Chapter 2 - Chemical Components of Cells PDF

Chemical Components of Cells Chapter 2 1 Chapter 2 Contents CHEMICAL BONDS Review pages 44 – 54 on your own. You should already be familiar with these chemistry concepts. SMALL MOLECULES IN CELLS MACROMOLECULES IN CELLS...

Chemical Components of Cells Chapter 2 1 Chapter 2 Contents CHEMICAL BONDS Review pages 44 – 54 on your own. You should already be familiar with these chemistry concepts. SMALL MOLECULES IN CELLS MACROMOLECULES IN CELLS 2 SMALL MOLECULES IN CELLS 3 Functional Groups Know the names, structures, and basic properties of these functional groups Influences the behavior of the molecule in which the group occurs! See pp. 70 -71 in text. 4  A Cell Is Formed from Carbon Compounds Carbohydrates Lipids Proteins Nucleic Acids C, O, H C, O, H C, O, H, N, S C, O, H, N, P Nearly all the molecules in a cell are carbon based (organic molecules). Can form many different types and sizes of molecules 5 Cells Contain Four Major Families of Small Organic Molecules Used as building blocks for cellular macromolecules Account for large fraction of a cell’s mass 6  Condensation Reactions Most cellular macromolecules are polymers (excludes lipids) Polymers are synthesized by condensation reactions in which monomers are linked together by the removal of water Energetically unfavorable; requires activation energy (generally ATP) and specific enzymes Condensation reaction Macromolecules have directionality - The chemistry differs at each end of the polymer 7 Hydrolysis Reactions To break down polymers, cells use a process called hydrolysis. Energetically favorable; requires enzymes but does not require (or release) energy. 8 KNOW! For all the basic molecules we are covering in this chapter (both monomers and macromolecules) recognize their molecular structure. Example Amino acid 9 Sugars Are both Energy Sources and Subunits of Polysaccharides 10 1 Sugars Carbohydrates Simple Complex Monosaccharides Disaccharides Polysaccharides Most common Glucose Sucrose Starches (glucose and Have general formula fructose) Fructose Glycogen CnH2nOn where n = 3, 4, 5, 6 Lactose Fibers Galactose (glucose and galactose) 11 Monosaccharides Monosaccharides can contain an aldehyde group and are called aldoses or aldosugars a ketone group and are called ketoses or ketosugars Most sugars have between three and six carbons and are classified as Trioses (three carbons) Pentoses (five carbons) Hexoses (six carbons) 12 FYI: Monosaccharides are Reducing Sugars Reduces another compound and is itself oxidized. Significance Spontaneous chemical reactions between the carbonyl groups of monosaccharides and the amino groups of amino acids in tissue proteins - Glycation Forms advanced glycation end-products (AGEs). AGEs affect nearly every type of cell and molecule in the body and are thought to be one factor in aging and some age-related chronic diseases such as diabetes mellitus, atherosclerosis, Alzheimer's disease. Glycation of lysine residues in histone has been implicated in contributing to cancer formation and metastasis. Induce oxidative stress and ROS formation, leading to inflammation and tissue damage. 13 Ring Formation In aqueous solutions, the aldehyde or ketone group of a sugar tends to react with a -OH group of the same molecule, closing the molecule into a ring. NOTE: carbons are numbered! 14 Isomers and Enantiomers Isomers Same formula but different arrangement of atoms. Changes chemical properties Can have major biological effects Recognized by different enzymes and proteins C6H12O6 Generate large variety in sugars Common among other organic molecules Enantiomers Mirror images L-glucose vs D-glucose L-glucose would be potential low- calorie sweetener but too expensive to manufacture. 15  Dexibuprofen Importance of Isomers and Enantiomers One enantiomer of a drug may have a desired beneficial effect while the other may cause (R)-ibuprofen serious and undesired side effects, or sometimes Isomerase even beneficial but entirely different effects. converts R- to S- Ibuprofen contains therapeutic activity only in the S- isomer form. https://link-springer-com.usd.idm.oclc.org/article/10.1007/BF03342662 (S)-ibuprofen (Dexibuprofen) Metamphetamine Meth (D) vs decongestant (L) 16  Glucose 𝛼 and β Links 4 1 4 1 The hydroxyl group on the carbon that carries the aldehyde or ketone can rapidly change from one position to the other. 𝛼: hydroxyl group downward α-D-glucose polymers generally form a spiral structure that is accessible to ⍺-glycosidic link enzymes and more easily hydrolyzed. β: hydroxyl group upward β-D-glucose polymers form straight β-glycosidic link chains Optimal for the construction of high tensile strength fibers Exclude water – hydrolysis very difficult 17 Di- and Polysaccharides Disaccharides Two monosaccharide units covalently linked via a glycosidic bond (condensation reaction). Common disaccharides Maltose, two glucose units Lactose, one glucose linked to one galactose Sucrose, one glucose linked to one fructose Polysaccharides Monosaccharides can link together to create complex, large, and branched structures. Energy storage Starch and glycogen Structural polysaccharides Cellulose, chitin, dietary fiber What is the molecular formula for a disaccharide containing two glucose molecules? 18 Carbohydrates are a source of energy Glucose has a central role as an energy source for cells. Cellular respiration oxidizes glucose (and other molecules) and uses the chemical energy to produce ATP. Cells store polysaccharides composed of only glucose units as longer-term storage for glucose Starch in plants Glycogen in animals Energy storage polysaccharides are composed of α-D-glucose units 19 Storage Polysaccharides 1 Starch Glucose reserve commonly found in plant tissue Starch grains Stored as starch grains within amyloplast in amyloplasts organelles It occurs both as unbranched amylose (10– 30%) and branched amylopectin (70–90%) 20 FYI: Amylose and Amylopectin Amylose Amylopectin Absorbs less water Absorbs more water Molecules form tight clumps Molecules have more open structure Slower rate of digestion Faster rate of digestion Lower glycemic index Higher glycemic index Beans, lentils, peanuts, veggies,.. Potatoes, white bread,…. 21 FYI: Resistant Starch Starches that do not get broken down by the enzymes in our small intestine but are used as a food source by beneficial bacteria in the colon. Benefits Doesn’t raise blood glucose levels. Improved GI health because it feeds beneficial bacteria. Increased feeling of fullness, prevents constipation, decreases blood cholesterol levels, and lowers risk of colon cancer. Regular digestible starch can be made resistant by cooking and cooling. Cooking causes starch to gelatinize. Cooling causes the starch to re-associate to form more H2O ordered structures. H2O Can cut the ability of our body to absorb and use as H2O H2O H O 2 calories by ½. After retrogradation Gelatinized 22 Storage Polysaccharides Glycogen Protein Highly branched core Stored mainly in the liver and muscle tissues of animals with a lot of water molecules surrounding it. Explains why dieting can initially cause a lot of weight loss. Glycogen in liver 23 Structural Polysaccharides 1 Some polysaccharides are used for mechanical support. Cellulose Composed of repeating monomers of β-D-glucose Forms plant cell walls Mammals cannot digest cellulose Considered “insoluble fiber” Creates bulk in intestines to promote regular bowel movements and other functions related to intestinal health Termites have protists in their digestive system which can break down cellulose Ruminants such as cows break it down via anaerobic bacteria in their digestive systems – produces methane 24 Structural Polysaccharides Sugar derivatives The hydroxyl groups of a simple monosaccharide can be replaced by other groups (carboxyl, amine, …) Chitin Type of polysaccharide composed of a sugar derivative called N- acetylglucosamine Makes up insect exoskeletons and fungal cell walls 25 Dietary Fiber Two types of structural polysaccharide fiber Insoluble fibers like cellulose Soluble fibers like pectin, gums, mucilage Absorb water to become a gelatinous, viscous substance and are fermented by bacteria in the digestive tract. Considered a pre-biotic Induces the growth or activity of microorganisms in the digestive system 26 If this interests you, read “Colonocyte metabolism shapes the gut microbiota” D2L link Modified carbohydrates Glycoproteins and glycolipids Small polysaccharides covalently linked to proteins or lipids. Found on cell membranes. Allow cells to adhere to one another and for protection. Allows cells to recognize and interact with each other. Which organelle glycosylates proteins or lipids? 27 Fatty Acid Chains Are Components of Cell Membranes 28 Categories of Lipids Sterols Cholesterol Plant sterols Steroid Vitamin D hormones C D A B 29  Palmate Fatty Acids Acid A fatty acid is a long amphipathic, hydrocarbon chain with a carboxyl group at one end The polar carboxyl group is the “head” Chemically reactive: in aqueous near neutral solution is ionized and very hydrophilic Name of ionized f.a. ends in -ate Palmate vs palmitic acid (under lower pH conditions) Fatty The nonpolar hydrocarbon chain is the “tail” Chemically not very reactive; hydrophobic Are the building blocks of several classes of lipids 30 Saturated and Unsaturated Fatty Acids Saturated hydrocarbon chains Consist of only single bonds between the carbons Found in meat, dairy products, coconut oil,… Tend to be solid at room temperature Unsaturated hydrocarbon chains Monounsaturated: one double bond Olive oil Polyunsaturated: more than one double bonds Corn oil, sunflower oil The more double bonds, the more fluid. Oxidizes (becomes rancid) more easily. 31 Essential Fatty Acids Must be ingested; cannot be synthesized by the body Only two fatty acids are essential for humans Alpha-linolenic acid: ω-3 fatty acid Linoleic acid: ω-6 fatty acid. Serve multiple functions. Balance between dietary ω-3 and ω-6 strongly affects function (4 ω-6 : 1 ω-3) 32 Trans-fats Hydrogenation: the addition of hydrogen atoms to unsaturated fatty acids. Converts liquid fats (oils) into a semi-solid (spreadable) or solid form Used to create margarine from plant oil Often creates trans fatty acids Linked to increased risk of heart disease and elevated cholesterol levels Listed on the food label as partially hydrogenated oil In the United States, if a food has less than 0.5 grams of trans fat in a serving, the food label can read 0 grams trans fat. 33 Triglycerides or Triacyglycerols Triglycerides are composed of three fatty acids linked to glycerol The three fatty acids on a triglyceride may vary in length and degree of saturation Are stored in cells as long-term energy storage. What other energy storage molecules are there? Glycerol Fatty acid tails 34 Triacylglycerol Triglyceride levels in blood Triglycerides containing mostly saturated fatty acids are usually solid or semisolid at room temperature and are called fats High triglyceride levels in blood increases risk for metabolic syndrome, fatty liver disease, pancreatitis Atherosclerosis To reduce triglyceride levels, reduce simple carb intake, exercise, lose weight, eat healthier fats,.. Triglycerides in plants are liquid at room temperature (e.g., vegetable oil) and are predominantly unsaturated Coconut oil is an exception 35 Triglycerides are a mixture of fatty acids with different saturation levels Olive oil Ω-6 Is coconut oil good for you? https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.119.044687 https://www.ahajournals.org/doi/pdf/10.1161/ https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.119.044687 CIRCULATIONAHA.119.044687 36  Phospholipids Choline Are the major constituents of cell membranes. Are amphipathic The head region contains highly polar covalent bonds Consists of a glycerol, a phosphate, and a polar/charged group The tail region is comprised of two nonpolar fatty acid chains When placed in solution, these lipids form membranes The length and degree of saturation of the fatty acids have profound effects on membrane fluidity 37 Glycolipids In addition to phospholipids, cell membranes contain differing amounts of glycolipids in the extracellular face of the membrane. Composed of a hydrophobic region with two long hydrocarbon tails and a polar region containing one or more sugars. H-substance Do not contain phosphate (sphingolipid) Maintain cell membrane stability and facilitate cellular recognition. Example: ABO blood types Unfortunately, can also be used as receptors for viruses and other pathogens to enter cells. 38 Lipid Aggregates 39 Steroids Derivative of a four-ringed hydrocarbon skeleton Relatively nonpolar and hydrophobic Differ from one another in the positions of double bonds and functional groups Most common steroid in animal cells is cholesterol Used for the synthesis of steroid (sex hormones, corticosteroids) hormones and found in cell membranes as a fluidity buffer 40 KNOW the names, abbreviations, structures, properties of all amino acids! Ionized form at neutral pH Amino Acids Are the Subunits of Proteins 41 Amino acids 1 The monomers of proteins are amino acids Twenty kinds of amino acids are used in protein synthesis Some proteins contain additional amino acids, usually the result of modification No two different proteins have the same amino acid sequence BUT two proteins with the same amino acid sequence can have different functions depending on how the protein folds Depends on conditions in the environment of the protein or different protein modifications Examples Cytoplasm vs matrix of mitochondria Phosphorylation Prion vs functional protein 42 Amino Acids Every amino acid has the same basic structure Can exist as L- or D-amino acids Only L-a.a. used to make proteins At pH 7, both amino and carboxyl groups are ionized The specific properties of amino acids depend on the nature of their R-groups Acidic, basic, uncharged polar, nonpolar Enantiomers 43 Families of Amino Acids (1 of 3) Acidic R groups Basic R groups Negatively charged Positively charged Families of Amino Acids (2 of 3) Uncharged polar R groups - Contain nitrogen or oxygen Families of Amino Acids (3 of 3) Nonpolar R groups Electronegativity H 2.20 C 2.55 S 2.58 O 3.44 N 3.04 Supplementing your diet with amino acids School is stressful; you can’t sleep and tend to get depressed  How about taking some L-tryptophan supplements to make you feel better and help you sleep? Is there evidence that this would help? 47  Where in the cell does this occur? Peptide Bond Amino acids are linked together by a covalent C—N peptide bond Polypeptides have directionality The end with the amino group is called the N- (or amino) Condensation reaction terminus The end with the carboxyl group is called the C- (or carboxyl) terminus 48 Proteins and Polypeptides Immediate product of amino acid polymerization (synthesis) is a polypeptide A polypeptide does not become a protein until it has assumed a unique, stable, three-dimensional shape and is biologically active 49 How many amino acids are in this peptide? Which are the peptide bonds? How many? 50 Modified Amino Acids And Proteins Post-translational modifications such as phosphorylation (-PO42-), acetylation (-COCH3), methylation (-CH3), and others are critical regulators of protein activity and function. 51 Nucleotides Are the Subunits of DNA and RNA 52 Nucleic Acids Coding DNA, 2% Nucleic acids store, transmit, and UTRs, express genetic information introns, 27% Repetitive DNA - DeoxyriboNucleic Acid sequences Serves as the repository of genetic 46% Regulatory information elements, RNA - RiboNucleic Acid RNA genes, All RNA in a cell is a copy of DNA 25% sequences Many roles, including gene Human DNA regulation and protein synthesis 53 Nucleotides DNA and RNA are built from nucleotide subunits. Consist of a nitrogen- containing base, a five-carbon sugar, and one or more phosphate groups. 54 Nucleic Acid Sugars 55  This is the molecule Nucleic Acid Bases caffeine. How would you classify caffeine? Specific to RNA A U C G T Specific to DNA 56 Nucleosides and Nucleotides Nucleoside can be Ribonucleosides (sugar is ribose) Deoxyribonucleosides (sugar is deoxyribose) Nucleotide can be either Ribonucleotides Deoxyribonucleotides 57 Is Adenosine a nucleotide or nucleoside? DNA or RNA? Adenosine 58 Phosphates Number of phosphates can differ Nucleoside monophosphate Or nucleotide Nucleoside diphosphate Nucleoside triphosphate The phosphate makes nucleotide negatively charged. 59 Phosphodiester Bond To form nucleic acid polymers, nucleotides form a covalent bond called phosphodiester bond. Polynucleotide has directionality with a 5ʹ phosphate group at one end and a 3ʹ hydroxyl group at the other The linear sequence of nucleotides in a nucleic acid chain is abbreviated using the one-letter code of the bases starting at the 5’ end of the chain. i.e. 5’ G A T C 3’ 60 Nucleotide Functions Nucleotides and their DNA or RNA? derivatives have many other functions aside from carrying Vitamin B5 genetic information 1. Carry chemical energy Modified Cysteine 2. Form coenzymes 3. Small intracellular signaling molecules 61 Adenosine and Sleep Promotes sleep 62 Self-Assembly of Macromolecules Many macromolecules can self-assemble to form complex structures due to the interactions (noncovalent bonds) within the molecule Can’t self assemble monomers into polymers but fold into final shape or associate with other structures via noncovalent bonds. 63 Chapter 2 Macromolecule Summary 1. Name of macromolecule. Is it a polymer? 2. Name and basic chemical structure of monomer. Are there different kinds? How do they differ from each other? 1. Functional groups 2. Recognizing chemical structures 3. Name of bond that forms between monomers to create polymer 4. Basic functions of macromolecule 5. Any additional important characteristics of monomer or polymer 64 Chapter 2 READ the chapter!!! Know the key terms Quiz on chapter 2 65