LECTURE I

SZL 311: Molecular Biology I

Course outline
2
SZL 311: MOLECULAR BIOLOGY 1


Essential techniques in molecular Biology: Safety in the molecular biology
laboratory. Macromolecules; techniques for purifying and characterizing
proteins. Nucleic acids: DNA, RNA; genomic and non-genomic nucleic acids:
nuclei acid. Karyotin and eukaryotic chromosome structure; bacteria and
bacteriophages. Recombinant DNA technology: extraction of DNA, digestion of
DNA with restriction animals. DNA cloning with plasmid and lambda phage
vectors; other vectors; construction of genomic and
C
DNA libraries.
Transformation. Applications of molecular biology: to the study of human
diseases ( microbial, genetic and neoplastic disorders) and of animal diseases.
MACROMOLECULES
.
MACROMOLECULES
What is a molecule?
A group of two or more atoms held
together by covalent bonds
Ex: H
2
O, Glucose,

What is a macromolecule?
A very large molecule made up of
repeating molecules or subunits
(monomers) linked (polymerized)
together to make a polymer.

Polymer is a long molecule
consisting of many similar
building blocks referred to as
monomers




.
Synthesis & Breakdown of Polymers
Dehydration synthesis: is an
anabolic process by which two
molecules are chemically bonded
through the use of enzymes and a
loss of water. Example: glucose +
glucose = maltose + water.


Hydrolysis: is a catabolic process by
which the bond between monomers
are broken by the enzyme and the
addition of water. Example: Sucrose +
water = glucose + fructose.






Classification of Macromolecules
.
.
Carbohydrates
Nucleic Acids Proteins
Lipids
CARBOHYDRATES
Monosaccharide: one sugar unit (monomer), contain formula
CH
2
O

Examples: glucose
deoxyribose
ribose
Fructose
Galactose



Carbohydrates are sugars
There are 3 levels of carbohydrate complexity:
Monosacharides
Dissacharides
Polysacharides
Use: Main fuel for cells
Monosaccharides that are left unused become linked by dehydration
synthesis to form disaccharides & polysaccharides.
Monosaccharide
Monosaccharide: one sugar unit (monomer), contain formula
CH
2
O
Monosaccharides are classified by

The location of the carbonyl group (as aldose or ketose)

The number of carbons in the carbon skeleton

Examples: glucose (most abudant)
deoxyribose
ribose
Fructose
Galactose etc
Use: -Main fuel for cells
-Raw materials for building blocks (Monosaccharides that are left
unused become linked by dehydration synthesis to form disaccharides
& polysaccharides.

Disaccharide
Disaccharide: two monosaccharides joined together
through a dehydration reaction (polymer), contain
formula CH
2
O. The monosaccharides are joined via a
glycosidic bond.

These are double sugars with the formula C
12
H
22
O
11
.
(Notice that one molecule of water is missing from the formula).


Examples: Sucrose = glucose + fructose.
Maltose = glucose + glucose,
Lactose = glucose + galactose.

Use: - Provide fuel after hydrolysis





Polysaccharide
Polysaccharides: the polymers of hundreds to thousands of sugars.

The structure and function of a polysaccharide are determined by its sugar
monomers and the positions of glycosidic linkages

The basic formula is ( C
6
H
10
O
5
)
n
. These are macromolecules capable of acting as
structural or storage molecules

Storage polysaccharides
Starch: a storage polysaccharide of plants, consists entirely of glucose monomers
linked via a 14 glycosidic bond. Plants store surplus starch as granules within
chloroplasts and other plastids. Two forms of starch exist: Amylose (linear) and
Amylopectin (branched)

Glycogen is a storage polysaccharide in animals, consists entirely of glucose
monomers linked via a 14 glycosidic bond . Humans and other vertebrates
store glycogen mainly in liver and muscle cells


Structural Polysaccharides
Cellulose: Is a major component of the tough wall of plant cells. It is a
polymer of glucose with a b 14 linkage of glucose monomers.

Chitin: Found in the exoskeleton of arthropods
Chitin also provides structural support for the cell walls of many fungi Chitin
is used to make a strong and flexible surgical thread that decomposes
after the wound or incision heals.








LIPIDS
Lipids are macromolecules that ARE NOT polymers
Lipids are mostly hydrocarbons and, therefore, are hydrophobic


Functions of lipids:
1. Long term energy storage (adipose tissue)
2. Protection against heat loss (insulation)
3. Protection against physical shock
4. Protection against water loss
5. Chemical messengers (hormones)
6. Major component of membranes (phospholipids)

Biologically important Lipids : Fats
Phospholipids
Steroids






Hydro=
Water
Phobic=feari
ng
FATS
(a) Saturated fat
(b) Unsaturated fat
Structural
formula of a
saturated fat
molecule
Space-filling
model of stearic
acid, a saturated
fatty acid
Structural
formula of an
unsaturated fat
molecule
Space-filling model
of oleic acid, an
unsaturated fatty
acid
Cis double bond
causes bending.
Each molecule is made of 1 glycerol & 3 fatty acids, Bonds form by dehydration synthesis
Saturated fat = no double bonds between in fatty acid chain (mainly warm blooded animals)
Unsaturated fat = 1 or more double bonds between in fatty acid chain (mainly Fish & Plants)
The fat molecules in animals are stored in adipose Tissues

PHOSHOLIPIDS
Charged
phosphate group
makes the head
hydrophilic
composed of: two fatty acids and a phosphate group are attached to glycerol
The two fatty acid tails are hydrophobic, but the phosphate group and its
attachments form a hydrophilic head
Phospholipids are the major component of all cell membranes
Hydrophilic
head
Hydrophobic
tail
WATER
WATER
Bilayer
STEROIDS
Steroids: Lipids characterized by a carbon skeleton consisting of four fused rings.
Cholesterol is a major component of animal cell membranes
Many sex hormones are made from cholesterol
Although cholesterol is essential in animals, high levels in the blood may contribute to
cardiovascular disease



This functional
group makes this
molecule
cholesterol.






PROTEINS
This macromolecule that comprise >50% of the Dry Weight of Most
Cells.

Proteins are made of a monomer of amino acids which are held
together by peptide bonds which are formed by a dehydration
reaction resulting in a polypeptide chain.

Each of the 20 different amino acids has a different R group which
gives it its unique characteristics

When a polypeptide chain folds it forms the functional
macromolecule called the PROTEIN













Genetic code
The start codon is AUG. Methionine is the only amino acid specified by just one codon, AUG. The
stop codons are UAA, UAG, and UGA. They encode no amino acid. The ribosome pauses and falls
off the mRNA.
The stretch of codons between AUG and a stop codon is called an open reading frame (ORF).
The code defines how sequences of these nucleotide triplets,
called codons, specify which amino acid will be added during
protein synthesis.
Classification of amino acids
.
.
19
Levels of protein structure
.
.
Secondary
structure
Tertiary
structure
Quaternary
structure
Hydrogen bond
a helix
b pleated sheet
b strand
Hydrogen
bond
Primary
structure
Primary Structure: a proteins
unique, linear sequence of
amino acids which is
determined by genetic
information
Secondary Structure: the
result of H-bonding between
partially negative oxygen &
nitrogen of the polypeptide
backbone and hydrogen on
the backbone ( a helix and b
sheets)
Tertiary structure:
the overall
shape of the
polypeptide
resulting from
interactions
between R-
groups of
amino acids.
Quaternary
structure: forms
when two or more
polypeptide chains
aggregate to
make one
molecule
Function of proteins
.
.
Enzymatic proteins Defensive proteins
Storage proteins Transport proteins
Enzyme
Virus
Antibodies
Bacterium
Ovalbumin Amino acids
for embryo
Transport
protein
Cell membrane
Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
Function: Storage of amino acids Function: Transport of substances
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.
Function of Proteins (2)
.
.
Hormonal proteins
Function: Coordination of an organisms activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
High
blood sugar
Normal
blood sugar
Insulin
secreted
Signaling
molecules
Receptor
protein
Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.
Muscle tissue
Actin Myosin
Collagen
Connective
tissue
Contractile and motor proteins
Function: Movement
Examples: Motor proteins are responsible for the
undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of
muscles.
Structural proteins
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.
NUCLEIC ACIDS
Nucleic Acids: Complex macromolecule that stores
information in cells important for heredity. Nucleic
acids are polymers made of smaller subunits called
nucleotides.

Two types Nucleic acids exist:
DNA = Deoxyribonucleic acid
RNA = Ribonucleic acid











.
Flow of genetic information:
DNA RNA Protein
Synthesis of
mRNA
mRNA
DNA
NUCLEUS
CYTOPLASM
mRNA
Ribosome
Amino
acids Polypeptide
Movement of
mRNA into
cytoplasm
Synthesis
of protein
2
3
Nucleic Acid Structure
.
Nucleic acids are polymers
of nucleotides.
Each nucleotide has 3
parts: 5-carbon sugar,
phosphate group, & a
nitrogenous base

DNA
Purines = Adenine, Guanine
Pyrimidines= Cytosine, Thymine

RNA
Purines = Adenine, Guanine
pyrmidines= Cytosine , Uracil
DNA double helix
Phosphodiester
bond

Adenine pairs with Thymine while Cytosine pairs with
Guanine on the double helix. The two strands of the
double helix are antiparallel, running in the 5-3 direction

.
.