General Biology

Bio 110

Chapter 3
CONTENTS

Part 1 Life on Earth: An Overview Chapter 1

PART II Chemistry of Life
a. Basic Chemistry Chapter 2

b. Chemistry of Organic Molecules Chapter 3

PART III The Cell
a. Cell Structure and Function Chapter 4
b. Membrane Structure and Function Chapter 5
 Part II

CHEMISTRY OF LIFE
b. Chemistry of Organic Molecules
3.1 Organic Molecules
 Chemistry is divided into organic chemistry, the chemistry of
organisms and inorganic chemistry, the chemistry of the non-
living world.
 Organic molecules should contain both carbon and hydrogen
atoms (Table 3.1).
 Classes of organic
compound(biomolecules):
 Carbohydrates.
 Proteins
 Lipids
 Nucleic acids

• A bacterial cell contains 5,000

different organic molecules and a
plant or animal cell has twice that
number.
 3.1 Organic Molecules
a. The Carbon Atom:
 Carbon has a total of six electrons: two electrons in the first shell and
four electrons in the outer shell.
 In order to acquire four electrons to complete its outer shell, a carbon
atom almost always shares electrons with CHNOPS, the elements that
make up most of the weight of living things.
 Methane ( CH4) is one of the simplest organic compounds.
 Four covalent bonds link four hydrogen atoms to the carbon atom.
 Each of the four lines in the formula for Methane represents a pair of
shared electrons
 3.1 Organic Molecules

 Carbon can share electrons with another

carbon atom. The C-C bond is quite
stable, and the result is carbon chains
that can be quite long.
 Branching at any carbon atom is
possible and hydrocarbon can turn back
on itself to form a ring compound.
 Carbon can form double bonds with itself
and other atoms. In acetylene, H-C≡C-H,
carbon is also capable of forming a triple
bond with itself.
 Organic molecules containing carboxyl
(acidic) groups (‒COOH) are highly
polar.
3.1 Organic Molecules:
b. The Biomolecules of Cells:
 Certain foods are rich in biomolecules.
 Ex., bread is rich in carbohydrate and meat is rich in protein.
 When you digest food, it gets broken down into smaller
molecules; digestion of bread releases glucose AND digestion of
meat releases amino acids. Your body then takes these subunits
and make up your cells. Table 3.2

Biomolecules

Category Example Subunit

Carbohydrate Polysaccharide Monosaccharide
Lipids Fat Glycerol and fatty acid
Proteins Polypeptide Amino acid
Nucleic Acids DNA, RNA Nucleotide
3.1 Organic Molecules:

c. Synthesis and Degradation:

 Synthesis: A cell uses a
condensation (or dehydration)
reaction to synthesize (build up) any
type of biomolecule, where a water
molecule; OH (hydroxyl group) and H
(hydrogen atom), is removed as
subunits are joined (Figure 3.1a).
 Degradation :To break down
biomolecules, a cell uses an opposite
type of reaction; namely hydrolysis,
where OH group from water attaches
to one subunit and H from water
attaches to the other subunit (Figure
3.1b).
Figure 3.1 Synthesis and dehydration of
 Enzymes are required for cells to biomolecules.
carry out dehydration and hydrolysis
reactions.
 3.1 Organic Molecules:
c. Synthesis and Degradation
(continued):
 An enzyme is a molecule that
speeds a reaction by bringing
reactants together.
 Enzymes participate in the
reaction, but it is unchanged by it.
 Polymers are the largest of the
biomolecules constructed by
linking together a large number of
the same type of subunit; called
monomer.
 Ex., Polysaccharide, protein
and nucleic acid are polymers
that contain many monomers, Figure 3.1 Synthesis and dehydration of
i.e., monosaccharides, amino biomolecules.
acids and nucleotides,
respectively.
 Part IIb

3.2 Carbohydrates
 3.2 Carbohydrates

 The term carbohydrate includes single or a chain of sugars.

 Carbohydrates are immediate energy source in living things and
play structural roles in a variety of organisms.
 The majority of carbohydrates have a carbon to hydrogen to
oxygen ratio of 1:2:1.
a. Monosaccharides: Ready Energy
 Monosaccharide is a single sugar molecule with a carbon backbone
of three to seven carbons.
 The molecular formula for a simple
sugar is a multiple of CH2O.
 As sugars have many hydroxyl groups,
their polar functional group makes them
soluble in water.
 Glucose (Figure 3.2), with six carbon
atoms, is a hexose with a molecular
formula of C6H12O6. Figure 3.2 Glucose.
3.2 Carbohydrates

a. Monosaccharides: Ready Energy (continued)

 Glucose functions:
 major source of cellular fuel for all living things.
 transports in the blood of animals.
 broken down in nearly all types of organisms during cellular
respiration, with the resulting buildup of ATP molecules.
 Ribose and deoxyribose are pentoses, with five carbon atoms,
that are found in the nucleic acids RNA and DNA, respectively.

Figure 3.2 Glucose.

 3.2 Carbohydrates

b. Disaccharides: Varied Uses

 They contain two monosaccharides joined during a dehydration

reaction.
 Figure 3.3 shows how disaccharide maltose (an ingredient used in
brewing) arises.
 Sucrose, a disaccharide used at home to sweeten food, is glucose
combined with fructose.
 We acquire sucrose from sugarcane and sugar beets.
 Lactose, a disaccharide found in milk, is glucose combined with
galactose. Individuals that are lactose intolerant cannot break this
disaccharide down and have subsequent medical problems.

Figure 3.3 Synthesis and degradation of maltose; a disaccharide.

3.2 Carbohydrates

c. Polysaccharides- Energy Storage Molecules:

 Polysaccharides is polymers of monosaccharides.

 When an organism requires energy, the polysaccharide is
broken down to release sugar molecules.
 Plants store glucose as starch (non-branched or branched,
Figure 3.4a), while animals store glucose as glycogen (highly
branched, Figure 3.4b).

Figure 3.4a Starch structure.

3.2 Carbohydrates

c. Polysaccharides- Energy Storage Molecules (cont.):

 After we eat, the release of the hormone insulin from the
pancreas promotes the storage of glucose as glycogen.
 Polysaccharides serve as storage molecules because they are
larger than a sugar and not as soluble in water, therefore, cannot
easily pass through the plasma membrane.

Figure 3.4b Glycogen structure.

 3.2 Carbohydrates

d. Polysaccharides- Structural Molecules:

 Structural polysaccharides include cellulose in plants, chitin in
animals and fungi and peptidoglycan in bacteria. In all three,
monomers are joined by the type of bond shown for cellulose in
Figure 3.5.

Figure 3.5 Cellulose Fibers.

 3.2 Carbohydrates

d. Polysaccharides: Structural Molecules (cont.)

 The cellulose monomer is simply glucose, but in chitin, the
monomer has an attached amino group.
 The structure of peptidoglycan is even more complex because
each monomer also has an amino acid chain.
 Cellulose is the most abundant organic molecule on Earth. Wood,
a cellulose plant product, is used for construction and cotton is
used for cloth.
 Chitin, like cellulose, cannot be digested by animals.
 Seeds are coated with chitin, and this protects them from attack
by soil fungi.
 Because chitin also has antibacterial and antiviral properties, it is
processed and used in medicine as a wound dressing material
and is useful in cosmetics.
Part Iib

3.3 Lipids
 3.3 Lipids
 Lipids are insoluble in water due to their hydrocarbon chains (Table
3.3), where hydrogen bonded only to carbon has no tendency to
form a bond with water molecules.
 Fat is used for both insulation and long-term energy storage by
animals, while plants use oil, instead.
 Phospholipids and steroids serve as major components of the
plasma membrane in cells.
a. Triglycerides: Long-Term Energy
Storage
 Fats and oils contain two types
of subunit molecules; fatty acids
and glycerol.
 Fatty acid consists of a long
(16-18 atoms) hydrocarbon
chain with a ‒COOH (carboxyl)
group at one end.
3.3 LIPIDS:
a. Triglycerides: Long-Term Energy Storage (continued):

 Fatty acids are either saturated or unsaturated. Saturated fatty acids

have no double bonds between the carbon atoms, while unsaturated
fatty acids have (C=C).
 Glycerol is a compound with three polar ‒OH groups, therefore, it is
soluble in water.
 During dehydration reaction to form a fat molecule, the acid portions
of three fatty acids react with the ‒OH groups of glycerol and three
molecules of water result (Figure 3.6).

Figure 3.6 Formation of a fat.

.
 3.3 LIPIDS
a. Triglycerides: Long-Term Energy Storage (cont.):
 During hydrolysis reaction, fats are degraded. Because there are three
fatty acids attached to each glycerol molecule, fats and oils are
sometimes called triglycerides. As triglycerides have many C‒H bonds,
they do not mix with water. Notice that unsaturated bond (C=C) melts at
lower temperature than those containing only saturated fatty acids.
 Fats are mostly of animal origin and oils are of plant origin.
 Diets high in animal fat are associated with circulatory disorders
because fatty material accumulates inside the blood vessels and blocks
blood flow.

Figure 3.6 Formation of a fat.

 3.3 LIPIDS:

a. Triglycerides: Long-Term Energy Storage (cont.)

 Butter, a fat that is solid at room temperature, contains

primarily saturated fatty acids, while corn oil, a liquid even
when placed in the refrigerator, contains primarily unsaturated
fatty acids (Figure 3.7).

Figure 3.7 Types of fatty acids and fats.

3.3 LIPIDS:
a. Triglycerides- Long-Term Energy Storage (cont.):

 This difference is useful to living things, ex., the feet of penguins

contain unsaturated triglycerides to help them protect exposed
parts from freezing.
3.3 LIPIDS :
b. Phospholipids- Membrane Components:
 A phospholipid is constructed like a fat, except that in place of
the third fatty acid attached to glycerol, there is a polar
phosphate group usually bonded to another organic group,
indicated by R (Figure 3.8).
 This portion of the molecule becomes the polar head
(hydrophilic), while the hydrocarbon chains of the fatty acids
become the non-polar tails (hydrophobic).

A kink causes fluidity of

plasma membrane

Figure 3.8 Phospholipid structure.

3.3 LIPIDS :-

b. Phospholipids: Membrane Components (continued):

 Therefore, when surrounded by water, phospholipids become a

bilayer (double layer) in which the hydrophilic heads project
outward and the hydrophobic tails project inward as in plasma
membrane (Figure 3.9).
 A plasma membrane is essential to the structure and function of a
cell.

Figure 3.9 Plasma membrane of a cell.

 3.3 LIPIDS
c. Steroids: Four Fused Rings:
 Each type of steroid differs primarily by the types of functional
groups attached to the carbon skeleton.
 Cholesterol (Figure 3.10) is essential component of an animal
cell’s plasma membrane and the precursor of several other
steroids, such as the hormones testosterone and estrogen.
 Cholesterol can also contribute to circulatory disorders.

 The presence of cholesterol encourages the

accumulation of fatty material inside the
lining of blood vessels and, therefore, high
blood pressure.

Figure 3.10 Cholesterol.

 Part II b

3.4 Proteins
3.4 Protein:

• Proteins are large biomolecules and

macromolecules that are comprise of one or
more amino acid residues.
 As much as 50% of the dry weight of most
cells are proteins.
 Presently, over 100,000 proteins have been
identified.
3.4 Proteins

Functions in animals:

 Metabolism: Enzymes bring reactants together and thereby

speed chemical reactions in cells.
 Support: Some proteins have a structural function; keratin
makes up hair and nails, while collagen lends support to
tendons and skin.
 Transport: Carrier proteins in the plasma membrane allow
substances to enter and exit cells. Also, hemoglobin transport
oxygen in the blood.
 Defense: Antibodies combine with foreign substances, called
antigens to prevent them from destroying cells.
 Regulation: Hormones serve as intercellular messengers that
influence the metabolism of cells; insulin regulates the
content of glucose in the blood.
 Motion: Actin and myosin allow parts of cells to move and
cause muscles to contract.
 3.4 Proteins

a. Amino Acids:
 Amino acid is the monomer of protein.
 The amino acid has three groups:
 ‒NH2 (amino group)
 ‒COOH (acid group
 R group for an amino acid

Besides, the central carbon atom in an amino acid bonds to a hydrogen

atom (‒H).
The 20 amino acids differ according to their R group, shaded in blue in
Figure 3.12. Some of which are shown in figure 13.12
b. Amino Acids:

Figure 3.12 Amino acids.

 a. Amino Acids: (cont.)

 The R group
 Range in complexity
from a single hydrogen
atom to a complicated
ring compound.
 Some are polar and
some are non-polar.
 The amino acid cysteine
has an R group that ends
with an ‒SH group, which
serves to connect one
chain of amino acids to
another by a disulfide
bond, ‒S‒S‒.

Figure 3.12 Amino acids.

3.4 Proteins:

a. Peptides:
 Proteins are polymers with amino acid monomers joined
together by a covalent bond called a peptide bond through
dehydration reaction between the carboxyl group of one and
the amino group of another (Figure 3.11).
 A peptide is two or more amino acids bonded together and a
polypeptide is a chain of many amino acids joined by peptide
bonds.
 A protein may contain more than one polypeptide chain, each
has its own sequence that influences the three-dimensional
shape of the protein.

Figure 3.11 Synthesis and degradation of a peptide.

 3.4 Proteins:-

c. Shape of Proteins:
 Protein has four levels of
structure.
 The primary structure is the
particular sequence of amino
acids.
 The secondary structure
occurs when the polypeptide
coils or folds (Figure 3.13)
resulting in an α (alpha) helix
or a pleated sheet called a β
(beta) sheet.
 Hydrogen bonding holds the
secondary structure.

Figure 3.13 Levels of protein organization.

 3.4 Proteins

c. Shape of Proteins:
 Hydrogen bonding between every fourth amino acid accounts for the
spiral shape of the α helix. In β sheet, the polypeptide turns back upon
itself.
 A tertiary structure is the folding that results in a three-dimensional shape
called globular protein. Bonds contribute to the tertiary structure are:
 Hydrogen bonds
 Ionic bonds
 Covalent bonds

Figure 3.13 Levels of protein organization.

3.4 Proteins

c. Shape of Proteins:
 Strong disulfide linkages in particular help maintain the tertiary shape.
 When a protein loses its natural shape, it is said to be denatured.
 Some globular proteins representing quaternary structure consist of
more than one polypeptide; hemoglobin consist of four polypeptides.
Each polypeptide in hemoglobin has a primary, secondary and tertiary
structure.

Figure 3.13 Levels of protein organization.

 Part IIb

3.5 Nucleic Acids

3.5 Nucleic Acids

 Nucleic acids are polymers of nucleotides:

 DNA (deoxyribonucleic acid) is the genetic material that
stores information regarding the order in which amino acids
are to be joined to make a protein.
 RNA (ribonucleic acid), three major types:
 Messenger RNA or mRNA
 Ribosome RNA or rRNA
 Transfer RNA or tRNA
 mRNA is an intermediary in the process of protein
synthesis, conveying information from DNA to a protein.
 Some nucleotides have independent metabolic functions in
cells; coenzymes, to facilitate enzymatic reactions, e.g., ATP
(adenosine triphosphate) supplies energy for energy-requiring
reactions.
3.5 Nucleic Acids
a. Structure of DNA and RNA
 Nucleotide; a complex of three types of molecules (Figure 3.14a)
contains:
 phosphorous (phosphoric acid)
 pentose sugar; deoxyribose for DNA and ribose for RNA (Figure
3.14b)
 nitrogenous base; pyrimidine or purine; single or double ring (Fig.
3.14c)

Figure 3.14 Nucleotides.

 3.5 Nucleic Acids:
a. Structure of DNA and RNA (cont.):

 In DNA, the pyrimidine base can be

cytosine (C) and thymine (T).
 In RNA, the pyrimidine bases are
cytosine (C) and uracil (U).
 In both DNA and RNA, the purine bases
are adenine (A) or guanine (G).
 The polynucleotide is a linear molecule
called a strand in which the backbone is
made up of a series of sugar-phosphate-
sugar-phosphate molecules.
 RNA is single-stranded, while DNA is
double-stranded, with the two strands
usually twisted about each other in the
form of a double helix (Figure 3.15a &
b). Figure 3.15 DNA structure.
.
3.5 Nucleic Acids:
a. Structure of DNA and RNA (cont.)

 The two strands are held together by hydrogen bonds between

pyrimidine and purine bases; thymine (T) is always paired with
adenine (A) and guanine (G) is always paired with cytosine (C).
 This is called complementary base pairing. Therefore, the number of
purine bases (A+G) always equals the number of
pyrimidine bases (T+C) (Figure 3.15c).

Figure 3.15 DNA structure.

 3.5 Nucleic Acids :

a. Structure of DNA and RNA (continued):

 Table 3.3summarizes the differences between DNA and RNA.
 3.5 Nucleic Acids
b. ATP (Adenosine Triphosphate):
 ATP is composed of adenine and ribose and triphosphate stands for
the three phosphate groups attached together and to ribose (Figure
3.16).
 ATP is a high-energy molecule. In cells, the terminal phosphate bond
is usually hydrolyzed to give the molecule ADP (adenosine
diphosphate) and a phosphate molecule.
 The energy that is released by ATP breakdown is coupled to energy-
requiring processes in cells, like muscle contraction and nerve
impulse conduction.

Figure 3.16 ATP and ADP.

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