Section 2.3 Carbon Compounds PDF

Carbon Compounds ❧ ❧ Section 2.3  4 Categories of Organic Molecules Lipids Carbohydrates Fats/Oils/Steroids/Wax Glucose/Fructose Starch...

Carbon Compounds ❧ ❧ Section 2.3  4 Categories of Organic Molecules Lipids Carbohydrates Fats/Oils/Steroids/Wax Glucose/Fructose Starch/Cellulose Molecules of Life Proteins Biochemicals Nucleic Acids Enzymes/Structure/ (CHON) Movement/Protection (DNA/RNA)  Carbon Compounds Organic Compounds Carbohydrates Lipids Proteins Nucleic Acids Monomer: Monomer: Nucleotide Monomer: Monomer: Glycerol and 1) 5 Carbon sugar, Monosaccharide Amino Acid Fatty Acids 2) phosphate group 3)nitrogenous base Made up of: Made up of: Made up of: Made up of: Carbon, Hydrogen, Carbon, Hydrogen, Carbon, Hydrogen, Carbon, Hydrogen, Oxygen Oxygen Oxygen, Nitrogen Oxygen, Nitrogen and (H:O in 2:1 ratio) (H:O not in 2:1 ratio) (sometimes Sulfur) Phosphorus  Organic Compounds ❧ All compounds are either ORGANIC, containing carbon bonded to hydrogen and oxygen, or INORGANIC. ❧ The chemistry of carbon is the chemistry of life.  Organic Compounds ❧ >11 million compounds ❧ Contain a C-C or C-H bond in combination with N, O, S, P or halogens ❧ Simplest = CH4 ❧ Most complex = DNA  Organic Compounds Allotropes of carbon Allotropes: Different forms of an element in same physical state Catenation: ability of an element to form chains and/or rings of covalently bonded atoms Carbon has high bond energies C-C 346 kJ/mol C-H 418 kJ/mol  Diamond ❧ tetrahedral array of C atoms o sp3 hybridized ❧ high mp (>3500°C) ❧ hardest material known to man ❧ brittle ❧ most dense (3.5x that of H2O) ❧ Industrial uses: cutting, drilling, grinding  Graphite ❧ layers of hexagonal arrays of C atoms o sp2 hybridized (planar) ❧ high mp ❧ no covalent bonds between layers – C atoms too far apart from each other (London Dispersion forces) ❧ layers slip past one another ❧ lubricant and pencil “lead” ❧ Graphite fibers (stronger and less dense than steel)- sporting goods and aircraft  Soot ❧ amorphous form of carbon (no structure) ❧ impure carbon particles resulting from incomplete combustion  Carbon Bonding: ❧ How many protons does carbon have? Electrons? ❧ Carbon has FOUR valence electrons o Needs eight electrons to be stable ❧ Carbon readily forms four covalent bonds with other atoms, including carbon  Carbon Bonding ❧ Carbon can form straight chains, branched chains, or rings o Leading to a great variety of organic compounds Isomers  Arrangement of Atoms ❧ Isomers – compounds that have the same molecular formula but different structures Isomers of C6H14 ❧ More C atoms in formula, more isomers o 18 isomers for C8H18 o 35 isomers for C9H20 o 75 isomers for C10H22  Ex #1) Butane, C4H10 Ex #2) Butene, C4H8 ISOMERS Ex #3) 2-Butene, C4H8 Ex #4) methyl propene, C4H8  Structural Formula ❧ Indicates the number and types of atoms present in a molecule and also shows the bonding arrangement of the atoms ❧ One possible isomer of C4H10 ❧ Does not show 3D shape  Structural Isomers ❧ Isomers in which the atoms are bonded together in different orders. ❧ C4H10 (note continuous chain of C atoms) butane methylpropane  Physical Properties of Structural Isomers Melting Boiling Density at Point (°C) Point (°C) 20°C Butane -138.4 -0.5 0.5788 Methylpropa ne -159.4 -11.633 0.549  Hydrocarbons ❧ Only have carbon and hydrogen ❧ Simplest organic compounds ❧ From petroleum (crude oil)  Carbon Bonding Single Bond Sharing 2 electrons A single line Double Bond Sharing 4 electrons Two parallel lines Triple Bond Sharing 6 electrons Three parallel lines  Naming Carbon Compounds ❧ Organic PREFIXES ❧ Indicates the number of carbon atoms in the hydrocarbon chain ❧ Hydrocarbon: any organic compound that contains only the elements, hydrogen and carbon # of C prefix # of C prefix 1 Meth- 6 Hex- 2 Eth- 7 Hept- 3 Prop- 8 Oct- 4 But- 9 Non- 5 Pent- 10 Dec-  Organic PREFIXES ❧ Prefixes for alkanes that have 1-4 carbons are rooted historically. o These are methane, ethane, propane, and butane, respectively. o An easy way to remember the first four names is the anagram Mary Eats Peanut Butter (methane, ethane, propane, butane) ❧ Prefixes for 5 carbons and up are derived from the Greek language. Naming Carbon Compounds ❧ Organic SUFFIXES ❧ Indicates the types of covalent bonds that are present in the hydrocarbon chain o Identifies the series to which it belongs Formula Type of Series Ending determines the # H atoms Bond(s) Alkane -ane CnH2n+2 Single Alkene -ene CnH2n Double Alkyne -yne CnH2n-2 Triple  Aliphatic Hydrocarbons - hydrocarbons without aromatic rings Saturated Hydrocarbons: compounds that contain all SINGLE bonds Alkanes: each carbon is bonded to 4 atoms – Only contain single bonds – Skeleton: C-C Molecular formula: C nH 2n+2  Unsaturated Hydrocarbons Compounds that contain at least one double bond or triple bond 1. Alkenes : compounds that contain a double bond Skeleton: C=C Molecular formula = C nH 2n  Unsaturated Hydrocarbons 2. Alkynes : compounds that contain a triple bond – Skeleton: C≡C – Molecular formula = C nH 2n-2  Naming Alkanes ❧ To give an alkane a name, a prefix indicating the number of carbons in the molecule is added to the suffix ane o identifies both the kind of molecule (an alkane) and how many carbons the molecule has (the prefix). ❧ The name pentane tells you that the molecule is an alkane (-ane ending) and that it has 5 carbons (pent- indicates 5)  Naming Alkenes 1. Locate the carbon atoms in the longest carbon chain that contains the double bond. Use the stem with the ending –ene. 2. Number the carbon atoms of this chain sequentially, beginning at the end nearer the double bond. If the parent chain has more than 3 carbons, insert the number describing the position of the double bond (indicated by its 1st carbon location) before the base name. 1-butene 2-butene http://wps.prenhall.com/wps/media/objects/476/488316/index.html  Naming Alkynes ❧ Named just like the alkenes except the suffix –yne is added ethyne 1-butyne propyne 2-butyne  Write the names of the organic compounds methane propyne 2-butyne 1-pentene nonane 3-hexene 2-pentene  Give the structural formulas for the organic compounds 1. ethene 2. heptane 3. 3-decyne 4. butane 5. 2-octene  Functional Groups ❧ An atom or group of atoms, that replaces hydrogen in an organic compound and that defines the structure of a family of compounds and determines the properties of the family. ❧ FUNCTIONAL GROUP - a cluster of atoms that influence the properties of the molecules that they compose, and determine the characteristics of the compound. Lactic Acid OH Estradiol Carboxyl (estrogen) { HO Hydroxyl Female lion OH Carbonyl (middle) Wohler 1828 O Testosterone Amino Male lion Urea  Hydroxyl Group Structure Compound Alcohols Name Polar, attracts water Properties (good solvent) Naming -ol Carbonyl Group  Carbonyl (end): Structure Compound Aldehydes Name Structural isomers Properties with different properties Naming -al  Carbonyl (middle): Structure Compound Ketones Name Structural isomers Properties with different properties Naming -one  Carboxyl Group Structure Compound Carboxylic acid Name (organic acids) Acidic Properties properties Naming -oic acid  Amino Group Structure Compound Name Amines Basic Properties properties Naming -amine  Phosphate Group Structure Compound Name Phosphates DNA Makes the molecule Properties and anion Transfer energy  Methyl Group Structure Compound Methylated Name compounds May affect gene Properties expression  Sulfhydryl Group Structure Compound Name Thiols Methanethiol - It is a colorless gas with a distinctive putrid smell. It Stabilize proteins is a natural substance found in the blood and brain of humans and Properties Some can have a other animals as well as plant stinky odor – skunk, tissues. It occurs naturally in rotten eggs, garlic certain foods, such as some nuts and cheese. It is also one of the main compounds responsible for Naming -thiol bad breath and the smell of flatus.  Large Carbon Molecules: ❧ In many carbon compounds, the molecules are built up from smaller, simpler molecules known as MONOMERS. ❧ Monomers can bind to one another to form complex molecules known as POLYMERS. o Large polymers are also called MACROMOLECULES o The process of reacting monomer molecules together in a chemical reaction to form polymer chains or three-dimensional networks - POLYMERIZATION  Biological Reactions ❧ WATER is the most important inorganic compound in the body and it participates in two biological reactions: o Hydrolysis o Dehydration Synthesis  Hydrolysis ❧ Breaking down polymers by adding a water molecule.  Hydrolysis ❧ Breaking down polymers by adding a water molecule. C12H22O11 + H2O → C6H12O6 + C6H12O6  Hydrolysis Polymers are broken down to monomers Animation: Hydrolysis of sucrose H2O H OH Hydrolysis H OH OH H  Dehydration Synthesis ❧ Build up large molecules by releasing a molecule of water.  Dehydration Synthesis ❧ Build up large molecules by releasing a molecule of water. C6H12O6 + C6H12O6 → C12H22O11 + H2O  Dehydration Synthesis o Cells make most of their large molecules by joining smaller organic molecules into chains called polymers o Cells link monomers to form polymers H OH OH H OH H Short polymer Unlinked monomer H2O Dehydration Dehydration reaction reaction H OH H OH Longer polymer  Energy Currency: ❧ Energy necessary for processes is available in the form of certain compounds that contain a large amount of energy in their overall structure. ❧ One of these is adenosine triphosphate or ATP  Energy Currency: ❧ ATP has three linked phosphate groups ( PO4-2) attached to one another by covalent bonds. ❧ The bond holding the last one is easily broken and when broken much more energy is released then was required to make the bond. ❧ This conversion of energy is used by cells to drive chemical reactions that enable organisms to function.  Molecules of Life ❧ The four main classes of organic compounds essential to all living things are made from CARBON, HYDROGEN, and OXYGEN atoms, but in different ratios giving them different properties.  Carbohydrates: ❧ Made of carbon, hydrogen, and oxygen with H to O in a 2:1 ratio ❧ Monosaccharides are a single sugar - MONOMER ❧ Source of energy ❧ Can be in straight or ring form ❧ -ose ending for sugars Glucose (C6H12O6) Ribose (C5H10O5)  Carbohydrates: ❧ Glucose, galactose, and fructose all have the same molecular formula but differ in the arrangement of atoms = ISOMERS ❧ General formula for the monomer = (CH2O)n o Molecular formula = C6H12O6 (hexoses) C5H10O5 (pentoses)  Carbohydrates: Type of Name of Description of Sugar Sugar Sugar Pentose ribose Found in RNA Pentose deoxyribose Found in DNA In blood; cell’s main Hexose glucose energy source (ATP) In fruit; sweetest of Hexose fructose monomers (honey) Hexose galactose In milk  Carbohydrates ❧ Disaccharides are double sugars ❧ Two monosaccharides condense to form disaccharides o Formed by dehydration synthesis o Molecular formula = C12H22O11  Carbohydrates: ❧ Bond that joins monosaccharides (carbohydrates) = glycosidic bond  Carbohydrates A disaccharide is produced by joining 2 monosaccharide (single sugar) units. In this animation, 2 glucose molecules are combined using a condensation reaction, with the removal of water. Glucose molecules joining to form a disaccharide Condensation of Monosaccharides Enzyme Catalytic Cycle  Common Disaccharides 2 single sugars that join Name of to form the Description of Sugar Disaccharide disaccharide Table Sugar; Sucrose Glucose + Fructose transportable energy (sugar beets, sugar cane) In milk of mammals; Lactose Glucose + Galactose provides energy for suckling animals In malt (grains) Maltose Glucose + Glucose From starches (cereal, pasta, potatoes)  Carbohydrates ❧ Polysaccharides many sugars: ❧ General formula – (C6H10O5)n plus H2O (n = # monomers) ❧ Formed by dehydration synthesis ❧ Long chains of glucose molecules  Carbohydrates: Name of Description of Sugar Polysaccharide Animal polysaccharide - stores excess sugar Stored in liver and muscles Glycogen Muscle contraction & movement (animal starch) Broken down into glucose and released into blood for quick energy Plant polysaccharide Starch Stores excess sugar Gives plants strength and rigidity Major component of wood and paper Cellulose Component of cell wall  o Starch and glycogen are polysaccharides That store sugar for later use o Cellulose is a polysaccharide found in plant cell walls – provides structure STARCH Glucose Starch granules in monomer potato tuber cells O O O O O O O O O O O Glycogen granules in muscle tissue GLYCOGEN O O O O O O O O O O O O O Cellulose fibrils in CELLULOSE a plant cell wall OO Cellulose OO O OH molecules OO OO O OH OO O O O O OO OO O O O Figure 3.7  Lipids: Fats, Oils, and Waxes ❧ Elements – carbon, hydrogen, and oxygen (NOT a 2:1 H:O ratio) ❧ Do not dissolve in water ❧ Lipids contain a large number of C-H bonds which store more energy than C-O bonds in carbohydrates ❧ Monomers: glycerol and fatty acid  Lipids ❧ Fatty Acids: o Fatty acids are unbranched C-chains → (12-28 C) with a carboxyl group (acid) at one end The carboxyl end is POLAR and attracted to water – HYDROPHILIC The hydrocarbon end is NONPOLAR and does not interact with water – HYDROPHOBIC  Fatty Acid General Structure Saturated (single bonds) Unsaturated (double bonds)  Functions of Lipids in living organisms ❧ Lipids can be used to store energy – long term E storage ❧ Lipids are important parts of biological membranes ❧ Lipids are waterproof coverings – nonpolar ❧ Heat insulation and protection around internal organs ❧ Steroids and hormones are lipids that send messages to cells (eg. estrogen, progesterone, testosterone) o anabolic steroids - synthetic ❧ Cholesterol, an important steroid, is an important component of the animal cell wall Steroid – 4 fused rings  Wax ❧ Long fatty acid chain joined to an alcohol chain ❧ Highly waterproof o Plant parts (leaves, fruit) form a protective coating on the outer surface (reduce transpiration) ❧ In animals → ear wax  Lipids Look at the structures of the fatty acids and explain the differences between saturated, unsaturated and polyunsaturated fats. Saturated and Unsaturated Fatty Acids: Lipids (4:52)  Saturated & Unsaturated Fatty Acids Carbon atoms with 4 atoms High melting points Saturated covalently bonded Solid @ room temperature Fatty Acids All single bonds Ex.) animal fat, shortening Carbon not bonded to the Liquid @ room temperature Unsaturated maximum # of atoms Primarily in plants Fatty Acids There are double bond(s) Energy storage in animals polyunsaturated Saturated vs. Unsaturated Fatty Acids  Trans fats ❧ A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits ❧ Hydrogenation – process of converting unsaturated fats to saturated fats by adding hydrogen ❧ Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds o These trans fats may contribute more than saturated fats to cardiovascular disease  Lipids ❧ Lipids (fats, oils, and waxes) are formed by a glycerol molecule bonding to fatty acid(s) o formed by dehydration synthesis Dehydration Synthesis Ester Linkage  Triglycerides ❧ Three fatty acids attached to glycerol Formation of a Triglyceride  Phospholipids ❧ Two fatty acids joined to a glycerol ❧ Makes up cell membrane - PHOSPHOLIPID BILAYER Phospholipid  Proteins ❧ Elements: Carbon, Hydrogen, Oxygen, Nitrogen ❧ Monomer: AMINO ACID (20 different kinds) ❧ Each amino acid has a central carbon atom bonded to 4 other atoms or functional groups 20 Amino Acids  Essential and Nonessential Amino Acids ❧ Essential Amino Acids: Cannot be synthesized in the animal body and should be obtained from diet ❧ Nonessential Amino Acids: Can be synthesized in the animal body o Some may be conditionally essential in newborns or during illness o Amino acids absorbed from food are used to synthesize structural proteins, functional proteins, protein hormones, carrier proteins, and proteins essential for growth, development and tissue repair.  Proteins ❧ Bond that joins amino acids (protein) = PEPTIDE BOND  Formation of a peptide bond Formation of a peptide bond Peptide bond amino acid 1 amino acid 2 dipeptide water Proteins  Functions of Proteins 1. Structural component of cell 2. Transport substances into or out of cells 3. Regulate cell processes 4. Control the rate of reactions - enzymes 5. Skin, hair, muscles, parts of skeleton (structural proteins – collagen and elastin in tissue) 6. Help to fight disease – antibodies 7. Hemoglobin – transport O2  Types of Proteins: Type Example(s) Description Ligase Speed up reactions (catalyst) Enzymes Pepsin Have a specificity for one Lactase substance IgM Highly specific Antibodies IgA Bind to foreign antigens (Immunoglobulins) IgG First line of defense against IgD disease-causing organisms Insulin Produced at one site – function at Hormones Thyroxin another Epinephrine Small amount to bring about a response Keratin Structural Proteins Collagen Build body and cell parts Actin & Myosin  Structural Proteins: Structural Description/Function Protein Tubulin Found in microtubules – cell skeleton Actin & Myosin In muscle for contraction Keratin In hair and nails Collagen Elasticity of skin Histones Proteins in chromosomes for support  Proteins Protein Structure: Proteins can only function properly if they have the proper shape Levels of Protein Structure: ❧ Primary Structure: the sequence of amino acids. ❧ Secondary Structure: the folding or coiling of the polypeptide chain. ❧ Tertiary Structure: the complete 3D arrangement of polypeptide chain. ❧ Quaternary Structure: the arrangement of the different polypeptide in a protein. A protein’s specific shape determines its function o A protein consists of one or more polypeptide chains folded into a unique shape that determines the protein’s function Groove Groove  Protein Structure (Conformation): The way the amino acids are lined up Primary Structure Dictated by your genes Alpha Helix - coil/spiral Secondary Structure Beta Pleated - formed due to hydrogen bonding between functional groups Determines protein’s function – Active Tertiary Structure Conformation Bonds between R groups: Ionic, Hydrogen, Hydrophobic, Disulfide Only get this if there is more than 1 Quaternary Structure polypeptide chain Ex.) Collagen (makes skin elastic) – 3 chains; Hemoglobin 2 α & 2β  Protein Structure (Conformation)  Primary Structure Secondary structure Amino acids Levels of Protein Structure Hydrogen O HH C N C CN O LeuMet Pro AsnVal Ala C bond C O C NH C O C NH H R O H H CC N C CN O H CC N C CN O H Val Ile NH N N HO C CC N C C N Cys Lys Val Arg HOC C H CR O O H C Gly Glu Ala His ValPhe O C C C C N H H C N CCN O O H O Thr SerLys Val N HO C C C H O Primary structure Gly LeuAspAla Val ArgGly SerPro Secondary structure N HO OC C NH O C C NH H O C C N CN H O C C N CCN H O C H C H O C C N CN H O C Alpha helix Pleated sheet Amino acids Tertiary Structure Quaternary Structure Quaternary structure Tertiary structure Transthyretin, with Polypeptide four identical (single subunit polypeptide subunits of transthyretin) Protein Structure (Conformation): Enzymes and Substrates: Enzyme + Substrate = ES complex → EP complex = Enzyme + product(s) Enzymes (Proteins) Enzyme Catalytic Cycle Got Lactase? o Many people in the world suffer from lactose intolerance Lacking an enzyme (lactase) that digests lactose, a sugar found in milk “ase” = enzyme “ose” = sugar  Enzymes Each enzyme is the specific helper to a specific reaction o each enzyme needs to be the right shape for the job o enzymes are named for the reaction they help sucrase breaks down sucrose proteases breakdown proteins lipases breakdown lipids DNA polymerase builds DNA Catalase breaks down hydrogen peroxide Enzymes - a fun intro (4:46)  Regulation of Enzyme Activity ❧ Most enzymes work the best at certain pH and temperature. ❧ Denaturation: a change in the shape of the enzyme. o Cause the enzyme to ineffective because the active site and the substrate no longer fit together. o Changes in pH and increases in temperature can denature enzymes. Animation  Denaturing Proteins ❧ Protein that has lost its active conformation, or shape ❧ Denaturing caused by: o Temperature o Solute (salt) Concentration o pH Enzyme concentration reaction rate amount of enzyme http://www.kscience.co.uk/animations/anim_ 2.htm Substrate concentration reaction rate amount of substrate  Temperature reaction rate 37°C temperature  Temperature on Enzymes ❧ Temperature effect on rates of enzyme activity o Optimum temperature greatest number of collisions between enzyme & substrate human enzymes = 35°- 40°C (body temp = 37°C) o Raise temperature denature protein = unfold = lose shape o Lower temperature molecules move slower decrease collisions  pH levels stomach intestines pepsin trypsin reaction rate 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 pH Pepsin breaks down proteins in stomach Trypsin is produced in the pancreas and breaks down proteins in the small intestine ❧ pH effects on rates of enzyme activity o pH changes protein shape o most human enzymes = pH 6-8 depends on where in body pepsin (stomach) = pH 3 trypsin (small intestines) = pH 8 ❧ Some enzymes can be turned on and off by regulator molecules that bind to the enzyme causing the active site to change shape. Enzyme function and inhibition (1:07)  Nucleic Acids ❧ Large, complex organic compounds that store information in cells, using a system of four compounds to store hereditary information, arranged in a certain order as a code for genetic instructions of the cell. ❧ Elements: Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus ❧ Monomer: Nucleotide 1. Phosphate group (Phosphoric Acid) 2. 5-carbon (pentose) sugar (Deoxyribose or Ribose) 3. Nitrogenous Base  Nucleic Acids Polymer: polynucleotide ❧ Polynucleotides are formed when the phosphate group of one nucleotide binds to the sugar of another nucleotide. Function: ❧ Provides instructions to the cell on how to make proteins - Dictates the amino acid sequence which controls protein synthesis ❧ Stores and transmits genetic information - allows genetic information to be passed on from one generation to the next. ❧ Specificity determined by the fact that only certain bases bond with each other o Said to be complementary A –T C-G  There are FOUR Nitrogenous Bases Nitrogen bases  Nitrogen Bases ❧ Purines - 2 ring base Adenine (A) Guanine (G) ❧ Pyrimidines - 1 ring base Cytosine (C) Thymine (DNA) (T), Uracil (RNA) (U)  Nucleic Acids ❧ Nucleotides combine, in DNA to form a double helix, and in RNA a single helix ❧ The sides of the ladder are made up of the phosphate group and the sugar and the rungs of the ladder are nitrogen bases ❧ Examples of Nucleic Acids: 1. Deoxyribonucleic Acid (DNA) 2. Ribonucleic Acid (RNA) Nucleic Acids and Dehydration Synthesis  Nucleic Acids: Type of Bond Bond Between…… phosphodiester phosphate group and sugar N-glycosidic sugar (glycosidic) and nitrogen base hydrogen nitrogen bases  Functions of Nucleic Acids: ❧ Dictate the amino acid sequence – controls protein synthesis ❧ Stores and transmits genetic information ❧ Specificity determined by the fact that only certain bases bond with each other o Said to be complementary A –T C-G  Making a Polymer ❧ The glue contains long strands of molecules like spaghetti. ❧ If the long molecules slide past each other easily, then the substance acts like a liquid because the molecules flow. ❧ If the molecules stick together at a few places along the strand, then the substance behaves like a rubbery. ❧ Borax is the compound that is responsible for hooking the glue’s molecules together to form the putty-like material  Making a Polymer 1. Measure 20 ml of solution a into a small beaker 2. Use a graduated cylinder to measure 10 ml of solution B, add it to the beaker. Add food coloring if you want 3. Stir with a glass rod and knead with fingers 4. Put it into a plastic cup and cap. Label with your name and pick up at the end of the day