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Organic ChemistryMs. NapolitanoHonors Biology
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Introduction to Orgo Organic chem – the study of C based
compounds (must have both C & H)
Why Carbon? It’s versatile! 4 valence electrons (4 covalent bonds) Form simple or complex compounds C chains form backbone of most biological
molecules (straight, bent, double bond, rings)
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Hydrocarbons Hydrocarbons
ONLY consist of C & H
Importance – store energy
Hydrophobic
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Organic Shorthand
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Isomers Isomers – same number of
atoms per element, different arrangement
3 types: Structural – differ in covalent
partners Geometric – differ in
arrangement around a double bond
Enantiomers – mirror images of each other
Different structure means different function!
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Functional Groups Functional groups – parts of organic molecules
that are most commonly involved in chemical reactions
replace H in hydrocarbons
Most are hydrophilic
Variation of life is due to molecular variation
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Functional Groups
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Isomers
Structural Isomers
Geometric Isomers
Enantiomers
cis trans
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10/29 – Do Now Draw the following compounds using organic
shorthand.
Draw out all hydrogens and carbons for the following compounds. What is the chemical formula?
C4H9OH1. 2. 3.
4. C4H8
5. 6. 7. 8.
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Practice Problem Draw the following compound (Retinol – Vitamin A)
using organic shorthand.
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Isomers Isomers – same number of
atoms per element, different arrangement
3 types: Structural – differ in covalent
partners Geometric – differ in
arrangement around a double bond
Enantiomers – mirror images of each other
Different structure means different function!
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Cyanide is an organic compound.
1 2
0%0%
1. True2. False
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What kind of isomers are these?
1 2 3
0% 0%0%
1. Structural2. Geometric3. Enantiomers
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This is a fatty acid. What type of isomer would you expect to see?
1 2 3
0% 0%0%
1. Structural2. Geometric3. Enantiomers
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Functional Groups Functional groups – parts of organic molecules
that are most commonly involved in chemical reactions
replace H in hydrocarbons
Most are hydrophilic
Variation of life is due to molecular variation
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Functional Groups
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Macromolecules Huge biological
molecules!
4 classes: Carbohydrates Lipids Proteins Nucleic Acids
Polymers – long molecule made of monomers
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Polymerization
Building dimers or polymers Condensation rxn AKA dehydration
synthesis: Monomer-OH + monomer-H dimer + H2O
Breaking down dimers or polymers Reverse rxn called hydrolysis Dimer + H2O monomer-OH + monomer-H
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The breaking down of foods during digestion is an example of dehydration synthesis.
1 2
0%0%
1. True2. False
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The breaking down of foods during digestion is an example of dehydration synthesis.
1 2
0%0%
1. True2. *False
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Amino acids (shown below) are linked together to form proteins. This is an example of dehydration synthesis.
1 2
0%0%
1. True2. False
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Amino acids (shown below) are linked together to form proteins. This is an example of dehydration synthesis.
1 2
0%0%
1. *True2. False
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Carbohydrates Cells get most of their energy from carbs
Carbs are sugars, most end in “-ose”
Multiple of molecular formula: CH2O Glucose: C6H12O6
Carbonyl group
Multiple hydroxyl groups
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Carbohydrates Monosaccharides
Monomers: simple sugars w/ 3-7 carbons Ex. (C6H12O6): Glucose, Fructose, Galactose
Disaccharide – formed by 2 monosaccharides forming a glycosidic linkage by dehydration synthesis
Ex: glucose + glucose maltose + H2O glucose + fructose sucrose + H2O glucose + galactose lactose + H2O
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Carbohydrates
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Carbohydrates Polysaccharides: 100’s – 1000’s of monosaccharides
joined by glycosidic linkages
Storage polysaccharides Starch
Plants – stored in plastids Made entirely of glucose - helical
Glycogen Animals – stored in liver & muscle (in vertebrates) Made entirely of glucose - branched
Structural polysaccharides Cellulose – plant cell walls
Made of glucose – linear Chitin
Exoskeleton of arthropods & fungi cell walls
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A compound has the molecular formula C5H10O5. Is it a carbohydrate?
1 2
0%0%
1. Yes2. No
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A compound has the molecular formula C5H10O5. Is it a carbohydrate?
1 2
0%0%
1. *Yes2. No
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Two monosaccharides are joined together by hydrolysis to form a disaccharide.
1 2
0%0%
1. True2. False
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Two monosaccharides are joined together by hydrolysis to form a disaccharide.
1 2
0%0%
1. True2. *False
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Which of the following is only made in animals?
1 2 3
0% 0%0%
1. Collagen2. Glycogen3. Starch
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Which of the following is only made in animals?
1 2 3
0% 0%0%
1. Collagen2. *Glycogen3. Starch
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Which of the following is only made by fungi?
1 2 3 4
0% 0%0%0%
1. Collagen2. Glycogen3. Starch4. Chitin
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Which of the following is only made by fungi?
1 2 3 4
0% 0%0%0%
1. Collagen2. Glycogen3. Starch4. *Chitin
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11/6 - Do Now Grab your clickers!
Take out your carbohydrates lab.
Draw the dehydration synthesis reaction that joins the following two molecules:
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Lipids No polymers!
Hydrophobic (mostly hydrocarbons)
Store energy efficiently (2x more than carbs!)
Types : Fats & oils Phospholipids Steroids Waxes
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Fats & Oils Fat = dehydration synthesis of:
Glycerol C3H5(OH)3
Fatty acid: 16 or 18 carbon hydrocarbon chain w/ carboxyl group
Glycerol + 3 fatty acid chains = triglyceride + 3 H2O
Function: Energy storage Insulation Protective cushioning around organs
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Saturated Fats No double bonds between carbons
Saturated with hydrogens
Solid at room temperature
Mostly animal fat
Ex: butter, lard, adipose
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Unsaturated Fats 1 or more double bonds between carbons
Bent or kinked chains
Liquid at room temperature
Mostly plant or fish fat
Ex: olive oil, cod liver oil, corn oil
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Phospholipids Glycerol + 2 fatty acids + phosphate
Phosphate head = hydrophilic
Fatty acid tails = hydrophobic
Form a bilayer in water
Makes up cell membranes
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Phospholipids
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Steroids 4 fused carbon rings
with various functional groups
Ex: cholesterol Component of cell
membrane & many hormones
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11/12 – Do Now Take out your lipids HW from the
weekend.
Grab your clickers!
Fill out the the Venn Diagram comparing carbs and lipids.Carb
sLipids
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Which of the following is a class of molecules that encompasses all of the
other molecules listed?
1 2 3 4 5 6
0% 0% 0%0%0%0%
1. Triglycerides2. Waxes3. Lipids4. Fatty acids5. Sterols6. Phospholipids
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Which of the following is a class of molecules that encompasses all of the
other molecules listed?
1 2 3 4 5 6
0% 0% 0%0%0%0%
1. *Triglycerides2. Waxes3. Lipids4. Fatty acids5. Sterols6. Phospholipids
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One molecule of fat is made by joining three molecules of _________ to one
molecule of _________ .
1 2 3 4
0% 0%0%0%
1. Glycerol, fatty acid
2. Sterols, phosphate
3. Phosphate, sterols
4. Fatty acid, glycerol
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One molecule of fat is made by joining three molecules of _________ to one
molecule of _________ .
1 2 3 4
0% 0%0%0%
1. Glycerol, fatty acid
2. Sterols, phosphate
3. Phosphate, sterols
4. *Fatty acid, glycerol
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Which of the following is most likely to have all single bonds in its fatty acid
chain?
1 2 3 4
0% 0%0%0%
1. Coconut oil2. Sunflower oil3. Canola oil4. Olive oil
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Which of the following is most likely to have all single bonds in its fatty acid
chain?
1 2 3 4
0% 0%0%0%
1. *Coconut oil2. Sunflower oil3. Canola oil4. Olive oil
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Which of the following statements about saturated fats is true?
1 2 3 4
0% 0%0%0%
1. They contain 1+ double bonds in the hydrocarbon tail.
2. They contain the maximum number of hydrogens in the hydrocarbon tail
3. They make up the majority of plant oils.
4. They are healthier for you then unsaturated fats.
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Which of the following statements about saturated fats is true?
1 2 3 4
0% 0%0%0%
1. They contain 1+ double bonds in the hydrocarbon tail.
2. *They contain the maximum number of hydrogens in the hydrocarbon tail
3. They make up the majority of plant oils.
4. They are healthier for you then unsaturated fats.
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Little Debbie Swiss Rolls Hostess Cupcakes
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11/14 – Do Now Get your clickers! Answer the following questions:
1. Which two amino acids are shown as the reactants?2. Draw the product.3. What type of reaction is this?4. What is the name of the newly formed bond? 5. Predict the following: The long chain made by the joining of
MANY amino acids using the newly formed BONDS is called a _____________.
+
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Proteins Functions: enzymes, structural support, storage,
transport, cellular communication, movement, defense
Monomer = amino acid Short C chain Amino group Carboxylic acid group “R” group determines type
Cells use 20 different amino acids to build 1000’s of different proteins
Amino acids linked by peptide bonds via dehydration synthesis to form polymers – polypeptides
Chaperonins assist in protein folding
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Protein Structure 10 Structure
- Sequence of amino acids (length vary)- Determined by genes
20 Structure How polypeptide folds or coils Α helix β pleats
30 Structure - 3D (fold onto itself) H bonds Hydrophobic interaction Disulfide bridges
40 Structure – bonds to other polypeptides 2 or more polypeptide chains bonded together
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Protein Conformation Structure of a protein is directly related to function
Protein conformation is determined when it is synthesized, and it is maintained by chemical interactions
Protein conformation also depends on environmental factors: pH, salt concentration, temp…etc
Protein can be denatured – unravel and lose conformation, therefore biologically inactive. When conditions change again, protein can be renatured
(restored to normal)
http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter3/protein_denaturation.html
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11/18 – Do Now Happy Monday!
Please get your clickers!
Take out your lipids & proteins lab.
Add proteins to your Venn Diagram! Draw & fill in the following:
Carbs Lipids
Proteins
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All of the following are true about both amino acids and monosaccharides EXCEPT:
1 2 3 4
0% 0%0%0%
1. They are monomers.
2. The are linked to other amino acids & monosaccharides (respectively) by dehydration synthesis.
3. They are organic molecules.
4. They are always arranged in a ring.
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All of the following are true about both amino acids and monosaccharides EXCEPT:
1 2 3 4
0% 0%0%0%
1. They are monomers.
2. The are linked to other amino acids & monosaccharides (respectively) by dehydration synthesis.
3. They are organic molecules.
4. *They are always arranged in a ring.
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All amino acids contain all of the following groups EXCEPT:
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1. amino2. hydroxyl3. carboxyl4. central carbon
between 2 functional groups
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All amino acids contain all of the following groups EXCEPT:
1 2 3 4
0% 0%0%0%
1. amino2. *hydroxyl3. carboxyl4. central carbon
between 2 functional groups
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All proteins have a primary structure.
1 2
0%0%
1. True2. False
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All proteins have a primary structure.
1 2
0%0%
1. *True2. False
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The helix that forms in a protein chain as a result of hydrogen bonds & other
weak forces is an example of:
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1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Nonlinear structure
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The helix that forms in a protein chain as a result of hydrogen bonds & other
weak forces is an example of:
1 2 3 4
0% 0%0%0%
1. Primary structure
2. *Secondary structure
3. Tertiary structure
4. Nonlinear structure
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In the stable form of a protein, what is generally oriented to the interior of
the protein molecule?
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0% 0%0%0%
1. Hydrophilic portions
2. Hydrophobic portions
3. Large portions4. Random
portions
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In the stable form of a protein, what is generally oriented to the interior of
the protein molecule?
1 2 3 4
0% 0%0%0%
1. Hydrophilic portions
2. *Hydrophobic portions
3. Large portions4. Random
portions
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Nucleic Acids 2 types:
DNA (deoxyribonucleic acid) Found in nucleus of eukarya Double stranded helix Provides directions for its own replication Also directs RNA synthesis
Though RNA controls 10 structure of proteins
RNA (ribonucleic acid) Single stranded, variety of shapes Transfers information from nucleus to cytoplasm (where
proteins are made)
DNA RNA Proteins
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Structure of Nucleic Acids
Monomers – nucleotides composed of 3 parts: Pentose (ribose or deoxyribose) Phosphate group Nitrogenous base
Pyrimidines – 6 membered rings of C & N Cytosine (C) Thymine (T)….DNA only Uracil (U)… RNA only
Purines – 6 membered ring fused to 5 membered ring of C & N Adenine (A) Guanine (G)
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Nucleotide Structure
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Bonding of Nucleotides
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Bonding of Nucleotides
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Write the complementary DNA strand for the
following:1. CGTAAGCGCTAATTA
2. TCTTAAATGATCGATC
3. AATGAATAGCTAGCTT
4. GGCATTCGCGATCATG
5. CGTTAGCATGCTTCAT
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Write the complementary DNA strand for the
following:1. CGTAAGCGCTAATTA
GCATTCGCGATTAAT
2. TCTTAAATGATCGATC
AGAATTTACTAGCTAG
3. AATGAATAGCTAGCTT
TTACTTATCGATCGAA
4. GGCATTCGCGATCATG
CCGTAAGCGCTAGTAC
5. CGTTAGCATGCTTCAT
GCAATCGTACGAAGTA
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Write the complementary RNA strand for the
following:1. CGTAAGCGCTAATTA
2. TCTTAAATGATCGATC
3. AATGAATAGCTAGCTT
4. GGCATTCGCGATCATG
5. CGTTAGCATGCTTCAT
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Write the complementary RNA strand for the
following:1. CGTAAGCGCTAATTA
GCAUUCGCGAUUAAU
2. TCTTAAATGATCGATC
AGAAUUUACUAGCUAG
3. AATGAATAGCTAGCTT
UUACUUAUCGAUCGAA
4. GGCATTCGCGATCATG
CCGUAAGCGCUAGUAC
5. CGTTAGCATGCTTCAT
GCAAUCGUACGAAGUA
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ATP Not a macromolecule, but still important
for life!
Adenosine Triphosphate (ATP) – primary energy transferring molecule in the cell
ATP ADP + Pi + Energy