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Chapter 3. The Structure and Function of Macromolecules. Macromolecules. Are large molecules (polymers) composed of smaller molecules (monomers) Are complex in their structures. Protein. Macromolecules. Most macromolecules are polymers , built from monomers
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Chapter 3 The Structure and Function of Macromolecules Macromolecules
  • Are large molecules (polymers) composed of smaller molecules (monomers)
  • Are complex in their structures
  • Protein Macromolecules
  • Most macromolecules are polymers, built from monomers
  • Four classes of life’s organic molecules are polymers
  • Carbohydrates
  • Proteins
  • Nucleic acids
  • Lipids
  • A polymer
  • Is a long molecule consisting of many similar building blocks called monomers
  • Specific monomers make up each macromolecule
  • Amino acids are the monomers for proteins
  • Monosaccharides make up carbohydrates
  • Glycerol and Fatty acids for Lipids
  • Nucleotides for Nucleic acids
  • 1 HO H 3 2 H HO Unlinked monomer Short polymer Dehydration removes a watermolecule, forming a new bond H2O 1 2 3 4 HO H Longer polymer (a) Dehydration reaction in the synthesis of a polymer Figure 5.2A The Synthesis and Breakdown of Polymers
  • Monomers form larger molecules by condensation reactions called Dehydration synthesis orCondensation
  • Is an anabolic reaction (building up)
  • Condensation of amino acids Dehydration Synthesis of Carbohydrates 1 3 HO 4 2 H Hydrolysis adds a watermolecule, breaking a bond H2O 1 2 H HO 3 H HO Figure 5.2B (b) Hydrolysis of a polymer The Synthesis and Breakdown of Polymers
  • Polymers can disassemble by
  • Hydrolysis (addition of water molecules)
  • Is a catabolic or breakdown reaction
  • Hydrolysis of a Disaccharide
  • Although organisms share the same limited number of monomer types,each organism is unique based on the arrangement of monomers into polymers
  • An immense variety of polymers can be built from a small set of monomers
  • How many words can be made using the English alphabet?
  • Carbohydrates
  • C, H, O w/ a H:O ratio of 2:1
  • Serve as fuel and building material
  • Sugars and their polymers (starch, cellulose, etc.)
  • Tend to end in “ose”
  • Sugars
  • Monosaccharides
  • Are the simplest sugars
  • Most are: C6H12O6
  • Can be used for fuel
  • Can be converted into other organic molecules
  • Can be combined into polymers
  • Glucose, Galactose, Fructose, Ribose…
  • Pentose sugars(C5H10O5) Hexose sugars(C6H12O6) Triose sugars(C3H6O3) H H H H O O O O C C C C H C OH H C OH H C OH H C OH H C OH H C OH HO C H HO C H Aldoses H H C OH H C OH HO C H H C OH H C OH H C OH Glyceraldehyde H C OH H C OH H Ribose H H Glucose Galactose H H H H C OH H C OH H C OH C O C O C O HO C H H C OH H C OH Ketoses H C OH H C OH H Dihydroxyacetone H C OH H C OH H C OH H Ribulose H Fructose Figure 5.3
  • Examples of monosaccharides
  • O H 6CH2OH 1 C 6CH2OH 2 CH2OH H C OH 5C H 5C O O 6 3 H O H H H H H 5 HO C H HOH HOH H 4 4C 1 C 1C 4C 4 1 OH H H H C OH 3 2 O HO OH OH OH 5 OH 2 C 3 C 3 C 2C OH H C H OH 6 H H OH OH H C OH H Figure 5.4 (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.
  • Monosaccharides
  • May be linear
  • Can form rings in solution
  • Disaccharides
  • C12H22O11
  • Consist of two monosaccharides
  • Are joined by a glycosidic linkage
  • Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. CH2OH CH2OH CH2OH CH2OH 1– 4glycosidiclinkage O O O O H H H H H H H H HOH HOH HOH HOH 4 1 H H H H OH OH O H OH HO HO OH O H H H OH H OH OH OH H2O Glucose Maltose Glucose CH2OH CH2OH CH2OH CH2OH O O O O H 1–2glycosidiclinkage H H H H H HOH Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring. HOH 2 1 OH H H HO H HO H HO H O O HO CH2OH CH2OH OH H OH H H H OH OH H2O Sucrose Fructose Glucose Figure 5.5 Maltose Glucose Glucose 1– 2glycosidiclinkage Polysaccharides
  • Polysaccharides
  • Are polymers of sugars
  • Serve many roles in organisms
  • Starch, glycogen, cellulose, chitin
  • Chloroplast Starch 1 m Amylose Amylopectin (a) Starch: a plant polysaccharide Figure 5.6 Storage Polysaccharides
  • Starch - Amylose
  • Is a polymer consisting entirely of glucose monomers
  • Is the major storage form of glucose in plants in amyloplasts
  • Mitochondria Giycogen granules 0.5 m Glycogen Figure 5.6 (b) Glycogen: an animal polysaccharide
  • Glycogen
  • Consists of glucose monomers
  • Is the major storage form of glucose in animal livers
  • Structural Polysaccharides
  • Cellulose
  • Is a polymer of glucose
  • H O CH2OH C CH2OH OH OH H C H O O H H H H HO OH OH C H 4 4 1 H H HO OH HO OH H H C OH OH H OH H C H OH  glucose C  glucose H (a)  and  glucose ring structures CH2OH CH2OH CH2OH CH2OH O O O O OH OH OH OH 1 4 4 4 1 1 1 HO O O O O OH OH OH OH (b)Starch: 1– 4 linkage of  glucose monomers OH OH CH2OH CH2OH O O OH OH O O OH OH HO OH 4 O 1 O O CH2OH CH2OH OH OH (c) Cellulose: 1– 4 linkage of  glucose monomers Figure 5.7 A–C
  • Has different glycosidic linkages than starch
  • – C6 is on the top left on both monomers – C6 is flipped from top to bottom OH OH OH OH Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. A cellulose molecule is an unbranched glucose polymer. Plant cells Cellulose molecules
  • Is a major component of the tough walls that enclose plant cells
  • Hydrogen bonds Figure 5.9
  • Cellulose is difficult to digest
  • Cows have microbes in their stomachs to facilitate this process
  • CH2OH O OH H H OH H H H NH O C CH3 OH (b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. (a) The structure of the chitin monomer. Figure 5.10 A–C
  • Chitin, another important structural polysaccharide
  • Is found in the exoskeleton of arthropods
  • Can be used as surgical thread
  • Lipids
  • Lipids are a diverse group of hydrophobic molecules
  • Lipids
  • Are the one class of large biological molecules that do not consist of polymers
  • Not considered a true macromolecules
  • Made up mostly of chains of hydrocarbons
  • Share the common trait of being hydrophobic
  • Fats, oils, waxes, phospholipids and steroids
  • Carbon, Hydrogen & Oxygen with H:O ratio >2:1
  • Involved in long term energy storage
  • Fats
  • Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids
  • Vary in the length and number and locations of double bonds they contain
  • Saturated fatty acids Have the maximum number of hydrogen atoms possible Have no double bonds Lard, butter, animal fat, palm oil, coconut oil, palm kernel oil Stearic acid Figure 5.12 (a) Saturated fat and fatty acid cis double bond causes bending Oleic acid Figure 5.12 (b) Unsaturated fat and fatty acid
  • Unsaturated fatty acids
  • Have one or more double bonds
  • Olive oil
  • What to eat?
  • The following foods are high in monounsaturated fats:
  • peanut butter
  • olives
  • nuts – almonds, pecans, pistachios, cashews
  • avocado
  • seeds – sesame
  • oils – olive, sesame, peanut, canola
  • The following foods are high in polyunsaturated fats:
  • walnuts
  • seeds – pumpkin, sunflower
  • flaxseed
  • fish – salmon, tuna, mackerel
  • oils – safflower, soybean, corn
  • Phospholipids
  • Have only two fatty acids
  • Have a phosphate group instead of a third fatty acid
  • Typical of a cell membrane
  • ***The kink in the H-C chain due to a double bond is what gives the cell membrane its fluidity + CH2 Choline N(CH3)3 CH2 O Phosphate Hydrophilic head – P O O O CH2 CH CH2 Glycerol O O C O C O Fatty acids Hydrophilic head Hydrophobic tails Hydrophobic tails (b) Space-filling model (c) Phospholipid symbol Figure 5.13 (a) Structural formula
  • Phospholipid structure
  • Consists of a hydrophilic “head” and hydrophobic “tails”
  • WATER Hydrophilic head Hydrophobic tail WATER Figure 5.14
  • The structure of phospholipids
  • Results in a bilayer arrangement found in cell membranes
  • H3C CH3 CH3 CH3 CH3 HO Figure 5.15 Steroids
  • Steroids
  • Are lipids characterized by a carbon skeleton consisting of four fused rings
  • One steroid, cholesterol
  • Is found in cell membranes
  • Is a precursor for some hormones like estrogen & testosterone
  • Proteins
  • Proteins have many structures, resulting in a wide range of functions
  • Building and regulatory functions
  • Proteins do most of the work in cells and act as enzymes
  • Most hormones are protein derived
  • Proteins are made of monomers called amino acids
  • Made up of Carbon, Hydrogen, Oxygen, Nitrogen & sometimes Sulfur
  • Table 5.1
  • An overview of protein functions
  • Substrate binds to enzyme. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. 2 2 Substrate (sucrose) Glucose Enzyme (sucrase) OH H2O Fructose H O 4 Products are released. 3 Substrate is converted to products. Figure 5.16
  • Enzymes
  • Are a type of protein that acts as a catalyst, speeding up chemical reactions (by reducing the amount of activation energy needed)
  • Polypeptides
  • Polypeptides
  • Are polymers (chains) of amino acids
  • A protein
  • Consists of one or more polypeptides
  • Amino acids
  • Are organic molecules possessing both carboxyl and amino groups
  • Differ in their properties due to differing side chains, called R groups
  • CH3 CH3 CH3 CH CH2 CH3 CH3 H CH3 H3C CH3 CH2 CH O O O O O H3N+ H3N+ H3N+ H3N+ C H3N+ C C C C C C C C C O– O– O– O– O– H H H H H Valine (Val) Leucine (Leu) Isoleucine (Ile) Glycine (Gly) Alanine (Ala) Nonpolar - Hydrophobic CH3 CH2 S H2C CH2 O NH CH2 H2N C C CH2 CH2 O– CH2 O O O H H3N+ H3N+ C C C C H3N+ C C O– O– O– H H H Phenylalanine (Phe) Proline (Pro) Methionine (Met) Tryptophan (Trp) Figure 5.17 Twenty Amino Acids (you do not need to memorize these!!)
  • 20 different amino acids make up proteins
  • OH NH2 O C NH2 O Polar - Hydrophilic C OH SH CH2 CH3 OH CH2 CH CH2 CH2 CH2 CH2 O O O O O O H3N+ H3N+ H3N+ H3N+ H3N+ H3N+ C C C C C C C C C C C C O– O– O– O– O– O– H H H H H H Glutamine (Gln) Tyrosine (Tyr) Asparagine (Asn) Cysteine (Cys) Serine (Ser) Threonine (Thr) Basic Acidic NH3+ NH2 NH+ O– O –O O NH2+ Electrically Charged - Ionic CH2 C C C NH CH2 CH2 CH2 CH2 CH2 O O H3N+ H3N+ CH2 CH2 C CH2 C C C O O– H3N+ O– CH2 C CH2 C H O H H3N+ O– C C CH2 H O O– H3N+ C C H O– H Lysine (Lys) Histidine (His) Arginine (Arg) Glutamic acid (Glu) Aspartic acid (Asp) Amino Acid Polymers
  • Amino acids
  • Are linked by peptide bonds through Dehydration synthesis
  • Protein Conformation and Function
  • A protein’s specific conformation (shape) determines how it functions
  • Amino acid subunits +H3NAmino end Pro Thr Gly Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Arg Val Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Tyr Trp Lys Ala Leu Gly lle Ser Pro Phe His Glu His Ala Glu Val Thr Phe Val Ala Asn lle Thr Asp Ala Tyr Arg Ser Ala Arg Pro Gly Leu Leu Ser Pro Tyr Ser Tyr Ser Thr Thr Ala o Val c Val Glu – Lys o Thr Pro Asn Carboxyl end Figure 5.20 Four Levels of Protein Structure
  • The specific order of amino acids in a polypeptide interacts with the environment to determine the overall structure of the protein.
  • The interactions of the R group of the amino acid determines structure and function of the R region of the protein.
  • Hydrophobic, hydrophilic or ionic
  • Primary structure
  • Is the unique sequence of amino acids in a polypeptide
  • Linear
  • H H H H H H O O O O O O O H H H H H H R R R R R R R C C C C C C C C C C C C C N N N N N N N N N N N N N C C C C C C C C C C C C C C R R R R R R H H H H H H H O O O O O O O H H H H H H H  pleated sheet H O H H Amino acidsubunits C C N N N C C C R H O H H H H H H N N N N N N  helix C C O C H H H C C C R R R R R H H C C C C C C O O O O H C R O C C O H C O N N H C C H R H R Figure 5.20
  • Secondary structure
  • Is the folding or coiling of the polypeptide into a repeating configuration due to Hydrogen bonds
  • Includes the  helix and the  pleated sheet
  • Hydrophobic interactions and van der Waalsinteractions CH CH2 CH2 H3C CH3 OH Polypeptidebackbone H3C CH3 Hyrdogenbond CH O HO C CH2 CH2 S S CH2 Disulfide bridge O -O C CH2 CH2 NH3+ Ionic bond
  • Tertiary structure
  • Is the overall three-dimensional shape of a polypeptide
  • Results from interactions between amino acids and R groups - Disulfide bridge formed
  • Polypeptidechain Collagen  Chains Iron Heme  Chains Hemoglobin
  • Quaternary structure
  • Is the overall protein structure that results from the aggregation of two or more polypeptide subunits
  • +H3N Amino end Amino acid subunits helix Review of Protein Structure Sickle-Cell Disease: A Simple Change in Primary Structure
  • Sickle-cell disease
  • Results from a single amino acid substitution in the protein hemoglobin
  • Valinefor Glutamic acid
  • Caused by a point mutation
  • Sickle-cell hemoglobin Normal hemoglobin Primary structure Exposed hydrophobic region Primary structure . . . . . . Glu Glul Val His Leu Thr Pro Val His Leu Pro Val Glu Thr 5 6 7 7 2 3 4 5 6 1 1 2 3 4 Secondaryand tertiarystructures Secondaryand tertiarystructures  subunit  subunit Hemoglobin A Hemoglobin S     Quaternary structure Quaternary structure  Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.    Molecules donot associatewith oneanother, eachcarries oxygen. Function Function 10 m 10 m Red bloodcell shape Normal cells are full of individualhemoglobinmolecules, eachcarrying oxygen Red bloodcell shape Figure 5.21 Fibers of abnormalhemoglobin deform cell into sickle shape. What Determines Protein Conformation?
  • Protein conformation depends on the physical and chemical conditions of the protein’s environment
  • Temperature, pH, [salt], etc. influence protein structure
  • Denaturation Normal protein Denatured protein Renaturation Figure 5.22 Denaturation is when a protein unravels and loses its native conformation(shape) The Protein-Folding Problem
  • Amino acid sequences of 875,000 proteins are known.
  • 3D shapes of 7,000 are known.
  • aka, Scientists don’t know the structure of most proteins
  • Most proteins
  • Probably go through several intermediate states on their way to a stable conformation
  • Denaturated proteins no longer work in their unfolded condition
  • Proteins may be denaturated by extreme changes in pH or temperature
  • Correctlyfoldedprotein Polypeptide Cap Hollowcylinder Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end. The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide. Chaperonin(fully assembled) The cap comesoff, and the properlyfolded protein is released. 2 3 1 Figure 5.23
  • Chaperonins (aka, chaperone proteins)
  • Are protein molecules that assist in the proper folding of other proteins
  • X-raydiffraction pattern Photographic film Diffracted X-rays X-ray beam X-raysource Crystal Nucleic acid Protein (b) 3D computer model (a) X-ray diffraction pattern
  • X-ray crystallography
  • Is used to determine a protein’s three-dimensional structure
  • Rosalind Franklin & DNA
  • Figure 5.24 Nucleic Acids
  • Nucleic acids store and transmit hereditary information
  • Polymers of nucleotides
  • Genes
  • Are the units of inheritance
  • Program the amino acid sequence of polypeptides
  • Are made of nucleotide sequences on DNA
  • The Roles of Nucleic Acids
  • There are two types of nucleic acids
  • Deoxyribonucleic acid (DNA)
  • Ribonucleic acid (RNA)
  • Deoxyribonucleic Acid
  • DNA
  • Stores information for the synthesis of specific proteins
  • Found in the nucleus of cells
  • DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore Ribosome 3 Synthesis of protein Aminoacids Polypeptide Figure 5.25 DNA Functions
  • Directs RNA synthesis (transcription)
  • Directs protein synthesis through RNA (translation)
  • 5’ end 5’C O 3’C O O 5’C O 3’C 3’ end OH Figure 5.26 The Structure of Nucleic Acids
  • Nucleic acids
  • Exist as polymers called polynucleotides
  • (a) Polynucleotide, or nucleic acid
  • Each polynucleotide
  • Consists of monomers called nucleotides
  • 5C Sugar + phosphate group + nitrogen base
  • Nucleotide Monomers
  • Nucleotide monomers
  • Are made up of nucleosides (sugar + base) and phosphate groups
  • Nucleotide Polymers 5` 3`
  • Nucleotide polymers
  • Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next
  • 3` 5` Gene
  • The sequence of bases along a nucleotide polymer
  • Is unique for each gene
  • The DNA Double Helix
  • Cellular DNA molecules
  • Have two polynucleotides that spiral around an imaginary axis
  • Form a double helix
  • 3’ end 5’ end Sugar-phosphatebackbone Base pair (joined byhydrogen bonding) Old strands Nucleotideabout to be added to a new strand 3’ end A 5’ end Newstrands 3’ end 3’ end 5’ end Figure 5.27
  • The DNA double helix
  • Consists of two antiparallel nucleotide strands
  • Look at the C’s on the ribose molecule. The 5th C bonded to the Phosphate group is the 5` end.
  • A,T,C,G
  • The nitrogenous bases in DNA
  • Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)
  • DNA and Proteins as Tape Measures of Evolution
  • Molecular comparisons
  • Help biologists sort out the evolutionary connections among species
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