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Organic Chemistry & Macromolecules
CP Biology
Building Blocks of Life ch 6
SPI.3210.1.3; SPI.3210.1.4
Vocabulary Activity
• Organic compound
A i id
• Nucleic acid
• Nucleotide• Amino acid
• Carbohydrate
• Lipid
• Macromolecule
• Polymer
• Protein
The Importance of Carbon
• Most versatile building blocks of
molecules
• Variation in carbon skeletons = diversity of
organic molecules
Carbon
• 4 valence electrons – little tendency to gain or loose electrons
• Capable of forming double and triple covalent bonds
• Can form 4 single covalent bonds
• Can combine with atoms of many different elements
Organic Compounds
• Carbon forms by far the greatest number of different compounds.
• Compounds containing only hydrogen and carbon are called hydrocarbons
– Simplest: methane (CH4)
Valences for the major elements of organic molecules
carbon dioxidecarbon dioxide
The structural formula, O = C = O, shows that each atom has completed its valence shells
CO2 can be classified as either organic or inorganic
CO2 is the source for all organic molecules in organisms via the process of photosynthesis.
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• Carbon chains form the skeletons of most organic molecules.
Skeletons vary in length and may be
Variation = Diversity
– Skeletons vary in length and may be straight, branched, or closed rings.
– Single and double bonds
Arrangement of Carbon Atoms
Double bond
Methane
Ethane
Ethene
Hydrocarbons
Butane
IsobutaneIsobutane
Hexane
Cyclohexane
The shapes of three simple organic molecules
Alkanes
• C‐H single bonds
• Hydrocarbons
• Straight chains, branched or cyclicStraight chains, branched or cyclic
• Name ends in –ane– Methane
– Ethane
– Propane
– Butane
Alkane Chemical Formulas
Notice hexane is a straight chain whereas the otherswhereas the others are branched.
The numbers show to which carbon the side chain is attached.
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Alkenes
• Double carbon bonds and single carbon‐hydrogen
bonds:
C=C and C‐H
• Name ends in ene• Name ends in ‐ene
• Simplest is ethene (ethylene)– C2H4
– Formed when fruit ripens
• Propene used to make rubbing alcohol and some plastics
Variations in carbon skeletons:Alkanes and Alkenes
Alcohols
• One or more ‐OH groups (hydroxyl)
• Name ends in –ol
– Methanol
– Ethanol
• Behave similarly to water molecules
• Liquid at room temp
• Much higher boiling point than other organic molecules of the same size
Part 2
Biochemical Compounds
• Naturally occurring organic compounds
• Important to living things
– Carbohydrates– Carbohydrates
– Proteins
– DNA
• All are polymers
Polymers
• Form when small organic molecules bond to form long chains (string of pearls)
Natural Man MadeNatural
•Cotton
•Wool
•Wood
•Rubber
•DNA
Man Made
•Plastic (flexible, easily molded)
•Fibers ( long thin chains)
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Polymers
• Some are long strings, like cooked spaghetti, that slide past each other
– Bending or flexingg g
– Ex. plastic soda bottle
• Some are meshed like a net
– Elastic property or memory
– Ex. rubber band
Carbohydrates
• Sugar
– Glucose
– Stored as glycogenStored as glycogen
• Starch
– Many glucose molecules bonded together
• Repeating glucose units
• Provide energy
Chapter 3Carbohydrates
Chapter 3Disaccharides
Tests for Carbohydrates
• Reducing sugar– Benedict’s reagent and heat– Orange precipitate indicates the presence of reducing sugar
• Non‐reducing sugar– Test done on solutions known not to contain reducing sugars
– Hydrolyze by heating with dilute HCl, then neutralize with sodium hydrogen carbonate, then carry out the test for reducing sugar
• Starch– Use iodine in potassium iodide solution– Blue‐black color indicates the presence of starch
Amino Acids
• Made of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.
• Bond together to make proteins‐ building bl kblocks
• 20 amino acids in naturally occurring proteins
• Have amino and carboxyl groups
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Chapter 3Amino Acid
Amino Acids
• Two amino acids can link together
– Condensation reaction
– Forms a dipeptideForms a dipeptide
– Bond is called a peptide bond
Condensation Reaction(or Dehydration Synthesis)
• The process of connecting monomers to make a polymer.– This process requires energy and is aided by enzymes.
– Removes water molecule
– One monomer provides a hydroxyl group and the other provides a hydrogen
Amino Acids
• Dipeptide can be broken with hydrolysis reaction
– Bond breaks by adding water moleculey g
Proteins• Proteins are large molecules made of long chains of amino acids
• 20 different amino acids
Each has:
– Amine groupAmine group
Carboxyl group
R group: represents a range of different groups
– Amine group
– Carboxyl group
– A variable R group (side chain)
• The R group determines the characteristics of the amino acid
– All are attached to a central carbon
group group
Central Carbon
• Determines the activity of the protein
• Primary structure: (The first l l) th f i
Conformation
level) the sequence of amino acids
• Secondary structure
• Tertiary structure
• Quaternary structure
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• Primary– Chain of amino acids
• Secondary structure– Alpha helix
– Held together by hydrogen bonds
• Tertiary– Held together by either
Beta‐
• Hydrogen bonds
• Ionic bonds
• Disulfide bonds
• Hydrophobic interactions
– Globular structure
• Quaternary– Same bonds as tertiary
– More than one A.A. chain
Beta‐
Proteins continued
Physical & Chemical Changes
• Alterations in pH, salt concentration, temperature, or other factors can denaturethe proteinthe protein.
• Disrupt bonds that hold them together– Ex. Mutations in DNA
Proteins continued
• Function in:
– support
– storage
– transport of other substances
i t ll l i li– intercellular signaling
– movement
– and defense against foreign substances
Test for proteins
• Add biuret solution.
• Purple color indicates presence of a protein
LipidsDiverse Hydrophobic Molecules
• Most are hydrophobic due to covalent bonds
• Highly diverse in form and function• Highly diverse in form and function
–3 forms
• fats
• phospholipids
•steroids
Fats
• Constructed of glycerol and fatty acids
• Used for energy
• Insulation and cushions vital organs• Insulation and cushions vital organs
• Fatty acid chains are very hydrophobic
– may vary in length and in types of bonds
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Chapter 3Fatty Acids
The structure of a phospholipid
Saturated and Unsaturated fats and fatty acids
Notice the straight and kinked nature
Triglyceride
Fats continued
• Saturated Fats:
– Straight chains
– Have no double bonds between carbons• they are “saturated” with hydrogen
– Solid at room temperature
– Most come from animal sources
– May lead to heart disease
Fats continued
• Unsaturated Fats
–One or more double bonds between carbons
Causes fatty acid chain to kink or–Causes fatty acid chain to kink or bend
– Liquid at room temperature
–Plant and fish fats (also called oils)
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Phospholipids
• Two fatty acids
– a glycerol and a phosphate group
• Phosphate group makes the head hydrophilicy p
• Tails are still hydrophobic
• Major component of cell membranes
Steroids
• Lipids with 4 fused carbon rings
• Steroids are different due to the functional groups attached
– Cholesterol is an important component of cellCholesterol is an important component of cell membranes
– Many are hormones
Test for Lipids
• Mix the substance to be tested with absolute ethanol.
• Decant the ethanol into water
• A milky emulsion indicates the presence of lipid
DNA
• Genetic Material
• DNA must copy itself
• Certain proteins unzip• Certain proteins unzip, pair, and reconnect DNA strands
DNA is made up of Nucleotides
Structure:
• Each nucleic acid is made of nucleotides
A it b i (A d– A nitrogen base: purines (A and G), and pyrmidines (C, T and U)
– Pentose sugar: Ribose or Deoxyribose
– Phosphate group
• The sequence of the bases are unique for each gene.
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DNA and RNA protein
Enzymes
• Enzymes speed up chemical reactions and bind to specific substrates.
– Lock and keyy
– binding of a substrate with an enzyme causes a change in the enzyme’s shape and reduces the activation energy of the reaction.
Enzyme: Important Properties
• Enzymes are catalytic proteins
• They can be used again and again
• They are influenced by temperature and pH• They are influenced by temperature and pH
• Regulate the movement of molecules through metabolic pathways
Factors that Affect Enzyme Activity
‐Temperature
*Cold temps slow the reaction.
*Hot temps denature the enzyme.
*Warm temps are just right
‐pH
*The proper pH depends on the enzyme.
enzyme
substrate A
The substrate molecules fit the shape of the enzyme
substrate B
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substrates combine temporarily with enzyme
enzyme joins substrates together
new compound releasedby enzyme
enzyme unchangedand ready fornext reaction
A ‘breaking‐down’ reaction
the shape of the substrate molecule fits the enzyme shapethis is called
the active siteof the enzyme
Intermediate stage (1)
substrate combinestemporarily with enzyme
enzyme will breakmolecule here
Intermediate stage (2)
substrate splits andseparates from enzyme
Final break‐down products
end‐products
enzyme ready fornext reaction
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The Digestive Enzymes
Site
Mouth
Stomach
Small intestine(from pancreas)
Enzyme Role in Digestion
Salivary amylase
Pepsin
Amylase
Breaks down starches into disaccharides
Breaks down proteins into large peptides
Continues the breakdown of starch
Small intestine
Trypsin
Lipase
Maltase, sucrase, lactase
Peptidase
Continues the breakdown of protein
Breaks down fat
Breaks down remaining disaccharides into monosaccharides
Breaks down dipeptides into amino acids.
Resources
Campbell et.al. (2004) Biology: Exploring Life. Prentice Hall
Campbell, N., Reece, J. (2005). AP Edition Biology, 7th ed. San Francisco,
CA: Benjamin Cummings Publishing Company.
Jones, M., Fosbery, R., Taylor , D., & Gregory, J. (2007). AS Level and A
Level Biology, 2nd ed. Cambridge, UK: Cambridge University Press.
Mackean, D. (2009). IGCSE Biology, 2nd ed. London, UK: Hodder
Education.