Bioprocess Fundamentals CENV 2200 PDF

1 Bioprocess Fundamentals CENV 2200 Dr. Ali Al Jibouri, P.Eng. Office: SW01-1580 Email: [email protected]  2 The Molecules of Life Organic Molecules Carbohydrates Prot...

1 Bioprocess Fundamentals CENV 2200 Dr. Ali Al Jibouri, P.Eng. Office: SW01-1580 Email: [email protected]  2 The Molecules of Life Organic Molecules Carbohydrates Proteins Most important large molecules Nucleic acids found in all living things Lipids  3 Macromolecules Macromolecules Large molecules composed of thousands of covalently connected atoms Most macromolecules are polymers Polymer = a long molecule consisting of many similar building blocks called monomers  4 Macromolecules Organic Molecules Carbohydrates Proteins Polymers Nucleic acids repeated Lipids  5 Polymers Monomers form larger molecules by condensation reactions called Dehydration Reactions one molecule loses hydrogen, one loses OH “adding water” Polymers are disassembled to monomers by Hydrolysis – a reaction that is essentially the reverse of the dehydration reaction  6 Polymers Short polymer Dehydration removes a water Unlinked monomer molecule, forming a new bond Longer polymer Dehydration reaction in the synthesis of a polymer Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer  7 Polymers Each cell has thousands of different kinds of macromolecules Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species An immense variety of polymers can be built from a small set of monomers  8 Carbohydrates Carbohydrates include sugars and the polymers of sugars Simple carbohydrates = monosaccharides Monosaccharides = Single sugars Carbohydrate macromolecules are polysaccharides Polysaccharides = polymers composed of many sugar building blocks  9 Monosaccharides Monosaccharides have molecular formulas that are usually multiples of CH2O Glucose is the most common monosaccharide Monosaccharides are classified by the location of the carbonyl group and by the number of carbons in the carbon skeleton  10 Triose sugars Pentose sugars Hexose sugars (C3H6O3) (C5H10O5) (C6H12O6) Sugars Glyceraldehyde Ribose Glucose Galactose Dihydroxyacetone Ribulose Fructose  11 Monosaccharides Monosaccharides serve as a major fuel for cells and as raw material for building molecules Although we draw them as linear skeletons, in aqueous solutions they form rings – most stable form  12 Monosaccharides Linear and ring forms Abbreviated ring structure  13 Disaccharides Disaccharides are formed when a dehydration reaction joins two monosaccharides The covalent bond formed is called a glycosidic bond Lactose = Glucose and Galactose Maltose = Glucose and Glucose Sucrose = Glucose and Fructose  14 Disaccharides 1–4 Dehydration glycosidic reaction in the linkage synthesis of maltose Glucose Glucose Maltose 1–2 Dehydration glycosidic reaction in the linkage synthesis of sucrose Glucose Fructose Sucrose  15 Polysaccharides Polysaccharides, the polymers of sugars, have storage and structural roles The structure and function of a polysaccharide are determined by its sugar monomers and the positions of the glycosidic linkages  16 Storage Polysaccharides Starch granules Starch (amylose) in a potato tuber cell Glucose monomer Glycogen granules in muscle tissue Glycogen Cellulose microfibrils in a plant cell wall Cellulose Cellulose Hydrogen bonds molecules between —OH groups (not shown) attached to carbons 3 and 6  17 Storage Polysaccharides Chloroplast Starch Starch – storage polysaccharide of plants, consists entirely of glucose monomers Two types of starch – amylose and amylopectin 1 µm Plants store surplus starch as granules within chloroplasts and other plastids Amylose Amylopectin Starch: a plant polysaccharide  18 Storage Polysaccharides Mitochondria Glycogen granules Glycogen – storage polysaccharide in animals Humans and other vertebrates store glycogen in liver and muscle 0.5 µm cells Glycogen Glycogen: an animal polysaccharide  19 Structural Polysaccharides Cellulose is a major component of the tough wall of plant cells Cellulose is a polymer of glucose, like starch, but the glycosidic linkages differ The difference is based on two ring forms for glucose: Alpha (α) Beta (β)  20 Structural Polysaccharides α Glucose β Glucose α and β glucose ring structures Polymers with α glucose are helical Polymers with β glucose are straight Starch: 1–4 linkage of α glucose monomers. Cellulose: 1–4 linkage of β glucose monomers.  21 Structural Cellulose microfibrils in a plant cell wall Polysaccharides Cell walls Microfibril In straight structures H atoms on 0.5 µm one strand can bond with OH Plant cells groups on other strands Parallel cellulose molecules held together in this way are grouped Cellulose into microfibrils  strong building molecules material for plants β Glucose monomer  22 Structural Polysaccharides Enzymes that digest starch by hydrolysing alpha linkages can’t hydrolyse beta linkages in cellulose Cellulose in human food passes through the digestive tract as insoluble fiber Some microbes use enzymes to digest cellulose Many herbivores (from cows to termites) have a symbiotic relationship with these mibrobes  23 Structural Polysaccharides Chitin – another structural polysaccharide is found in the exoskeleton of arthropods & provides structural support for the cell walls of many fungi  24 Lipids Lipids are the one class of large biological molecules that do not form polymers The unifying feature of lipids is having little or no affinity for water Lipids are hydrophobic because they consist mostly of hydrocarbons which form nonpolar covalent bonds The most biologically important lipids are fats, phospholipids and steroids  25 Fats Fats are constructed from two types of smaller molecules: glycerol and fatty acids Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon A fatty acid consists of a carboxyl group attached to a long carbon skeleton  26 Fats Fatty acid (palmitic acid) Glycerol Dehydration reaction in the synthesis of a fat  27 Fats Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride  28 Fats Ester linkage Fat molecule (triacylglycerol)  29 Fats Fatty acids vary in length (number of carbons) and in the number and locations of double bonds Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds Unsaturated fatty acids have one or more double bonds The major function of fats is energy storage  30 Fats (a) Saturated fat (b) Unsaturated fat Structural formula of a saturated fat molecule Structural formula of an unsaturated Space-filling fat molecule model of stearic acid, a saturated Space-filling fatty acid model of oleic acid, an unsaturated fatty acid Double bond causes bending.  31 Phospholipids In a phospholipid, two fatty acids and a phosphate group are attached to glycerol The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head  32 Phospholipids Hydrophilic head Choline Phosphate Glycerol Hydrophobic tails Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid (d) Phospholipid symbol bilayer  33 Phospholipids When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior The structure of phospholipids results in a bilayer arrangement found in cell membranes Phospholipids are the major component of all cell membranes  34 Phospholipids WATER Hydrophilic head Hydrophobic tails WATER  35 Steroids Steroids are lipids characterized by a carbon skeleton consisting of four fused rings Cholesterol, an important steroid, is a component in animal cell membranes  36 Steroids Estradiol Testosterone Cholesterol 37  38 Proteins Proteins account for more than 50 % of the dry mass of most cells Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances  39 Enzymatic proteins Defensive proteins Function: Selective acceleration of Function: Protection against disease chemical reactions Example: Antibodies inactivate and help Example: Digestive enzymes catalyze the destroy viruses and bacteria. hydrolysis of bonds in food molecules. Antibodies Enzyme Virus Bacterium Storage proteins Transport proteins Function: Storage of amino acids Function: Transport of substances Examples: Casein, the protein of milk, is Examples: Hemoglobin, the iron-containing the major source of amino acids for baby protein of vertebrate blood, transports mammals. Plants have storage proteins oxygen from the lungs to other parts of the in their seeds. Ovalbumin is the protein body. Other proteins transport molecules of egg white, used as an amino acid across cell membranes. source for the developing embryo. Transport protein Ovalbumin Amino acids for embryo Cell membrane  40 Hormonal proteins Receptor proteins Function: Coordination of an organism’s Function: Response of cell to chemical activities stimuli Example: Insulin, a hormone secreted by Example: Receptors built into the the pancreas, causes other tissues to membrane of a nerve cell detect signaling take up glucose, thus regulating blood molecules released by other nerve cells. sugar concentration. Receptor protein Insulin Signaling molecules High secreted Normal blood sugar blood sugar Structural proteins Contractile and motor proteins Function: Support Function: Movement Examples: Keratin is the protein of hair, Examples: Motor proteins are responsible horns, feathers, and other skin appendages. for the undulations of cilia and flagella. Insects and spiders use silk fibers to make Actin and myosin proteins are their cocoons and webs, respectively. responsible for the contraction of Collagen and elastin proteins provide a muscles. fibrous framework in animal connective tissues. Actin Myosin Collagen Muscle tissue 30 µm Connective tissue 60 µm  41 Polypeptides Polypeptides are polymers of amino acids A protein is a biologically functional molecule composed of one of more polypeptides  42 Amino Acid Monomers An Amino Acid is an organic molecule with both an amino group and a carboxyl group Amino acids differ in their properties due to differing side chains – R groups Proteins are constructed from the same set of 20 amino acids, linked in unbranched polymers  43 α carbon Amino Acid Amino Carboxyl group group  44 Proteins All proteins consist of a backbone of an amino group (-NH2) and a carboxyl group (-C(=O)OH) 20 different amino acids are involved in Amino Group the structure of a variety of proteins which Carboxyl have various functions Various Group R Groups Store energy Immune system Hormones Amino Acid Structure S. Manahan, Environmental Chemistry. CRC Press, 2017.  45 Nonpolar side chains; hydrophobic Side chain (R group) Glycine Alanine Valine Leucine Isoleucine (Gly or G) (Ala or A) (Val or V) (Leu or L) (Ιle or Ι) Methionine Phenylalanine Tryptophan Proline (Met or M) (Phe or F) (Trp or W) (Pro or P)  46 Polar side chains; hydrophilic Serine Threonine Cysteine (Ser or S) (Thr or T) (Cys or C) Tyrosine Asparagine Glutamine (Tyr or Y) (Asn or N) (Gln or Q)  47 Electrically charged side chains; hydrophilic Basic (positively charged) Acidic (negatively charged) Aspartic acid Glutamic acid Lysine Arginine Histidine (Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)  48 Amino Acid Polymers Amino acids are linked by peptide bonds A polypeptide is a polymer of amino acids Polypeptides range in length from a few monomers to more than a thousand Each polypeptide has a unique linear sequence of amino acids Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N- terminus) NCC-NCC-NCC-NCC  49 Peptide bond New peptide bond forming Side chains Back- bone Amino end Peptide Carboxyl end (N-terminus) bond (C-terminus)  50 Protein Structure and Function A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape The sequence of amino acids determines a protein’s three- dimensional conformation A protein’s conformation determines its function Ribbon models and space-filling models can depict a protein’s conformation  51 G. Miller and S. Spoolman, Living in the environment: principles, connections, and solutions. Nelson Education, 2011.  52 Antibody protein Protein from flu virus  53 Protein Structure The primary structure of a protein is its unique sequence of amino acids Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain Tertiary structure is determined by interactions among various side chains (R groups) Quaternary structure results when a protein consists of multiple polypeptide chains  54 Primary structure Primary Structure Amino acids 1 5 10 Primary structure, the sequence of Amino end amino acids in a protein, is like the 30 25 20 15 order of letters in a long word 35 40 45 50 Primary structure is determined by Primary structure of transthyretin 55 inherited genetic information 70 65 60 75 80 85 90 95 115 110 105 100 120 125 Carboxyl end  55 Secondary Structure Secondary structure The coils and folds of secondary structure result from hydrogen bonds between repeating α helix constituents of the polypeptide backbone Hydrogen bond Typical secondary structures are β pleated sheet a coil called an alpha helix and a β strand folded structure called a beta pleated sheet Hydrogen bond 56  57 Tertiary Structure A proteins tertiary structure is Tertiary structure superimposed on the patterns of the secondary structure Tertiary structure is the overall shape of a polypeptide resulting from interactions between the Transthyretin side chains (R groups) of various polypeptide amino acids 58  59 Quaternary Structure Quaternary structure results Quaternary structure when two or more polypeptide chains form one macromolecule Collagen is a fibrous protein consisting of three polypeptides Transthyretin protein coiled like a rope Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains  60 Quaternary Structure Polypeptide chain β Chains Iron Heme α Chains Polypeptide chain Collagen Hemoglobin  61 https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/a/orders-of-protein-structure  62 Protein Folding Cap It is hard to predict a protein’s conformation from its primary structure Hollow Most proteins probably go cylinder through several states on their way to a stable conformation Chaperonins are protein molecules that assist the proper Chaperonin folding of other proteins (fully assembled)  63 Correctly Polypeptide folded protein Steps of Chaperonin The cap attaches, causing The cap comes Action: the cylinder to change off, and the An unfolded poly- shape in such a way that properly folded peptide enters the it creates a hydrophilic protein is released. cylinder from one environment for the end. folding of the polypeptide.  64 Protein Structure In addition to primary structure, physical and chemical conditions can affect conformation Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein’s native conformation is called denaturation A denatured protein is biologically inactive  65 Protein Structure Denaturation Normal protein Denatured protein Renaturation 66  67 Activity Make a list of some types of proteins, their function and specific examples.  68 S. Manahan, Environmental Chemistry. CRC Press, 2017.  69 5 challenges we could solve by designing new proteins  70 Nucleic Acids The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid  71 Nucleic Acids There are two types of nucleic acids: Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis Protein synthesis occurs in ribosomes  72 DNA Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA Movement of mRNA into cytoplasm Ribosome via nuclear pore Synthesis of protein Amino Polypeptide acids  73 Nucleic Acids - Structure Nucleic acids are polymers called polynucleotides Each polynucleotide is made of monomers called nucleotides Each nucleotide consists of a nitrogenous base, a pentose sugar and a phosphate group The portion of a nucleotide without the phosphate group is called a nucleoside  74 Nucleotide Monomers Nucleotide monomers are made up of nucleosides and phosphate groups Nucleoside = nitrogenous base + sugar There are two families of nitrogenous bases: Pyrimidines have a single six-membered ring Purines have a six-membered ring fused to a five-membered ring In DNA, the sugar is deoxyribose In RNA, the sugar is ribose  5′ end 75 Nucleoside Nitrogenous base Phosphate group Pentose sugar Nucleotide 3′ end Polynucleotide, or nucleic acid  76 Nitrogenous bases Pyrimidines Cytosine Thymine (in DNA) Uracil (in RNA) C T U Purines Adenine Guanine A G Pentose sugars Deoxyribose (in DNA) Ribose (in RNA) Nucleoside components  77 Nucleotide Polymers Nucleotide polymers are linked together, building a polynucleotide Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages The sequence of bases along a DNA or mRNA polymer is unique for each gene  78 Sugar-phosphate backbone 5′ end (on blue background) Nitrogenous bases Pyrimidines 5′C 3′C Nucleoside Nitrogenous Cytosine (C) Thymine Uracil base (T, in DNA) (U, in RNA) Purines Phosphate 5′C group Sugar (pentose) Adenine (A) Guanine (G) 3′C (b) Nucleotide Sugars 3′ end (a) Polynucleotide, or nucleic acid Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components  79 DNA Double Helix A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix In the DNA double helix, the two backbones run in opposite 5´ to 3´ directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C  80 5′ 3′ Sugar-phosphate backbones Hydrogen bonds 3′ 5′ Base pair joined by hydrogen bonding  81 5′ end 3′ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 5′ end New strands 3′ end 5′ end 5′ end 3′ end 82  83 DNA Replication and RNA Transcription and Translation https://www.youtube.com/watch?v=6gUY5NoX1Lk  84 Sources  J. B. Reece et al., Campbell Biology, Canadian Edition,. Pearson Education, 2014. Chapter 5.  S. Manahan, Environmental Chemistry, 10th Edition. Boca Raton: CRC Press, 2017.  Khan Academy, “Orders of protein structure,” Khan Academy. [Online]. Available: https://www.khanacademy.org/science/biology/macromolecules/proteins-and- amino-acids/a/orders-of-protein-structure. [Accessed: 01-Feb-2019].  85 Review Questions Why is butter solid at room temperature, while vegetable oil is a liquid? a) Butter is a saturated fat and vegetable oil is an unsaturated fat b) Butter is a nonpolar molecule and vegetable oil is a polar molecule c) Butter is an unsaturated fat and vegetable oil is a polar molecule d) Butter is a polar molecule and vegetable oil is a nonpolar molecule  86 Review Questions What type of carbohydrate is sucrose? a) Trisaccharide b) Monosaccharide c) Polysaccharide d) Disaccharide Figure 1: Structure of Sucrose  87 Review Questions Which of the following statements is true of the carbohydrate glucose? a) Glucose is a polysaccharide b) Glucose contains carbon, hydrogen and oxygen atoms c) Glucose is a structural isomer of galactose d) Glucose is a pentose sugar  88 Review Questions How are triglycerides formed? a) Triglycerides are formed through hydrolysis, which results in the loss of H2O molecules b) Triglycerides are formed through dehydration synthesis, which results in the loss of H2O molecules c) Triglycerides are formed through hydrolysis, which results in the production of H2O molecules d) Triglycerides are formed through dehydration synthesis, which results in the addition of H2O  89 Review Questions Which of the following is a characteristic of lipids? a) They are not soluble in water b) They are either fats or oils c) They are composed of nitrogenous chains d) They are polar molecules  90 Review Questions Which of the following occurs when hydrogen is reacted with vegetable oil? a) The hydrogenated vegetable oil will contain fewer trans fats b) The hydrogenated vegetable oil will become solid at room temperature c) The hydrogenated vegetable oil will become polarised d) The hydrogenated vegetable oil will become a saturated fat  91 Review Questions What are the components of a triglyceride molecule? a) One glycerol and one cholesterol b) One cholesterol and two fatty acids c) One glycerol and three fatty acids d) One glycerol and two fatty acids  92 Review Questions Which of the following categories includes all others in the list? a) Disaccharide b) Polysaccharide c) Starch d) Carbohydrate  93 Review Questions The enzyme amylase can break glycosidic linkages between glucose monomers only if the monomers are in the α form. Which of the following could amylase break down? a) Glycogen, starch and amylopectin b) Glycogen and cellulose c) Cellulose and chitin d) Starch, cellulose and chitin  94 Review Questions Which of the following is true of unsaturated fats? a) They are more common in animals than in plants. b) They have double bonds in their fatty acid chains. c) They generally solidify at room temperature. d) They contain more hydrogen than do saturated fats having the same number of carbon atoms.  95 Review Questions The molecular formula for glucose is C6H12O6. What would be the molecular formula for a polymer made by linking ten glucose molecules together by dehydration reactions?? a) C60H120O60 b) C60H102O51 c) C60H100O50 d) C60H111O51  96 Review Questions The structural level of a protein least affected by a disruption in hydrogen bonding level is: a) Primary level b) Secondary level c) Tertiary level d) Quaternary level e) All structural levels are affected equally  97 Review Questions What parts of a polypeptide participate in the bonds that hold together: a) Secondary Structure b) Tertiary Structure a) Secondary structure involves hydrogen bonds between atoms of the polypeptide backbone b) Tertiary structure involves interactions between atoms of the side chains of the amino acid subunits  98 Review Questions Which of the following statements is true regarding protein structure? a) Proteins in a quaternary structure consist of a simple polypeptide chain b) The two types of primary structure are α helices and β pleated sheets c) Secondary structures are formed by multiple polypeptide chains d) Interactions between the R groups in amino acids form tertiary structure  99 Review Questions Which of the following is an example of protein denaturation? a) Several amino acids are joined together via peptide bonds b) A protein binds with a substrate, lowering the activation energy of a reaction c) Amino acids fold into repeating patterns due to hydrogen bonding of the peptide backbone d) A protein is exposed to extremely high heat, causing it to lose its secondary structure and be left with only its primary structure  100 Review Questions Why does a denatured protein no longer function normally?  The function of a protein is a consequence of its specific shape, which is lost when it is denatured  101 Credentials This presentation was crafted by Dr. Deirdre Lynch.