lecture02 BIO 181 2017 fall 1spp.pdf

BIO 181: General Biology I Biological Macromolecules Instructor: Dr. Cayle Lisenbee Office: UCENT 355 Phone: (602) 496-0641 Email: [email protected] Office Hours: Posted on Blackboard Ariz...

BIO 181: General Biology I Biological Macromolecules Instructor: Dr. Cayle Lisenbee Office: UCENT 355 Phone: (602) 496-0641 Email: [email protected] Office Hours: Posted on Blackboard Arizona State University Downtown Phoenix Campus College of Integrative Sciences and Arts  Learning Objective Describe the general composition, synthesis, and breakdown of organic macromolecules. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 2 Organic Macromolecules  Living organisms are composed of four types of carbon-based (organic) macromolecules. The four types differ substantially in structure and function.  Lipids  Carbohydrates  Proteins  Nucleic acids  Do these look familiar to you? Provide two examples of where you may have seen them before. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 3 Organic Macromolecules BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 4 Organic Macromolecules  Organic macromolecules are polymers composed of subunits, or building blocks, called monomers. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 5 Organic Macromolecules – Reactions  Organic polymers are synthesized iteratively by linking together monomers with special types of covalent bonds.  These “joining” processes are called condensation reactions.  Each reaction yields a single molecule of water. Think of the water molecule “condensing” out of the reaction. Some people refer to these processes as dehydration synthesis reactions. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 6 Organic Macromolecules – Reactions  Organic polymers are degraded (broken down) by severing the covalent bonds that link the monomers.  These “breakdown” processes are called hydrolysis reactions.  Each reaction uses a single molecule of water. Think of the water molecule lysing, or splitting, a large molecule into its monomeric subunits. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 7  Learning Objective Apply your understanding of the structure of lipids and their fatty acid building blocks to their various functions in living organisms. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 8 Lipids – Fatty Acids  A lipid is a carbon-containing biological molecule that is largely nonpolar and hydrophobic. Most are hydrocarbons that contain primarily carbon and hydrogen atoms.  Lipids are composed of building blocks called fatty acids.  A fatty acid is a hydrocarbon chain that is bonded to a carboxylic acid (COOH) functional group.  Most fatty acids have an even number of carbon atoms – they are synthesized by joining two-carbon acetyl groups. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 9 Lipids – Saturation  In lipid biochemistry, saturation refers to the degree to which the carbon atoms in a fatty acid are linked to hydrogen atoms.  Unsaturated fatty acids possess one or more double covalent bonds between adjacent carbon atoms. The double bonds produce kinks that prevent rotation, limit flexibility, and change the overall shape of the fatty acid. Carboxyl group Does the saturation Double level of a fatty acid covalent bond affect its chemical Hydrocarbon properties at room chain temperature? Stearic Acid Oleic Acid Fully-saturated 18-carbon fatty Monounsaturated 18-carbon fatty acid with no double bonds acid with one double bond BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 10 Lipids – Saturation The linear shape of saturated fatty acid molecules allows them to pack closely together; they tend to form solids at room temperature. How does this concept apply to cis and trans unsaturated fatty acids? Examples of some common fatty acids BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 11 Lipid Types  The structures and functions of cellular lipids vary widely. Four important types are found in cells.  Fats (triglycerides)  Phospholipids  Steroids  Waxes The glossy coating on the leaves of some plant species are composed of special lipids called waxes.  Let’s take a closer look at each of these types of lipid polymers. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 12 Lipid Types – Fats (Triglycerides)  Fats are composed of three fatty acid monomers linked together via a glycerol molecule. These are called triglycerides.  They are synthesized through a series of condensation reactions that join the carboxylic acid groups of fatty acids to the hydroxyl groups of glycerol. These special covalent bonds are called ester linkages. Condensation reaction Ester linkage Fats function as energy storage molecules in animals and plants! BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 13 Lipid Types – Phospholipids  Phospholipids consist of a glycerol molecule that is linked to a phosphate group (PO43-) and two fatty acid chains.  They are synthesized in the same way as are fats (triglycerides).  They are amphipathic molecules, meaning that they contain both hydrophilic (polar) and hydrophobic (nonpolar) regions.  The hydrophilic “head” region contains polar covalent bonds and charged atoms.  The hydrophobic “tail” region consists of the nonpolar hydrocarbon chains of the fatty acids. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 14 Lipid Types – Phospholipids  The primary function of phospholipids is to form membranes.  Membranes establish the boundaries between the inside and outside of the cell and its organelles.  When placed in an aqueous solution, the polar head groups interact with water while the nonpolar tails do not. These interactions cause the phospholipids to arrange themselves into a bilayer membrane.  We’ll discuss membranes in more detail later. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 15 Lipid Types – Steroids  Steroids are a unique family of lipids distinguished by a four-ring structure. General structure of a steroid lipid  They are synthesized by cyclizing a special triterpenoid hydrocarbon (a special type of fatty acid building block) known as squalene.  Steroid hormones are important signaling molecules, and sterols like cholesterol are integral components of mammalian cell membranes. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 16 Lipid Types – Steroids Do you recognize the names of any of these important steroid lipids? (You don’t have to memorize their structures!) BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 17  Learning Objective Understand how the functions of carbohydrates are related to the structures and bonding configurations of their monosac- charide building blocks. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 18 Carbohydrates  Carbohydrates are “hydrated hydrocarbons” composed primarily of carbon, hydrogen, and oxygen atoms arranged as (CH2O)n.  Repeating chains of hydrated carbons form monosaccharides, or simple sugars, that are the building blocks of carbohydrates. Carbohydrates also are known as polysaccharides. (CH2O)n Simple sugar Carbohydrate (monosaccharide) (polysaccharide) BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 19 Carbohydrates – Monosaccharides  The structures of simple sugars differ in several key ways that help biologists and chemists define sugar building blocks.  Number of carbon atoms. Aldose Sugar  Triose sugars have three carbon atoms.  Pentose sugars have five carbon atoms. Carbonyl group at end  Hexose sugars have six carbon atoms. of carbon chain  Location of the carbonyl group.  Aldose sugars have a carbonyl group at the end of the monosaccharide that forms a highly reactive aldehyde. Ketose Sugar  Ketose sugars have a carbonyl group in the middle of the monosaccharide that Carbonyl forms a reactive ketone. group in middle of carbon chain BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 20 Carbohydrates – Monosaccharides ... (continued).  Spatial arrangement of their atoms.  Most of the carbon atoms in simple sugars are chiral centers – the same groups of atoms can be linked to these carbons in different orientations.  The arrangement of the hydroxyl (-OH) groups at each carbon atom defines the type of simple sugar. Glucose Galactose Glucose and galactose are hexose sugars that differ only in the orientation of the hydroxyl group on carbon-4. Are glucose and galactose aldose or ketose sugars? Different configuration of hydroxyl BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA groups! 21 Carbohydrates – Monosaccharides  Dissolved in water at pH 7 or in solid form, glucose (and many other hexoses) form six-membered rings called hemiacetals.  The cyclization process produces two different forms, or anomers, of glucose. Oxygen from carbon-5 bonds to carbon-1, resulting in a ring structure α-Glucose β-Glucose Ring forms of Linear form of glucose glucose (Fischer projection) (Haworth projections) BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 22 Carbohydrates – Polysaccharides  Polysaccharides are polymeric carbohydrates that are formed through condensation reactions between the hydroxyl groups on separate monosaccharides. The condensation reactions produce special covalent bonds called glycosidic linkages.  The monomers (monosaccharides) joined by glycosidic linkages can be identical or different.  The glycosidic linkages can form between any two hydroxyl groups, so the location and geometry of these bonds varies widely. Glycosidic BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA linkage 23 Carbohydrates – Functions  Carbohydrates are critically important molecules that perform a wide variety of functions!  They serve as building blocks in the synthesis of other molecules.  They indicate cell identity.  They store chemical energy.  They provide cells with fibrous structural materials. Let’s explore the functions of carbohydrates in a bit more detail.... BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 24 Carbohydrate Fxns – Cell Identity  Although polysaccharides are unable to store information, they do display information on the outer surfaces of cells. Here, they are present in the form of glycoproteins and glycolipids – sugars that have been joined to proteins and lipids, respectively, by strong covalent bonds. glycoprotein  Glycoproteins are key Outside of cell identification badges that function in cell-cell recognition and cell-cell signaling. Inside of cell BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 25 Carbohydrate Fxns – Energy Storage  Plants store carbohydrates as starch, and animals store sugars as glycogen. Both are made of many α-glucose monomers joined by α-1,4-glycosidic linkages. These linkages cause the sugar chains to form distinct helical structures.  Branching occurs when glycosidic linkages form between carbon-1 of a glucose monomer on one strand and carbon-6 of a glucose monomer on another strand.  Starch can be unbranched (amylose) or branched (amylopectin).  Glycogen is highly branched.  The enzymes amylase and phosphorylase catalyze the hydrolysis of α-glycosidic linkages in glycogen and starch, respectively. The released subunits then can be used for ATP production. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 29 Carbohydrate Fxns – Energy Storage BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 30 Carbohydrate Fxns – Structural Mat’l  Unlike starch and glycogen with α-glycosidic linkages, structural carbohydrates possess β-1,4-glycosidic linkages that are difficult to hydrolyze – very few enzymes have active sites that accommodate their geometry or have the reactive groups necessary.  Structural carbohydrates form long strands with bonds between adjacent strands. These may be organized into fibers or layered in sheets to give cells and organisms great strength and elasticity. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 31 Carbohydrate Fxns – Structural Mat’l  Cellulose is a polymer of β-glucose monomers linked by β-1,4-glycosidic linkages. It is found in plant cell walls.  Chitin is a polymer of N-acetylglucosamine monomers linked by β-1,4-glycosidic linkages. It is found in fungal cell walls and insect and crustacean exoskeletons.  Peptidoglycan is made up of two types of mono- saccharides linked by β-1,4-glycosidic linkages. Each monomer is cross-linked to a chain of amino acids, and peptide bonds link the amino acid chains of adjacent strands. It is a component of bacterial cell walls. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 32 BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 33  Learning Objective Explain how the functional diversity of proteins is related to the chemical properties and structures of their component amino acids. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 34 Proteins – Amino Acids  Proteins are “aminated hydrocarbons” that are composed primarily of carbon, hydrogen, oxygen, and nitrogen. These elements are arranged into various amino acid monomers, the building blocks of proteins (polypeptides).  All amino acids have a central carbon atom (a-carbon) attached by covalent bonds to an amine group (NH2), a carboxylic acid group (COOH), a hydrogen atom (H), and a variable side chain (R). How is this shorthand form of an amino acid’s structure similar to the expanded structure on the left? BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 35 Proteins – Amino Acids  Proteins in most living organisms are built from a standard set of 20 different amino acids. They differ only in the structure of their side chains (R-groups).  R-groups differ in size, shape, and chemical reactivity.  In general, amino acids with hydroxyl (OH), amino (NH3), carboxylic acid (COOH), or sulfhydryl (SH) functional groups in their side chains are more reactive than those with side chains composed of only carbon and hydrogen.  Side chains also dictate an amino acid’s interactions with water.  Nonpolar R-groups can’t form hydrogen bonds; amino acids that possess these groups are hydrophobic and tend to avoid water molecules.  Polar R-groups form hydrogen bonds readily; amino acids with these groups are hydrophilic. Let’s look at the 20 standard amino acids grouped according to their chemical properties... BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 36  Chemical property R-group Name Name abbreviations You don’t have to memorize this chart! But you should be able to deduce the properties of an amino acid if given its chemical structure. Wanna try it? BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 37 How likely is phenylalanine to interact with water? Start by determining the chemical properties of its side chain (R-group). Nonpolar R-group Conclusion: not likely. Does this mean that our water-filled cells can’t use hydrophobic amino acids? No. In water (pH 7), the amino and carboxylic acid groups in all amino acids ionize to NH3+ and COO–. This helps the amino acids interact with water and stay in solution. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 38 Proteins – Amino Acids  With one exception (glycine), all amino acids may exist as either a left-handed or right-handed optical isomer.  Isomers are molecules that have the same molecular formula but different structures.  Optical isomers are mirror images – they differ in the arrangement of groups around a carbon atom that has four different groups attached to it. Their structures cannot be superimposed, and a left-handed isomer may not substitute functionally for a right-handed Non-superimposable optical isomers of the one, and vice versa. amino acid alanine  Formulate a hypothesis that explains why cells utilize selectively only left-handed amino acid isomers for protein synthesis. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 39 Proteins – Polypeptides  Polypeptides are formed by joining amino acids together covalently via condensation reactions. These reactions link the carboxylic acid group of one amino acid to the amino group of another amino acid to form a peptide bond.  Peptide bonds are special single covalent bonds between a carbon and a nitrogen atom. The arrangements of the atoms in a peptide bond makes it an unusually strong bond. Electrons within the carbonyl group contribute double bond characteristics to the peptide bond, making the latter much stronger than a typical single covalent bond. Carboxylic Amino Peptide acid group group bond BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 40 Proteins – Polypeptide Structure  Polypeptides are flexible polymers that have a clear organization and orientation (directionality).  The backbone (magenta) includes the repeating pattern of amine groups, a-carbons, and carboxylic acid groups that are attributed to each of its component amino acids.  The amino acids are linked together with peptide bonds. Finding these within the backbone helps you locate each individual amino acid in the chain.  One end of the backbone terminates in a free amine group (NH3+), the other in a free carboxylic acid group (COO-). They define the N terminus and C terminus. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 41 Proteins – Polypeptide Structure  The size, shape, and function of a polypeptide is dictated by its component amino acids. These characteristics are understood and interpreted at four basic levels.  Primary structure  Secondary structure  Tertiary structure  Quaternary structure BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 42 Proteins – Polypeptide Structure  A polypeptide’s primary structure is its unique sequence of amino acids.  By convention, biologists always write amino acid sequences with the N-terminus on the left and the C-terminus on the right. Does the order, or sequence, of amino acids in a polypeptide matter? In other words, will you have the same poly- peptide if you change its amino acid sequence? The chemical properties of the amino acids determine the function of the protein, so a single amino acid change can alter function radically! BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 43 Proteins – Polypeptide Structure  In water, polypeptides twist and bend into more complex forms. However, the double bond character of peptide bonds makes them stiff – the carbon and nitrogen atoms can’t twist about each other. Flexible polypeptide Peptide bond  The primary structure of a protein thus consists of alternating “stiff ” segments that rotate around the α-carbon atoms of its constituent amino acids. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 44 Proteins – Polypeptide Structure  Secondary structure results in part from hydrogen bonding between the carbonyl oxygen of one amino acid residue and the amino hydrogen of another. A polypeptide chain must bend to allow this hydrogen bonding to occur – this bending forms two types of folds, namely a-helices or -pleated sheets. These two ribbons represent different Hydrogen portions of the same bonds polypeptide chain BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 45 Proteins – Polypeptide Structure  Note how secondary structure depends entirely on the primary structure of the polypeptide! Some amino acid sequences are more likely to form α-helices, whereas others are more likely to form β-pleated sheets. = = a-helix -pleated sheet BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 46 Proteins – Polypeptide Structure  The tertiary structure of a polypeptide results from interactions between R-groups or between R-groups and the polypeptide’s backbone. These contacts cause the secondary structures to bend and fold upon themselves into the unique, three-dimensional final fully-folded functional form of the polypeptide. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 47 Proteins – Polypeptide Structure  R-group interactions include hydrogen bonds, van der Waals interactions, disulfide bonds, and ionic bonds. In general, these represent intramolecular interactions that determine shape! Hydrogen bond between side chain and carbonyl oxygen Ionic bond Hydrophobic interactions (van der Waals Hydrogen bond between interactions) two side chains Disulfide bond BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 48 Proteins – Polypeptide Structure  Complex proteins contain several distinct polypeptide chains that engage in intermolecular interactions. Quaternary structure occurs when two or more polypeptide chains form a single entity. Hemoglobin is a tetrameric protein that exhibits quaternary structure. It consists of four polypeptide subunits. Could the quaternary structure of hemoglobin be affected by a single amino acid change in one or two of its four component polypeptides? Yes! This is the basis for the disease known as sickle-cell anemia! BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 49 Proteins – Folding  Protein folding often is spontaneous, because the formation of hydrogen bonds and other interactions make the folded molecule more stable energetically than the unfolded molecule.  A given sequence of amino acids MUST assume a specific tertiary or quaternary structure (as appropriate) in order to become fully and completely functional.  Proteins called molecular chaperones help newly-synthesized polypeptides fold correctly in cells.  Proteins can become unfolded, or denatured, in response to changes in temperature and pH. Denatured proteins typically do not function normally! BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 50 Proteins – Functions BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 51  Learning Objective Describe how the information storage and catalytic functions of nucleic acids are determined by the structures of their nucleotide building blocks. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 52 Nucleic Acids  Nucleic acids are “phosphorylated hydro- carbons” composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus.  These elements combine in regular patterns to form the two main types of nucleic acid, namely ribonucleic acid (RNA) and deoxyri- bonucleic acid (DNA).  Other than viruses, most living organisms utilize both DNA and RNA as their genetic material. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 53 Nucleic Acids – Nucleotides  Nucleic acid polymers are composed of monomeric building blocks called nucleotides.  Each nucleotide building block is composed of a phosphate group, a sugar group, and a nitrogenous base. Biologists often refer to nucleotides as “bases” in reference to their nitrogenous bases.  The phosphate group functions as a critical linkage site for nucleotide polymerization (more later). The use of phosphate in nucleic acids is unique among the biological molecules, and it gives nucleic acids an overall nega- tive electrical charge. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 54 Nucleic Acids – Nucleotides  The sugar is a pentose (five-carbon) monosaccharide called ribose in ribonucleotides and deoxyribose in deoxyribonucleotides. The carbon atoms on the sugar are numbered in a clockwise pattern.  The structures of ribose and deoxyribose differ only in the presence or absence, respectively, of a hydroxyl (OH) group on the 2' carbon.  The nitrogenous base is attached to the 1' carbon and the phosphate group to the 5' carbon. The 3' and 5' carbon atoms are used to link nucleotides together (via the phosphate groups) to form nucleic acid polymers. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 55 Nucleic Acids – Nucleotides  The nitrogenous bases contribute unique chemical properties to each type of nucleotide.  Pyrimidine bases include cytosine [C], uracil [U], and thymine [T]. Note that uracil is found only in ribo- nucleic acids (RNA), and thymine is found only in deoxyribonucleic acids (DNA).  Purine bases include adenine [A] and guanine [G]. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 56 Nucleic Acids – Polymers  Polymerization involves the formation of a special covalent bond called a phosphodiester bond between the phosphate group on the 5' carbon of one nucleotide and the hydroxyl (OH) group on the 3' carbon of another nucleotide.  Phosphodiester bonds form via condensation reactions. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 57 Nucleic Acids – Structure  The primary structure of a nucleic acid is defined by its unique sequence of nucleotide bases.  Nucleic acid polymers consist of a backbone of alternating sugar and phosphate groups contributed by successive nucleotides in the chain. The nitrogenous bases jut out and away from the backbone.  The sugar-phosphate backbone of a nucleic acid is directional – one end has an unlinked 5' phosphate, and the other end has an unlinked 3' hydroxyl (OH) group.  Nucleotide sequences are written conventionally in the 5' 3' direction because this reflects the mechanism by which nucleotides are added to a growing nucleic acid molecule during its synthesis. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 58  Sugar-phosphate or phosphodiester backbone Unlinked 5' phosphate group Unlinked 3' hydroxyl group BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 59 Nucleic Acids – Structure of DNA  James Watson and Francis Crick, American and British scientists, respectively, are credited with discovering the secondary structure of DNA. Their discovery very much was a team effort that benefitted from the contributions of many prominent people.  Erwin Chargaff, an Austrian biochemist, established two empirical rules for DNA in 1950.  The total number of purines and pyrimidines is the same.  The numbers of A’s and T’s are equal, and the numbers of C’s and G’s are equal.  Maurice Wilkins, a New Zealand molecular biologist, devised new methods for producing and photographing crystals of DNA. He also was the first to suggest that double-stranded DNA forms a helical structure. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 60 Nucleic Acids – Structure of DNA  Rosalind Franklin, a British chemist and biologist, produced the x-ray crystallo- graphic data that Watson and Crick used to devise the helical structure of DNA.  Watson and Crick determined that...  DNA consists of two antiparallel nucleic acid strands that twist upon each other to form a double helix.  The hydrophilic sugar-phosphate backbones of both strands face the exterior of the DNA molecule, and purine–pyrimidine pairs of nitrogenous bases face the interior.  The DNA strands form complementary base pairs A-T and G-C.  The double helix has two types of grooves, specifically the major groove and the minor groove, that differ in size and provide access to the nucleotide bases. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 61 Nucleic Acids – Structure of DNA  The DNA double helix exhibits two very important features:  Strict adherence to base pairing rules allows one strand to be “read” from the other, i.e., the strands are complementary to each other.  Base pairing rules and hydrogen bonding chemistry cause the two strands to run in opposite directions, i.e., the strands are antiparallel. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 62 Nucleic Acids – DNA  The elegance of the double helix is best appreciated by studying three- Major groove dimensional interactive models of the DNA molecule.  Check one out for yourself! Length of one complete  On Apple devices, download the app turn of helix (10 rungs per Minor groove turn) 3.4 nm “Molecules.” On Android devices, try the app “Molecule 3D.” Both are free (at last check) and come pre-loaded Distance between bases 0.34 with structures for B-form DNA. nm  On the web: https://www.rcsb.org/pdb/explore.do?structureId=1BNA Width of the helix 2.0 nm BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 63 Nucleic Acids – Structure of RNA  The primary structure of RNA differs from DNA in two ways:  RNA contains ribose sugars instead of deoxyribose sugars.  RNA contains uracil instead of thymine.  The secondary structure of RNA results from complementary base pairing between sequences on the same RNA strand.  Single-stranded RNA folds over on itself to form a hairpin loop. The bases on one side of the Loop fold align with an antiparallel and complementary Hairpin Single segment on the other side of the fold. stranded Double stranded Stem  RNA molecules can assume very intricate tertiary and quaternary structures, too! Nitrogenous bases BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 67 Nucleic Acids – Structure of RNA These images represent a stereo pair. Cross your eyes slightly to merge the two images and then let your eyes relax. Can you see the structure in 3-D? BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 68 Nucleic Acids – Structure of RNA BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 69  Learning Objective Analyze each of the four types of biological macromolecules for their potential contributions to the emergence of life on earth. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 70 Origin of Life Experiments Could life have originated from chemical origins? Could this “chemical evolution” have occurred on ancient Earth?  Research results suggest...YES!  Stanley Miller combined methane (CH4), ammonia (NH3), and hydrogen (H2) in a closed system with water and applied heat and electricity as an energy source. These conditions mimicked the composition and weather of early earth’s atmosphere.  The products of Miller’s experiment included hydrogen cyanide (HCN) and formaldehyde (H2CO), two important precursors that can form the building blocks of complex organic macromolecules.  In recent experiments, two-carbon acetaldehydes, amino acids, and other organic molecules have been formed easily in these conditions. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 71 Origin of Life Experiments  Carbohydrates and lipids likely had little to no role in the origin of life because they lack the structural and chemical complexity seen in molecules that are able to catalyze chemical reactions.  Catalysis is important because it allows molecules to make copies of themselves and persist through time. This is a key feature of life!  Proteins may have been the first self-replicating molecules to exist on the planet, but there are problems with this hypothesis.  Amino acids were abundant in the prebiotic soup.  Proteins are the most efficient catalysts known.  However, the first self-replicators probably needed to have a mold or a template – something not found in proteins. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 72 Origin of Life Experiments – DNA  DNA’s stability makes it a reliable storage molecule for genetic information.  DNA is less reactive than RNA and therefore is more resistant to chemical degradation. It’s resistance largely is attributed to the lack of a hydroxyl (OH) group at the 2' positions of the ribose sugars in each nucelotide. However...  Stable molecules such as DNA generally make poor catalysts.  If DNA can’t catalyze chemical reactions, it probably can’t catalyze its own replication! It is for this reason that biologists think the first life-form was made of RNA, not DNA. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 73 Origin of Life Experiments – RNA  Can RNA function both as a template for copying itself and as a catalyst for the polymerization reaction that is required to make the complementary copy?  The presence of an extra hydroxyl (OH) group in RNA building blocks makes RNA much more reactive and less stable than DNA.  The RNA world hypothesis states that the first life-form on earth was a self-replicating RNA molecule. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 74 BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 75 Origin of Life Experiments – RNA Researchers found that an RNA replicase could be isolated that could catalyze the addition of ribonucleotides to a complementary RNA strand! BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 76 Origin of Life Experiments – RNA  RNA is not very stable, but early RNAs might have survived long enough in the prebiotic soup to replicate themselves and become the first life forms. However...  Simulations of chemical evolution have NOT yet produced DNA or RNA nucleotides from early earth molecules.  Sugars and purines are made easily, but pyrimidines and ribose are not easily synthesized.  Ribose would have had to have been dominant on ancient earth for nucleic acids to form!!! BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 77