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

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