5IP Organic Macromolecules and Other Biological Molecules

Organic Macromolecules and Other Biological Molecules

Lecture Goals:

• Examine the importance and role of carbon in biological function
• Understand the defining structure and characteristics of the four major groups of biological molecules
• Understand the function of the major groups of macromolecules

Course Competencies: 4. Compare and contrast the most stable subatomic particles and describe how they affect the chemical characteristics of matter. (II) 5. Describe the relationship between atoms and molecules and the importance of chemical bonds to atomic stability, molecular structure and chemical characteristics. (II) 6. Describe the relationships between the structure and functions of the four major kinds of organic macromolecules found in living things. (II)

Presentation Links

Day 1 Content

Building Macromolecules

The Element Carbon

Carbohydrates

Day 2 Content

Lipids

Proteins

Nucleic Acids

The Element Carbon

Filled Valence Electron Spots

The "backbone" of organic molecules

Open Valence Electron Spots

• Carbon is one of two elements required for organic molecules
• It has four available valence electron slots. This allows the possiblity of:
• up to four covalent bonds
• complex shapes by bonding to other carbons
• formation of benzene rings (6 carbon rings that are structurally stable)

The Element Carbon

Hydrocarbons

• The smallest hydrocarbon, methane (CH4)
• Smallest "unit" of an organic molecule.
• Composed of one carbon and four hydrogens
• Covalent bonds are equal distances apart from each other

• Hydrocarbon Chains
• Form when one (or more) hydrogen-carbon bonds are replaced with carbon-carbon bonds.
• Carbon can either be single, double, or triple bonded to another carbon

Note: Quadruple bonded carbon theoretically exists but it would NOT be an organic molecule. There are molecules where a triple bond behaves like a quadruple bond due to electron sharing. This is often covered in o-chem 3 courses.

The Element Carbon

Hydrocarbons

• Hydrocarbon Rings
• Highly stable structure (especially benzene rings)
• Electrons are shared (evenly) around the entire ring

The Element Carbon

Substituted (Modified) Hydrocarbons

• Parts of hydrocarbons can bond to other elements.
• Common elements are oxygen and nitrogen
• Can occur:
• within rings
• branches off rings
• along chains
• branches off the chains
• These often occur in specific variations that have properties that allow the macromolecule to "perform" certain functions
• We call these functional groups.

The Element Carbon

Functional Groups

• Functional groups:
• Define different types of macromolecules
• Cause molecules to fold into different shapes that can do different chemical "work".
• React to or are inert against other macromolecule structures, allowing for control over when or where certain reactions take place.

Note: When we are focusing on a particular functional group in a molecule we will often represent the rest of the molecule as R.

The Element Carbon

Isomers

• Due to the same elements being used many organic compounds are isomers
• Have the same chemical formula, but the arrangement is different
• Different isomers will react and function differently!

C2OH4

C2OH4

The Element Carbon

Types of Isomers

• Structural isomers
• Different arrangement
• Geometric isomers
• Parts are flipped (typically over a double bond)
• Enantiomers
• Mirror

Watch out for the way connecting lines representing the covalent bonds look. The cone shape indicates direction.

Check your notes

• Number of bonds carbon forms
• The different types of hydrocarbons
• What a substituted hydrocarbon is
• Functional groups
• The three types of isomers and why they matter
• How to recognized polar and non-polar parts of molecules

02:00

Building Macromolecules

Parts of a macromolecule

• Biological Macromolecule
• Large molecules built from smaller organic molecules
• Four major classes
• carbohydrates
• lipids
• proteins
• nucleic acids
• Make up most of the body's "dry mass" (non-fluid parts of the body)

Building Macromolecules

Parts of a macromolecule

• Monomer
• A subunit of a macromolecule
• Each class of macromolecule has a different type of monomer:
• carbohydrates = simple sugar
• lipids = glycerol and fatty acids
• proteins = amino acids
• nucleic acids = nucleotide
• Polymers
• Multiple monomers linked through covalent bonds

Building Macromolecules

Parts of a macromolecule

Dehydration Synthesis

• Monomers bond together through the removal of an OH- ion from one end of the monomer and a H+ ion from a different monomer.
• The result is a polymer and water
• It is called dehydration because the molecule has "lost" a water.

Building Macromolecules

Parts of a macromolecule

Hydrolysis

• Polymers break into monomers bond together through the addition of an OH- ion to one end of the monomer and a H+ ion to a different monomer.
• The result is a monomer
• It is called hydrolysis because the molecule has "drank" a water.

Test your Knowledge

H2O

OH

OH

Check your notes

• Define
• macromolecule
• monomer
• polymer
• How to recognize dehydration synthesis VS hydrolysis

02:00

Carbohydrates

"The Sugars" and more

• Polymers composed of simple sugars
• Key features:
• Composed of carbon, hydrogen, and oxygen
• This is where the name comes from
• Carbo- = carbon
• -hydrate = water (2H and O)
• Due to the repeating numbers of C, H, and O the formula will often be written as a stoichiometric formula (CH2O)n
• Have three main types:
• Monosaccharides
• Disaccarides
• Polysaccarides

Carbohydrates

C6H12O6 -or- (CH2O)6

Monosaccharides

• Mono = one Sacchar = sweet
• These are the monomers of carbohydrates
• Type is defined by
• What type of functional group is attached to the sugar
• How many carbons it has:
• Trioses (three carbon)
• Pentoses (five carbon)
• Hexoses (six carbon)
• Which structural isomer they are

Test your Knowledge

C6H12O6

Carbohydrates

Disaccharides

• Di = two Sacchar = sweet
• Form when two monosaccharides undergo a dehydration reaction
• Common examples:
• sucrose (aka table sugar)
• joined glucose and fructose monomers
• most common
• lactose (aka milk sugar)
• joined glucose and galactose monomers

• maltose (aka malt sugar)
• joined glucose monomers

Carbohydrates

Disaccharides - Lactose Intolerance

• Lactose intolerance is when the small intenstine doesn't produce enough lactase.
• Lactase is an enzyme that causes lactose to undergo hydrolysis.
• If lactose isn't broken down in the small intenstine it cannot be absorbed by the intenstinal lining.
• Instead it moves into the colon, where bacteria will begin to break it down.
• The waste products from the bacteria is what causes the symptoms of lactose intolerance

Carbohydrates

Polysaccharides

• Poly= many Sacchar = sweet
• May be composed of many different monosaccharides
• Types: branched or unbranched
• Examples:
• starch (energy storage in plants)
• glycogen (energy storage in animals, fungi, and bacteria)
• cellulose (cell walls in plants, some fungi, and some bacteria)
• chitin (exoskeleton in arthropods, cell walls in many fungi)

Carbohydrates

C6H12O6

Functions of Carbohydrates

• Mono = one Sacchar = sweet
• These are the monomers of carbohydrates
• Type is defined by
• What type of functional group is attached to the sugar
• How many carbons it has:
• Trioses (three carbon)
• Pentoses (five carbon)
• Hexoses (six carbon)
• Which structural isomer they are

Check your notes

• Define
• carbohydrate
• monosaccharide
• disaccharide
• polysaccharide
• Recognize the different types of within each class
• Why isomers matter with monosaccarides
• What stoichiometric formulas are

02:00

Lipids

"The Fats and Oils" (and sterols and more)

Lipids

"The Fats and Oils"

• Polymers composed of glycerol and fatty acids
• glycerol: an alcohol (a type of organic compound that carries at least one hydroxyl ( −OH) functional group)
• fatty acid: a long chain of carbon (between 4 and 36, with most being around 15) with a carboxyl group at the end

Lipids

"The Fats and Oils"

• Key features:
• Largely hydrophobic
• "water fearing"
• insoluble in water
• The fatty acid portion has two main forms:
• saturated fatty acid
• unsaturated fatty acid

Lipids

"The Fats and Oils"

• Saturated Fatty Acid
• No double bonds in carbon chain
• Typically solid at room temperature
• Example: Stearic acid (energy storage in animals, "meat fat")

Lipids

"The Fats and Oils"

• Unsaturated Fatty Acid
• "The oils"
• Has double bonds in carbon chain
• monounsaturated: one double bond (example olive oil)
• polyunsaturated: more than one double bond (example canola oil)
• Typically liquid at room temperature
• example oleic acid "olive oil"

Lipids

"The Fats and Oils"

• Unsaturated Fatty Acid
• Have two main forms:
• Cis Fat
• hydrogens are on the same side of the double bond
• bent shape
• Trans Fat
• hydrogens are on the opposite sides of the double bond
• "straighter" shape

Test your Knowledge

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Lipids

Functions of Lipids

• Essential Fatty Acids
• Fatty acids that are required by our body to function, but cannot produce on its own
• Omega-3 (heart health and blood function)
• Form a range of substances:
• fats
• vitamin absorption
• long-term energy storage
• insulation

Lipids

Functions of Lipids

• Form a range of substances (continued):
• waxes
• water repellent (duck feathers, otter fur)
• water loss reduction (cactus)
• phospholipids
• plasma/cell membranes(!)
• steroids
• plasma membrane components (e.g., cholesterol)
• hormones (signaling molecules e.g., estrogen, testosterone)
• interesting note: steroids are the only lipids with ring structures

Lipids

Functions of Lipids

• Form a range of substances (continued):
• waxes and oils
• water repellent (duck feathers, otter fur)
• water loss reduction (cactus)
• phospholipids
• plasma/cell membranes(!)
• steroids
• plasma membrane components (e.g., cholesterol)
• hormones (signaling molecules e.g., estrogen, testosterone)
• interesting note: steroids are the only lipids with ring structures

Check your notes

• Define
• saturated fatty acid
• unsaturated fatty acid
• cis fat
• trans fat
• Types of substances made of lipids
• Functions of lipids

03:00

Proteins

"The worker organic molecules"

Proteins

"The worker organic molecules"

• Polymers composed of amino acid monomers
• Most diverse organic molecules
• 20 common amino acids that make proteins
• 9 are essential amino acids in humans (we need to eat them since our bodies can't make them)
• Joined together through dehydration synthesis to form a peptide bond
• Protein chains are called polypeptides

Proteins

R groups (AKA side chains) give amino acids their unique properties

Proteins

Protein structure

• Polypeptides are long chains of amino acids
• The sequence of the chain is known as a protein's primary structure
• Hydrogen bonds exist between certain functional groups within amino acids
• This causes local folding in the polypeptide, which is considered a protein's secondary structure
• alpha-helix
• beta-pleated sheet

Proteins

Protein structure

• Looking at the folding on a "large" scale shows us the the protein's tertiary structure. Examining the shape we can see:
• the three-dimensional structure of the protein
• where its interactions sites are
• where its "movable" sites are

• When several polypeptides interact together to form a single protein it is known as the protein's quaternary structure

Test your Knowledge

Proteins

Protein structure: Denaturation

• Protein structure relies on a set of conditions:
• pH
• temperature
• surrounding chemicals
• Changes to these can "break" the shape of the protein, which is called denaturation
• Whether this is reversable varies between proteins
• Sometimes your body "intentionally" denatures proteins
• digestion
• fevers (defense)

Proteins

Protein functions

• Enzymes
• catalysts (helpers) in biochemical reactions
• example: digestion
• Transport
• example: hemoglobin in blood
• Structure
• example: keratin (mammal nails)

Proteins

Protein functions

• Hormones
• typically between cells
• example: insulin
• Defense
• example: immunoglobins
• Movement
• example: myosin (muscle movement)
• Storage
• example: albumin (egg white)

Check your notes

• Amino Acid Structure
• Four "levels" of protein structure
• Denaturation
• Seven main functions of proteins

03:00

Nucleic Acids

"The Data Storage"

Nucleic Acids

"The Data Storage"

• Polymers composed of nucleotides
• nitrogenous base
• pentose sugar
• phosphate group
• Combine to form polynucleotides, which has as two major forms:
• deoxyribonucleic acid (DNA)
• ribonucleic acid (RNA)

Nucleic Acids

Nucleotide structure

DNA and RNA are named for they type of pentose sugar they have

The nucleotide is named for the type of nitrogenous base it has

Nucleic Acids

Nitrogenous Bases

• Purines (two rings)
• adenine and guanine (found in DNA and RNA)
• Pyrimidines (one ring)
• cytosine (found in DNA and RNA)
• thymine (found in DNA)
• uracil (found in only RNA)

Nucleic Acids

Thymine

Adenine

Guanine

Cytosine

T G G C A G T A

A C C G T C A T

DNA Structure

• Deoxyribonucleic acid (DNA)
• double helix structure
• phosphates and sugars bind to form the "backbone"
• nitrogenous bases pair with its complement through hydrogen bonds

Nucleic Acids

Hydrogen Bonds between Complements

Nucleic Acids

RNA Structure

• Four types of Ribonucleic acid (RNA)
• messenger (mRNA)
• carries information from DNA
• protein synthesis
• ribosomal RNA (rRNA)
• part of the ribosome organelle
• transfer RNA (tRNA)
• transports amino acids for protein synthesis
• microRNA (miRNA)
• gene regulation

Check your notes

• Define
• DNA
• Four types of RNA
• Know the two purines and three pyrimidines
• Complimentary pairs
• Functions of lipids

03:00