Organic ChemistryMs. NapolitanoHonors 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

Structural Isomers

Geometric Isomers

Enantiomers

cis trans

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.

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.

1 2

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1. True2. False

What kind of isomers are these?

1 2 3

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1. Structural2. Geometric3. Enantiomers

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

1 2 3

0% 0%0%

1. Structural2. Geometric3. 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.

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1. True2. False

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

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1. True2. *False

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

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1. True2. False

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

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1. *True2. 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?

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1. Yes2. No

A compound has the molecular formula C5H10O5. Is it a carbohydrate?

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1. *Yes2. No

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

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1. True2. False

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

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1. True2. *False

Which of the following is only made in animals?

1 2 3

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1. Collagen2. Glycogen3. Starch

Which of the following is only made in animals?

1 2 3

0% 0%0%

1. Collagen2. *Glycogen3. Starch

Which of the following is only made by fungi?

1 2 3 4

0% 0%0%0%

1. Collagen2. Glycogen3. Starch4. Chitin

Which of the following is only made by fungi?

1 2 3 4

0% 0%0%0%

1. Collagen2. Glycogen3. Starch4. *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.Carb

sLipids

Which of the following is a class of molecules that encompasses all of the

other molecules listed?

1 2 3 4 5 6

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1. Triglycerides2. Waxes3. Lipids4. Fatty acids5. Sterols6. Phospholipids

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

One molecule of fat is made by joining three molecules of _________ to one

molecule of _________ .

1 2 3 4

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1. Glycerol, fatty acid

2. Sterols, phosphate

3. Phosphate, sterols

4. Fatty acid, glycerol

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

Which of the following is most likely to have all single bonds in its fatty acid

chain?

1 2 3 4

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1. Coconut oil2. Sunflower oil3. Canola oil4. Olive oil

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

Which of the following statements about saturated fats is true?

1 2 3 4

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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.

Which of the following statements about saturated fats is true?

1 2 3 4

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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.

Little Debbie Swiss Rolls Hostess Cupcakes

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 _____________.

+

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

- 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:

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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.

All of the following are true about both amino acids and monosaccharides EXCEPT:

1 2 3 4

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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.

All amino acids contain all of the following groups EXCEPT:

1 2 3 4

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1. amino2. hydroxyl3. carboxyl4. central carbon

between 2 functional groups

All amino acids contain all of the following groups EXCEPT:

1 2 3 4

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1. amino2. *hydroxyl3. carboxyl4. central carbon

between 2 functional groups

All proteins have a primary structure.

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1. True2. False

All proteins have a primary structure.

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1. *True2. False

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

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1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Nonlinear structure

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

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1. Primary structure

2. *Secondary structure

3. Tertiary structure

4. Nonlinear structure

In the stable form of a protein, what is generally oriented to the interior of

the protein molecule?

1 2 3 4

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1. Hydrophilic portions

2. Hydrophobic portions

3. Large portions4. Random

portions

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

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:1. CGTAAGCGCTAATTA

2. TCTTAAATGATCGATC

3. AATGAATAGCTAGCTT

4. GGCATTCGCGATCATG

5. CGTTAGCATGCTTCAT

Write the complementary DNA strand for the

following:1. CGTAAGCGCTAATTA

GCATTCGCGATTAAT

2. TCTTAAATGATCGATC

AGAATTTACTAGCTAG

3. AATGAATAGCTAGCTT

TTACTTATCGATCGAA

4. GGCATTCGCGATCATG

CCGTAAGCGCTAGTAC

5. CGTTAGCATGCTTCAT

GCAATCGTACGAAGTA

Write the complementary RNA strand for the

following:1. CGTAAGCGCTAATTA

2. TCTTAAATGATCGATC

3. AATGAATAGCTAGCTT

4. GGCATTCGCGATCATG

5. CGTTAGCATGCTTCAT

Write the complementary RNA strand for the

following:1. CGTAAGCGCTAATTA

GCAUUCGCGAUUAAU

2. TCTTAAATGATCGATC

AGAAUUUACUAGCUAG

3. AATGAATAGCTAGCTT

UUACUUAUCGAUCGAA

4. GGCATTCGCGATCATG

CCGUAAGCGCUAGUAC

5. 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