Introduction to Molecular forces and Macromolecules

1. Introduction to Molecular forces and Macromolecules

2. Announcements • There will be a quiz in next lab. Session. Like • always, it will cover materials from the previous • lab and from upcoming lab. • Next lab. is cell biology, • Instead of the BLC project for this lab, I’m giving • the choice to write a report on amino acids and • nucleotides. However, you may choose to do the • project and in all cases it is a total of 12 points

3. Today • atoms and how they behave • chemical bonds • biological macromolecules and their building • blocks. • in class exercises • BLC project

4. Atoms • smallest part of any element • made up of a positively charged central nucleus • surrounded by negatively charged cloud of • electrons. • -the nucleus contains protons (positively charged) • and neutrons (electrically neutral). • -number of protons equal the number of electrons, so • any atom is electrically neutral. • -atoms of the same element but with different • number of neutrons are termed isotopes

5. Atoms • electrons are arranged in shells around the nucleus, • with the inner most (1st) able to hold two electrons • and 2nd and 3rd able to hold eight electrons. • -the outer most shell of determines how chemically • an element is active and how • it will behave in chemical • reaction. • …Helium and Neon are • chemically inert • … Carbon, Nitrogen, • oxygen and fluorine

6. Molecules • molecule is a collection of atoms that are held • together. • -carbon is a major molecule forming atom (all life • forms contain carbon) • -molecular weight of any molecule is the sum of • the atomic weights of all its atoms.

7. Chemical bonds -forces that hold atoms and molecules together -Intramolecular bonds 1-covalent bond .electron(s) sharing between two non metallic atoms. .electron(s) either shared evenly between the atoms or not (this create ionic character). H2O… O- H+ H+

8. Chemical bonds 2-ionic bond .attraction for an anion and a cation after an electron is transferred from the metal to the non-metal 3-metallic bond . a sea of electrons

9. Chemical bonds Intermolecular bonds 1-hydrogen bonds.attraction of the partially positive end of one highly polar molecule for the partially negative end of another highly polar molecule is called a hydrogen bond

10. Chemical bonds 2-van der Waals Forces .weak attractive forces that hold non-polar molecules. H2, He, Ne 3-Molecule-Ion Attractions .a molecule (water) is attracted to an ion (sodium)

11. Chemical bonds 4-hydrophobic bond .Force that bring two non-polar molecules together when they exist in polar environment. …oil in water

12. Experiments 1-hydrogen bonds and surface tension .water, mineral oil, and ethanol .fill eppendorf tubes (by submerging into the beaker) with different types of liquids supplied. Invert the tubes while still submerged and determine which one resist pouring out. 2- hydrophobicity (1) .veg. oil, detergent, water. .fill petri dish with water and/or detergent and add drops of oil Hydrophobicity (2) Magic sand and/ or ethanol

13. 3- diffusion, temperature, osmosis .agar plates .dye (three different molecular weight dyes)

14. Biological Macromolecules amino acids carbohydrates monosaccharides proteins fatty acids DNA/RNA nucleotides lipids

15. Carbohydrates -polymers of monosaccharides. -short term energy storage material -cell wall in bacteria and plants are complex carbohydrates. -they contain C, H, and O -interaction between carbonyl group (>C=O) and hydroxyl group (COOH) result in ring structure. monosaccharides…glucose, fructose polysaccharides…cellulose, starch, glycogen

16. Experiment 4- starch and amylases .use the small Petri dishes to mix starch and a source of amylases. .incubate at room temp. for 15 min. . Test for the presence of monosaccharides using Benedict’s reagent

17. Proteins • -composed of one (or more) poly peptide chain. • -each polypeptide chain is a polymer of amino acid • -amino acids are tied together by covalent bond • termed; peptide bond. The reaction leading to • peptide bond formation is termed dehydration • reaction because it exclude a water molecule • each amino acid has an amino group (NH2) at one • end and a carboxyl group (COOH ) at the other end. • this makes proteins have amino terminal end and • carboxyle terminal end. • -there are 20 a.a. and some of them are essential ones

18. proteins • -proteins are the architectural and functional unit of • the cell. They are parts of membranes and all • enzymes are proteins in structure. • the amino acid sequence in any protein is termed • primary structure. This primary structure can fold • on itself forming a secondary structure and this in • turn can fold on itself forming a tertiary structure. • -protein function is dependant on correct folding • of this protein.

19. Experiment 5-enzymes/ protein folding . Ready made jell-o (on ice), fruits pieces, .add a piece of raw or heated fruit (cooled on ice) onto jello surface. .examine during next two hours (effect of gelatinase from plant origin on the jell-O .

20. Lipids -they are diverse in their structure, not true polymer -contain primarily C and H -hydrophobic -four major groups .fats or triglycerides .phospholipid .steroids .trepens ….lipoproteins

21. Nucleic acids • these include DNA and RNA • DNA store the genetic code. The genetic code is • translated into amino acids (proteins). • -RNA store also the genetic code but it has an • enzymatic function (ribozyme catalyze the peptide • bond formation in cell). • both are polymere of nucleotides. Each nucleotide • contain sugar molecule, 1 phosphate group • attached to carbon # 5 and a nitrogenous base • attached carbon # 2

22. Nucleic acids -nitrogenous bases either purines ( adenine,guanine) and pyrimidines (cytosine, thymine, uracil) -RNA is single stranded and some RNA species can fold in a similar manner to proteins. -DNA exist in a double helix

23. Nucleic acids

24. Nucleic acids

25. purines

26. pyrimidines

27. Experiment 6- DNA is a large molecule . Add equal amount of salmon sperm DNA and absolute ethanol and try to spool using pasteur pipette. .repeat the same after shearing the DNA using syringe. .dispose the syringe while the needle still attached in sharps discard .dispose glass pasteur pipettes Experiment 7-Detecting co2 using BaOH2 .use the designated flask and mix dry ice with water and direct the pipette into BaOH2. Observe what happens

28. BLC project • -get acquainted to molecules • -make a typed report identifying 6 a.a. and • 2 nucleotides. • nucleotides……! • Amino acids • “http://www.chemie.fu-berlin.de/chemistry/bio/ • amino-acids_en.html”