds of nucleotides are strung
together to form large single or double-stranded
molecules.
B. Each strand's backbone consists of joined sugars
and phosphates with nucleotide bases projecting
toward the interior from the sugars.
Phosphate
Sugar
Nitrogenous
base
Single strand of DNA or RNA
phosphate
connected by
covalent bond
sugar
base
The two most important nucleic acids are DNA and RNA.
A. DNA is a double-stranded helix carrying encoded
hereditary instructions.
1. deoxyribose
2. A to T, C to G
B. RNA is single stranded and functions in translating the
code to build proteins.
1. ribose
2. Uracil (U) in place of Thymine (T)