1. Unit 2 Molecular Biology

2. Essential Ideas 2.1 - Living organisms control their composition by a complex web of chemical reactions

3. Basic Background Organic chemistry = carbon Biochemistry – attempts to explain the chemical characteristics of living organism 4 categories of organic compounds – Carbohydrates – Lipids – Proteins – Nucleic acids

4. Basic Background Water is the medium of life Proteins act as enzymes Genetic information stored in DNA Compounds of carbon, hydrogen and oxygen are used to supply and store energy

5. Section 2.1 Molecules to Metabolism Understandings: Molecular biology explains living processes in terms of the chemical substances involved. Carbon atoms can form four covalent bonds, allowing a diversity of stable compounds to exist. Life is based on carbon compounds, including carbohydrates, lipids, proteins, and nucleic acids. Metabolism is the web of all the enzymes-catalysed reactions in a cell or organism.

6. Understandings continued: Anabolism is the synthesis of complex molecules from simpler molecules, including the formaion of macromolecules from monomers by condensation reactions. Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

7. Molecular biology – the chemistry of living organisms Interactions between organic molecules Example of Metabolism  Insulin (protein hormone)  Facilitates the movement of glucose from the bloodstream into the cell’s interior  Interacts with protein channels to open them  Glucose moves high to low

8. Molecular biology – the chemistry of living organisms Insulin cont.  Why can’t glucose go through the phospholipid bilayer?  Polarity  Insulin and channels are both proteins  Coded by DNA  What category of organic molecule is glucose Each organic molecule is represented

9. Carbon-based life Are all compounds that contain carbon organic? Atomic # of carbon is ______ Carbon has ___ valence electrons Carbon always forms 4 __________ bonds (share) Covalent bonds are strong bonds. Carbon dioxide

10. Challenge yourself Read through the following example of molecular interactions leading to a physiological response. Try to classify each of the named molecular components as a carbohydrate, lipid, protein or nucleic acid.

11. Reading When a predator, such as a snake, catchers and eats a small rodent, one of the main sources of nutrition that the snake is consuming is the muscle of the prey animal. That muscle is primarily composed of two molecules: actin and myosin. When the ingested muscle reaches the intestines of the snake, enzymes (such as trypsin) help the snake digest the actin and myosin into amino acids. Other enzymes (such as lipase) help the snake digest the triglyceride fats within the adipose tissue of the rodent.

12. Biochemical compounds important to living organisms nucleotidesAmino acids Glycerol Fatty acids monosaccharides Carbohydrates (C, H, O) 1:2:1 Lipids (C, H, O) Nucleic Acids (C, H, O, N, P) Proteins (C, H, O, N & Sometimes S)

13. Common categories

14. Skill: Drawing Molecules Glucose:

15. Skill: Drawing Molecules Ribose:

16. Skill: Drawing Molecules Saturated Fatty Acid

17. Skill: Drawing Molecules Generalized amino acid:

18. Skill: Identification of biochemicals as carbohydrates, lipids, proteins and nucleic acids.

19. Metabolism: reactions controlled by enzymes all the reactions within all of the cells (and fluids such as blood or digestion in the small intestines) comprise the metabolism of the organism. Catalyzed by enzymes

20. Factors determining if reactions occur Identity of the colliding molecules Orientation of the colliding molecules (where they hit each other) The speed of the molecules when they collide

21. Examples of a reaction Creating ATP – cellular respiration Replication of DNA Synthesis of RNA Synthesis of proteins Photosynthesis

22. Metabolism Anabolism Synthesis of complex molecules Require energy (ATP) Condensation/dehydration synthesis Examples: – Protein synthesis – DNA synthesis – Photosynthesis Catabolism Breakdown of complex molecules Release energy Hydrolysis Examples – Digestion of food – Digestion of dead organic matter by decomposers

23. Application: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.

24. Urea (organic) was discovered in urine – 1720’s It was widely believed that organic compound could only be made with help of a “vital principle” (vitalism) Vitalism = living organism and inanimate things differed fundamentally because living organisms contained a non-physical element.

25. Application Urea is in nitrogenous waste In humans – Produced in the liver – Enters the bloodstream – Filtered out by the kidneys – A component of urine

26. Application Wohler – German physician & chemist – 1828 Mixed cyanic acid and ammonium – Crystalline substance formed Crystals were urea Organic molecule synthesized from inorganic substances

27. Work is published Click here

28. Importance Scientific theories undergo modifications Important discoveries are made accidentally Scientific discovery is not always appreciated immediately for its importance

29. 2.2. Water Understanding: – Water molecules are polar and hydrogen bonds form between them. – Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water. – Substances can be hydrophilic or hydrophobic

30. Structure of Water Water is the solvent = aqueous What type of bond is between the oxygen and the hydrogen atoms of water? – Polar covalent bond Because of that bonding, it has – Dipolarity And thus short-lived hydrogen bonds

31. Cohesion Same type of molecules Why – Water forms into droplets when it splits – Water has a surface tension – Water is able to move a water ‘column’ in the vascular tissues of plants

32. Adhesion Attraction between two unlike molecules Water is attracted to cellulose Leads to capillary action

33. Application Use of water as a coolant in sweat.

34. Thermal properties High specific heat – Water can absorb or give off a lot of heat without changing temp much – Ocean/beach day vs night High heat of vaporization – Water absorbs a lot of heat when it evaporates Water evaporates through stomata – cools plant

35. Examples Basilisk lizards can run on water

36. Application Modes of transport of glucose, amino acids, cholesterol, fats, oxygen, and sodium chloride in blood in relation to their solubility in water.

37. Solvent properties Water is solvent to other polar molecules – Proteins, carbs, nucleic acids Excellent medium for transport – Xylem carries water & dissolved minerals – Phloem moves dissolved sugar Blood most common transport in animals – Blood plasma – Glucose, amino acids, fibrinogen, hydrogen carbonate ions

38. Substance High or low relative solubility in water Mode of transport in an aqueous environment GlucosePolar molecule/high solubility No special mode of transport needed/dissolves directly in aqueous plasma Amino acidsVarying polarity but all are reasonably soluble No special mode of transport needed/ dissolves directly in aqueous plasma CholesterolLargely non-polar/very low solubility Transported by blood proteins that have polar amino acids on the outer portion to give water solubility, & non-polar amino acids internally to bind the non-polar cholesterol FatsNon-polar fatty acid components/very low solubility Transported by blood proteins that have polar amino acids on the outer portion to give water solubility, & non-polar amino acids internally to bind the non-polar cholesterol

39. SubstanceHigh or low relative solubility in water Mode of transport in an aqueous environment OxygenTravels as diatomic O 2 /low solubilityRelatively low solubility in water is exacerbated by the relatively high temperature of warm-blooded animals (oxygen is less soluble in warm aqueous solutions)/haemoglobin is used to bind & transport oxygen molecules reversibly Sodium chlorideIonizes/high solubilityNo special mode of transport needed/sodium chloride is an ionic compound, it ionizes into separately charged Na + and Cl - ions in aqueous plasma

40. Hydrophobic & hydrophilic Polar substances = hydrophilic Non-polar substances = hydrophobic – Organic non-polar = carbon & hydrogen OR large areas of only hydrogen & carbon (methane) fatty acids, some proteins depending on the arrangement of the amino acids (think integral proteins)

41. Application Comparison of the thermal properties of water with those of methane.

42. Methane vs Water Polar covalent Non- polar covalent