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Hydrocarbons & Macromolecules Mrs. Daniels Advanced Biology Sept. 2005 (modified Sept. 2008)

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1 Hydrocarbons & Macromolecules Mrs. Daniels Advanced Biology Sept (modified Sept. 2008)

2 Hydrocarbons What are they? Where do we find them? What do we use them for? Old arguments of organic molecules: vitalism vs. mechanism

3 Drawing Hydrocarbons How many bonds can carbon form? This enables it to form long chains (branched or unbranched) Skeleton structures Isomers

4 Structural: same formula - different structure or arrangement of atoms Ex. C 2 H 6 O H H H H | | | | H - C - C - OH or H - C - O - C - H | | | | H H H H

5 Isomers Geometric: same formula - different spatial arrangement around double bond Ex. Butene C 4 H 8 CH3HCH3CH3 C = C C = C HCH3 H H

6 Isomers Optical (also called enantiomers): same formula - mirror images of the same covalent bonds Ex. Lactic acid 22 1 C 33C1 44

7 Naming Alkanes Rules to naming alkanes (see handout)

8 Saturation If a hydrocarbon has the greatest number of “openings” filled with hydrogen, then it is said to be SATURATED This means it is full and can hold no more If a hydrocarbon has a double bond, does it have the potential to hold more hydrogen than it has now? Yes…it is UNSATURATED

9 ATTACHMENTS TO HYDROCARBONS There are many places along the hydrocarbon chain where functional groups can be attached These areas are the regions of the organic molecule which are often chemically reactive Depending on their # and arrangement, they determine the unique chemical properties of the molecule in which they occur

10 Functional Groups Polar and hydrophilic: Hydroxyl –An OH group –Alcohols Carbonyl –Double bonded Oxygen –Ex. Aldehydes & ketones

11 Functional Groups Carboxyl –An end carbon is double bonded to an O and is single bonded to a hydroxyl group Amino -weak base -NH 2 Sulfhydryl –SH –Called thiols Phosphate –PO 4 -3

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13 Most macromolecules are polymers Monomer- subunit/building block molecule of a polymer. Monomer- subunit/building block molecule of a polymer. Polymer - Polymer - -poly means “many” and mer means “part” -large molecule consisting of many identical or similar parts or subunits connected together Polymerization Reaction: the process of Polymerization Reaction: the process of creating a polymer from its constituent parts -A chemical rxn that links two or more small molecules to form larger molecules with repeating structural units

14 Condensation reaction(Dehydration reaction) = most Condensation reaction(Dehydration reaction) = most polymerization rxns for organisms are condensation rxns. Monomers covalently linked, producing a net removal of water for each covalent linkage. Monomers covalently linked, producing a net removal of water for each covalent linkage. One monomer loses a H+ and the other loses an OH-. One monomer loses a H+ and the other loses an OH-. This process requires NRG and the presence of biological enzymes and catalysts. This process requires NRG and the presence of biological enzymes and catalysts. Hydrolysis = rxn that breaks the covalent bonds between monomers by the addition of water molecules. Hydrolysis = rxn that breaks the covalent bonds between monomers by the addition of water molecules. H bonds to one monomer and OH bonds to another monomer thus connecting the two. H bonds to one monomer and OH bonds to another monomer thus connecting the two.

15 A limitless variety of polymers can be built from a small set of monomers Macromolecules are: large organic polymers Macromolecules are: large organic polymers 4 Main Categories of Macromolecules: 4 Main Categories of Macromolecules: Carbohydrates Carbohydrates Lipids Lipids Proteins Proteins Nucleic acids Nucleic acids

16 Unity and diversity of all life is tied to the specific arrangement and resultant emergent properties of these universal monomers. Unity and diversity of all life is tied to the specific arrangement and resultant emergent properties of these universal monomers. There is unity in life as there are only about common monomers used to construct all macromolecules There is unity in life as there are only about common monomers used to construct all macromolecules There is diversity in life as new properties emerge when these universal monomers are arranged in different ways There is diversity in life as new properties emerge when these universal monomers are arranged in different ways

17 Organisms use carbohydrates for fuel and building material Carbohydrates = organic molecules made from sugars and their polymers. Carbohydrates = organic molecules made from sugars and their polymers. Carbohydrates are classified according to the number of simple sugars Carbohydrates are classified according to the number of simple sugars

18 Monosaccharides = simple sugars Monosaccharides = simple sugars CH 2 O ratio CH 2 O ratio major nutrients for cells - Glucose is most common(produced by photosynthesis) major nutrients for cells - Glucose is most common(produced by photosynthesis) Chemical bond energy is harvested during cellular respiration Chemical bond energy is harvested during cellular respiration carbon skeletons are the raw materials for other organic molecules carbon skeletons are the raw materials for other organic molecules incorporated into di and polysaccharides. incorporated into di and polysaccharides. EX = triose (3 C), pentose (5 C), hexose (6 C) EX = triose (3 C), pentose (5 C), hexose (6 C) Sugars end with “ose” Sugars end with “ose” Aldose- sugar with a carbonyl group at a terminal carbon (aldehyde) Aldose- sugar with a carbonyl group at a terminal carbon (aldehyde) Ex. Glucose (Galactose is its enantiomer) Ex. Glucose (Galactose is its enantiomer) Ketose- sugar with carbonyl group within the carbon skeleton (ketone) Ketose- sugar with carbonyl group within the carbon skeleton (ketone) Ex. Fructose Ex. Fructose

19 In aqueous solution, many form rings Many monosaccharides can form rings in aqueous solns Many monosaccharides can form rings in aqueous solns O CH 2 OH H OH H OH H OH H H O C H- C-OH HO-C- H H- C-OH H

20 Disaccharides = two monosaccharides joined by glycosidic linkage Disaccharides = two monosaccharides joined by glycosidic linkage Glycosidic linkage =covalent bond formed by condensation rxn between two sugar monomers. Glycosidic linkage =covalent bond formed by condensation rxn between two sugar monomers. Ex = maltose, lactose, sucrose Ex = maltose, lactose, sucrose Maltose: glucose and glucose (sugar important in brewing beer) Maltose: glucose and glucose (sugar important in brewing beer) Lactose: glucose and galactose (sugar present in milk) Lactose: glucose and galactose (sugar present in milk) Sucrose: glucose and fructose (table sugar; most prevalent disaccharide) Sucrose: glucose and fructose (table sugar; most prevalent disaccharide)

21 Polysaccharides = macromolecules made of 100s to 1000s of monosaccharides. Enzyme mediated condensation rxns - NRG storage and structural support Polysaccharides = macromolecules made of 100s to 1000s of monosaccharides. Enzyme mediated condensation rxns - NRG storage and structural support Storage Polysaccharides- cells hydrolyze these into sugars as needed Storage Polysaccharides- cells hydrolyze these into sugars as needed Starch- storage polysaccharide of plants- stored in plastids(granules) Starch- storage polysaccharide of plants- stored in plastids(granules) Glycogen- glucose polymer - storage polysaccharide in animals Glycogen- glucose polymer - storage polysaccharide in animals Large glucose polymer - highly branched- stored in muscle & the liver Large glucose polymer - highly branched- stored in muscle & the liver Structural Polysaccharides Structural Polysaccharides Cellulose- linear unbranched polymer- major component of plant cell walls Cellulose- linear unbranched polymer- major component of plant cell walls Chitin- structural polysaccharide- polymer of an amino sugar Chitin- structural polysaccharide- polymer of an amino sugar

22 Lipids are mostly hydrophobic molecules with diverse functions Lipids- Lipids- diverse group of organic compounds diverse group of organic compounds insoluble in water insoluble in water 1. Fats, Triacylglycerol, or Triglycerides 1. Fats, Triacylglycerol, or Triglycerides hydrophobic due to many C-H bonds hydrophobic due to many C-H bonds variation arises from fatty acid composition, number, & arrangement variation arises from fatty acid composition, number, & arrangement Glycerol = 3 carbon alcohol Glycerol = 3 carbon alcohol Fatty acids (carboxylic acids)= carboxylic acid group at one end =“head” and an attached hydrocarbon chain as a “tail” Fatty acids (carboxylic acids)= carboxylic acid group at one end =“head” and an attached hydrocarbon chain as a “tail” Saturated- no dbl bonds (solid at room temp.; animal fats) Saturated- no dbl bonds (solid at room temp.; animal fats) Unsaturated-one or more dbl bonds present (liquid; plants & fish) Unsaturated-one or more dbl bonds present (liquid; plants & fish)

23 Triacylglycerol -A fat made of 3 fatty acids bonded to one glycerol by ester linkages (triglyceride) Triacylglycerol -A fat made of 3 fatty acids bonded to one glycerol by ester linkages (triglyceride) Major fxn of fat is energy storage Major fxn of fat is energy storage Humans and other mammals stock their long-term food reserves in adipose cells (expandable as needed) Humans and other mammals stock their long-term food reserves in adipose cells (expandable as needed) A gram of fat stores more than twice as much energy as a gram of a polysaccharide such as starch A gram of fat stores more than twice as much energy as a gram of a polysaccharide such as starch

24 Phospholipids = Glycerol + 2 F.A. + phosphate Phospholipids = Glycerol + 2 F.A. + phosphate a chemical group can be attached to the phosphate a chemical group can be attached to the phosphate Micelle: the phospholipids will form around a nonpolar particle with their hydrophobic (hydrocarbon) tails towards the particle and the hydrophilic (phosphate) head facing the water Micelle: the phospholipids will form around a nonpolar particle with their hydrophobic (hydrocarbon) tails towards the particle and the hydrophilic (phosphate) head facing the water This is how particles can be washed away This is how particles can be washed away Cell Membrane:a phospholipid bilayer makes up the majority of the cell membrane Cell Membrane:a phospholipid bilayer makes up the majority of the cell membrane Two layers of phospolipids arrange themselves so that the hydrocarbon tails are facing each other and the phosphate heads form a hydrophilic sheet on both sides of the membrane Two layers of phospolipids arrange themselves so that the hydrocarbon tails are facing each other and the phosphate heads form a hydrophilic sheet on both sides of the membrane

25 Steroids = Steroids = Lipids made of 4 fused carbon rings with various functional groups attached Lipids made of 4 fused carbon rings with various functional groups attached Cholesterol- (C 27 ) Cholesterol- (C 27 ) Common component of animal cell membranes Common component of animal cell membranes Precursor to many other steroids Precursor to many other steroids Too much cholesterol can lead to atherosclerosis (see p. 835) – Too much cholesterol can lead to atherosclerosis (see p. 835) – plaques build up in lining of arteries and constrict the blood flow HO

26 Amino acids connected= polypeptide Amino Acid = building block molecule of a protein Amino Acid = building block molecule of a protein most consisting of an asymmetric carbon most consisting of an asymmetric carbon Since the AA can exist in three ionic states (weak acid, weak base, and neutral) the pH of the solution determines the dominant ionic state Since the AA can exist in three ionic states (weak acid, weak base, and neutral) the pH of the solution determines the dominant ionic state Every AA includes the following around a central  carbon: Every AA includes the following around a central  carbon: Hydrogen atom Hydrogen atom Carboxyl group Carboxyl group Amino group Amino group Variable R group Variable R group

27 There are 20 amino acids There are 20 amino acids 10 are essential AA’s and must be obtained from dietary sources because they cannot be synthesized in the body 10 are essential AA’s and must be obtained from dietary sources because they cannot be synthesized in the body Amino acids exist as zwitterions - dipolar ions Amino acids exist as zwitterions - dipolar ions Peptide bonds=covalent bond formed by a condensation rxn that links the carboxyl group of one amino acid to the amino group of another. N-C-C-N- C-C repeating sequence Peptide bonds=covalent bond formed by a condensation rxn that links the carboxyl group of one amino acid to the amino group of another. N-C-C-N- C-C repeating sequence

28 Polypeptide chains- range in length from a few monomers to more than a thousand with unique linear sequences of AA Polypeptide chains- range in length from a few monomers to more than a thousand with unique linear sequences of AA N-terminus and C-terminus N-terminus and C-terminus Polypeptide chain = polymers of AAs that are arranged in a linear sequence and linked by peptide bonds Polypeptide chain = polymers of AAs that are arranged in a linear sequence and linked by peptide bonds Chains of 50 or less AA’s = peptide Chains of 50 or less AA’s = peptide Chains of more than 50 AA’s = protein Chains of more than 50 AA’s = protein

29 Proteins are molecular tools Proteins = macromolecule consisting of one or more polypeptide chains folded and coiled into specific conformations Proteins = macromolecule consisting of one or more polypeptide chains folded and coiled into specific conformations Important functions include: Important functions include: Structural support Structural support storage (of amino acids) storage (of amino acids) transport (hemoglobin) transport (hemoglobin) signaling(chemical messengers) signaling(chemical messengers) cellular response to chemical stimuli(receptor proteins) cellular response to chemical stimuli(receptor proteins) movement(contractile proteins) movement(contractile proteins) Defense(antibodies) Defense(antibodies) and catalysis of biochemical rxns(enzymes) and catalysis of biochemical rxns(enzymes)

30 Protein’s fxn depends upon specific conformation Four Levels of Protein Structure Four Levels of Protein Structure Primary- determined by genes- sequenced in lab Primary- determined by genes- sequenced in lab Secondary-regular, repeated coiling & folding of a polypeptide backbone Secondary-regular, repeated coiling & folding of a polypeptide backbone Alpha helix- helical coil stabilized by H bonding by every 4th peptide bond(found in fibrous proteins) Alpha helix- helical coil stabilized by H bonding by every 4th peptide bond(found in fibrous proteins) Beta pleated- sheet of antiparallel chains folded into accordion pleats- held together by intrachain or interchain H bonds between adjacent polypeptides(some fibrous and many globular protein cores) Beta pleated- sheet of antiparallel chains folded into accordion pleats- held together by intrachain or interchain H bonds between adjacent polypeptides(some fibrous and many globular protein cores)

31 Tertiary- irregular contortions of a protein due to bonding between side chains(R groups) superimposed upon the primary and secondary structure- bonding is weak interactions and covalent linkage Tertiary- irregular contortions of a protein due to bonding between side chains(R groups) superimposed upon the primary and secondary structure- bonding is weak interactions and covalent linkage Hydrophobic interaction= clustering of hydrophobic molecules as a result of their mutual exclusion from water Hydrophobic interaction= clustering of hydrophobic molecules as a result of their mutual exclusion from water Disulfide bridges(covalent linkage)=formed between two cysteine monomers brought together by folding of the protein(strong bond). Disulfide bridges(covalent linkage)=formed between two cysteine monomers brought together by folding of the protein(strong bond). Quaternary-protein with two or more polypeptide chains Quaternary-protein with two or more polypeptide chains

32 Protein conformation Protein conformation **Physical and chemical conditions influence conformation** **Physical and chemical conditions influence conformation** -Denaturation = alteration of a protein’s native conformation and emergent biological activity -Denaturation = alteration of a protein’s native conformation and emergent biological activity -Proteins can be denatured by: -Proteins can be denatured by: Organic solvents- turns the hydrophobic chains normally inside the core of the protein towards the outside- hydrophilic chains turn away from the solvent towards the interior of the protein. Organic solvents- turns the hydrophobic chains normally inside the core of the protein towards the outside- hydrophilic chains turn away from the solvent towards the interior of the protein. Chemical agents that disrupt the H bonds, pH, ionic bonds, and disulfide bridges. Chemical agents that disrupt the H bonds, pH, ionic bonds, and disulfide bridges. Excessive heat- disrupts the weak interactions with increased thermal“agitation”. Excessive heat- disrupts the weak interactions with increased thermal“agitation”.

33 Protein folding- most proteins pass thru several intermediate stages to reach their final conformation Protein folding- most proteins pass thru several intermediate stages to reach their final conformation Chaperone proteins= newly discovered “brace” to a folding protein- this bracing plays an important role as a protein conforms to its “final” 3D shape Chaperone proteins= newly discovered “brace” to a folding protein- this bracing plays an important role as a protein conforms to its “final” 3D shape

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35 Nucleic acids store and transmit hereditary information Remember that Protein conformation is determined by primary structure. -Primary structure, in turn is determined by genes -Gene = hereditary units of DNA Remember that Protein conformation is determined by primary structure. -Primary structure, in turn is determined by genes -Gene = hereditary units of DNA

36 Two types of nucleic acids Two types of nucleic acids 1.Deoxyribonucleic acid (DNA) 1.Deoxyribonucleic acid (DNA) Coded information that programs all cell activity Coded information that programs all cell activity Contains directions for its own replication Contains directions for its own replication Copied and passed from one generation of cells to the next Copied and passed from one generation of cells to the next In Eukaryotes- found primarily in the nucleus (but is also found in mitochondria of cells) In Eukaryotes- found primarily in the nucleus (but is also found in mitochondria of cells) Make up genes-contain instructions for making mRNA, which in turn is responsible for protein synthesis Make up genes-contain instructions for making mRNA, which in turn is responsible for protein synthesis

37 2.Ribonucleic acid (RNA) 2.Ribonucleic acid (RNA) Functions in actual synthesis of proteins coded by DNA Functions in actual synthesis of proteins coded by DNA Site of protein synthesis=ribosomes in the cytoplasm of the cell Site of protein synthesis=ribosomes in the cytoplasm of the cell 3 main types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA) 3 main types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA) mRNA carries the encoded genetic message from nucleus to cytoplasm mRNA carries the encoded genetic message from nucleus to cytoplasm Two processes : Transcription and translation (we will examine more closely when we know more about the cell) involve rRNA and tRNA Two processes : Transcription and translation (we will examine more closely when we know more about the cell) involve rRNA and tRNA

38 A DNA strand is a polymer with an information-rich sequence of nucleotides Nucleic acid=polymer of nucleotides linked by condensation rxns Nucleic acid=polymer of nucleotides linked by condensation rxns Nucleotide=Building block molecule of a nucleic acid Nucleotide=Building block molecule of a nucleic acid Made of : Made of : 5 carbon sugar 5 carbon sugar Phosphate group Phosphate group Nitrogenous base Nitrogenous base

39 Pyrimidine-6 membered ring made up of carbon and nitrogen atoms Pyrimidine-6 membered ring made up of carbon and nitrogen atoms Cytosine(C) Cytosine(C) Thymine(T)-found only in DNA Thymine(T)-found only in DNA Uracil(U)-found only in RNA Uracil(U)-found only in RNA Purine-5 membered ring fused to a 6 membered ring Purine-5 membered ring fused to a 6 membered ring Adenine(A) Adenine(A) Guanine(G) Guanine(G)

40 Nucleotides have several fxns: Many are monomers for nucleic acids Many are monomers for nucleic acids Many transfer chemical energy from one molecule to another (ex. ATP) Many transfer chemical energy from one molecule to another (ex. ATP) Many are electron acceptors in enzyme controlled redox rxns of cell Many are electron acceptors in enzyme controlled redox rxns of cell

41 Inheritance is based on precise replication of DNA Double helix-Proposed by Watson and Crick(1953) Double helix-Proposed by Watson and Crick(1953) Rosalind Franklin Rosalind Franklin Two nucleotide chains wound in a double helix Two nucleotide chains wound in a double helix Sugar-phosphate backbones are outside the helix Sugar-phosphate backbones are outside the helix Nitrogenous bases paired in the interior of the helix(H bonds) Nitrogenous bases paired in the interior of the helix(H bonds) Adenine to Thymine, Cytosine to Guanine pairing rule Adenine to Thymine, Cytosine to Guanine pairing rule

42 Two strands are complimentary thus they serve as templates to make new strands- it is this mechanism of precise copying that makes inheritance possible Two strands are complimentary thus they serve as templates to make new strands- it is this mechanism of precise copying that makes inheritance possible Most DNA molecules s to s of base pairs long Most DNA molecules s to s of base pairs long

43 Species that have many characteristics in common, are found to have many of the same DNA sequences which cause the production of similar amino acids and proteins Species that have many characteristics in common, are found to have many of the same DNA sequences which cause the production of similar amino acids and proteins Other structures and their functions (which ultimately are based on the DNA code) in many cases are very similar as well Other structures and their functions (which ultimately are based on the DNA code) in many cases are very similar as well


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