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Lab 6 – Organic II – Amines and Amides in Health CHEM 2701 – Pre-Health Chemistry II (standard) Overview • Amines and amides are abundant in nature. • They are a major component of proteins and enzymes, nucleic acids, drugs and much more. Amines • A class of functional group containing a nitrogen (N) atom bonded to carbon atoms (C) Amides • A class of functional group containing a nitrogen (N) atom bonded to a carbonyl group (C = O) Examples of Amines and Amides Many drugs and hormones contain amines, amides or both. Common name Description Molecular formula Trimethylamine Responsible for the odor of rotting fish Putrescine Very strong smell, found in rotting flesh; partially responsible for the odor of urine and bad breath NH2 – CH2 – CH2 – CH2 – CH2 – NH2 Morphine Painkiller Heroin More powerful than morphine. Crosses the blood brain barrier more readily than morphine. Cocaine Stimulant made from the coca plant. Causes large amounts of dopamine to build up in the brain. Feelings range from sensations of energy and alertness to irritability and paranoia. Caffeine Blocks adenosine receptors in the brain. Adenosine in the brain helps humans feel tired. When adenosine receptors are blocked, you feel more alert. Melatonin A naturally occurring hormone released by the pineal gland. Triggered in darkness. Causes drowsiness. Urea Crystalline compound; main product in the breakdown/metabolism of proteins; excreted in urine Dopamine A hormone and neurotransmitter. Role in motor control, motivation and arousal. Parkinson’s disease, a condition resulting in “resting tremors” and motor impairment, results when the dopamine production pathway in neurons is reduced. CHEM 2701 – Lab 6 – Organic II Chemistry II for Pre-Health Sciences (online) ____/23 marks (6% of final grade) Rationale Organic molecules may look like 2D objects when drawn on paper. But just like you learned about VSEPR (i.e. tetrahedral, trigonal pyramidal etc.) in CHEM 1701, molecules have a 3D shape. In this lab you will get a chance to build organic molecules to see their 3D shape come to life. You will also explore applications of amines and amides in healthcare. Learning objectives The following learning objectives are covered in this lab. · CLO 8 Prepare for and conduct laboratory experiments to investigate scientific questions using appropriate techniques. · LO 4.30 Identify the amine and amide functional groups in organic compounds · LO 4.31 Name common examples and uses of amines and amides (i.e. neurotransmitters) · LO 4.32 Discuss the importance of hydrogen bonding in amines and amides Procedure & Observations · Be sure to review the lab in its entirety before beginning. · Throughout the lab you are required to photograph parts of your experiment and include these photos in your final submission. Handing in your lab When complete, submit your work to the appropriate folder in DC Connect under Activities Assignments. Other notes · A maximum 10% penalty may be applied for spelling, grammar and mechanics. · When rounding final answers, apply the rounding rules as discussed in this course. · Make sure all answers are in full sentences using appropriate scientific terminology. · Note how many marks are associated with a question and use that as a guide when structuring your response. Materials Soft materials to act as “atoms” and a more sturdy material to join the atoms and to represent bonds as you build molecules in this lab. Below are some suggestions but please use whatever you already have at home. Do not go out to a store to purchase materials. Practice social distancing. If you are struggling with finding materials at home, email me and I will suggest some alternatives. · toothpicks (or some other object for connecting, even a hair pin will work) · ~10 small marshmallows of one color [or raisins, candy, cereal, beans of one color etc.] · ~20 small marshmallows of a second color [or raisins, candy, cereal, beans of a second color etc.] · ~20 small marshmallows of a third color [or raisins, candy, cereal, beans a third color etc.] Experiment 1 – Building Organic Models[14 marks] Background: The following functional groups learned in this course do not contain oxygen: alkane, alkene, alkyne. The following functional groups learned in this course do contain oxygen: amide, alcohol, carboxylic acid, aldehyde, ketone, ester, ether. Materials Remember you can use something other than marshmallows – anything you have at home – the items just have to have the right texture to build molecules below. · toothpicks (or some other object for connecting, even a hair pin will work) · ~10 small marshmallows of one color · ~20 small marshmallows of a second color · ~20 small marshmallows of a third color Procedure 1. [1 mark] Each of your marshmallows (or other material) will represent an element. Identify which element each of your materials will represent. Carbon atoms (C) Hydrogen atoms (H) Oxygen atoms (O) 2. Use your toothpicks and marshmallows (or other items) to build each of the organic molecules below. 3. As you work, complete the table below to provide the missing information for each organic molecule. a. Identify the functional group (i.e. alkene, alcohol etc.) b. Provide the IUPAC name c. Write the condensed formula d. Write the molecular formula (CxHy) e. Identify the bond type (i.e. single, double, triple) 4. Photograph each molecule and include the photo below. Data and Analysis 1. [3 marks] Use your materials to build each molecule shown below. Then record the information indicated and photograph your molecules. Insert photos below. Click directly on the photo space holder to insert your photo. Table 1: Functional groups without oxygen Functional group IUPAC name Condensed formula Molecular formula Bond type Photo of molecule CH3 – CH = CH2 propyne propane 2. [1 mark] As you add more bonds between carbons, what happens to the number of hydrogen atoms in the molecule? Comment in 1-2 sentences. 3. [1 mark per row = 4 marks] Use your materials to build each molecule shown below. Then record the information indicated and photograph your molecules. Insert photos below. Click directly on the photo space holder to insert your photo. Table 2: Functional groups with oxygen Functional group Common name IUPAC name Structural formula Photo of molecule acetone formaldehyde isopropyl alcohol OH | CH3 – CH – CH3 formic acid 4. [3 marks] How are a carbonyl group and hydroxyl group similar? How are they different? Comment in 2-3 sentences. Carbonyl Hydroxyl What it looks like Similarity Difference 5. Rubbing alcohol often contains a mixture of isopropyl alcohol and ethanol. The structural formula for isopropyl alcohol is provided in Table 2: Functional groups with oxygen above. a. [1 mark] Draw the structural formula for ethanol. b. [1 mark] Which alcohol, isopropyl alcohol or ethanol, would you expect to be more soluble in water? Why? [HINT: consider the length of each alcohol]. Experiment 2 – Amines and Amides in Health[6 marks] Procedure 1. Refer to the printed resources in the lab 6 assignments folder for additional information to complete this section. 2. Summarize the function of each molecule in 1-2 points. Data and Analysis 1. [1 mark per row = 5 marks] Record all information below. Molecule Common name Function 2. [1 mark] What is the key difference between the amine and amide functional group? Experiment 3 – Hydrogen Bonding in Amines and Amides[3 marks] Background: The presence of nitrogen in amines and amides results in polarity in these molecules. The polarity allows these molecules to take part in hydrogen bonding. The N-H bond is not as polar as the O-H bond thus the hydrogen bonding seen is not as strong. The ability of amines and amides to take part in hydrogen bonding is important for maintaining the structure of proteins and DNA. Hydrogen bonding holds nitrogenous base pairs together in the DNA double helix. Hydrogen bonding between neighboring amides Hydrogen bonding between neighboring amines Data and Analysis 1. [1 mark] Highlight/circle the hydrogen bonds in the nucleotide base pairing below. [HINT: there are two hydrogen bonds] 2. [1 mark] Which nitrogenous base, adenine and thymine, contains an amide?__________________ 3. [1 mark] What do you think would happen if hydrogen bonding did not happen in DNA? CHEM 2701 – Lab 6 – Organic IIPage 4 of 4