LAB 1 MOLECULAR CELL BIOLOGY Lab 1 Molecular

LAB (1) MOLECULAR CELL BIOLOGY

Lab (1) Molecular Biology Definition : 1 -Modern field of science 2 -To understand the basic of living organisms’ chemical reactions necessary to build cell’s nutrients and to perform biological functions. Structural organic order is as follows: Organism–System–Organs–Tissues–Cells–Organelles– Molecules-Atoms The body of Living organisms consists of : two types of Molecules: Inorganic molecules : (water, salts, acids and bases) they are basic simple materials that composes more complicated materials of living cell. Organic molecules: composed primarily of carbon atom (C). Cellular organic molecules are four kinds of macromolecules: Proteins - Carbohydrates - Lipids - Nucleic acids

• Proteins: 1 -One of the 4 macromolecules in living organisms, 2 -composed of amino acids that binding by peptide bonds to each other Amino Acids: 1 - Definition : 1 -Building of proteins. 2 - consists of : Amine group (NH 2) with basic properties, and Carboxyl group (COOH) with acidic properties, in addition to a side group (R) which determines the distinctive properties of amino acids. Amine Carboxyl group Chemical formula of Amino acid

2 - Kinds of Amino acids : • Neutral non polar amino acids: e. g. Tryptophan. • Neutral polar amino acids: e. g. Cysteine. • Non-neutral amino acids: e. g. Arginine. 3 -Levels of Structure in Proteins I- Primary Structure: The binding of amino acids with peptide bond to form a linear chain of poly peptide. H 2 N His Tyr Ser (Peptide bond) Met Glu Phe Glu Arg His Ser Sequence of amino acids to form linear chain of polypeptide COOH

H 2 N II- Secondary Structure: Tyr Ser The specific shape of protein results from Hydrogen (H)-bonding of Met Ala the poly-peptide chain. Glu Val Hbond Cys Met Ser There are 2 forms of secondary structure: His Phe 1 - α-helix : e. g. Collagen protein in white fibers, and Elastine in elastic Glu Lys Ser Thr fibers (both in connective tissues). 2 - β- plated sheet: e. g. Keratin protein in hair and horny layer of skin. Both forms are fibrous proteins that do not dissolve in water (insoluble) Glu Arg COOH Secondary structure is formed by formation of H bonds of Hydrogen atom of Amine group in one amino acid with Oxygen atom of carboxyl group of another amino acid.

III- Tertiary Structure: There are 3 main types of chemical bonds that contributes to the formation of tertiary structure: 1 -H-bond : ( Binding between parts of near region and far region from poly-peptide ) 2 -Ionic bond : (Binding between free of Amine group at one side of the poly-peptide with free of Carboxyl group on the other side of the poly-peptide 3 -di-sulfide bond (-S-S-) : (Binding between two atom of sulfide in two amino acide Distanced from each other by a specific distance , which result in formation of a Globular protein that dissolves in water (soluble). e. g. enzymes.

IV- Quaternary Structure: The joining of multiple polypeptide molecules(units) into one large complex structure. and that are in the form of bundle , and have the same chemical bonds that also this structure are non-covalent. ( chain) (Iron) ( chain) (Heme) Quaternary structure: example is Hemoglobin, it consists of 4 polypeptid coiled chains to form one complex globular structure. ( OC 1 – OC 2 – B 1 – B 2 )

Slide Reagents and dyes Object Features (For read) Intestine with protein inclusions Tissue parts Bromophenol stained blue indicates ninhydrin Schiff Staining technique: presence of Chloramine-T bromophenol blue. Proteins Schiff Muscle with protein inclusion Tissue parts stained violet Pseudo-iso-cyanin Insulin in pancreas indicates Immuno-peroxidase presence of stain Insulin Secondary Structure Elastic (yellow) fibers Elastin Tissue parts stained black indicates presence of elasic fibers Gieson Stain Proteins in cells Insulin Protein hormone Elastine (Fibrous helical protein)

Secondary Structure Tissue parts stained Collagen (white) blue indicates fibers presence of collagen fibers Upper part: fibrous keratin Secondary Structure In horny layer Keratin in Skin Tertiary Structure Tissue parts staines Phosphatase in lung blue indicates presence of protein Tertiary Structure enzyme Phosphatase in alimentary duct Red blood cells Quaternary (RBCs) sained red Structure naturally due to Hemoglobin in red presence of blood cell hemoglobin. Tri chrome stain Collagen (Fibrous helical protein) Keratin (Fibrous H&E plated protein) Phosphatase globular ) enzyme ) Hemoglobin (blood pigment that binds and transfers oxygen)

Chemical Experiments Detection of Amino Acids - Studying Proteins Characteristics Detection of amino acids in egg white and milk: • A) Detection of Tryptophan, phenylalanine: (1) in 2 test tubes Add 3 ml of each sample (egg white, milk) (2) Add 1 ml of conc. Nitric acid, then heat tube over flame for 1 min. , a yellow color will occur. (3) Cool tube (in ice ), then add 4 ml of 40% Na. OH. Observation: Yellow color converts to orange (formation of orange precipitant) indicates presence of both amino acids. Results: Amino acid Milk Tryptophan + light orange Phenylalanin + Egg white + dark orange +

2 -Detection of amino acids Cyseine and Methionine 1 - Put 5 ml of each sample (milk, egg white) in test tubes 2 - Add 2 ml Na. OH (40%), heat tubes on flame for 5 or more minutes till yellow color develop. 3 - Cool tubes, then add 2 ml of lead acetate (5%). Observation: dark brown or gray to black ppt. (darken with time) Result: Amino acid Milk Cysteine + dark brown ppt Methionine + dark brown ppt Egg white + black ppt

(1) Affecting Factors on Protein Denaturation: 1) In 5 test tubes, add 5 ml of egg white in each. Mark tubes from 1 to 5. 2) Put tube 1 in boiling water bath (or heat over flame) 3) In tube 2, add 3 ml of Na. Cl solution (ionic solution) 4) In tube 3, add 3 ml Na. HCO (base) 5) In tube 4, add 5 ml HCl (acid) 6) In tube 5, add 5 ml ethanol alcohol (organic compound) Results: Tube # 1 2 3 4 5 Added factor Boiling water bath / flame Na. Cl (ionic compound) Na. HCO (base) HCL (acid) Ethanol (organic compound) Observation (+) Coagulation (like boiled egg) (-) no change (+) bubbles burst that disappears quickly (+) coagulation (white color) (+) white ring in middle

Conclusion: -In normal conditions, proteins exists in their natural state. -Some factors affects the nature of proteins and can change structure of proteins. -Factors like high temperature, exposure to some chemicals causes denaturation of proteins, function of protein is lost.