Week 2 Organic Chem

Our bodies depend on carbon-based materials. The study of carbon-based structures is known as organic chemistry and will be the first topic of this lesson.​

In this concept, we will learn about the four major organic macromolecules: carbohydrates, lipids, nucleic acids, and proteins. ​

We will discuss the chemical reactions that are used to build and breakdown molecules. ​

We will also learn about the structure and functions of proteins. These versatile biomolecules serve in many key roles in the body and is key in areas from the digestion of sugar to the synthesis of DNA.​

Finally, we will discuss nutrients and biomolecules.

Functional Groups​

True or False: Functional groups are sets of atoms that are ionically bonded to the carbon framework; False

Which is the monomer of a polysaccharide?​; Monosaccharide

A nucleotide is made up of a sugar, a phosphate group and a; Nitrogen Base

Carbon Overview​

Carbon is the most important atom for life. Without this atom, life would likely not be possible in any form based on our current understanding of life.​

Organic chemistry starts with a carbon (element: C). It is important that you remember that carbons have 4 unpaired valance electrons (electrons in the outer shell, available for bonding). This will allow the potential for each C to make 4 bonds. In fact, the golden rule of organic chemistry is that C is expected to make 4 bonds.

Carbon Overview​

Carbon is the most important atom for life. Without this atom, life would likely not be possible in any form based on our current understanding of life.​

Organic chemistry starts with a carbon (element: C). It is important that you remember that carbons have 4 unpaired valance electrons (electrons in the outer shell, available for bonding). This will allow the potential for each C to make 4 bonds. In fact, the golden rule of organic chemistry is that C is expected to make 4 bonds.

Functional Groups: Biomolecules​

When we study biomolecules, there are many functional groups present in biomolecules.  ​

The functional groups that we will be seeing most in our exploration of these biomolecules are alcohols, carboxylic acids, amines, and esters.​

The table shows the descriptions of these functional groups, as well as examples of the functional groups highlighted in condensed structural formulas (chemical formulas that show some of the structure of a molecule).​

As noted earlier, the functional groups determine what types of reactions are possible for a given organic chemical. Our bodies depend on these functional groups to build important biomolecules such as proteins, DNA, and fats. This building of biomolecules is known as anabolism. Our bodies also break down compounds, in a process known as catabolism. Both building up and breaking down of biomolecules involve functional groups.  

Recap​: Functional Groups

Carbon is unique because it can accept functional groups.​

Functional groups are sets of atoms that are covalently bonded to the carbon framework.​

Functional groups play significant roles in reactions with other compounds.

Dehydration Synthesis Reaction and Hydrolysis Reaction​

A dehydration synthesis reaction links two monomers together and removes a molecule of water. In cells, your body builds new molecules through this reaction. There are many reactions possible in organic chemistry. We will be focusing in this section on hydrolysis and dehydration; two important classes of reactions that are important in the human body.​

As mentioned in the last section, our body builds and breaks down biomolecules. These two reactions both involve water. In general, hydrolysis involves breaking down organic molecules and dehydration synthesis involves the building up organic molecules.

Hydrolysis​

In hydrolysis, water is inserted into an organic functional group, such as an ester, and breaks the molecule apart. This type of reaction is especially common in digestion as the body breaks down food.​

In this image, an organic molecule with an ester group is broken down by the addition of water.​

In the reaction, we see how the addition of water breaks the original molecule (methyl ethanoate) into a carboxylic acid and alcohol. Examples of hydrolysis reactions include the breaking down of sugar in the body as well as many of the reactions involved in digestion.

Dehydration Synthesis Reaction​

Dehydration synthesis reactions are used by the body to build a number of important compounds, including fats and proteins. In a dehydration reaction, water is synthesized from the formation of a new bond.​

In this image, we see how the carboxylic acid group reacts with an alcohol group to release a water molecule and form an ester group (COOC). We can see here how two molecules are joined to form a new molecule.

Dehydration Synthesis Reaction​

Dehydration synthesis reactions are used by the body to build a number of important compounds, including fats and proteins. In a dehydration reaction, water is synthesized from the formation of a new bond.​

In this image, we see how the carboxylic acid group reacts with an alcohol group to release a water molecule and form an ester group (COOC). We can see here how two molecules are joined to form a new molecule.

Hydrolysis, Dehydration, and Biomolecule Formation​

We see here that hydrolysis and dehydration are, in many ways, opposites. Hydrolysis typically results in the breaking down of molecules, while dehydration involves forming larger molecules. Both of these reactions are vital parts of metabolism. These reactions are also key for the formation and digestion of biomolecules we will be studying.

Hydrolysis Reactions: Using water to break down a large molecule into two or more smaller ones​. H2O + AB → A + B

Dehydration Reactions: The removal of water allows for two or more small molecules to combine to form a larger one.​ A + B → AB + H2O

Chemical Equations: Symbolizes the course of a chemical reaction​; Reactants (on left) → products (on right)

Monomers

Monomers are small, molecular building blocks that can exist alone or be linked to others of the same type to form a larger molecule called a polymer, i.e., either a dimer (by the joining or condensation of 2 monomeric units) or a trimer (3 monomeric units) or a polymer (∝monomeric units). ​

​There are 3 important biological monomers:​

Monosaccharides: Polymerize (combine or cause to combine to form a polymer) to form polysaccharides

Amino Acids: Polymerize (combine or cause to combine to form a polymer) to form polypeptides  (proteins)

Nucleotides: Polymerize (combine or cause to combine to form a polymer) to form polynucleotides (nucleic acids)​

Polymers

Glucose- C6H12O6

A polymer is a substance formed by the linkage of many smaller molecules known as monomers. ​

• ​Mono = single

• ​Poly = many​

​Polymerization is a process that constructs a polymer from many small molecules, like links in a chain. An example of a monomer is glucose, whose molecules link together to form glycogen, a polymer.​

Substances that have macromolecules are composed of many repeating structural units (known as ‘mers’). The mers are contributed by the reacting monomers, but, constitutionally, need not be identical with them.

Polymeric Substances in the Diet​

The polymeric substances contained in the diet (proteins, carbohydrates, nucleic acids, and fats) cannot be used by the organism directly. Digestive enzymes first have to degrade them into monomers (amino acids, sugars, nucleotides, fatty acids) which are then absorbed by the cells of the intestinal mucosa and made available for metabolism.

Structure of Carbs Versus Lipids Versus Proteins​

Carbohydrates contain carbon (C), hydrogen (H), and oxygen (O) but lack nitrogen and are water-soluble.

Proteins are organic energy-yielding nutrients or macronutrients also containing C, H, and O that contain nitrogen and are water-soluble.

Lipids (fats) are organic energy-yielding nutrients or macronutrients, also containing C, H, and O, also lack nitrogen, and are not water-soluble.

Carbohydrates: Definition, Structure, Source, and Function​

Review the tabs to learn about carbohydrates definition, structure, source, and function.

• Definition and Structure: Carbohydrates are essential energy-yielding nutrients or macronutrients which are organic and are mainly composed of carbon, hydrogen, and oxygen. ​

Carbohydrates lack nitrogen.

• Dietary Sources: Main dietary sources of carbohydrates are grains, milk, fruits and starchy vegetables like potatoes.

Function; Provide energy​

• Naturally occurring sweeteners (sucrose and fructose)​

• Brain and nerve tissues require glucose as fuel

Cardinal Functions of Carbs​

Your body converts most dietary carbohydrates to glucose, a simple sugar compound that is found in the body’s circulation and provides a source of energy for cells. ​

​Cardinal functions of carbohydrates:​

• Provides energy ​

• Dietary fiber helps with naturally lowering cholesterol and helps with bowel movements

• Provides naturally occurring sweeteners (sucrose and fructose) in food

• Brain and nerve tissues require glucose as fuel

• Protein-sparing effect

Classification of Carbs​

Simple Carbohydrates:​

• Monosaccharides ​

  • Mono = one​

  • Saccharide = sugar​

• Disaccharide ​

Complex Carbohydrates:​

• Polysaccharides 

Classification of Carbs

Monosaccharides, also called simple sugars, are the simplest forms of sugar and the most basic units (monomers) from which all carbohydrates are built. Remember “FGG”:​

• F for Fructose​

• G for Glucose​

• G for Galactose

Disaccharides (also called a "double sugar" or biose) are the sugars formed when two monosaccharides are joined by glycosidic linkage. For example:​

• Sucrose: glucose + fructose​

• Maltose: glucose + glucose​

• ​Lactose: glucose + galactose

Polysaccharides are "complex carbs", composed of many units of monosaccharides held together by different kinds of chemical bonds.​

Examples of polysaccharides:​

• ​Glycogen: storage form of glucose in animals (including humans)​

• Starch: storage form of glucose in plants​

• Cellulose: cell walls of plants are composed of cellulose​

• Fiber 

Definition of Proteins​

Proteins are an organic energy-yielding nutrient or macronutrient which contains hydrogen, oxygen, carbon, and nitrogen.​

• Recall that carbohydrates and lipids are organic macronutrients that lack nitrogen.

Proteins are unique because they contain nitrogen. Proteins are comprised of chains of amino acids in chemical linkage with one another, known as polypeptides.​

• Amino acids are the building blocks of proteins.

Examples of Proteins in the Human Body​

Hemoglobin: Iron, Heme, Oxygen molecules, Polypeptide chain

Enzymes are proteins that catalyze (speed up) a chemical reaction by lowering the energy of activation. The energy of activation is the energy that must be overcome in order for a reaction to proceed forward.​

Hemoglobin is a protein molecule that binds oxygen molecules inside red blood cells. The red blood cell containing the hemoglobin-oxygen bound complex delivers this oxygen to different parts of the body.

Two Types of Amino Acids​

Amino acids are building blocks of proteins and exist in two types:​

• ​Essential (indispensable) amino acids: those amino acids that must be obtained from the diet.​

• Non-essential (dispensable) amino acids: our bodies contain sufficient stores of these types of amino acids, and therefore they do not have to be exclusively derived from the diet.

Glucogenic Amino Acids

Glucogenic amino acids have a carbon skeleton that can serve as a non-carbohydrate substrate for de novo (making new glucose from non-carbohydrate precursors) glucose synthesis. This is also known as gluconeogenesis.​

Glucogenic amino acids are those that can be converted to glucose, whereas ketogenic amino acids can enter a metabolic cycle to produce fatty acids and be stored as fat.​

Ketogenic Amino Acids

In the body, we also categorize some amino acids as ketogenic acids as they can be used by tissues and organs as an alternate source of energy. Ketogenic amino acids have carbon skeletons that can serve as precursors of the ketone bodies.​

• Leucine and lysine are exclusively ketogenic amino acids​.

Most organs and tissues can use ketone bodies as an alternative source of energy. The brain uses them as a major source of energy during periods where glucose is not readily available. 

Complete Versus Incomplete Proteins

Complete Proteins: Source: Animal foods generally provide complete protein.​

Definition: Proteins that have all nine of the essential amino acids in sufficient quantities are considered complete (high-quality) proteins. ​

• The most complete protein sources are foods derived from animals, including egg whites, meat, poultry, fish, and milk. ​

• Animal foods contain all the essential amino acids in approximately the right proportions.

Incomplete Proteins: Source: With the exception of soy protein and beans, the protein in plant foods is incomplete​

Definition: An incomplete protein lacks one or more essential amino acids and does not match the body’s amino acid needs as closely as animal foods do.​

• Proteins that do not contain all of the essential amino acids in sufficient quantities to support growth & health are called incomplete (low-quality) proteins.

Structure of Proteins​

Primary: It consists of one or more linear chains of a number of amino acid units linked together by peptide bonds. 

Secondary: The primary protein manifesting as a linear, unfolded structure consisting of the polypeptide chain assumes a helical shape to produce the secondary structure of a protein. ​

• Alpha (α) helix coils resemble a spring​

• Beta (β) pleated sheets resemble accordion ribbons​

Tertiary: The secondary structure of a protein, in turn, may fold in certain specific patterns to produce the twisted three-dimensional or the tertiary structure of the protein molecule.

Quaternary: Finally, certain other proteins are made up of subunits of similar or dissimilar types of the polypeptide chains.​

• These subunits interact with each other in a specific manner to give rise to the so-called quaternary structure of the protein​.

Definition of Lipids (Fats)​

Chemical reactions: triglycerides

Lipids are essential energy-yielding nutrients or macronutrients which are organic.​

​Structure:

• Composed of carbon, hydrogen, and oxygen – but lacks nitrogen​

​Characteristics:​

• Lipids are characterized by their insolubility in water, meaning that lipids do not dissolve in water.​

• All lipids are hydrophobic. ​

• Most of the fat we eat is in the form of triglycerides.

Classification of Lipids​

Simple Lipids:​

• Triglycerides are the main simple lipids. ​

Compound Lipids:​

• Phospholipids ​

Derived Lipids:​

• Saturated vs. unsaturated Fatty acids​

• Steroids consist of 4 fused rings.​

Classification of Lipids: Simple Lipids-TAG​

Triglycerides (abbreviated TAG) are composed of:​

• 3 fatty acid (abv. FA) molecules:​

  • FA: long chains of carbon atoms surrounded by hydrogen atoms​

• PLUS 1 Glycerol molecule:​

  • Glycerol: a 3-carbon molecule that is the backbone of TAG

Plasma Membrane: Phospholipid Bilayer​

The plasma membrane behaves amphipathically, meaning it has both hydrophilic ("water-loving", or water-soluble) and hydrophobic ("water-hating", or poorly water-soluble) regions.​

This phospholipid bilayer constitution contains both a hydrophilic component comprised of a phosphate head and a hydrophobic component consisting of 2 long fatty acid chains. ​

• While the 2 long fatty acid chains are hydrophobic, they are also lipophilic ("lipid-loving", or lipid-soluble) non-polar tails. ​

• The phosphate head, while hydrophilic, is also lipophobic ("lipid-hating", or poorly lipid-soluble) and polar, containing a negatively charged phosphate group. The phosphate group interacts freely with water molecules, rendering it more readily soluble in water than lipids. 

Hydrophilic: water-loving ​

Hydrophobic: water-hating ​

Lipophilic: lipid-loving ​

Lipophobic: lipid-hating 

Classification of Lipids: Derived Lipids​

Remember, lipids are essential energy-yielding nutrients or macronutrients which are organic. There are two types of derived lipids: saturated fatty acids and unsaturated fatty acids.​

• Saturated fatty acids: The carbon chain carries its full complement of hydrogen atoms and all the carbon atoms are linked by single bonds.​

• Unsaturated fatty acids: unsaturated fatty acids have one or more carbon-carbon double bonds in the molecule and double bonds can take up hydrogen.​

• Short-chain fatty acids: fatty acids of total carbon atom numbers from 1 to 6.​

• Medium-chain fatty acids: fatty acids of total carbon atom numbers from 7 to 12​.

• Long-chain fatty acids: fatty acids of total carbon atom numbers from 13 to 21.

Derived Lipids: Saturated Fatty Acids​

Saturation of fatty acids depends on how many hydrogen atoms bond to the four potential bonding sites of each carbon atom.​

If all four sites have a hydrogen atom bond, it's saturated.​

Because all the carbon atoms are bonded to as many hydrogen atoms as they can hold, no double bonds between carbon atoms exist.

Saturated Fatty Acids:​

• Solid at room temperature​

• Straight linear appearance.​

• Source: animals ​

• High melting point​

• Are less likely to become rancid 

Derived Lipids: Unsaturated Fatty Acids​

Unsaturated Fatty Acids

A monounsaturated fatty acid has only one double carbon bond, indicative of an unsaturated fat.

An unsaturated fatty acid is a fatty acid that isn't completely filled with all the hydrogen atoms it can hold.​

• This results in the formation of double bonds between carbon atoms. ​

• Originate from plant fat and oils​.

• Are soft or liquid at room temperature.

• Have lower melting points than saturated fats.​

• Can become rancid when exposed to extended periods of light and oxygen. 

Recap: Saturated Versus Unsaturated Fats​

Review the table to recap saturated and unsaturated fats. 

Deoxyribonucleic Acid and Ribonucleic Acid

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are macromolecules in the form of polymers (nucleic acids) which are involved in the storage of genetic & hereditary information consisting of building blocks called nucleotides (monomers).​

​DNA and RNA nucleic acids are the molecular repositories for genetic information and are jointly referred to as the ‘molecules of heredity’.​

• DNA serves primarily as the repository of genetic information.​

• RNA molecules play several different roles in expressing that information, in gene regulation and protein synthesis.​

DNA and RNA are nucleic acids (macromolecules in the form of polymers).​

Nucleic acids are comprised of building blocks of monomeric nucleotides.

Definition of Nucleotide

RNA (Ribonucleic acid) DNA (Deoxyribonucleic acid)

A nucleotide is a monomeric unit of nucleic acids, composed of three elements:​

• A phosphate​

• A pentose sugar (Ribose or Deoxyribose)​

• A nitrogenous base (Purine or Pyrimidine)​

DNA & RNA are polymers of nucleotides.

Purines

A purine has a 2-ringed heterocyclic nitrogenous base, containing 2 carbon-nitrogen rings and 4 nitrogen atoms.​

​Pyrimidine C4H4O2 is an organic heterocyclic, nitrogenous compound containing: ​

• 6-membered aromatic ring with​

  • 2 nitrogen atoms in the 1 and 3 positions

  • 3 double bonds at 1,3, and 5 positions

Purine: Guanine and Adenine ​

To remember which nitrogen bases are classified as pyrimidines, recall “CUT”, the pyramid (pyrimidine):​

• C – Cystine​

• U – Uracil​

• T – Thymine ​

DNA: The DNA double-stranded molecule exists as a double helix and the double helix shape of the DNA molecule is formed as the nitrogen bases pair up via hydrogen bonds.

• Sugar:​ Deoxyribose = DNA​

• Phosphate: Same in RNA and DNA

• Nitrogen Bases:​ DNA = A,T,G,C​

DNA forms a double strand through the binding of nitrogen bases. Nitrogen bases bind in accordance to complementary base-pairing rules. ​

Complementary base-pairing rules:​

• A always pairs with T​

• C always pairs with G

To help you remember:​

• Apple-Tree (A always pairs with T)​

• Car-Garage (C always pairs with G)

RNA: RNA is a single-stranded linear molecule that is active mostly outside the nucleus.​

• The single-stranded structural configuration of RNA is formed as the nitrogen bases pair up via hydrogen bonds. ​

• Contains ribose sugar (not deoxyribose)​

• Thymine is replaced with uracil​

• Three varieties of RNA carry out the DNA order for protein synthesis.​

1. Messenger RNA (mRNA)

2. Transfer RNA (tRNA)

3. Ribosomal RNA (rRNA)

• Sugar:​ Ribose = RNA​

• Phosphate: Same in RNA and DNA​

• Nitrogen Bases:​ RNA = replace T with U

Amino acids are the monomeric units of which macromolecules?​; Proteins

DNA and RNA are both nucleic acids that are made of monomeric subunits called nucleotides. 

Organic Biomolecules​

Biomolecules are organic macromolecules that drive the biochemical, metabolic and cellular processes inside living organisms. ​

​Examples:​

• Macronutrients: carbohydrates (carbs), lipids, and proteins ​

• ​Nucleic acids: DNA and RNA 

Macromolecules and Macronutrients

Macromolecules, which can also be classified as macronutrients, are energy-yielding essential nutrients and are classified biochemically (i.e., based on their biochemical makeup) into polymers:​

Carbohydrates: are divided into:​

• Polymers = polysaccharides​

• Monomers = monosaccharides ​

Proteins:​

• Polymers = polypeptides or proteins ​

• Monomer = monopeptide (amino acid consisting of one amino acid). Example: glycine ​

Lipids​

DNA and RNA  (These are micromolecules but not macronutrients) 

Properties of macronutrients: ​

• Organic ​

• Essential ​

• High-energy yielding ​

• Nutrients 

Nutrients

Nutrients are any substances in food that the body can use to obtain energy, synthesize tissues, or regulate functions.

A nutrient is a chemical which is absent in the diet for a long time which results in specific changes in health.

Essential Nutrients: Nutrients must be consumed from foods because they cannot be made in the body in sufficient quantities to meet its needs and support health. ​

​Substances must be obtained in the diet because the body either cannot make them or cannot make adequate amounts of them. ​

​When used to refer to nutrients, the word essential means more than just “necessary”; it means “needed from outside the body”-normally from foods. 

Energy-yielding nutrients are the nutrients that break down to yield energy the body can use, such as carbohydrates, proteins, and fats (lipids). ​

​"Macronutrients" is another name for energy-yielding nutrients.