Topic 2 Molecular Biology 2.1 Molecules to metabolism (Source: Biology, Course Companion. 2014 Edition, Allot and Mindorff, Oxford University Press)

Cornell Notes Style The following slides model the Cornell style of taking notes: Page is divided into 2 unequal columns Biggest column on the right is for writing important details Smaller column on the left is for writing main ideas or questions At the end of each major topic, a short summary is written Advantage? More organized notes and forces you to process with your brain as you write them.

Understanding: Molecular bio explains living processes in terms of chemical substances involved How is Bio related to Chem? What are examples of molecules in cells? What is the reductionist approach to studying Bio? We can explain bio processes by explaining the structure of molecules & how they interact Ex of important molecules in cells: water, DNA, RNA, proteins, enzymes Reductionist approach = breaking down processes into parts – helps explain processes but sometimes looking at the whole system is better than just looking at the parts (Emergent properties = “The whole is greater than the sum of its parts.”)

Understanding: Carbon atoms can form 4 bonds allowing diversity of compounds to exist What are some properties of C that make it a good biological molecule? C forms covalent bonds with other atoms Covalent = shared electrons Covalent – strongest type of bond so C-based molecules are stable C forms up to 4 bonds – more than most atoms (very reactive!) so can be complex rings or chains C can bond w/1 element or more Bonds w/C can be single or double

Understanding: Life is based on C compounds including carbs, lipids, proteins & nucleic acids What are the 4 main classes of C compounds important in living organisms? What are some properties of the 4 main classes of these C compounds? Each has diff properties and purposes Carbs: contain C, H, O; ~ratio 2H:1O (like H2O) Lipids: insoluble in water ~Ex: steroids, waxes, fatty acids, triglycerides (fats – solid at room temp; oils – liquid at r temp) Proteins: chains of amino acids ~contain C, H, O, N and sometimes S Nucleic acids: chains of nucleotides ~contain C, H, O N, P ~2 types – DNA, RNA

Which is NOT in one of the 4 main classes of organic compounds? Water Starch Fat DNA

2.1 Summary so far… (your turn to write a summary!)

Urea produced naturally Urea produced artificially Applications: Urea as ex of compound produced by living organisms but can also be artificially synthesized Urea produced naturally Urea produced artificially Not in liver No enzymes involved Urea is identical in both 100 million tons/year produced, mostly as nitrogen fertilizer for crops

Skills: Drawing molecular diagrams of glucose, ribose, saturated fatty acid, and general amino acid DRAW on your whiteboards, individually, without looking at notes: Glucose Ribose Amino Acid Fatty Acid Glycerol

Skills: ID biochems such as carbs, lipids or proteins from diagrams (Source: commons.wikimedia.org)

Diff between ribose & deoxyribose: (Source: commons.wikimedia.org)

What is this a picture of? Ribose Glucose Amino acid Fatty acid

Nature of Science: Falsification of theories the artificial synthesis of urea helped to falsify vitalism Urea discovered in 1720’s; assumed to be product of kidneys Widely believed organic compounds could only be made with help of a “vital principle” Vitalism = the theory that the origin and phenomena of life are dependent on a force or principle distinct from purely chemical or physical forces. (http://www.oxforddictionaries.com/us/definition/american_english/vitalism) Aristotle used the word “psyche” (Greek for “breath, life, soul”) for the vital principle Good discussion on diff between life and non-life: http://www.cod.edu/people/faculty/fancher/vitalism.htm

Understanding: Metabolism is the web of all enzyme-catalyzed rxns in a cell or organism. Students: add your question here! Metabolism = sum of all rxns in an organism Rxns are catalyzed by enzymes Rxns in cytoplasm of cells or extracellular Rxns can be straight chains or cycles Metabolism of prokaryotes = 1000+ diff rxns

Understanding: Anabolism is the synthesis of complex molecules from simpler molecules including formation of macromolecules from monomers by condensation rxns. Students: add your question here! Metabolism = anabolism + catabolism Anabolism = building larger molecules (Body builders use anabolic steroids!) Anabolic rxns need ATP for energy Examples of anabolism: ~ protein synthesis ~ DNA synthesis ~ photosynthesis ~ carb synthesis (starch, glycogen, cellulose)

Words defined… Macromolecules = “polymers” = large molecules Ex: DNA, proteins, starch, triglyeride Monomers = “one unit” = small molecules = building blocks Ex: nucleotides, amino acids, monosaccharides (glucose & ribose), fatty acids, glycerol * Condensation Rxns = rxns that build larger molecules from smaller ones, and in the process produce WATER (condensation). Also called “dehydration synthesis”.

Understanding: Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers. Students: add your question here! Catabolism = break down of larger molecules into smaller ones Energy is released & captured in ATP Ex: ~ digestion (by consumers & decomposers) ~ cell respiration * Hydrolysis = rxns that break down large molecules good night love u mom “hydro” = water “lysis” = breaking “hydrolysis” = using water to break molecules

Which is BREAKING down large molecules? Metabolism Anabolism Catabolism Cannibalism

Summary….