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 (-NH
•
Called amines
•
Molecular building
2
) 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
(-OPO
3
-2 )
•
Called phosphates
•
Transfers energy between organic molecules
•
Ex: glycerol phosphate

S2. Functional Groups
 Methyl (-CH
3
)
•
Called methylated compounds
•
Found on DNA and hormones
•
Ex: 5-Methyl cytidine

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

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

U3. Biochemical Molecules
Carbohydrate Classifications:
 Monosaccharides: single sugar
•
Examples: glucose, galactose, fructose, ribose
 Disaccharides: two sugars
•
Examples: ma ltose, 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: C
6
H
12
O
6
 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: C
6
H
12
O
6
Biologyatsandringham.pbworks.com

S1. Drawing Molecular Diagrams
Ribose: C
5
H
10
O
5
 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: C
5
H
10
O
5 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  www.Ib.bionija.com.au
maltose

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 nonliving matter

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