Biomolecules PDF

# Biomolecules ## Biomolecules: The Raw Materials of Biotechnology - Are the molecules of cells - The lowest level of organization ## Organization of Life - Entire organism - System - Tissue - Cells - Organelle - Molecules - Atoms - Molecular/atoms lowest level of organization ## Elements of L...

# Biomolecules ## Biomolecules: The Raw Materials of Biotechnology - Are the molecules of cells - The lowest level of organization ## Organization of Life - Entire organism - System - Tissue - Cells - Organelle - Molecules - Atoms - Molecular/atoms lowest level of organization ## Elements of Life - Organic chemistry - Chemistry of Carbon - CHNOPS - Carbon - Hydrogen - Nitrogen - Oxygen - Phosphorus - Sulfur - Several Trace Minerals ## Carbon - The Main Event - Forms a bond with 4 other atoms in which electrons are shared, forming a **covalent compound** ## Carbon - 4 Bonds to Other Atoms - **CH4** - H - H ¬ C ¬ H - H - **CH3OH** - H - H ¬ C ¬ OH - H - **CH3CH2OH** - H ¬ C ¬ C ¬ OH - H H - **CH2O** - O - H ¬ C ¬ H ## Four Main Types of Biomolecules - **All are polymers** - **All are organic (C) compounds** - **Carbohydrates** - Energy, support and recognition - **Proteins** - Enzymes, structure, recognition, transport, pigments, signals, movement - **Lipids** - Cell membrane structure, energy storage, signals, cellular metabolism - **Nucleic Acids** - Hereditary and protein information, energy, signals ## Carbohydrates - Common Features - **OH** - Several OH (alcohol) groups which LOVES water and makes sugars solids and water soluble - **C = 0** - C with a double bond to an oxygen - Aldehyde or Ketone, joins with OH to form a cyclic structure. ## Monosaccharide - Fructose - **D-Fructose** - Double bond oxygen becomes alcohol - CH2OH - C - CHHO - C - CH2OH - Beta Isomer - H - H ¬ C ¬ OH - C ¬ O - HO ¬ C ¬ H - H ¬ C ¬ OH - H ¬ C ¬ H - OH ## Monosaccharide - Galactose - H - C = 0 - H ¬ C ¬ OH - HO ¬ C ¬ H - HO ¬ C ¬ H - H ¬ C ¬ OH - CH2OH <start_of_image> Diagrams of Galactose in cyclic structure ## Monosaccharide - Glucose - O = C ¬ H - H ¬ C ¬ OH - HO ¬ C ¬ H - H ¬ C ¬ OH - H ¬ C ¬ OH - CH2OH Diagrams of Glucose in cyclic structure ## Comparing Two Different Sugars - Open Chain - H - C = O - H ¬ C ¬ OH - HO ¬ C ¬ H - HO ¬ C ¬ H - H ¬ C ¬ OH - CH2OH - Cyclic - Diagrams of sugars in cyclic structure ## Disaccharides - Two Sugars - Diagrams of Glucose, Fructose and Sucrose. - Dehydration Synthesis of Sucrose - Loss of H and OH - Loss of Water ## Disaccharide - Lactose - Lactose = Milk Sugar - Lactose = Glucose and galactose - Lactase = Enzyme that digests lactose - Most mammals express lactase only as juveniles. - Adults are lactose intolerant. - Once weaned = NO MILK!!!!! Diagrams of Lactose, Glucose, and Galactose. ## Polysaccharides - Diagrams of Starch and Cellulose - **Starch**...bonds between glucose can be digested - Amylose = plant - Glycogen = animal - Cellulose...bonds between glucose cannot be digested by mammals ## So...Both are GLUCOSE????? - **Starch** stores glucose molecules for energy - Amylose →Maltose - Amylase - Maltose → 2 Glucose - Maltase - **Cellulose** is a rigid molecule of support - Cellulose → Cellobiose - Cellulase - Cellobiose → 2Glucose - Cellobiase - **Good for providing energy** - **Good for making paper** ## Other Carbohydrates - Diagrams of Chitin and the following sulfates: - Heparin - Chondroitin-4-sulfate - Chondroitin-6-sulfate - Hyaluronate - Dermatan sulfate - Keratan sulfate ## To Test for Carbohydrate - **Benedict's** - Chemical test for reducing sugars - To test for the presence of monosaccharides and reducing disaccharide sugars in food, dissolve a small amount of Benedict's reagent in the food sample. - During heating, the solution should progress from blue (no glucose present) to green, yellow, orange, red, and then brick red or brown (high glucose present). - **Lugol's** - Chemical test for starch - An indicator test for the presence of starches, which turns a dark-blue/black. - Stains starches due to Iodine's interaction with the soil structure of the polysaccharide. ## Deeper Look - Biomolecule - Role in Cell - Monomer - Distinguishing Features - Carbohydrate - Energy/Support - Monosaccharide - C=O, OH group, Subsitute -OH, The way they are connected. ## Protein - Proteins (also known as polypeptides) are organic compounds made of amino acids.&#x20; - Proteins are essential parts of organisms. - Proteins participate in virtually every process within cells. - Proteins make up half the dry weight of an *Escherichia coli* cell (the other macromolecules, such as DNA and RNA, make up only 3% and 20%, respectively). - Proteins have diverse functions due to their ability to **bind** other molecules specifically and tightly. - **Protein Function** - WOW!! - **Structural** - Bones, skin, nails, hooves, hair - **Enzymatic** - Digest sugar, makes DNA, makes fatty acids&#x20; - **Transport** - Carries oxygen and fats in blood, Ca2+/CI- - **Contractile** - Muscles for movement, move chromosomes - **Hormone** -Regulate blood sugar, increase heart rate - **Immunity** -Antibodies fight foreign substance&#x20; - **Pigment** - Pigment in skin, eyes - **Recognition** - On cell surfaces—other molecules (receptors) - **Toxins** - Stops nerve transmission, effects movement of ions, enzymes that destroy red blood cells ## Protein Structure - Polypeptide - Polymer of many amino acids - Diagrams of Polypeptide - H ¬N ¬C¬C ¬OH ­ - Amino acid bond - R ## Amino Acids are Distinguished by the R Group - Twenty different amino acids are found in proteins. - Most microorganisms and plants can biosynthesize all 20. - Animals (including humans) must obtain some of the amino acids from the diet. - The amino acids that an organism cannot synthesize on its own are referred to as **essential amino acids**. - Humans require 8 essential amino acids. - Diagrams of amino acids in a polypeptide structure ## Amino Acids Combine by a Dehydration Synthesis Reaction - Diagram of Peptide Bond - Diagram of Octapeptide - A molecule of water is removed from two glycine amino acids to form a peptide bond. - Also called a condensation reaction ## Amino Acids Combine to Form Protein - The order in which amino acids are bonded is called the **sequence**. - The sequence of amino acids determines the **primary structure** of a protein. - Determined by the genetic code (sequence of DNA). - Diagram of primary, secondary, tertiary, and quaternary protein structure ## The Chemical Nature of R Groups Defines the Characteristics of the Protein - Some amino acid groups are attracted to each other. - Some amino acid groups are repelled by each other. - http://www.biog1105-1106.org/demos/105/unit1/proteinstructure.html ## Four Levels to Protein Structure - Amino acid groups determine the overall shape of protein. - Proteins are not long straight molecules, but are usually folded into a 3-D shape. ## Protein Shape = Protein Function - Diagrams of protein structure in 3D&#x20; ## Genetic Disease is Due to Incorrect Proteins - DNA - RNA (mRNA to be exact) - Protein - Central Dogma of Molecular Biology - List of genetic diseases: - Angelman's Syndrome - Color Blindness - Cystic Fibrosis - Duchenne muscular dystrophy - Hemophilia - Sickle Cell Disease - Tay Sachs - Phenylketonuria - Ataxia telangiectasia - Gaucher disease - Amyotrophic lateral sclerosis - Parkinson Disease - Huntington Disease - Alzheimer Disease - Cancer (Breast, Colon, etc..) - And the list goes on and on and on. ## Changes in DNA = Change in Protein = Change in Function - DNA - Transcription - RNA (mRNA to be exact) - Translation - Protein - Gene Expression - Regulation of transcription determines genes expressed (and proteins produced). - Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification. - Alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. ## Detecting Proteins - Chemical test used for detecting the presence of peptide bonds. - In a positive test, a copper (II) ion is reduced to copper (I). - Forms a complex with the nitrogen and carbon of the peptide bonds in an alkaline solution.&#x20; - A violet color indicates the presence of proteins. - **Biuret Test** - **Alternative protein assays include:** - **UV spectroscopy** - **Lowry protein assay** - **Bicinchoninic acid protein assay (BCA)** - **Amido black protein assay** - **Other Tests** ## Biomolecule - Role in Cell - Monomer - Distinguishing Features - Test - Carbohydrate - Energy/Support - Monosaccharide - C=O, OH group, Subsitute -OH, The way they are connected - Benedict's Test - Protein - Regulation/support - Amino Acid - Central C w/H, -NH2, -COOH, R groups - Biuret Reagent - Lipids - Energy Support Signaling - Glycerol and fatty acids, Cholesterol - Mostly C-H, insoluble in water - Grease spot test ## Lipids - What are They? - Sometimes used as a synonym for fats (which are a subgroup of lipids called triglycerides) - Lipids are defined as molecules that are hydrophobic or amphiphilic - Hydrophobic...they don't dissolve in water - Amphiphilic nature = some lipids form structures such as vesicles, liposomes, or membranes in a water environment - **Broad group of molecules that include:** - Fats - Sterols - Waxes - Fat-soluble vitamins such as vitamins A, D, E, and K - Monoglycerides - Diglycerides - Phospholipids - And others. - **The main biological functions include:** - Energy storage - Structural components of cell membranes - Important signaling molecules ## Lipids - What are They? - Made of mostly C-H - Some oxygen - Some phosphorus - Might see nitrogen - Made of mostly C-H - Diagram of fatty acids - **That's why they are hydrophobic**. (They don't like water). ## Three General Groups - **Triglycerides** - **Phospholipids** - **Steroids** ## Triglycerides - Animal fat and plant oils - Energy storage molecules - Composed of glycerol and fatty acids - Diagrams of Triglycerides ## Fat vs. Oil - It's All in the Fatty Acids - **Saturated Fats** - All C-C single bonds - **Unsaturated Fats** - A few to many C = C double bonds - Diagram of unsaturated fats molecules - **Saturated Fats** - Molecules pack together well - a solid - or fat - at room temperature - **Unsaturated Fats** - Molecules don't pack together - a liquid - or oil - at room temperature. ## Phospholipids - Found primarily in cell membranes. - Similar to triglycerides except...these have a phosphate group which makes the molecule capable of interactions with water.&#x20; - **Phosphate = polar head** - Diagrams of Phosphate molecule ## Phospholipids - **Phosphate** = A negative charge. - **Hydrophilic-phosphate (head)** - **Hydrophobic-fatty acid (tail)** - Make membrane bilayer in water environment (like the cell). Diagram of phospholipids ## Phospholipids Make Up Membranes - Diagram of Cell Membrane - Diagram of Phospholipid Bilayer - Diagram of Micelle - **Phospholipid Bilayer** - Hydrophilic - Hydrophobic - Carbohydrate - Glycoprotein - Glycolipid - Extrcellular Fluid - Cholesterol - Filaments of cytoskeleton - CYTOPLASM - Protein - **Liposome** - **Micelle** - **Bilayer sheet** - http://fig.cox.miami.edu/Faculty%20Dana/membrane.jpg ## Sterols - Overlapping rings of C-H - Complex molecules with many functions: - Hormone - Pigments - Vitamins - Cholesterol - one of the most important - Diagrams of Sterols and Cell Membranes ## Sterols - Diagrams of: - Cholesterol - Estrogen - Testosterone - Vitamin K - Vitamin D ## Test for Lipids - Grease-spot test for lipids has been used for centuries. - Produce a translucent stain on paper or fabric. ## Fatty Acids Used to Make Soap - Consists of sodium or potassium salts of fatty acids. - Made by reacting common oils or fats with a strong alkaline solution (the base, NaOH) in a process known as **saponification**. - The fats are split from glycerol by the base, yielding alkali salts of fatty acids (crude soap) and glycerol. - https://anitagrant.com/images/stories/ingredients/SiteUpdates/SAPprocess.gif ## Biomolecule - Role in Cell - Monomer - Distinguishing Features - Test - Carbohydrate - Energy/Support - Monosaccharide - C=O, OH group, Subsitute -OH, The way they are connected - Benedict's Test - Protein - Regulation/support - Amino Acid - Central C w/H, -NH2, -COOH, R groups - Biuret Reagent - Lipids - Energy Support Signaling - Glycerol and fatty acids, Cholesterol - Mostly C-H, insoluble in water - Grease spot test - Nucleic Acids - Information Energy, Signaling - Nucleotide - Sugar, Phosphate, Cyclic N-Base - Ethidium bromide, Sybersafe, Methylene Blue ## Nucleic Acids - A nucleic acid is a polymer composed of chains of monomeric nucleotides. - The most common nucleic acids are **deoxyribonucleic acid (DNA)** and **ribonucleic acid (RNA)**. - Nucleic acids are universal in living things, as they are found in all cells and viruses.&#x20; - Named for their role in the cell nucleus. ## Nucleic Acid - Function - These molecules carry genetic information or form structures within cells. - **DNA** is responsible for the long-term storage of information. - **DNA** is often compared to a set of blueprints. - **DNA** contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. - Diagram of DNA ## The Three Types of RNA - **RNA** Includes: - mRNA (messenger) - tRNA (transfer) - rRNA (ribosomal) - All used in protein synthesis - **mRNA** roles is the transcribed genetic information from deoxyribonucleic (DNA). - **rRNA** acts as assembly site for protein synthesis in complexes or protein and RNA known as ribosomes. - **tRNA** serves as an essential carrier molecule for amino acids to be used in protein synthesis. - **All encoded in the DNA** ## Nucleic Acid - Structure - The monomers from which nucleic acids are constructed are called nucleotides. - A sequence of nucleotides forms a polymeric chain that has the ability to interact with another chain, or other parts of the chain. - A double-stranded nucleic acid consists of two single-stranded nucleic acid chains held together by hydrogen bonds, such as in the DNA double helix. - RNA is usually single-stranded, but any given strand may fold back upon itself to from secondary structure as in tRNA and rRNA. ## Nucleic Acid - Structure - Diagram of DNA and RNA structure - **Nitrogenous bases** - Cytosine, Thymine, Guanine, Adenine, Uracil. - **DNA** - Deoxyribonucleic acid - **RNA** - Ribonucleic acid - **Base Pairs** - Sugar phosphate backbone ## Nucleotides - Each nucleotide consists of three components: - A carbon to carbon ringed structure with nitrogen. - Called a nitrogenous base - Either a purine or a pyrimidine - A 5-carbon sugar - A Phosphate group - Diagram of nucleotide ## Nucleic Acid Types Differ in the Structure of the Sugar - **DNA** contains **2-deoxyribose**. - **RNA** contains **ribose**. - The only difference is the presence or absence of OH (hydroxyl group) on the second carbon. - **That OH makes RNA less stable - easily degraded**. - **RNA is a transient molecule**. - Diagrams of ribose and deoxyribose sugar molecules ## Nitrogenous Bases Found in the Two Nucleic Acid Types are Different - Adenine, cytosine, and guanine are found in both RNA and DNA. - Thymine only occurs in DNA and uracil only occurs in RNA. - Diagrams of pyrimidines and purines - **DNA** = A T C G - **RNA** = A U C G ## All Nucleotides Have a Phosphate Group - Diagram of nucleotide - **Phosphate** - as found in phospholipids - **HPO4** - **Found between two adjacent nucleotides in a polypeptide** - **Sugar-phosphate backbone** ## Nucleotides are Joined in a Polymer - Diagram of nucleotide - **The addition of a nucleotide requires a nucleotide tri-phosphate… the energy necessary to create the bond between adjacent nucleotide is found in the phosphates that leave.** ## Creating a New Nucleotide is Template Driven...DNA Will be Copied - Making a new DNA or RNA polynucleotide requires a DNA molecule to be copied. - **DNA** is copied by matching complementary bases. - **Adenine** pairs with **thymine** (or uracil in RNA).&#x20; - **Cytosine** pairs with **guanine**. - Diagrams of bases in DNA ## Strict Complementary Rules - Diagram of DNA strands - **Resulting DNA molecule:** - Two chains of twisted nucleotides (two strands - a double helix) - Arranged anti-parallel - Just enough room for a purine (double ring) and a pyrimidine (single ring)...This determines the match ## Base Pairs are Complementary - Two chains are held together by a weak interaction between the bases. - **C = G** - **A = T** - Diagram of DNA molecule - The bond holding the nucleotides together within the strand is very strong. ## DNA Sequence - Order of bases on the polynucleotide chain is called the **DNA sequence**. - This determines the message encoded by the molecule. - **ATT CGC TTG AAC T....** - Although DNA is represented by a sequence of letters, it is important to remember that each nucleotide has a sugar and a phosphate. ## RNA is Very Similar - **Ribonucleic acid** - **Uses uracil instead of thymine**. - **-OH** group on the **second carbon of the sugar (its ribose-not deoxyribose)**. - **Single stranded**. - Diagram of RNA molecule ## Recall the Central Dogma of Molecular Biology - DNA - Transcription - RNA (mRNA to be exact) - Translation - Protein - **TACCGTCTCGAA** - **AUGGCAGAGCUU** (mRNA to be exact) - **Amino Acids....** - **How is RNA translated?** ## Genetic Code = 3 Nucleotides - **AUGGCAGAGCUU** - **AUG GCA GAG CUU** - **1st** amino acid - **Met** - **2nd** amino acid - **Ala** - **3rd** amino acid - **Glu** - **4th** amino acid - **Leu** - Diagram of ribosomes reading codons on mRNA ## Nucleotides are Used for Energy and Signaling - Diagram of ATP and GTPase - **ade** - **rib** - **ATP** - high-energy bond - **GTPase Activating Proteins (GAPS)** - **GTP Exchange Factors (GEFS)** - **"Active" GTP** - **GDP "inactive"** ## Detecting DNA/RNA - Electrophoresis with dyes that **bind** DNA - **Best is Ethidium Bromide** - **Sybersafe with comparable sensitivity** - Diagram of electrophoresis run ## Biomolecule - Role in Cell - Monomer - Distinguishing Features - Test - Carbohydrate - Energy/Support - Monosaccharide - C=O, OH group, Subsitute -OH, The way they are connected - Benedict's Test - Protein - Regulation/support - Amino Acid - Central C w/H, -NH2, -COOH, R groups - Biuret Reagent - Lipids - Energy Support Signaling - Glycerol and fatty acids, Cholesterol - Mostly C-H, insoluble in water - Grease spot test - Nucleic Acids - Information Energy, Signaling - Nucleotide - Sugar, Phosphate, Cyclic N-Base - Ethidium bromide, Sybersafe, Methylene Blue