Macromolecules


Introduction to Molecular Size

  • Benjamin Franklin's observation in 1773: "1 teaspoon of oil covers about ½ acre of water."

  • Size of an oil molecule: 3/5003/500 billionth of an inch =0.0000000063= 0.0000000063 inches =1.6= 1.6 nm.

Non-Contact Atomic Force Microscope (nc-AFM)

  • nc-AFM images of a molecule before and after a reaction greatly improve over scanning tunneling microscope images.

  • They resemble classic molecular structure diagrams.

  • Source: Robert Sanders, Media Relations, May 30, 2013.

Chemistry of Life

  • Major and minor grooves (likely referring to DNA structure).

  • Key elements: Hydrogen, Oxygen, Nitrogen, Carbon, Phosphorus.

  • Importance of metabolic pathways; refer to the metabolic pathways chart designed by Donald E. Nicholson.

Objectives

  • You are what you eat.

  • Understanding organic molecules and the effects of functional groups.

  • Living organisms are primarily composed of 4 macromolecules.

  • Macromolecules are built from simple building blocks (monomers).

  • Understanding how monomers form polymers.

  • Structure/function of building blocks and the 4 macromolecules.

  • Proteins: the factors determining their structure/function.

  • Protein denaturation: what it is and when it occurs.

Vocabulary

  • Amino acid

  • ATP

  • Cellulose

  • Complementary base pairing

  • Dehydration

  • Denaturation

  • DNA

  • Double helix

  • Essential

  • Fatty acid

  • Functional groups (Hydroxyl, Carbonyl, Carboxyl, Amino, Sulfhydryl, Phosphate, Methyl)

  • Glycogen

  • Hydrolysis

  • Lipid

  • Macromolecule

  • Monomer

  • Monosaccharide

  • Nitrogenous base

  • Nucleotide (Adenine, Thymine, Guanine, Cytosine, Uracil)

  • Organic

  • Phospholipid

  • Polypeptide

  • Polysaccharide

  • (Primary, secondary, tertiary & quaternary structure)

  • Protein

  • R-group

  • RNA

  • Saturated fats

  • Starch

  • Triglyceride

  • Unsaturated fats

  • Watson & Crick

Organic Chemistry

  • Carbon can form 4 covalent bonds.

  • The "big 6" elements in living organisms: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur.

Structure/Function of Organic Molecules

  • Hydrocarbons (only C & H)

    • Examples: Ethane, Ethylene, Acetylene, Octane, Benzene

  • Functional groups

    • Atoms or clusters of atoms covalently bonded to a carbon backbone.

    • Give organic compounds their different properties.

    • Methyl group is hydrophobic.

  • Energy coupling via ATP!

Four Major Macromolecules

  • Carbohydrates (Polysaccharides)

  • Lipids

  • Nucleic acids (DNA, RNA)

  • Proteins

Macromolecule - Monomer Relationships

  • Polysaccharides (Carbohydrates) - Monosaccharides

  • Lipids - Fatty acids + Glycerol

  • Proteins - Amino acids (20 types)

  • Nucleic acids - Nucleotides (5 types)

  • Life is modular: complex structures made of simple building blocks.

Bread Recipe & Nutritional Components

  • Basic bread recipe ingredients:

    • 3 cups flour

    • 2 T Table Sugar

    • 1 t Table Salt

    • 1 cup water

    • 2 T Canola Oil

    • 2 t yeast

  • Consideration of:

    • Calories

    • Carbohydrates

    • Fats

    • Proteins

    • Vitamins & Minerals

  • Nucleic acids not on label - but why?

Calories

  • Food energy.

  • Examples of activities to burn off calories from different drinks.

Carbohydrates

  • Simple organic molecules of C, H, & O. General formula: C<em>n(H</em>2O)nC<em>n(H</em>2O)_n

    • Monosaccharides

    • Disaccharides

    • Polysaccharides

  • These are the macromolecules in this group

Carbohydrates (Saccharides)

  • Structure/Function.

  • Hydrophilic.

  • Building blocks: Glucose (C<em>6H</em>12O6C<em>6H</em>{12}O_6).

  • Linear vs. Ring structure.

  • Functional groups.

Monosaccharides (Simple Sugars)

  • Most have 5 or 6 Carbon backbone.

  • -ose suffix

Functions of Monosaccharides

  • Glyceraldehyde (3 carbon sugar).

  • Part of RNA.

  • Part of DNA.

  • Short term energy source.

  • Building blocks of polysaccharides.

Disaccharides

  • Simple sugars composed of 2 monosaccharides.

  • Formed by dehydration reactions (condensation reactions) which release water.

  • Example: Glucose + Fructose -> Sucrose + Water.

Functions of Disaccharides

  • Energy source (e.g., maltose, lactose).

  • Transport (e.g., sucrose).

  • Examples: Lactose, Sucrose, Maltose (C<em>12H</em>22O11C<em>{12}H</em>{22}O_{11}).

  • Dehydration reaction occurs.

Polysaccharides

  • Complex carbohydrates made up of 100’s of monomers.

  • Three common examples (all made of just glucose monomers):

    • Cellulose

    • Starch

    • Glycogen

Cellulose (“Fiber” in Foods)

  • Function: major part of plant cell walls.

  • Holds up plants.

  • Resists digestion.

  • World’s most abundant polysaccharide.

Fiber in Diet

  • Function:

    • Reduces constipation.

    • Carbohydrates absorb water.

    • Feeds our microbiome.

    • May lower risk of colon cancer.

  • Foods high in fiber.

  • "9 g of added sugar": (2022, no longer “healthy” FDA).

Starch (Amylose)

  • Function: energy storage carbohydrate made by plants.

  • Easily digested.

  • Plants have more carbohydrates (amount and types) than animals do.

Glycogen

  • Function: energy storage in animals.

  • Found in liver and muscle cells.

  • Hormones insulin/glucagon control formation/degradation.

Polysaccharides List

  • Examples of different polysaccharides: Agar, Amylose, Cellulose, Chitin, Glycogen, Starch, etc.

Digestion of Simple Sugars and Starch

  • Part 1: Breakdown of the polymer.

  • Hydrolysis reactions - adding H2OH_2O cleaves a polymer.

  • Part 2: Building polymers.

  • Monosaccharides are transported from intestine -> blood -> cells.

  • Energy or build glycogen.

  • Reaction name: dehydration

Bread Recipe and Carbohydrates

  • Are carbohydrate monomers essential to your diet?

  • What about “low-carb” diets?

  • Which is the source of carbohydrates in bread?

  • How is 52g of starch different from 52g of “sugar”?

  • What if it were whole wheat flour?

Lipids: Fats, Oils, Waxes

  • "Hydrocarbons"

  • Building blocks: Glycerol + Fatty Acid chains.

  • Hydrophobic but may have hydrophilic heads.

  • Classes of Lipids:

    • Triglycerides (fats)

    • Phospholipids

    • Others

Fatty Acid Chains

  • Saturated fats

    • Solid at room temperature (liquid at "body temperature").

    • What organisms have saturated fats?

  • Unsaturated fats

    • Liquid at “room temperature”.

    • Monounsaturated- have one double bond.

    • Polyunsaturated- have more than one double bond.

    • What organisms have unsaturated fats?

  • Free fatty acids are rare.

Triglycerides (Fats)

  • Glycerol linked to 3 fatty acid chains.

  • Function:

    • Cushion organs (animals).

    • Energy storage (long term).

    • Insulation (adipose tissue).

Trans Fats

  • “Partially hydrogenated vegetable oils”.

  • Why are trans fats “bad”?

  • Why are trans fats “good”?

Phospholipids

  • Glycerol backbone.

  • 2 Fatty acids.

  • 1 phosphate hydrophilic head.

  • Structure/function: Fat sandwich.

Other Lipids

  • Waxes

  • Sterols (e.g., Vitamin D, bile salts, cortisone, estrogen, & cholesterol).

Digestion of Lipids

  • Lipids -> glycerol + FA into blood -> cells

  • Energy or building blocks for your lipids.

Bread Recipe and Lipids

  • Are lipids essential to your diet? Yes, 2 are: omega-3 (e.g. Alpha-linolenic acid) & omega-6 fatty acids (e.g. Linoleic acid).

  • Which is the source of lipids in bread?

  • "a good ratio" of 1:5.

Essential Oils

  • Aromatherapeutic.

  • "essence of" the plant.

Nucleic Acids

  • DNA & RNA.

  • Not listed on food labels.

Nucleic Acids

  • Deoxyribonucleic acid (DNA).

  • Ribonucleic acid (RNA).

  • Building blocks (monomers) are nucleotides.

  • A, T, G, C, U.

  • Pyrimidines and Purines.

DNA

  • Structure?

  • Function?

  • Vocabulary: Nucleus, Chromosome, Gene, Genome.

  • How many chromosomes do you have?

  • How many genes do you have?

DNA Structure

  • Double helix.

  • "Like rungs on a spiral ladder".

DNA Structure - Nucleotides

  • Each DNA nucleotide consists of 3 parts:

    • Nitrogenous base (G, A, C or T - not U).

    • Deoxyribose sugar (5 carbon sugar).

    • Phosphate group.

  • U is found in RNA, not DNA.

DNA - Double Helix

  • Like a twisted zipper.

  • Sides = Sugar-phosphate backbone.

DNA Structure

  • Sides of the zipper: Sugar-phosphate backbone.

  • Interlocking teeth of the zipper: join “complementary” nucleotides.

  • A ALWAYS pairs with T.

    • Forming 2 hydrogen bonds.

  • C ALWAYS pairs with G.

    • Forming 3 hydrogen bonds.

DNA - Complementary Base Pairing

  • What is the complementary base pair sequence for the following strand of DNA?

  • CTAATGT -> GATTACA

DNA Structure - Discoverers

  • DNA is a double-stranded helix (Watson & Crick 1953 from data “stolen” from Rosalind Franklin).

  • James Watson, Maurice Wilkins: 1962 Nobel prize in physiology, Francis Crick.

DNA - Supercoiling

  • DNA is often highly condensed “super-coiled” (unless it is being replicated or transcribed).

  • DNA is wrapped tightly around proteins & folded.

  • DNA must unwind for replication, or transcription to occur.

  • Prior to ~1940 genetic material was thought to be protein. Why?

Expressing Genetic Information

  • The information in the sequence of nucleotides of DNA must first be transcribed into a sequence of RNA.

RNA (Ribonucleic Acid)

  • Ribose.

  • 4 nitrogenous bases are A, G, C & U.

  • Single-stranded.

  • Function of RNA?

  • For exam 1: Be able to compare/contrast DNA vs. RNA structure.

Types of RNA

  • Three major types of RNA are transcribed from DNA:

    • tRNA (transfer RNA)

    • rRNA (ribosomal RNA)

    • mRNA (messenger RNA)

  • All 3 are involved in protein translation.

  • Language of nucleic acid sequence translated into language of amino acid sequence.

Central Dogma

  • Relationship between DNA and proteins.

  • DNA -> RNA -> Protein.

  • Proteins are responsible for biochemical metabolic reaction to make all the cells molecules (responsible for expressing genetic traits; hair color, eye color, blood type etc. etc. etc.

Function of Nucleotide Monomers

  • DNA building blocks- your genetic material.

  • RNA building blocks- Readers and relayers of the messages of DNA.

  • Other - Ex. ATP - Energy coupling molecule.

  • DNA & RNA are the nucleotide polymers.

Bread Recipe and Nucleic Acids

  • Nucleic acids are not analyzed or listed in nutritional information, BUT they are present.

  • Are nucleic acids essential to your diet?

  • Which is the source of nucleic acids in bread?

Proteins

  • Complex macromolecules made up of 100s or 1000s of building blocks.

  • Have defined structures/functions.

  • Protein suffix often -in or -ase for enzymes.

Proteins - Amino Acids

  • Building blocks (monomers) are (20) amino acids.

  • Most diverse/complex group of macromolecules.

Protein Formation

  • Chains of amino acids are put together by dehydration reaction.

  • Vocabulary: peptide bonds, polypeptides, Protein (A functional polypeptide).

  • This process occurs during translation of mRNA into protein.

Amino Acids

  • How do the 20 amino acids differ?

  • Note: R-groups; functional groups.

  • Note: they differ in characteristics (e.g., Hydrophobic/phylic, charged etc.).

Protein Function

  • A functional protein Must be correctly folded and modified.

  • Structure/Function determined by the sequence of the amino acids.

  • What is the function of the various amino acid R-groups?

  • What is the difference between a polypeptide and a protein?

Protein Structure

  • Primary, Secondary, Tertiary, Quaternary structures.

  • Primary - amino acid sequence.

  • Secondary - alpha helix, beta pleated sheet.

  • Tertiary - 3D folding.

  • Quaternary - multiple polypeptides.

Example - Hemoglobin

  • Four polypeptides come together to form the final functional protein, hemoglobin.

Protein Representation

  • Various ways to represent proteins: Ball and stick model, Space filling model, Ribbon model.

Protein Classes

  • General classes of ~ 1 million proteins:

    • Structural proteins (e.g., Keratin, Collagen, Cytoskeleton, etc.).

    • Active proteins:

      • receptors

      • movement proteins

      • carrier proteins - intercellular

      • membrane transporters

      • muscles (actin/myosin)

      • Enzymes- reaction catalysts

  • Plants have more types of proteins but less amount than do animals

Protein Structure Maintenance

  • What normally maintains protein structure?

  • Amino acids and the protein’s environment:

    • Covalent bonds

    • Ionic bonds

    • Hydrogen bonds

    • Hydrophobic/Hydrophilic interactions

    • van der Waals attractions

Protein Denaturation

  • Protein denaturation: Causes?

  • Can denaturation be reversed?

  • Protein denaturation is not the same as protein “breakdown”.

  • What happens when you cook carbohydrates, lipids and nucleic acids with (or change pH, solute concentration, heating, detergents, etc.)?

Cooking and Food Digestibility

  • Maillard reaction.

  • Heat-based hydrolysis in cooked food.

Protein Synthesis

  • Gene –a sequence of DNA that codes for a particular protein (i.e. codes for a sequence of amino acids).

Protein Structure and Mutations

  • The sequence of amino acids determine protein structure/function.

  • Mutations (altering amino acid sequence) can alter protein structure/function.

  • Mutations are the result of “errors” in the gene that codes for a particular protein.

Gluten Protein Example

  • Gliadin and glutenin.

  • 296 amino acids of gliadin.

Protein Digestion

  • Proteins -> Amino acids from intestine -> blood

  • Energy or building blocks to build up your proteins.

Bread Recipe and Proteins

  • Are proteins essential to your diet?

  • Are amino acids essential to your diet?

  • What is meant by “complete protein”?

  • Which is the source of protein?

  • How does cooking effect bread proteins?

SARS-COV-2 Proteins

  • 29 proteins coded by SARS-COV-2.

  • Mutations would result in changes in proteins' structure/function.

Macromolecules - Source of Building Blocks

  • From diet (“essential”) or metabolism.

  • Plants make all their own.

  • How are macromolecules made in your cells?

Other Macromolecules

  • Chitin (found in exoskeletons).

  • Lignin (found in plant cell walls).

Bread - Other Ingredients

  • Other essential ingredients from your diet: Vitamins & minerals.

  • So is my bread a good food?

Key Takeaways

  • You are what you eat.

  • 4 major macromolecules, their building-blocks, structure/function.

  • Increasing temperature tends to increase the rate of chemical reactions. Why is this not usually true in biological systems?

  • Maintain a “balanced” diet. Eat a variety of real food.

Functional Group Quiz

  • Match the functional group with its structural formula.

  • Circle those structural formulas that are likely hydrophobic.

  • What are the functional groups in this nucleotide?

  • How many Carbons does it have?

Polarity Quiz

  • Which molecule is polar?

  • Which is nonpolar?

  • What about the terms hydrophilic and hydrophobic?

Macromolecule Classification

  • Indicate which of the four major macromolecules.

  • Macromolecule’s building Blocks (i.e. its monomer or sub-unit)?

  • Indicate if this class is usually Hydrophobic and/or Hydrophilic?

  • Suffix? -ose -ase -in