Biology. Organic Chemistry, Hydrocarbons. Slide 1 / 140 Slide 2 / 140. Slide 4 / 140. Slide 3 / 140. Slide 5 / 140. Slide 6 / 140

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1 Slide 1 / 140 Slide 2 / 140 iology Large iological Molecules Slide 3 / 140 Slide 4 / 140 Vocabulary Large iological Molecules Unit Topics amino acid monosaccharide secondary structure lick on the topic to go to that section amphiphilic carbohydrate cellulose denaturation disaccharide N fatty acid fructose nucleic acid nucleotide peptide bond phosphodiester bond polysaccharide primary structure protein purine starch steroid sucrose tertiary structure trans fat triglyceride unsaturated waxes Organic hemistry, ydrocarbons arbohydrates, Polysaccharides Nucleic cids mino cids, Proteins Lipids Review glucose glycogen hydrocarbon lipid pyrimidine quaternary structure RN saturated Slide 5 / 140 Slide 6 / 140 Organic hemistry, ydrocarbons arbon arbon is the backbone of biological molecules. Organic chemistry is the chemistry of carbon compounds. arbon has the ability to form long chains, enabling the creation of large molecules: proteins, lipids, carbohydrates, and nucleic acids. Return to Table of ontents

2 Slide 7 / 140 Organic ompounds Slide 8 / 140 Organic hemistry Organic compounds range from simple molecules to colossal ones. Organic compounds contain: lways Often Occasionally N S arbon atoms can form diverse molecules by bonding to four other atoms which are in different directions. O P This allows the molecule to take on a 3 configuration. It is this 3 structure that defines the molecule's function. Si alogens Slide 9 / 140 Slide 10 / 140 Electron onfiguration 1 Organic chemistry is a science based on the study of. arbon has four valence electrons to make covalent bonds. You should remember from chemistry, electron configuration is the key to an atom s characteristics. Electron configuration determines the kinds and number of bonds an atom will form with other atoms. functional groups. carbon compounds. water and its interaction with other kinds of molecules. inorganic compounds. Slide 11 / 140 Slide 12 / Which property of the carbon atom gives it compatibility with a greater number of different elements than any other type of atom? arbon has 6 to 8 neutrons. arbon has a valence of 4. arbon forms ionic bonds. and only. E,, and. 3 What type(s) of bond(s) does carbon form? ionic hydrogen covalent and only E, and

3 Slide 13 / 140 Slide 14 / ow many electron pairs does carbon share to complete its valence shell? 5 Which of the following is an organic compound? 2O Nal 6 12O 6 O 2 Slide 15 / 140 ydrocarbons Slide 16 / 140 Saturated ydrocarbons These molecules consist of only carbon and hydrogen atoms. Each carbon atom makes 4 bonds. Each hydrogen atom makes 1 bond. arbonhydrogen bonds are non-polar, so those bonds are hydrophobic. In saturated hydrocarbons: every carbon atom is bonded to four different atoms no new atoms can be added along the chain Fossil fuels are examples of hydrocarbons that are formed from decaying organic matter. Slide 17 / 140 Unsaturated ydrocarbons 6 ydrocarbons. Slide 18 / 140 In unsaturated hydrocarbons: some of the carbon-carbon bonds are double or triple bonds those can be broken and replaced with a single bond double bond are polar are held together by ionic bonds contain nitrogen contain only hydrogen and carbon atoms at that point, additional atom(s) can be added

4 Slide 19 / What is the reason why hydrocarbons are not soluble in water? The majority of their bonds are polar covalent carbon to hydrogen linkages The majority of their bonds are nonpolar covalent carbon to hydrogen linkages They are hydrophilic They are lighter than water Slide 20 / ydrocarbons containing only single bonds between the carbon atoms are called. saturated polar non-polar unsaturated Slide 21 / ydrocarbons containing double or triple bonds between some of the carbon atoms are called. saturated polar non-polar unsaturated Slide 22 / Gasoline and water do not mix because gasoline is. less dense than water non-polar and water is polar volatile and water is not polar and water is non-polar Slide 23 / 140 iological Macromolecules ydrocarbons form the framework from which the 4 different classes of macromolecules (large molecules) have been derived. We have mentioned these 4 types of molecules before. List them below. Slide 24 / 140 Polymers Three of the classes of life s organic molecules are polymers: carbohydrates, nucleic acids, and proteins. lthough organisms share the same limited number of monomer types, each organism is unique based on the arrangement of how their monomers are used to make polymers. n immense variety of polymers can be built from a small set of monomers. (See the first slide in this chapter for a hint) Polymer : Proteins arbohydrates Nucleic acids Monomer they're made from: mino acids Simple sugars (monosaccharides) Nucleotides

5 Slide 25 / 140 Review: ehydration Synthesis Slide 26 / are to carbohydrates as are to proteins. short polymer O monomer nucleic acids; amino acids monosaccharides; amino acids amino acids; nucleic acids monosaccharides; nucleic acids O longer polymer water Slide 27 / ehydration synthesis reactions join monomers to form polymers. Which of the following illustrates a dehydration synthesis reaction? Slide 28 / 140 arbohydrates, Polysaccharides 6 12O O 6 --> 12 22O O 3 6O O 3 --> 6 12O O 6 + 2O --> 3 6O O 3 3 6O 3 + 2O --> 3 6O 4 Return to Table of ontents Slide 29 / 140 arbohydrates Slide 30 / 140 Formula for arbohydrates arbohydrates are compounds consisting of carbon, hydrogen and oxygen. arbohydrates have equal amounts of carbon and oxygen atoms, but twice as many hydrogen atoms. Simple carbohydrates also called sugars also called saccharides. The general formula for a carbohydrate is x 2x O x So some possible formulas for carbohydrates are: 6 12O O O 9

6 Slide 31 / 140 Slide 32 / In the carbohydrate described by the formula 14 In the carbohydrate described by the formula 8 x O 8 x =? x 14 O x x =? Slide 33 / In the carbohydrate described by the formula Slide 34 / 140 arbohydrates x 6 O x x =? Monosaccharides are the simplest carbohydrates. They are the monomers that are used to build more complex carbohydrates. The most common of these are glucose and fructose. isaccharides are formed by combining two monosaccharides. Table sugar, (sucrose) is made up of glucose and fructose. Polysaccharides are formed by combining chains of many monosaccharides. Slide 35 / 140 Monosaccharides Slide 36 / 140 arbohydrate Solubility Monosaccharides are the simplest sugars. Examples include glucose and fructose In solution, they form ring-shaped molecules. The basic roles of simple sugars are as: fuel to do work, the raw materials for carbon backbones the monomers from which larger carbohydrates are synthesized. Glucose Fructose (monosaccharides) Sugars all have several hydroxyl (O - ) groups in their structure that makes them soluble in water. Note: the names of sugars typically end in "ose"

7 Slide 37 / 140 arbohydrate Structures Slide 38 / 140 isaccharides In solution, sugars form cyclic structures. These can form chains of sugars. ells link 2 simple sugars together to form disaccharides isaccharide formation is another example of a dehydration synthesis reaction. The most common disaccharide is sucrose (glucose + fructose) What other molecule is produced when sucrose is formed? Slide 39 / Which of the following is an example of a monosaccharide? Slide 40 / isaccharides are formed by combining how many monosaccharides? sucrose glucose fructose & Slide 41 / What is another name for a simple carbohydrates? sugars saccharides monosaccharides all of the above Slide 42 / 140 Polysaccharides Polysaccharides are polymers of glucose. ifferent organisms link monosaccharides together, using dehydration reactions, to form several different polysaccharides. The most important 3 are starch, glycogen, and cellulose.

8 Slide 43 / 140 Polysaccharides: Starch Starch is used for long term energy storage in plants. starch can be branched or unbranched. Slide 44 / 140 Polysaccharides: Glycogen Glycogen has the same kind of bond between monomers as starch but it is always highly branched. It is used for long term energy storage in animals. It's used in muscles to provide a local supply of energy when needed. Glycogen is broken down to obtain glucose. What kind of reaction is used? Slide 45 / 140 Polysaccharides: ellulose Slide 46 / 140 reakdown of ellulose ellulose is a carbohydrate used to make cell walls in plants. ellulose has a different kind of bond between monomers, forming chains that are crosslinked by hydrogen bonds. ecause cellulose is the principle structural molecule in cell walls of plants, it needs to be strong. nimals cannot break down cellulose without the help of intestinal bacteria. It is commonly referred to as fiber. In order for cells to obtain energy from polysaccharides, they must be first broken down into monosaccharides. occurs, breaking the polysaccharide into glucose molecules. Slide 47 / 140 Getting Energy Slide 48 / The fundamental unit of a polysaccharide is fructose glucose sucrose and

9 Slide 49 / Simple sugars do not include Slide 50 / Starch and glycogen are similar molecules because monosaccharides disaccharides polysaccharides glucose they are both disaccharides they are both structural molecules they are both used to storage energy they are both highly branched Slide 51 / 140 Slide 52 / necropsy (an autopsy on an animal) is performed by a veterinarian. The stomach contents contain large amounts of cellulose. We can conclude that this animal is a/an. carnivore herbivore omnivore decomposer 23 In plants is used to for energy storage and is found in cell walls. glucose; starch starch; glycogen starch; cellulose cellulose; starch Nucleic cids Slide 53 / 140 Slide 54 / 140 Nucleic cids Nucleic acids are compounds consisting of carbon, hydrogen, oxygen, nitrogen, and phosphorus. The two main types of nucleic acids are N and RN Return to Table of ontents

10 Slide 55 / 140 Nucleic cids Slide 56 / In this diagram, the is the monomer. Nucleic acids are chains of nucleotides. nucleotide nucleotide nucleotide Nucleic cid Nucleotide Nucleic cid Nucleic cid Slide 57 / 140 Phosphodiester bond Slide 58 / 140 Parts of a Nucleotide The bonds between nucleotides are called phosphodiester bonds. Like bonds between saccharides, they are formed by dehydration synthesis. a base (a nitrogen compound) Nucleotides have three parts: a sugar a phosphate Slide 59 / 140 Sugars Slide 60 / 140 Ribonucleic cid (RN) uses the sugar ribose, while eoxyribonucleic cid (N) uses the sugar deoxyribose. Ribose eoxyribose ere's the difference.

11 Slide 61 / 140 Slide 62 / 140 Nucleotides Each strand is unique due to its sequence of bases. In this way, genetic information is stored in the sequence of nucleotides. Since the bases are not part of the sugar or the bond, the base sequence is independent of them. ny base sequence is possible. Slide 63 / The creation of a phosphodiester bond involves the removal of from the nucleotides: Slide 64 / Which of the following is not a component of a nucleotide? phosphates glucose water nucleic acids phosphate group nitrogenous base 5-carbon sugar glucose Slide 65 / Which base is found in RN but not N? ytosine Uracil Guanine denine Slide 66 / The only structural difference between RN and N is in their nitrogenous bases. True False

12 Slide 67 / 140 Slide 68 / denine would be characterized as a purine. True False 30 Uracil is a purine. True False Slide 69 / 140 Slide 70 / Pyrimidines are bases with single carbon rings. True False Slide 71 / 140 RN Slide 72 / 140 RN base pair bonding RN is a single strand of nucleotides. This strand folds in on itself, hydrogen bonds forming between the bases, and between bases and surrounding water. These bonds cause RN to form different shapes. onds form between bases in a predictable pattern. nucleotide with an adenine base () will hydrogen bond with a nucleotide with a uracil (U) base. nucleotide with a guanine (G) base bonds with a nucleotide with a cytosine () base. ifferent sequence of bases = different shapes U G

13 Slide 73 / 140 RN In early life, RN played many roles that have now been taken over by more specific molecules. RN's role is still essential, but more limited than it once was. Think back to last chapter and fill in the molecules which control these functions now. Function Then Now catalyze reactions store energy store genetic information RN RN RN N is double-stranded. It only forms one shape: the double-helix. Pair bonding between nucleotides still occurs, but in N it is between guanine (G) and cytosine () and between adenine () and thymine (T) T G Slide 74 / 140 N Thymine denine ytosine Guanine Slide 75 / 140 ouble elix Slide 76 / 140 N v. RN Instead of nucleotides being attracted to other bases in the same strand, to create shapes, they bond to matching nucleotides in a second strand, to create the double stranded helix. This makes N a better archive for genetic information since the bases are on the inside of the helix, protected. Thymine is also more stable than uracil. ut it also means that N can't directly work in the cell. It is a library of information, but the only way that information can be used is via RN. RN is chemically active in the cell, N is not. Slide 77 / 140 Storage and Implementation of the Genetic ode Slide 78 / 140 N and RN So N is more useful and stable as an archive, while RN is more useful working in the cells. RN carries genetic information from N to where it can be used. N is maintained in a safe environment to maintain the integrity of the genetic code. RN strands are shorter and less durable than N strands, but they are critical to communicate the instructions of the N code to the cell where they can be executed. Without RN, the information stored in N could not be used. nd without N, the information would not be as stable. RN is used throughout the cell to implement the genetic code that's stored within N.

14 Slide 79 / N is more stable than RN because. Slide 80 / N. RN it can form a double helix it contains the base uracil it can form a double helix and contains the base uracil it can form a double helix and contains the base thymine is a polymer of nucleic acid; is a polymer of glucose is always a double helix; forms many shapes has hydrogen bonds between its bases; bases do not form bonds acts as an enzyme; stores genetic code Slide 81 / 140 Slide 82 / 140 N N and RN RN double helix ribose sugar Proteins thymine base guanine doublestranded found inside and group multiple single adenine phosphate base outside the shapes strandedbase made up of nucleus deoxyribose remains in nucleotides sugar nucleus cytosine uracil bas base Return to Table of ontents Slide 83 / 140 Proteins are compounds consisting of carbon, hydrogen and oxygen, nitrogen, and sometimes sulfur. Proteins also called Proteins peptides also called polypeptides. Slide 84 / 140 mino cids Proteins are chains of amino acids. There are 20 amino acids used to construct the vast majority of proteins. While there are a few others that are sometimes used, these 20 are the "standard" amino acids. ll life on Earth uses virtually the same set of amino acids to construct its proteins.

15 Slide 85 / 140 omponents of mino cids mino cids always include an amine group (N3), a carboxyl group (OO) and a side chain that is unique to each amino acid. The side chain (sometimes called the R-group) determines the unique properties of each amino acid. ere it is symbolized by the letter "R". carboxyl group (OO) Slide 86 / 140 Peptide onds The chemical bond that is formed between amino acids is called a peptide bond. Like bonds between saccharides and nucleotides, they are formed by dehydration synthesis. amine group (N3) ydroxyl group atom Water side chain Slide 87 / 140 Peptide bonds Slide 88 / 140 mino cids The common "amine" group (N3) and "carboxyl" group (OO) are shown in black. The unique side chains are shown in blue. Peptide chain with 50 or more amino acids can form an individual protein The 8 amino acids in orange are nonpolar and hydrophobic.the others are polar and hydrophilic. The 2 in the magenta box are acidic ("carboxyl" group in the side chain). 1 The 3 in the light blue box are basic ("amine" group in the side chain). Slide 89 / Glucose molecules are to starch as are to proteins. oils fatty acids amino acids nucleic acids Slide 90 / Which of the following is not a component of amino acids? R-group mine Group ydroxyl Group arboxyl Group

16 Slide 91 / Which component of amino acids varies between the 20 different kinds? mine group arboxyl group ydroxyl group R-group Slide 92 / 140 Protein Shape and Structure Shape is critical to the function of a protein. protein's shape depends on four levels of structure: Primary Secondary Tertiary Quaternary Slide 93 / 140 Proteins: Primary Structure The primary structure of a protein is the sequence of amino acids that comprise it. Each protein consists of a unique sequence. lanine Valine Leucine Serine Lysine or Leucine Leucine lanine or Lysine lanine Serine Lysine or... Slide 94 / 140 hanges in Primary Structure hanges in the primary structure of a protein are changes in its amino acid sequence. hanging an amino acid in a protein changes its primary structure, and can affect its overall structure and ability to function. Sickle ell disease is an example of a single amino acid defect Slide 95 / 140 Sickle ell isease Slide 96 / 140 Secondary Structure Sickle ell isease is a blood disorder specifically involving hemoglobin, which carries oxygen in the blood. single glutamate amino acid is replaced in the primary sequence by a valine.the result changes the overall shape of the hemoglobin molecule and does not allow it to properly carry oxygen. Secondary Structure is a result of hydrogen bond formation between amine and carboxyl groups of amino acids in each polypeptide chain. epending on where the groups are relative to one another, the secondary structure takes the shape of an alpha helix or a pleated sheet. Note: R-groups do not play a role in secondary structure.

17 Slide 97 / 140 Secondary Structure Slide 98 / 140 Tertiary Structure pleated sheets Tertiary Structure is the overall 3- shape of the polypeptide. It results from the clustering of hydrophobic and hydrophilic R-groups and bonds between them along the helices and pleats. alpha helix Slide 99 / 140 Structure etermines Function The function of proteins is determined by their shape: it's tertiary structure. It's shape is driven by chemistry, but it is the shape, not the chemistry, that dictates function. Each sequence of amino acids folds in a different way as each amino acid in the chain interacts with water and the other amino acids in the protein uniquely. For instance, upon contacting water, a protein can fold into grooves that function as binding sites for other molecules. Slide 100 / 140 enaturation hanges in heat, p, and salinity can cause proteins to unfold and lose their functionality, known as denaturation. This egg's protein has undergone denaturation and loss of solubility, caused by the high rise in the temperature of the egg during the cooking process. Slide 101 / The tertiary structure of a protein refers to: its size the presence of pleated sheets its over all 3 structure the number of R-groups it contains Slide 102 / The structure of a protein consists of a chain of amino acids assembled in a specific order. primary secondary tertiary quaternary

18 Slide 103 / ydrophobic interactions have occurred between R groups of adjacent amino acids in a protein. This is the structural level and forms a/an. secondary; alpha helix secondary; pleated sheet tertiary; 3 shape primary; alpha helix Some proteins have a Quaternary Structure. Quaternary structure consists of more than one polypeptide chain interacting with each other through hydrogen bonds and hydrophobic/hydrophilic interactions. Slide 104 / 140 Quaternary Structure Primary Secondary Tertiary Slide 105 / 140 Level Structure Notes Quaternary bonds between amino acids hydrogen bonds between amine and carboxyl groups clustering of hydrophobic or hydrophilic R groups attractions between multiple peptide chains single chain of amino acids alpha helix, pleated sheet disulfide bonds not present in all proteins Slide 106 / enaturation causes a protein to lose its shape lose its function both and none of the above Slide 107 / t which structural level does a protein get its function? Primary Secondary Tertiary Quaternary Structural ontractile Slide 108 / 140 Types of Proteins Proteins have 7 different roles in an organism. Type Function hair, cell cytoskeleton as part of muscle and other motile cells Storage efense Transport Signaling Enzymatic/ chemical sources of amino acids antibodies, membrane hemoglobin, membrane hormones, membrane regulate speeds of reactions

19 Slide 109 / ormones are an example of what class of protein? Slide 110 / emoglobin is an example of what class of proteins? structural defense transport signaling Transport Signaling Enzymatic Structural Slide 111 / 140 Slide 112 / 140 Lipids Lipids Lipids are the one class of large biological molecules that do not consist of polymers. Main functions of lipids include energy storage the major component of cell membrane involved with metabolic activities Return to Table of ontents Slide 113 / 140 Review: molecules and water Slide 114 / 140 mphiphilic Recall the definitions of hydrophobic and hydrophilic. hydrophilic water water mphiphilic molecules have a hydrophobic "tail" and a hydrophilic "head". So one of its ends is attracted to water, while the other end is repelled. hydrophobic ydrophobic molecules ydrophilic molecules What molecule did we already learn about that was amphiphilic? Lipids are either hydrophobic or amphiphilic.

20 Slide 115 / 140 Triglicerides: ydrophobic Lipids Triglicerides are hydrophobic. They are constructed from two types of smaller molecules: a single glycerol and three fatty acids Fatty acids are carboxylic acids with a very long chain of carbon atoms. They vary in the length and the number and locations of double bonds they contain. 3 fatty acids added to glycerol produce a trigliceride. Slide 116 / 140 Triglicerides glycerol a fatty acid 2O 2O 2O OO Slide 117 / 140 Phospholipids: mphiphilic Lipids Phospholipids have 2 fatty acids and 1 phosphate group. The phosphate end is polar and hydrogen bonds with water. The fatty acids are made of long chains of carbon and hydrogen, making them non-polar. Slide 118 / ow are lipids different from other large biological molecules? they do not contain carbon they contain oxygen they are hydrophillic they are not polymers s a result, the phosphate end is hydrophilic and the fatty-acid end is hydrophobic. Overall, phospholipids are amphiphilic. 46 Lipids can be. Slide 119 / 140 Slide 120 / phospholipid is an example of a/an. E hydrophobic hydrophilic amphiphilic hydrophobic and amphiphilic hydrophilic and amphiphilic hydrophobic molecule hydrophilic molecule amphiphilic molecule hydrophobic and amphiphilic molecule

21 Slide 121 / 140 Saturated Lipids Slide 122 / 140 Unsaturated Lipids ave the maximum number of hydrogen atoms possible ave no double bonds in their carbon chain They are solid at room temperature ave one or more double bonds. Oils are liquids at room temperature. When hydrogenated (by adding more hydrogen) they become solid and saturated. Slide 123 / 140 Fatty cid onding Structure Slide 124 / 140 Trans Fats Saturated fatty acids Unsaturated fatty acids double bond The chemical process that's used to saturate unsaturated fatty acids can lead to transfats. These have a double bond that is rotated, resulting in a linear chain. These do not function well in biological systems and are a health hazard. Trans unsaturated fatty acids (transfats) click here to see a video on lipids twisted double bond Slide 125 / 140 Trans Fat: Margarine Slide 126 / 140 ealth azards of Trans Fats Margarine is a trans fat which which developed during World War II ue to a milk and butter shortage, scientists took corn oil and hydrogenated it. The double bonds became single bonds and a solid was formed Trans fats tend to stay in the bloodstream much longer than saturated or unsaturated fats. Trans fats are much more prone to arterial deposition and plaque formation. Trans fats are thought to play a role in the following diseases and disorders: cancer, alzheimers disease, diabetes, obesity, liver dysfunction, and infertity.

22 Slide 127 / 140 mphiphilic Lipids: Soaps and etergents Slide 128 / 140 Soaps and etergents The hydrophobic end of a soap or detergent is repelled by water, but attracted to other non-polar molecules, like grease and oil. The hydrophilic end of the soap or detergent hydrogen bonds with water. So the soap or detergent bonds with many stains (oil, grease, etc.) and pulls them from the surface being cleaned and into the surrounding water. The water then goes down the drain, along with the oil or grease, leaving the surface clean. detergent hydrophobic end hydrophilic end fabric being washed IRT IRT REMOVE Slide 129 / 140 Waxes Slide 130 / 140 Steroids Waxes are effective hydrophobic coatings formed by many organisms (insects, plants, humans) to ward off water. They consist of 1 long fatty acid attached to an alcohol. Steroids are lipids with backbones which form rings. holesterol is an important steroid as are the male and female sex hormones, testosterone and estrogen. Slide 131 / 140 Slide 132 / Fatty acids with double bonds between some of their carbons are said to be: saturated unsaturated triglycerides monoglycerides 49 Which of the following is not a lipid? wax cellulose cholesterol triglyceride

23 Slide 133 / ellulose is a lipid found in cell membranes. True False Slide 134 / Which of the following is not one of the four major groups of molecules found in living organisms? E glucose carbohydrates lipids proteins nucleic acids Slide 135 / 140 Slide 136 / 140 Review carbon-hydrogen-oxygen 1:2:1 monosaccharides simple sugar Return to Table of ontents primary source of energy plants (autotrophs) monosaccharides Glucose Fructose Starch ellulose Glycogen long chains of monosaccharides polysaccharides ring shaped table sugar Slide 137 / 140 Slide 138 / 140 types found in have phosphate store genetic information deoxyribose guanine make proteins thymine cytosine nucleotides ribose adenine carbon, hydrogen, uracil N nitrogen, oxygen, phophorus Nitrogenous base sugar RN enzymes amine group quaternary structure control the rate of chemical reactions muscle, hair cartilage, nails, meat we eat carboxyl group primary structure and sometimes tertiary structure r group secondary structure amino acids carbon, hydrogen, oxygen, nitrogen, sulfur body to function properly

24 Slide 139 / 140 Slide 140 / 140 are are energy storage amphilic carbon-hydrogen-oxygenphosphorus head and tail hydrophobic phospholipids triglicerides glycerol, fatty acid, phosphate saturated OR unsaturated hormones and cell membranes