LECTURE I

SZL 311: Molecular Biology I

Course outline

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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 CDNA libraries. Transformation. Applications of molecular biology: to the study of human diseases ( microbial, genetic and neoplastic disorders) and of animal diseases.

MACROMOLECULESMACROMOLECULES

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MACROMOLECULES

What is a molecule?A group of two or more atoms held

together by covalent bondsEx: H2O, 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

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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

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Carbohydrates

Nucleic AcidsProteins

Lipids

CARBOHYDRATES

Monosaccharide: one sugar unit (monomer), contain Monosaccharide: one sugar unit (monomer), contain formula CHformula CH22OO

Examples:Examples: glucose glucose deoxyribosedeoxyriboseriboseriboseFructoseFructoseGalactoseGalactose

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), Monosaccharide: one sugar unit (monomer), contain formula CHcontain formula CH22OO

Monosaccharides are classified by

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

The number of carbons in the carbon skeleton

Examples:Examples: glucose (most abudant)glucose (most abudant)deoxyribosedeoxyriboseriboseriboseFructoseFructose

Galactose etcGalactose etc

Use: 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 Disaccharide: two monosaccharides joined together through a dehydration reaction together through a dehydration reaction (polymer), contain formula CH(polymer), contain formula CH22O. The O. The monosaccharides are joined via a glycosidic monosaccharides are joined via a glycosidic bond.bond.

These are double sugars with the formula C12H22O11.

(Notice that one molecule of water is missing from the formula).

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

Use: Use: - - Provide Provide fuel after hydrolysis

Polysaccharide

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

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

The basic formula is ( C6H10O5)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 1→4 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 1→4 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 1–4 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:Functions of lipids:1.1. Long term energy storage (adipose tissue)Long term energy storage (adipose tissue)2.2. Protection against heat loss (insulation)Protection against heat loss (insulation)3.3. Protection against physical shockProtection against physical shock4.4. Protection against water lossProtection against water loss5.5. Chemical messengers (hormones)Chemical messengers (hormones)6.6. Major component of membranes (phospholipids)Major component of membranes (phospholipids)

Biologically important Lipids : Fats

Phospholipids

Steroids

Hydro= Water

Phobic=fearing

FATS

(a) Saturated fat (b) Unsaturated fat

Structuralformula of asaturated fatmolecule

Space-fillingmodel of stearicacid, a saturatedfatty acid

Structuralformula of anunsaturated fatmolecule

Space-filling modelof oleic acid, anunsaturated fattyacid

Cis double bondcauses 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

Hydrophilichead

Hydrophobictail

WATER

WATER

Bilayer

STEROIDS

Steroids: Lipids characterized by a carbon skeleton consisting of four fused rings.Cholesterol is a major component of animal cell membranesMany sex hormones are made from cholesterolAlthough 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

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19

Levels of protein structure

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Secondarystructure

Tertiarystructure

Quaternarystructure

Hydrogen bond

helix

pleated sheet

strand

Hydrogenbond

Primarystructure

Primary Structure: a protein’s 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 ( helix and 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 acidsfor embryo

Transportprotein

Cell membrane

Example: Digestive enzymes catalyze the hydrolysisof bonds in food molecules.

Function: Protection against disease

Example: Antibodies inactivate and help destroyviruses and bacteria.

Function: Storage of amino acids Function: Transport of substances

Examples: Casein, the protein of milk, is the majorsource of amino acids for baby mammals. Plants havestorage proteins in their seeds. Ovalbumin is theprotein of egg white, used as an amino acid sourcefor the developing embryo.

Examples: Hemoglobin, the iron-containing protein ofvertebrate blood, transports oxygen from the lungs toother parts of the body. Other proteins transportmolecules across cell membranes.

Function of Proteins (2)

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Hormonal proteins

Function: Coordination of an organism’s activities

Example: Insulin, a hormone secreted by thepancreas, causes other tissues to take up glucose,thus regulating blood sugar concentration

Highblood sugar

Normalblood sugar

Insulinsecreted

Signalingmolecules

Receptorprotein

Receptor proteins

Function: Response of cell to chemical stimuli

Example: Receptors built into the membrane of anerve cell detect signaling molecules released byother nerve cells.

Muscle tissue

Actin Myosin

Collagen

Connectivetissue

Contractile and motor proteins

Function: Movement

Examples: Motor proteins are responsible for theundulations of cilia and flagella. Actin and myosinproteins are responsible for the contraction ofmuscles.

Structural proteins

Function: Support

Examples: Keratin is the protein of hair, horns,feathers, and other skin appendages. Insects andspiders use silk fibers to make their cocoons and webs,respectively. Collagen and elastin proteins provide afibrous 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 ofmRNA

mRNA

DNA

NUCLEUSCYTOPLASM

mRNA

Ribosome

AminoacidsPolypeptide

Movement ofmRNA intocytoplasm

Synthesisof protein

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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

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