2.1 Molecules to Metabolism IB Biology HL 1 Mrs. Peters Fall 2014

2.1 Molecules to Metabolism EI: Living organisms control their composition by a complex web of chemical reactions. NOS: Falsification of theories: the artificial synthesis of urea helped falsify vitalism.

Background Information Organic: anything that contains carbon Organic Chemistry: The chemistry of carbon compounds Biochemistry: the chemistry characteristics of living organisms

U1. Molecular Biology Molecules are important to living organisms Molecules are classified into 4 biochemical groups and water

U1. Molecular Biology 4 biochemical groups Nucleic Acids Proteins Carbohydrates Lipids

U1. Molecular Biology Each molecule has a specific structure and function Biochemical molecules work together to ensure the cells needs are met

U1. Molecular Biology Cell Needs Example: Read the scenario.

U2. Carbon Versatile atom which acts as a building block for molecules Has 6 electrons, accepts 4 readily

U2. Carbon Uses covalent bonds to share electrons Carbon atoms can bond to each other, easily, forming chains or rings

U2.Carbon Structures Variation in structures Length: a chain of carbon atoms Branching: a chain of carbon atoms with a “branch” attached

U2.Carbon Structures Variation in structures Double Bonds: two bonds between two carbon atoms Rings: carbon atoms forming bonds with each other in a ring

U2. Hydrocarbons Simplest organic molecule containing only carbon and hydrogen Tend to be hydrophobic Examples: Fats petroleum

S2. Functional Groups A group of atoms bonded to carbon molecules

S2. Functional Groups Hydroxyl group (-OH) Called alcohols Name ends in –ol Polar molecules Ex: ethanol

S2. Functional Groups Carbonyl group (-C=O) Called aldehydes, if located at the end of carbon chain Ex: Propanol Called ketone, if located elsewhere on carbon chain Ex: Acetone

S2. Functional Groups Amino Group (-NH2) Called amines Molecular building blocks of proteins (amino acids) Ex: glycine

S2. Functional Groups Carboxyl Group (-COOH) Called carboxylic acids Carbon is double-bonded to oxygen (carbonyl group) with a hydroxyl group attached Ex: Acetic Acid

S2. Functional Groups Sulfhydryl group (-SH) Called thiols Interact to help stabilize protein structures Ex: cysteine

S2. Functional Groups Phosphate group (-OPO3-2) Called phosphates Transfers energy between organic molecules Ex: glycerol phosphate

S2. Functional Groups Methyl (-CH3) Called methylated compounds Found on DNA and hormones Ex: 5-Methyl cytidine

U3. Biochemical Molecules of Life Subcomponents (building blocks) Carbohydrate Monosaccharide Lipids Glycerol, fatty acids, phosphate groups

U3. Biochemical Molecules of Life Subcomponents (building blocks) Proteins (polypeptides) Amino Acids Nucleic Acids Nucleotides

U3. Biochemical Molecules Carbohydrate Classifications: Monosaccharides: single sugar Examples: glucose, galactose, fructose, ribose Disaccharides: two sugars Examples: maltose, lactose, sucrose

U3. Biochemical Molecules Carbohydrate Classifications: Polysaccharides: many sugars Examples: Starch, glycogen, cellulose, chitin

U3. Biochemical Molecules Lipid Classification Triglycerides: glycerol with three fatty acids Example: Fat stored in adipose cells

U3. Biochemical Molecules Lipid Classification Phospholipids: phosphate group with two fatty acids Example: Lipids forming a bilayer in cell membranes

U3. Biochemical Molecules Lipid Classification Steroids: rings of carbon with side chains Examples: cholesterol, vitamin D, and some hormones

U3. Biochemical Molecules Proteins: Examples: Enzymes, antibodies, peptide hormones Nucleic Acids: Examples: Deoxyribonucleic acid (DNA), Ribonucleic acid (RNA), adenosine triphosphate (ATP)

S1. Drawing Molecular Diagrams Glucose: C6H12O6 6 atom ring with a side chain 5 carbons are in the ring, one is with the side chain Carbons are numbered with 1 on the right Hydroxyl groups on C 1,2,3, and 4

S1. Drawing Molecular Diagrams Glucose: C6H12O6 Biologyatsandringham.pbworks.com

S1. Drawing Molecular Diagrams Ribose: C5H10O5 5 atom ring with a side chain 4 carbons are in a ring, one in side chain Carbon atoms are numbered with 1 on the right Hydroxyl groups are on C 1, 2, 3

S1. Drawing Molecular Diagrams Ribose: C5H10O5 dl.clackamas.cc.or.us

S1. Drawing Molecular Diagrams Saturated Fatty Acid: Carbon atoms form an unbranched chain Number of carbon atoms is between 14 and 20 One end is a carboxyl group The other end is a methyl group Carbon atoms in between have 2 hydrogen bonded

S1. Drawing Molecular Diagrams Saturated Fatty Acid: Courses.washington.edu

S1. Drawing Molecular Diagrams Amino Acid: Carbon atom in center with Amino group Carboxyl group Hydrogen atom R group (variable)

S1. Drawing Molecular Diagrams Amino Acid: Education-portal.com

U4. Metabolism All of the reactions within all the cells of an organism DNA replication, synthesis of RNA, synthesis of proteins, cell respiration, photosynthesis and many more

U4. Metabolism Reactions are controlled by enzymes Each enzyme has a specific job in one metabolic reaction Enzymes speed up the rate of reactions, by making the reaction take place

U4. Metabolism Metabolic pathway: when one molecule is transformed into another through a series of small steps, each performed by different enzymes

U4. Metabolism Metabolism has two parts: Anabolism: synthesis of complex molecules Catabolism: breakdown of complex molecules

Quick Vocab Introduction Monomer: small repeating units; the building blocks of polymers. EX: glucose, amino acids Polymer: a long molecule consisting of many similar or identical building blocks linked by covalent bonds; many monomers EX: carbohydrates, proteins, nucleic acids

Quick Vocab Introduction Polymer Example: Glucose is a monomer, Starch is a polymer of glucose

U5. Anabolism Larger molecules are created by the condensation reaction. Two molecules are joined by covalent bonds Water is a product of the reaction

U5. Condensation Reaction Condensation Reaction- building polymers Two molecules are joined to form a larger molecule, held by covalent bonds; requires an enzyme and produces one water molecule. Each monomer contributes to water that is made, one provides the -OH, one the -H.

U5. Condensation Reaction Condensation Example: Glucose + Galactose  Lactose + water (monomer) + (monomer)  (polymer) + water ** Lactose is really called a dimer (only two monomers are bonded together) Di- means 2 ** Polymer is for many monomers bonded together; Poly- means many

U5. Condensation Reaction Condensation Example: Amino acid + amino acid  dipeptide + water (monomer) + (monomer)  (polymer) + water **dipeptide is formed when two amino acids bond

U5. Condensation Reaction Condensation Diagram:

U5. Condensation Reaction Condensation Example: Glucose + glucose  maltose www.Ib.bionija.com.au

U5. Condensation Reaction Condensation Example: www.saburchill.com

U6. Catabolism Larger molecules (polymers) are broken down into monomers by the hydrolysis reaction Water is used to break the covalent bonds

U6. Hydrolysis Reaction Hydrolysis- breaking polymers into monomers bonds between monomers of a polymer are broken by the addition of water molecules; requires enzymes a H from water attaches to one monomer OH from water attaches to the other monomer

U6. Hydrolysis Reaction Hydrolysis Example: Lactose + water  glucose + galactose (polymer)+ water  (monomer) + (monomer) ** Lactose is really called a dimer (only two monomers are bonded together) Di- means 2 ** Polymer is for many monomers bonded together; Poly- means many

U6. Hydrolysis Reaction Hydrolysis Example: dipeptide + water  amino acid + amino acid (polymer) + water (monomer) + (monomer) **dipeptide is formed when two amino acids bond

U6. Hydrolysis Reaction Hydrolysis Diagram:

U6. Hydrolysis Reaction Hydrolysis Example: Lactose + water  galactose + glucose People.stfx.ca

U6. Hydrolysis Reaction Hydrolysis Example: En.wikibooks.org

Nature of Science Vitalism and Urea Theory of Vitalism: living organisms were composed of organic chemicals that could only be produced in living organisms because of a “vital force” required to make them.

Nature of Science Vitalism and Urea 1828: German Chemist Friedrich Wohler synthesized urea using silver isocyanate and ammonium chloride. He created an organic compound artificially without a vital force.

Nature of Science Vitalism and Urea This began the falsification of the theory Biologists now accept that living organisms are governed by the same chemical and physical forces as non-living matter

Nature of Science Vitalism and Urea There are still some complex proteins that have not been artificially synthesized: Hemoglobin