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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
Molecule Subcomponents (building blocks)
Carbohydrate Monosaccharide
Lipids Glycerol, fatty acids, phosphate groups
U3. Biochemical Molecules of Life
Molecule 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 ClassificationTriglycerides: glycerol with three fatty acids
• Example: Fat stored in adipose cells
U3. Biochemical Molecules
Lipid ClassificationPhospholipids: 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 chain5 carbons are in the ring, one is with the side chainCarbons are numbered with 1 on the rightHydroxyl 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 chain4 carbons are in a ring, one in side chainCarbon atoms are numbered with 1 on the rightHydroxyl 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 chainNumber of carbon atoms is between 14 and 20One end is a carboxyl groupThe other end is a methyl groupCarbon 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 withAmino groupCarboxyl groupHydrogen atomR 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 moleculesCatabolism: 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 UreaTheory 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 Urea1828: 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 UreaThis began the falsification of the theoryBiologists now accept that living organisms are governed by the same chemical and physical forces as non-living matter
Nature of Science
Vitalism and UreaThere are still some complex proteins that have not been artificially synthesized: Hemoglobin