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Molecular Biology

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Lesson 1: Molecules, Metabolism and Carbs

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What are these made of?

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Molecular Biology and Metabolism Explain living processes in terms of the chemical substances involved Many processes are controlled by protein catalysts called enzmyes. The sum of all enzyme- catalyzed reactions is called metabolism. Metabolism includes Catabolism (breaking large molecules into smaller molecules) Anabolism (building small molecules into larger molecules)

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Basic chemistry review Bohr Model of an atom Protons and Neutrons in nucleus Electrons orbit the nucleus Particle:Charge:Mass:Determines: ProtonNeutronElectron +1 0 -1 -1 ~1 amu ~0 (~1/1800 amu) elementisotope ion / charge Note that the electrons are actually much farther from the nucleus than shown.

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Bonding Gain / loss of electrons results in an ionic bond. Sharing electrons results in a covalent bond.

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Polar Covalent Bonds Sometimes atoms in a covalent bond do not share electrons equally. The result is a bond with a slightly positive end and a slightly negative end as seen in water molecules.

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Hydrogen Bonding Since water is polar, the positive ends attract the negative ends. This attraction creates hydrogen bonds. Hydrogen bonds are weak individually, but together they can be very important! Hydrogen Bonding in Water and DNA

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Carbon Biochemistry Life is based on atoms of the element CARBON Carbon can form a variety of stable compounds because it can form 4 covalent bonds Compounds are called organic if they contain carbon atoms bonded to hydrogen atoms (C-H) + a few others

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Organic molecules can be made by living things OR artificially Urea is made by living things (as a waste product) and also by artificial synthesis: Wohler Synthesis Helped show that there is no fundamental difference between organic molecules and other molecules same rules apply. (Disproved vitalism)

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Type of Carbon Macromolecule Monomer Elements Used FeaturesMajor functions Carbohydrate (sugars) Monosac- charide CHORing(s), CH 2 OStructure, energy storage Lipid (fats and oils) Fatty acid, steroid, glycerol CHO Long chain, O at one end, (4 rings in steroid) Energy storage, hormones, buoyancy, insulation Protein Amino acid CHON N-C-C backbone, R-group SO MANY THINGS! Enzymes, structure, movement, defense, etc. Nucleic AcidNucleotideCHOPS sugar +N-base +phosphate Information storage (genetics), production of proteins ElementSymbol Number of Covalent Bonds HydrogenH1 OxygenO2 NitrogenN3 CarbonC4 PhosphorusP5

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Carbohydrates Carbo = carbon, Hydrate = water Carbo = carbon, Hydrate = water Formula is (CH 2 O) n Formula is (CH 2 O) n Often have a ring structure Often have a ring structure Carbohydrate:3 examples:Use in animals:Use in plants: Monosaccharides (single sugars) Glucose Fructose Galactose Carried in blood to supply energy to the body Sweetens fruits to help seed dispersal (attracts animals) Disaccharides (two sugars) Lactose Sucrose Maltose In milk to provide energy to dependent young Carried by (some) phloem (sap) to supply energy Polysaccharides (many sugars) Glycogen Cellulose Starch In liver and muscles for short- term energy storage Forms strong fibers in cell wall for structure / support Energy storage

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Draw a Monosaccharide! How many carbons in your sugar? Draw a figure with that number of sides BUT one C will stick out and one O will go in ring Each carbon will have an O-H and H attached EXCEPT around the 2 carbons on the arm Count number of atoms and number of bonds! C C C CC O -O-H -H H|H| H- C 5 H 10 O 5

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Examples of monosaccharides Be able to DRAW and D-glucose Be able to DRAW D-ribose Fructose Other monosaccharides Galactose RNA found in DNA

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Disaccharides Two monosaccharides covalently bonded: + = + = Examples include: sucrose (table sugar) lactose (in milk) maltose (malt flavoring) Monosaccharides and disaccharides are called sugars and taste sweet!

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Condensation Reactions in Sugars Joins monosaccharides together (creates a covalent bond) Creates a water molecule (hydroxyl (OH) from one monomer and hydrogen (H) from the other)

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Hydrolysis Reactions in Carbs Condensation reactions in reverse Water is used up Produces monosaccharides from disaccharides

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Anabolism: Repeated Condensation Reactions Produces polymers from monomers Each covalent bond formed releases a water molecule Ex. Monosaccharides Polysaccharides + Water PolysaccharideFound inBuilt fromType of linksFunction Cellulose Plants-glucose1C-4C onlyStructure (cell wall) Starch (types of) Plants-glucoseEnergy storage Amylose 1C-4C only Amylopectin 1C-4C and 1C- 6C (some) Glycogen Humans (and some other animals) -glucose1C-4C and 1C- 6C (many) Energy storage (liver and muscles)

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Catabolism: Repeated Hydrolysis Reactions Produces monomers from polymers Each covalent bond broken uses a water molecule Ex. Polysaccharides + Water Monosaccharides H2OH2O

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Molecular Visualization Software See AWESOME jsmol interactives of most molecules here. here Visit interactives and build your own with Molecular Workbench Molecular Workbench Molecular Workbench Two rotations of ribose at biotopics. You may need to use a particular browser and/or update Java.

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Lesson 2: Lipids

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Lipids Lipids are mostly non-polar molecules. Used in energy storage, membrane structure, insulation, cell-to-cell communication, buoyancy, and more. Two building blocks of glycerides: / OH Glycerol:C 3 H 8 O 3 Fatty acid:CH 3 -(CH 2 ) x -C=O

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Condensation in Glycerides Glycerol bonded to a fatty acid makes a glyeride Monoglyceride + 1 water = glycerol + 1 fatty acid Diglyceride + 2 waters = glycerol + 2 fatty acids Triglyceride + 3 waters = glycerol + 3 fatty acids

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Lipids to know: Types of Fatty Acids Saturated Unsaturated Cis Trans Polyunsaturate d Be able to draw a saturated fatty acid.

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Lipids to know: Glycerides: Phospholipids: Steroids:

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Lipids v. Carbohydrates ~9 Calories / gram Long-term storage Non-polar (water insoluble) ~4 Calories / gram Short-term storage Polar, water soluble Why are lipids preferable to carbohydrates for long term energy storage in animals? Why are lipids used less frequently for energy storage in plants? Some seeds have high lipid content. Why?

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Body Mass Index BMI used as an indicator of health risks due to weight Does not take into account fat / muscle Calculate by formula or nomogram What would be the BMI for a person who is: a)80 kilos & 160 cm b)80 kilos & 145 cm

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Is BMI an effective predictor? What % of people had a BMI indicating they were overweight, but body fat did NOT confirm it?

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Lipids and Heath: Links for Methods and Evidence METHODS Animal models Randomized, controlled studies Before and after cohort studies MEASURE Levels of lipids in blood, lipid metabolism enzymes... Genetics (Alleles related to lipid metabolism) Health (CVD, cardiac events) Google scholar, JSTOR, etc. 2009 AU Review (on Haiku) LipidWorld (example of free journal) LipidWorld

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Health Risks of Trans Fats From WHO Scientific Update on Trans Fatty Acids (2009, Eur J Clin Nutr) on Haiku Meta-analysis esp. of research in humans Findings: Increased LDL-C bad cholesterol Decreased HDL-C good cholesterol Increased CHD (coronary heart disease) Increased coronary events (e.g. heart attack) Inflammatory effects Type of trans fat matters - 18:1 and 18:2 especially harmful Possible findings: Increased insulin resistance (Type II Diabetes) Increase membrane dysfunction Source may be important (natural source in some meats) Also a nice summary with some citations on WikipediaWikipedia

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Health Risks of Saturated Fats Currently evidence is contradictory Recent meta-analyses show (2010) and no significant evidence for concluding that dietary saturated fat is associated with an increased risk of CHD or CVD. (2010) and2010 Current evidence does not clearly support cardiovascular guidelines that encourage high consumption of polyunsaturated fatty acids and low consumption of total saturated fats (2014)2014 (showed saturated about the same as cis-monounsaturated, better than trans, and worse than polyunsaturated omega-3 and omega-6) Other recent meta-analyses show consuming PUFA in place of SFA reduces CHD events (2010) and2010 reducing saturated fat by reducing and/or modifying dietary fat reduced the risk of cardiovascular events by 14%. (2012)2012 See Wikipedia for further links to relevant studies.Wikipedia

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Lesson 3: Water

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Water molecules are polar Hydrogen bonds form between water molecules

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Properties of Water Cohesive Adhesive Solvent Thermal Heat capacity Boiling / freezing points Evaporative cooling

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Cohesion Water molecules stick to each other due to hydrogen bonds between them Surface tension Organisms benefit from cohesion. In plants, cohesion helps transport water up to the leaves. Surface tension and capillary action also involve cohesion.

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Cohesion from a bugs eye More cohesion: Basilisk Running On Water

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Adhesion Attraction between water molecules and other molecules (polar or charged) Living things benefit from adhesion when water sticks to cell walls allowing water to move to leaves.

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Versatile Solvent Because water has partial positive and negative charge, it can dissolve many substances that are polar, positively charged, or negatively charged Water does NOT dissolve non- polar, uncharged substances well (lipids / fats / oils) Living things benefit because they dissolve the molecules of life and metabolism in water, where they can interact and react.

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Substances Interact with Water HYDROPHILIC Water loving Polar or charged Gets wet or dissolves HYDROPHOBIC Water fearing Non-polar, uncharged Repels water, not soluble

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Transport in Blood by Solubility SubstanceChargeSolubilityMethod of Transport GlucosePolarHigh Dissolved in blood plasma Amino AcidsPolarHigh Dissolved in blood plasma CholesterolNon-polarLow In Lipoproteins (HDL, LDL) FatsNon-polarLow In lipoproteins such as chylomicrons OxygenNon-polarLow Attached to hemoglobin protein Sodium Chloride Ionic (charged) High Dissolved in blood plasma

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Thermal Properties High heat capacity: large amounts of energy are needed to raise the temperature of water High (latent) heat of vaporization: large amounts of energy are necessary to vaporize water Low density as a solid: because of packing of water molecules by hydrogen bonds ice is less dense than liquid water (at most temperatures)

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Water and Cooling Evaporative cooling: Terrestrial organisms may sweat, pant, or transpire. As water evaporates and breaks hydrogen bonds, it takes energy from the remaining water which becomes cooler High heat capacity: Water organisms may transfer heat to the environment without raising the water temperature by much; have a stable environment to live in

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Low Density as a Solid A frozen layer of ice can insulate a pond and prevent it from freezing solid during the winter. This allows organisms to survive in the pond year round.

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Thermal Properties of Water v. Methane Specific Heat Capacity (J/gK) Heat of Vaporization (kJ/mol) Freezing Point (C) Boiling Point (C) Water4.18440100 Methane2.268.2-182.6-161.7 What causes these differences? Why are they significant?

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