Lecture_2_updated.pdf

Lecture 2 Carbohydrates, Protein, and Lipids Dr. Sophie SHI Ling [email protected] School of Science and Technology 1 Contents I. Carbohydrates II. Proteins III. Lipids 2  What is car...

Lecture 2 Carbohydrates, Protein, and Lipids Dr. Sophie SHI Ling [email protected] School of Science and Technology 1 Contents I. Carbohydrates II. Proteins III. Lipids 2  What is carbohydrates? A biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen-oxygen atom ratio of 2:1, also called saccharides Most abundant class of organic compounds found in living organisms The empiric formula is (CH2O)n or CnH2nOn, “hydrates of carbon” Originate as products of photosynthesis, an endothermic reductive condensation of carbon dioxide requiring light energy and the pigment chlorophyll A major source of metabolic energy, both for plants and for animals that rely on plants for food 3  Classification of carbohydrates——Monosaccharides Based on the degree of polymerization, carbohydrates are divided into four major categories: monosaccharides, disaccharides, oligosaccharides, and polysaccharides Ø Monosaccharides (“mono” means one) The simplest carbohydrates and cannot be hydrolyzed into other smaller carbohydrates Building blocks of disaccharides and polysaccharides, also known as simple sugars Aldose: the monosaccharides containing the aldehyde group Ketose: the monosaccharides containing one ketone group 4 Classification of carbohydrates——Monosaccharides Ø Examples of monosaccharides Ø Glucose, mannose and galactose (C6H12O6) All three sugars have the same molecular formula (C6H12O6) and are hence isomers Glucose, mannose and galactose are stereoisomers that they have the same structure but differ in the spatial arrangement of the atoms Epimers are carbohydrates which vary in one position for the placement of the -OH group Glucose is the C-2 epimer of mannose, and C-4 epimer of galactose Ø Fructose (C6H12O6) Fructose differs in structure from glucose, mannose and galactose it has a ketone group rather than an aldehyde group hence a structural isomer 5 Classification of carbohydrates——Monosaccharides Ø Examples of monosaccharides Ø Ribose (C5H10O5) and deoxyribose (C5H10O4) Both ribose and deoxyribose are aldopentose A monosaccharide containing five carbon atoms that has an aldehyde functional group at one end Ribose sugar has a hydroxyl (OH) group at position 2, whereas deoxyribose sugar has a hydrogen (H) atom at position 2 6 Classification of carbohydrates——Monosaccharides Ø Functions of monosaccharides Glucose is the main and important source of energy in human, central to energy consumption Galactose is an essential carbohydrate for cellular metabolism, contributing to energy production and storage, can be obtained from milk sugar (lactose) Mannose is a constituent of mucoproteins and glycoproteins required for the proper functioning of the body Fructose exists in fruits and honey; can be metabolized by liver to produce mainly glucose, and minor amounts of glycogen, lactate and a small amount fatty acids in human Ribose is a component of the ribonucleotides from which ribonucleic acid (RNA) is built, and so this compound is necessary for coding, decoding, regulation and expression of genes Deoxyribose, along with phosphate, makes up the sugar-phosphate backbone in deoxyribonucleic acid (DNA), which is the genetic materials for living organisms 7 Classification of carbohydrates——Disaccharides Ø Disaccharides (“di” means two) Consist of two sugar units, can be broken (hydrolyzed) into two monosaccharides The hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide through a covalent bond, releasing a molecule of water The covalent bond formed between the two sugar molecules is known as a glycosidic bond Example: glucose + fructose sucrose 8 Classification of carbohydrates——Disaccharides Ø Disaccharides (“di” means two) Ø Common disaccharides Maltose (glucose + glucose) Cellobiose (glucose + glucose) differ in glycosidic bonds Sucrose (glucose + fructose) Lactose (glucose + galactose) 9 Classification of carbohydrates——Disaccharides Ø Sources of disaccharides Maltose naturally exists in fruit, such as apples, oranges, peaches, blueberries and cranberries Cellobiose occurs naturally as a basic component of cellulose, a substance produced by plants Sucrose can be found in sugarcane, sugar beets, dates Lactose naturally occurs in milk Ø Functions of disaccharides Maltose is an important intermediate in starch and glycogen digestion Cellobiose is a product of cellulose breakdown and plays a role in the metabolism of certain organisms that can utilize it Sucrose is a product of photosynthesis, providing essential carbon and energy for growth and development in plants Lactose is a source of energy in animals, primarily serving as a carbohydrate 10 found in milk Classification of carbohydrates——Oligosaccharides Ø Oligosaccharides (“Oligo” means a few) compounds that yield 3 to 10 molecules of the same or different monosaccharides on hydrolysis linked to either lipids or amino acid by N- or O-glycosidic bonds known as glycolipids or glycoproteins N-linked oligosaccharides: ü It involves the attachment of oligosaccharides to asparagine O-linked oligosaccharides: ü It involves the attachment of oligosaccharides to threonine or serine Ø Functions of Oligosaccharides Glycoproteins are carbohydrates attached to proteins, function as cell-surface receptors, cell- adhesion molecules, immunoglobulins, and tumor antigens Glycolipids are carbohydrates attached to lipids that are important for cell recognition and modulate membrane proteins that act as receptors 11 Classification of carbohydrates——Polysaccharides Ø Polysaccharides (“Poly” means many) A chain of more than 10 monosaccharides join together through glycosidic bond formation, also known as glycans Unlike mono- and disaccharides, polysaccharides are not sweet and, in general, they are not soluble in water Three Important polysaccharides: starch, glycogen and cellulose 12  Classification of carbohydrates——Polysaccharides Ø Functions of polysaccharides Starch is an energy storage polysaccharide found in plants, digestible for human Glycogen is an energy storage polysaccharide formed in the liver in animals Cellulose is a structural polysaccharide that is found in the cell wall of plants v Although cellulose is indigestible for human, it can act as digestive fiber to promote gut health Ø Other polysaccharides Chitin provides important structural stability to fungal cell walls Peptidoglycan is an essential component of bacterial cell walls. It provides strength to the cell wall and participates in binary fission during bacterial reproduction Agarose provides a supporting structure in the cell wall of marine algae Heparin acts as a natural anticoagulant that prevents blood from clotting Chondroitin is an essential component of cartilage that provides resistance against compression 13 Summary Carbohydrates Monosaccharides Disaccharides Oligosaccharides Polysaccharides 1 sugar molecule 2 sugar molecules 3-10 sugar molecules >10 sugar molecules Glucose Maltose Starch Fructose Cellobiose Glycogen Galactose Lactose Cellulose Mannose Sucrose 14 Contents I. Carbohydrates II. Proteins III. Lipids 15  Amino acids——Building blocks of proteins Amino acids are organic compounds mainly consisting of carbon, hydrogen, and nitrogen Structure of amino acid: a hydrogen atom, a carboxyl group, an amino group, and an R-group (side chain), sometimes referred to as a side chain The α-carbon, carboxyl, and amino groups are common to all amino acids R-group is the only unique feature in each amino acid All of the amino acids in proteins exist in two mirror image forms, L and D (except for glycine, which has a R-group as hydrogen atom) With only very minor exceptions, every amino acid found in cells and in proteins is in the L configuration There are 20 different amino acids that function as building blocks of proteins 16  Amino acids——Essential & Non-essential Ø Essential amino acids Cannot be synthesized by cell, must be obtained from diet Help the body repair muscle tissues and form precursor molecules for neurotransmitters Ø Non-essential amino acids Can be produced by cell Involved in proper brain function, the production of red blood cells and white blood cells, and the removal of toxins from the body 17 Amino acids——Classification Ø Amino acids with non-polar side chains (hydrophobic) 9 amino acids fall in the category of non-polar side-chain amino acids alanine (A), valine (V), leucine (L), glycine (G), isoleucine (I), methionine (M), tryptophan (W), phenylalanine (F) and proline (P) Alanine (Ala) 18 Amino acids——Classification Ø Amino acids with polar side chains 6 amino acids fall in the category of uncharged polar side-chain amino acids serine (S), threonine (T), cysteine (C), tyrosine (Y), asparagine (N) and glutamine (Q) 19  Amino acids——Classification Ø Positively charged amino acids (Basic) 3 amino acids fall in the category of positively charged amino acids lysine (K), arginine (R), histidine (H) NH2 group in the residue, ionized into NH3+ at a cellular pH Ø Negatively charged amino acids (Acidic) 2 amino acids fall in the category of negatively charged amino acids aspartic acid (D), glutamic acid(E) COOH group in the residue, ionized into COO- at a cellular pH 20  Proteins Ø Definition A biological macromolecule made up of one or several chains of amino acids linked to each other by peptide bonds forming a polypeptide chain Ø Peptide bond The amine group of one amino acid undergoes a reaction with the carboxylic acid of another amino acid A dehydration-condensation reaction, forming an amide group (CO−NH) The formation of a peptide bond is catalyzed by a ribosome Peptide: short chains of amino acids linked by peptide bonds Polypeptide: a longer, continuous, unbranched peptide chain 21  Proteins——Structure Ø Primary structure defined as the linear sequence of amino acids linked together to form a polypeptide chain determined by the encoding sequence of nucleotides in the gene (DNA) The sequence of codons in DNA, copied into messenger RNA, specifies a sequence of amino acids in a protein 22  Proteins——Structure Ø Secondary structure As protein synthesis progresses, interactions between amino acids close to each other begin to occur, giving rise to local patterns called secondary structure Include the well known α-helix and β-strands Ø α-helix A coiled structure, with 3.6 amino acids per turn of the helix (5 helical turns = 18 amino acids) In the α-helix, hydrogen bonds form between C=O groups and N-H groups in the polypeptide backbone that are four amino acids distant These hydrogen bonds are the primary forces stabilizing the α-helix 23  Proteins——Structure Ø β-strands A flat, side-by-side arrangement of polypeptide chains linked together by hydrogen bonds Rather than coils, β-strands have bends and these are sometimes referred to as pleats can be organized to form elaborately organized structures, such as sheets and barrels Higher order β-strand structures are sometimes called super-secondary structures, stabilized by hydrogen bonds In higher order structure, strands can be arranged parallel or anti-parallel amino to carboxyl orientations the same amino to carboxyl orientations opposite of each other 24  Proteins——Structure Ø Tertiary Structure The tertiary structure of proteins represents overall folding of the polypeptide chains, further folding of the secondary structure H-bonds, electrostatic forces, disulfide linkages, and Vander Waals forces stabilize this structure The specific folding of proteins into their tertiary structure is crucial for their biological function Changes in this structure can affect enzyme activity, binding affinity, and overall stability Gives rise to two major molecular shapes called fibrous and globular c c 25  Proteins——Structure Ø Tertiary Structure Difference between fibrous and globular protein Fibrous Globular Shape Long and narrow Round/spherical Purpose Structural – which means these Functional – this means globular proteins helps to maintain cell proteins carry out a specific shape by providing a scaffolding biological function in the body Amino acid sequence Repetitive amino acid sequence Irregular amino acid sequence Resilience Less sensitive to changes in pH and More sensitive to changes in pH temperature and temperature Solubility Typically insoluble in water Typically soluble in water Examples Collagen, myosin, fibrin, actin, Haemoglobin, myoglobin, keratin, elastin immunoglobin, insulin, enzymes 26 Proteins——Structure Ø Quaternary Structure The spatial arrangement of various tertiary structures gives rise to the quaternary structure composed of two or more smaller protein chains, referred to as subunits describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex In contrast to the first three levels of protein structure, not all proteins will have a quaternary structure since some proteins function as single units Examples of proteins with quaternary structure: hemoglobin, DNA polymerase 27 Proteins——Structure Ø Summary of Protein Structure q Primary structure The most basic level of protein hierarchy Represents the specific linear sequence of amino acids in a single polypeptide chain q Secondary structure The next level of organization beyond primary structure Involves local folding patterns, such as α-helix and β-sheets, stabilized by hydrogen bonds within the polypeptide chain q Tertiary structure The unique three-dimensional arrangement of all amino acids in a single polypeptide chain Tertiary structure is critical to the function of proteins q Quaternary structure Involves the specific spatial arrangement and interactions of multiple polypeptide chains, forming a functional protein complex 28 Denaturation of proteins A process in which proteins lose the quaternary structure, tertiary structure, and secondary structure which is present in their native state Can be caused by changes in temperature, pH, or exposure to chemicals Reversible: if the denaturing agent is removed, allowing the protein to resume its function Irreversible: loss of function, example: boiled eggs (high temperature applied) Denaturing method Effect on Protein Structure Supplies kinetic energy to protein molecules, causing their Heat above 50°C, ultraviolet (UV) radiation, or atoms to vibrate more rapidly and disrupting intermolecular agitation force such as hydrogen bonding Disrupt the salt bridges and hydrogen bonding formed Acids or Bases between the side chains Use of organic compounds, such as Disrupt intramolecular hydrogen bonding within the protein isopropyl alcohol Form strong bonds with the carboxylate anions of aspartic Salts of heavy metal ions, such as mercury, acid and glutamic acid or SH groups of cysteine, disrupting copper, silver, and lead ions ionic bonds and disulfide linkages Soaps and Detergents Disrupt the hydrophobic interactions in the protein 29 Protein folding Protein folding is the process by which a linear chain of amino acids (the polypeptide) acquires its functional three-dimensional structure Mainly guided by hydrophobic interactions, formation of intramolecular hydrogen bonds, van der Waals forces The correct folding gives rise to the function of proteins Misfolding of proteins can cause disorders and diseases, including neurodegenerative disease, such as Alzheimer's disease and Parkinson’s disease ü Chaperone: a functionally related group of proteins assisting protein folding in the cell ü UPS: Ubiquitin–Proteasome System, degrading short-lived regulatory or structurally abnormal proteins ü Autophagy: self-degradation process of the cell that removes unnecessary or dysfunctional components through a lysosome- dependent regulated mechanism 30 Functions of proteins Class of Protein Function Examples Collagen is in tendons and cartilage; Structural Provide structural components Keratin is in hair, skin, wool, and nails mediate contraction of cardiac Contractile Myosin and actin contract muscle fibres and skeletal muscle Carry essential substances Haemoglobin transports to oxygen; Transport throughout the body Lipoproteins transport lipids Casein stores protein in milk; Storage Store nutrients Ferritin contains iron and is stored in the spleen and liver Regulate body metabolism and Insulin regulates the blood glucose level; Hormonal the nervous system Growth hormone regulates body growth Trypsin catalyzes the hydrolysis of Catalyze biochemical reactions in proteins; Enzyme the cells Amylase helps change starches into sugars Recognize and destroy foreign Immunoglobulins stimulate immune Protection substances responses 31 Summary Building block of Macromolecular proteins Amino acid chains polypeptides Essential & Non- Primary essential structure Linked by peptide bonds Secondary Polar & Non-polar structure Peptide & Tertiary Acidic & Basic Polypeptide structure Quaternary structure 32 Contents I. Carbohydrates II. Protein III. Lipids 33 Introduction to lipids Ø Definition Organic compounds that contain hydrogen, carbon, and oxygen atoms, which form the framework for the structure and function of living cells Ø Structure Lipids are primarily composed of two types of molecules: glycerol and fatty acids A glycerol molecule is made up of three carbon atoms with a hydroxyl group attached to it and hydrogen atoms occupying the remaining positions Fatty acids consist of an acid group at one end of the molecule and a hydrocarbon chain, which is usually denoted by the letter ‘R’ May be saturated or unsaturated 34  Physical properties of lipids Soluble in non-polar solvents such as acetone, chloroform, and alcohol Insoluble in water Hydrophobic Energy-rich organic molecules Either liquid or non-crystalline solid at room temperature Greasy in texture Devoid of ionic charges Present either in saturated or unsaturated structural form Stored in adipose tissues in the body 35  Chemical properties of lipids Ø Hydrolysis of triglycerides Triglycerides, the main constituents of body fat in humans and other vertebrates, can be hydrolyzed to produce glycerol and three fatty acids Ø Saponification (皂化反應) The process in which triglycerides are combined with a strong base to form fatty acid metal salts during the soap-making process 36  Chemical properties of lipids Ø Hydrogenation the process of combining unsaturated fat with hydrogen in order to partially or completely convert it into saturated fat Unsaturated fat: a fat or fatty acid in which there is at least one double bond within the fatty acid chain Saturated fat: a type of fat in which the fatty acid chains have all single bonds between the carbon atoms Monounsaturated fat: have one unsaturated carbon bond in the molecule Polyunsaturated fat: have more than one unsaturated carbon bond in the molecule 37  Chemical properties of lipids Ø Halogenation Unsaturated fatty acids have the ability to bind halogens like Cl2, Br2 and I2 to their double bonds; resulting in de-colorization, in which the halogen solution loses its original color Ø Rancidity Oxidation and hydrolysis of fats and oil are responsible for causing rancidity, in which the fat or oil develops a disagreeable odor 38  Classification of lipids Ø Simple lipids The components made out of fatty acids forming ester bond with alcohol Fat and oils: esters of fatty acids with glycerol Waxes: esters of fatty acids with high molecular weight and long-chain alcohol (fatty alcohol) Ø Complex lipids Esters of fatty acids with alcohols and molecules with other groups Phospholipids: a class of lipids whose molecule has a hydrophilic "head" containing a phosphate group and two hydrophobic "tails" derived from fatty acids, joined by an alcohol residue Glycolipids: lipids with a carbohydrate attached by a glycosidic bond Ø Derived lipids lipids obtained after hydrolysis of simple and complex lipids that possess characteristics of lipids Examples: Steroids, fatty acids, glycerol, ketone bodies, lipid-soluble vitamins, and hormones 39  Phospholipids Ø Classification Glycerophospholipids: phospholipids with a glycerol backbone Sphingolipids: phospholipids with a sphingosine backbone The main lipid component of cell membranes and are important in the cells semi-permeability Biological membranes usually involve two layers of phospholipids, called a phospholipid bilayer Each phospholipid has a hydrophilic head and a hydrophobic tail The hydrophobic tails face inward , ensuring their protection from the aqueous environment Glycerophospholipid Sphingolipid 40 Glycolipids Ø Classification q Glycoglycerolipid composed of glycerol, fatty acids, and carbohydrates, more commonly found in plants Examples: galactolipids, sulfolipids q Glycosphingolipids composed of sphingosine, fatty acids, and carbohydrates; predominant in human and animals Examples: cerebrosides, gangliosides galactolipid galactose sulfolipid sulfated glucose 41  Glycolipids are found on the cell membranes of all eukaryotic and some prokaryotic cells Attached to the lipid bilayer and extend into the extracellular environment Exert several functions in cell recognition, cell-cell communication and signal transduction 42 Functions of phospholipids and glycolipids Phospholipids Glycolipids Structural role in membranes Membrane stability Major building blocks of biological membranes, creating a bilayer Maintain the stability the cell membrane; that provides a barrier between the inside and outside of the cell Contribute to the structural integrity of membranes Membrane fluidity Cell proliferation Influence the fluidity and flexibility of the membrane, allowing the Play a role in the regulation of cell growth via interactions with movement of proteins and lipids within the bilayer growth factor receptors Calcium signalling Cell signaling and communication Gangliosides are associated with calcium ions which is thought Act as second messengers in signal transduction to have a role in neuronal function Energy storage Cell recognition The fatty acid tails of phospholipids can be enzymatically cleaved Serve as recognitions sites for cell-cell interaction, act as cell to generate energy markers Immune response Precursors for bioactive lipids Immune responses are generated when the carbohydrate The precursor for the production of bioactive lipids such as attached to the glycolipid binds to a specific of leukocytes and prostaglandins is released from phospholipids endothelial cells Membrane protein function Surface receptors Have the ability to interact directly with particular membrane The carbohydrate part of the glycolipid have particular binding proteins, controlling their activity, location, and function sites; receptors will bind to the sugar part of the glycolipid Cellular trafficking and membrane remodeling Involved in cellular activities involving membrane trafficking, including vesicle production, exocytosis, and endocytosis 43  Steroids A type of lipid molecule containing fused ring structure Important components of cell membranes that alter membrane fluidity Signaling molecules Examples: cholesterol, sex hormones estradiol and testosterone q Cholesterol principal sterol of all higher animals, distributed in body tissues a structural component of cell membranes regulate membrane fluidity during changes in temperature building block for synthesizing various steroid hormones (vitamin D, and bile acids) 44  At high temperatures, cholesterol acts to stabilize the cell membrane and increase its melting point At low temperatures, it inserts into phospholipids and prevents them from interfering with each other to avoid aggregation Contributes to the integrity and rigidity of cell membranes 45  Fatty acids A carboxylic acid with an aliphatic chain, which is either saturated or unsaturated important dietary sources of fuel for animals important structural components for cells q Saturated fatty acids Fatty acids whose hydrocarbon chains do not contain any double bonds Associated with high levels of total plasma cholesterol, increased risk of heart disease and stroke Rich sources of dietary saturated fatty acids include butter fat, meat fat, and tropical oils q Unsaturated fatty acids Fatty acids whose hydrocarbon chains contain one or more double bonds Monounsaturated fatty acids: contain one unsaturated or double bond Polyunsaturated fatty acids: have more than one unsaturated carbon bonds in the molecule Can be found in avocado, fish oil Involved in many body functions, including neuro-protective, 46 antioxidant, anti-inflammatory effects and cardiovascular health  Polyunsaturated Fatty acids (PUFA) Ø Classification q Omega-3 fatty acids Have a terminal carbon-carbon double bond in the omega three-position, the third bond from the end of the carbon chain (the omega end) important constituents of animal lipid metabolism, play an important role in the human diet and physiology Three important types: α-linolenic acid (ALA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) DHA and EPA are found in algae and fish, while ALA can be found in plants Intake of omega-3 fatty acids levels are associated with lower incident risk for cardiovascular disease q Omega-6 fatty acids Have a terminal carbon-carbon double bond in the Omega end omega six-position, the sixth bond from the end of the carbon chain (the omega end) Help stimulate skin and hair growth, maintain bone health, regulate metabolism, and maintain the reproductive system Foods like nuts, seeds, eggs, and vegetable oils are all excellent sources of omega-6 fatty acids Examples: linoleic acid, arachidonic acid 47  Cis- and Trans-fatty acids q Cis-fatty acids The term "cis" and "trans" describe the positions of the two hydrogen atoms located next to the carbon atoms where the double bond exists Cis fatty acid has both hydrogen atoms located on the same side found naturally in foods such as nuts, fish, and corn oil, and are generally considered beneficial for human consumption q Trans-fatty acids Trans fatty acid has the two hydrogen atoms on opposite sides Mainly come from fried and bakery products with hydrogenated vegetable oil Intake of dietary trans-fatty acids disrupt the body‘s ability to metabolize essential fatty acids Leading to changes in the phospholipid fatty acid composition of the arterial walls, increase risk of heart disease 48  Functions of lipids Storage form of energy Structural components of bio-membranes Metabolic regulators (steroid hormones) Act as surfactants detergents and emulsifying agents Act as electric insulators in neurons Provide insulation against changes in external temperature (subcutaneous fat) Protect internal organs (pads of fat) Help in absorption of fat soluble vitamins (A, D, E and K) Serve as second messenger in hormone action 49 Summary Lipids Simple lipids Complex lipids Derived lipids Fat and oils Phospholipids Steroid Waxes Glycolipids Fatty acids 50