Ms. Napolitano Honors Biology Organic Chemistry Ms. Napolitano Honors Biology

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)

Hydrocarbons Hydrocarbons ONLY consist of C & H Importance – store energy Hydrophobic

Organic Shorthand

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!

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

Functional Groups

Isomers Geometric Isomers Structural Isomers cis trans Enantiomers

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? 1. 2. 3. C4H9OH 4. C4H8 5. 6. 7. 8.

Practice Problem Draw the following compound (Retinol – Vitamin A) using organic shorthand.

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!

Cyanide is an organic compound. True False

What kind of isomers are these? Structural Geometric Enantiomers

This is a fatty acid. What type of isomer would you expect to see? Structural Geometric Enantiomers

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

Functional Groups

Macromolecules Huge biological molecules! 4 classes: Carbohydrates Lipids Proteins Nucleic Acids Polymers – long molecule made of monomers

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

The breaking down of foods during digestion is an example of dehydration synthesis. True False

The breaking down of foods during digestion is an example of dehydration synthesis. True *False

Amino acids (shown below) are linked together to form proteins Amino acids (shown below) are linked together to form proteins. This is an example of dehydration synthesis. True False

Amino acids (shown below) are linked together to form proteins Amino acids (shown below) are linked together to form proteins. This is an example of dehydration synthesis. *True False

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

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

Carbohydrates

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

A compound has the molecular formula C5H10O5. Is it a carbohydrate? Yes No

A compound has the molecular formula C5H10O5. Is it a carbohydrate? *Yes No

Two monosaccharides are joined together by hydrolysis to form a disaccharide. True False

Two monosaccharides are joined together by hydrolysis to form a disaccharide. True *False

Which of the following is only made in animals? Collagen Glycogen Starch

Which of the following is only made in animals? Collagen *Glycogen Starch

Which of the following is only made by fungi? Collagen Glycogen Starch Chitin

Which of the following is only made by fungi? Collagen Glycogen Starch *Chitin

11/6 - Do Now Grab your clickers! Take out your carbohydrates lab. Draw the dehydration synthesis reaction that joins the following two molecules:

Lipids No polymers! Hydrophobic (mostly hydrocarbons) Store energy efficiently (2x more than carbs!) Types : Fats & oils Phospholipids Steroids Waxes

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

Saturated Fats No double bonds between carbons Saturated with hydrogens Solid at room temperature Mostly animal fat Ex: butter, lard, adipose

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

Phospholipids Glycerol + 2 fatty acids + phosphate Phosphate head = hydrophilic Fatty acid tails = hydrophobic Form a bilayer in water Makes up cell membranes

Phospholipids

Steroids 4 fused carbon rings with various functional groups Ex: cholesterol Component of cell membrane & many hormones

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. Carbs Lipids

Which of the following is a class of molecules that encompasses all of the other molecules listed? Triglycerides Waxes Lipids Fatty acids Sterols Phospholipids

Which of the following is a class of molecules that encompasses all of the other molecules listed? *Triglycerides Waxes Lipids Fatty acids Sterols Phospholipids

One molecule of fat is made by joining three molecules of _________ to one molecule of _________ . Glycerol, fatty acid Sterols, phosphate Phosphate, sterols Fatty acid, glycerol

One molecule of fat is made by joining three molecules of _________ to one molecule of _________ . Glycerol, fatty acid Sterols, phosphate Phosphate, sterols *Fatty acid, glycerol

Which of the following is most likely to have all single bonds in its fatty acid chain? Coconut oil Sunflower oil Canola oil Olive oil

Which of the following is most likely to have all single bonds in its fatty acid chain? *Coconut oil Sunflower oil Canola oil Olive oil

Which of the following statements about saturated fats is true? They contain 1+ double bonds in the hydrocarbon tail. They contain the maximum number of hydrogens in the hydrocarbon tail They make up the majority of plant oils. They are healthier for you then unsaturated fats.

Which of the following statements about saturated fats is true? They contain 1+ double bonds in the hydrocarbon tail. *They contain the maximum number of hydrogens in the hydrocarbon tail They make up the majority of plant oils. They are healthier for you then unsaturated fats.

Little Debbie Swiss Rolls Hostess Cupcakes

11/14 – Do Now + Get your clickers! Answer the following questions: Which two amino acids are shown as the reactants? Draw the product. What type of reaction is this? What is the name of the newly formed bond? Predict the following: The long chain made by the joining of MANY amino acids using the newly formed BONDS is called a _____________.

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

Protein Structure 10 Structure 20 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

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

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

All of the following are true about both amino acids and monosaccharides EXCEPT: They are monomers. The are linked to other amino acids & monosaccharides (respectively) by dehydration synthesis. They are organic molecules. They are always arranged in a ring.

All of the following are true about both amino acids and monosaccharides EXCEPT: They are monomers. The are linked to other amino acids & monosaccharides (respectively) by dehydration synthesis. They are organic molecules. *They are always arranged in a ring.

All amino acids contain all of the following groups EXCEPT: hydroxyl carboxyl central carbon between 2 functional groups

All amino acids contain all of the following groups EXCEPT: *hydroxyl carboxyl central carbon between 2 functional groups

All proteins have a primary structure. True False

All proteins have a primary structure. *True False

The helix that forms in a protein chain as a result of hydrogen bonds & other weak forces is an example of: Primary structure Secondary structure Tertiary structure Nonlinear structure

The helix that forms in a protein chain as a result of hydrogen bonds & other weak forces is an example of: Primary structure *Secondary structure Tertiary structure Nonlinear structure

In the stable form of a protein, what is generally oriented to the interior of the protein molecule? Hydrophilic portions Hydrophobic portions Large portions Random portions

In the stable form of a protein, what is generally oriented to the interior of the protein molecule? Hydrophilic portions *Hydrophobic portions Large portions Random portions

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

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)

Nucleotide Structure

Bonding of Nucleotides

Bonding of Nucleotides

Write the complementary DNA strand for the following: CGTAAGCGCTAATTA TCTTAAATGATCGATC AATGAATAGCTAGCTT GGCATTCGCGATCATG CGTTAGCATGCTTCAT

Write the complementary DNA strand for the following: CGTAAGCGCTAATTA GCATTCGCGATTAAT TCTTAAATGATCGATC AGAATTTACTAGCTAG AATGAATAGCTAGCTT TTACTTATCGATCGAA GGCATTCGCGATCATG CCGTAAGCGCTAGTAC CGTTAGCATGCTTCAT GCAATCGTACGAAGTA

Write the complementary RNA strand for the following: CGTAAGCGCTAATTA TCTTAAATGATCGATC AATGAATAGCTAGCTT GGCATTCGCGATCATG CGTTAGCATGCTTCAT

Write the complementary RNA strand for the following: CGTAAGCGCTAATTA GCAUUCGCGAUUAAU TCTTAAATGATCGATC AGAAUUUACUAGCUAG AATGAATAGCTAGCTT UUACUUAUCGAUCGAA GGCATTCGCGATCATG CCGUAAGCGCUAGUAC CGTTAGCATGCTTCAT GCAAUCGUACGAAGUA

ATP Not a macromolecule, but still important for life! Adenosine Triphosphate (ATP) – primary energy transferring molecule in the cell ATP   ADP + Pi + Energy