Large Biological Molecules

Large_iological_Molecules_Presentation 2013 08 30.notebook New Jersey enter for Teaching and Learning Progressive Science Initiative This material is made freely available at www.njctl.org and is intended for the non commercial use of students and teachers. These materials may not be used for any commercial purpose without the written permission of the owners. NJTL maintains its website for the convenience of teachers who wish to make their work available to other teachers, participate in a virtual professional learning community, and/or provide access to course materials to parents, students and others. Large iological Molecules www.njctl.org lick to go to website: www.njctl.org www.njctl.org www.njctl.org Vocabulary Large iological Molecules Unit Topics amino acid amphiphilic carbohydrate cellulose denaturation disaccharide N fatty acid fructose glucose glycogen hydrocarbon lipid monosaccharide nucleic acid nucleotide peptide bond phosphodiester bond polysaccharide primary structure protein purine pyrimidine quaternary structure RN saturated secondary structure starch steroid sucrose tertiary structure trans fat triglyceride unsaturated waxes Organic hemistry, Hydrocarbons arbohydrates, Polysaccharides Nucleic cids mino cids, Proteins Lipids Review lick on the topic to go to that section Vocabulary Table of ontents Organic hemistry, Hydrocarbons 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 Organic hem, Hydrocarbons arbon 1

Large_iological_Molecules_Presentation 2013 08 30.notebook Organic hemistry Electron onfiguration arbon has four valence electrons to make covalent bonds. arbon atoms can form diverse molecules by bonding to four other atoms which are in different directions. This allows the molecule to take on a 3 configuration. It is this 3 structure that defines the molecule's function. 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 3 Electron onfiguration 1 Organic chemistry is a science based on the study of. functional groups. carbon compounds. 2 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. water and its interaction with other kinds of molecules. arbon has a valence of 4. inorganic compounds. arbon forms ionic bonds. and only. E,, and. Question 1 Question 2 3 What type(s) of bond(s) does carbon form? ionic 4 How many electron pairs does carbon share to complete its valence shell? hydrogen covalent E and only, and Question 3 Question 4 2

Large_iological_Molecules_Presentation 2013 08 30.notebook 5 Which of the following is an organic compound? H2O Nal 6H12O6 iological Macromolecules Hydrocarbons form the framework from which the 4 different classes of macromolecules (large molecules) have been derived. O2 arbohydrates Nucleic cids Proteins Lipids Question 5 iomolecular Polymers 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. Review: ehydration Synthesis short polymer monomer OH H n immense variety of polymers can be built from a small set of monomers. Polymer : Proteins Monomer they're made from: mino acids longer polymer H OH water arbohydrates Simple sugars (monosaccharides) Nucleic acids Nucleotides Polymer Types ehydration Syn. 6 are to carbohydrates as are to proteins. nucleic acids; amino acids monosaccharides; amino acids amino acids; nucleic acids monosaccharides; nucleic acids 7 ehydration synthesis reactions join monomers to form polymers. Which of the following illustrates a dehydration synthesis reaction? 6H 12O 6 + 6H 12O 6 > 12H 22O 11 + H 2O 3H 6O 3 + 3H 6O 3 > 6H 12O 6 6H 12O 6 + H 2O > 3H 6O 3 + 3H 6O 3 3H 6O 3 + H 2O > 3H 6O 4 Question 11 Question 12 3

Large_iological_Molecules_Presentation 2013 08 30.notebook arbohydrates, Polysaccharides arbohydrates arbohydrates are compounds consisting of carbon, hydrogen and oxygen. Simple carbohydrates also called sugars also called saccharides. Return to Table of ontents arbohydrates Elements in arbs Formula for arbohydrates arbohydrates have equal amounts of carbon and oxygen atoms, but twice as many hydrogen atoms. 8 In the carbohydrate described by the formula 8 H xo 8, x =? The general formula for a carbohydrate is x H 2x O x So some possible formulas for carbohydrates are: 6 H 12 O 6 ; 8 H 16 O 8 ; 9 H 18 O 9 arb Formula Question 13 9 In the carbohydrate described by the formula xh 14 O x, x =? 10 In the carbohydrate described by the formula x H 6 O x, x =? Question 14 Question 15 4

Large_iological_Molecules_Presentation 2013 08 30.notebook arbohydrates 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. Monosaccharides 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. Saccharides Monosaccharides arbohydrate Solubility arbohydrate Structures Sugars all have several hydroxyl (OH ) groups in their structure that makes them soluble in water. In solution, sugars form cyclic structures. Glucose (monosaccharides) Fructose Note: the names of sugars typically end in "ose" These can form chains of sugars. Solubility yclic Structure isaccharides 11 Which of the following is an example of a monosaccharide? ells link 2 simple sugars together to form disaccharides isaccharide formation is another example of a dehydration reaction, the same reaction used to create proteins sucrose glucose fructose & The most common disaccharide is sucrose (glucose + fructose) isaccharides Question 16 5

Large_iological_Molecules_Presentation 2013 08 30.notebook 12 isaccharides are formed by how many monosaccharides? 13 What is another name for simple carbohydrates? 2 3 4 5 sugars saccharides monosaccharides all of the above Question 17 Question 18 Polysaccharides Polysaccharides are polymers of glucose. ifferent organisms link monosaccharides together, using dehydration reactions, to form several different polysaccharides. Polysaccharides: Starch Starch is used for long ifferent term energy organisms link monosaccharides together to form storage several in different plants. polysaccharides. The most important 3 are starch, glycogen, and cellulose. an Starch be branched is used or for long term energy storage in plants. unbranched. an be branched (amylopectin) or unbranched (amylose). The most important 3 are starch, glycogen, and cellulose. Polysaccharides Starch Polysaccharides: Glycogen Glycogen has the same kind of bond between monomers as starch ifferent but it is organisms always highly link branched. monosaccharides together to form It is several used for different long term polysaccharides. energy storage in animals. It's used in muscles The to most provide important a local 3 supply are starch, of energy glycogen, when and needed. cellulose. Starch is used for long term energy storage in plants. an be branched (amylopectin) or unbranched (amylose). Glycogen is broken down to obtain glucose. Polysaccharides: ellulose ellulose ifferent is a organisms link monosaccharides together to form carbohydrate several different used polysaccharides. to make The cell most walls important in 3 are starch, glycogen, and cellulose. plants. Starch is used for long term energy storage in plants. ellulose an be has branched a different (amylopectin) or unbranched (amylose). kind of bond between monomers, forming chains that are crosslinked by hydrogen bonds. Glycogen ellulose 6

Large_iological_Molecules_Presentation 2013 08 30.notebook reakdown of ellulose Getting Energy ecause ifferent cellulose organisms link monosaccharides together to form the several principle different structural polysaccharides. molecule The most in cell important walls 3 are starch, glycogen, and cellulose. of plants, it needs to Starch is used for long term energy storage in plants. be strong. an be branched (amylopectin) or unbranched (amylose). 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. Hydrolysis occurs, breaking the polysaccharide into glucose molecules. reakdown of ellulose Energy 14 The fundamental unit of polysaccharides is 15 Simple sugars do not include fructose monosaccharides glucose disaccharides sucrose and polysaccharides glucose Question 19 Question 20 16 Starch and glycogen are similar molecules because they are both disaccharides they are both structural molecules they are both used to storage energy they are both highly branched 17 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 Question 21 Question 22 7

Large_iological_Molecules_Presentation 2013 08 30.notebook 18 In plants is used to for energy storage and is found in cell walls. Nucleic cids glucose; starch starch; glycogen starch; cellulose cellulose; starch Return to Table of ontents Question 23 Nucleic cids Nucleic cids Nucleic cids Nucleic acids are compounds consisting of carbon, hydrogen, oxygen, nitrogen, and phosphorus. Nucleic acids are chains of nucleotides. nucleotide nucleotide nucleotide The two main types of nucleic acids are N and RN Nucleic cid Elements of N Nucleotides Phosphodiester bond 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 Phophodiester ond Parts of Nucleotide 8

Large_iological_Molecules_Presentation 2013 08 30.notebook Sugars ases Ribonucleic cid (RN) uses the sugar ribose, while eoxyribonucleic cid (N) uses the sugar deoxyribose. RN uses the bases adenine, guanine, cytosine, and uracil (GU) N uses the bases adenine, guanine, cytosine, and thymine (GT) Ribose eoxyribose denine Guanine ytosine Thymine Uracil Here's the difference. RN RN RN N RN N N N The difference is that N uses thymine (T) rather than uracil (U). Sugars ases Purines and Pyrimidines Nitrogen containing bases composed of 2 ringed structures are known as purines. Nitrogen containing bases composed of single ring structures are known as pyrimidines. 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. denine Guanine ytosine Thymine Uracil Purines/Pyrimidines Nucleotides 19 The creation of a phosphodiester bond involves the removal of from the nucleotides: 20 Which of the following is not a component of a nucleotide? phosphate group phosphates nitrogenous base glucose 5 carbon sugar water nucleic acids glucose Question 24 Question 25 9

Large_iological_Molecules_Presentation 2013 08 30.notebook 21 Which base is found in RN but not N? ytosine Uracil Guanine denine 22 The only structural difference between RN and N is in their nitrogenous bases. True False Question 26 Question 27 23 denine would be characterized as a purine. 24 Uracil is a purine. True False True False Question 28 Question 29 25 Pyrimidines are bases with single carbon rings. 26 This base would be characterized as a: True False purine pyrimidine Question 30 Question 31 10

Large_iological_Molecules_Presentation 2013 08 30.notebook RN 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. RN base pair bonding 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 RN RN ase Pairs 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. Function Then Now catalyze reactions store energy store genetic information RN RN's phosphate group RN Proteins TP N N is double stranded. It only forms one shape: the double helix. N Pair bonding between nucleotides still occurs, but in N it is between guanine (G) and cytosine () and between adenine () and thymine (T) T G Thymine denine ytosine Guanine RN Functions N ouble Helix 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. ouble Helix N vs. RN 11

Large_iological_Molecules_Presentation 2013 08 30.notebook Storage and Implementation of the Genetic ode One cannot live without the other 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 is used throughout the cell to implement the genetic code that's stored within N. 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. Genetic ode RN + N 27 N is more stable than RN because. 28 N. RN it can form a double helix is a polymer of nucleic acid; is a polymer of glucose 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 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 Question 32 Question 33 N N and RN RN Proteins phosphate group multiple shapes found inside and outside the nucleus double stranded deoxyribose sugar uracil base cytosine base double helix made up of nucleotides single stranded remains in nucleus guanine base thymine base ribose sugar adenine base Return to Table of ontents Venn iagram mino cids, Proteins 12

Large_iological_Molecules_Presentation 2013 08 30.notebook Proteins mino cids Proteins are compounds consisting of carbon, hydrogen and oxygen, nitrogen, and sometimes sulfur. Proteins also called peptides also called polypeptides. 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. Proteins mino cids omponents of mino cids mino cids always include an amine group (NH 3 ), a carboxyl group (OOH) 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. Here it is symbolized by the letter "R". carboxyl group (OOH) 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 (NH 3 ) Hydroxyl group H atom Water side chain Parts of mino cids Peptide onds Peptide bonds mino cids The common "amine" group (NH3) and "carboxyl" group (OOH) are shown in black. 1 2 The unique side chains are shown in blue. The 8 amino acids in orange are nonpolar and hydrophobic.the others are polar and hydrophilic. 1 2 Peptide chain with 50 or more amino acids can form an individual protein. http://www.bioss.ac.uk/~dirk/genomeodyssey/go_1955_to_66.html The 2 in the magenta box are acidic ("carboxyl" group in the side chain). The 3 in the light blue box are basic ("amine" group in the side chain). Peptide onds 20 mino cids 13

Large_iological_Molecules_Presentation 2013 08 30.notebook 29 Glucose molecules are to starch as are to proteins. 30 Which of the following is not a component of amino acids? oils fatty acids amino acids nucleic acids R group mine Group Hydroxyl Group arboxyl Group Question 34 Question 35 31 Which component of amino acids varies between the 20 different kinds? Protein Shape and Structure mine group Shape is critical to the function of a protein. protein's shape depends on four levels of structure: arboxyl group Hydroxyl group R group Primary Secondary Tertiary Quaternary Question 36 Protein Shape & Structure Proteins: Primary Structure hanges in Primary Structure The primary structure of a protein is the sequence of amino acids that comprise it. Each protein consists of a unique sequence. 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. lanine Leucine Serine Lysine Sickle ell disease is an example of a single amino acid defect Valine or Leucine Leucine lanine or Lysine lanine Serine Lysine or... Primary Structure hanges in P.S. 14

Large_iological_Molecules_Presentation 2013 08 30.notebook Sickle ell isease 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 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. Sickle ell Secondary Structure Secondary Structure 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 Mar 16 6:55 PM Tertiary Structure Structure determines 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. enaturation hanges in heat, ph, 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. Structure = Function enaturation 15

Large_iological_Molecules_Presentation 2013 08 30.notebook 32 The tertiary structure of a protein refers to: 33 The structure of a protein consists of a chain of amino acids assembled in a specific order. its size the presence of pleated sheets its over all 3 structure the number of R groups it contains primary secondary tertiary quaternary Question 37 Question 38 34 Hydrophobic 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. Quaternary Structure Question 39 Quaternary Structure Structure Summary 35 enaturation causes a protein to Level Structure Notes Primary Secondary Tertiary Quaternary bonds between amino acids single chain of amino acids hydrogen bonds between alpha helix, pleated amine and carboxyl sheet groups clustering of hydrophobic disulfide bonds or hydrophilic R groups attractions between multiple peptide chains not present in all proteins lose its shape lose its function both and none of the above Structure Summary Question 40 16

Large_iological_Molecules_Presentation 2013 08 30.notebook 36 t which structural level does a protein get its function? Types of Proteins Primary Proteins have 7 different roles in an organism. Secondary Type Function Tertiary Quaternary Structural hair, cell cytoskeleton ontractile as part of muscle and other motile cells Storage sources of amino acids efense antibodies, membrane proteins Transport hemoglobin, membrane proteins Signaling hormones, membrane proteins Enzymatic regulate speeds of chemical reactions Question 41 Types of Proteins 37 Hormones are an example of what class of protein? 38 Hemoglobin is an example of what class of proteins? structural defense transport signaling Transport Signaling Enzymatic Structural Question 42 Question 43 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 Lipids Lipids 17

Large_iological_Molecules_Presentation 2013 08 30.notebook Review: molecules and water 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 Hydrophobic molecules Hydrophilic molecules Lipids are either hydrophobic or amphiphilic. Hydrophobic/Hydrophilic mphiphilic Triglicerides: Hydrophobic Lipids Triglicerides are hydrophobic. They are constructed from two types of smaller molecules: a single glycerol and three fatty acids Triglicerides 3 fatty acids added to glycerol produce a trigliceride 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 glycerol H 2OH H 2OH H 2OH H H H H H H H H H a fatty acid H H H H OOH H H H H Triglicerides Triglicerides Phospholipids: mphiphilic Lipids 39 How are lipids different from other large biological molecules? 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. s a result, the phosphate end is hydrophilic and the fatty acid end is hydrophobic. Overall, phospholipids are amphiphilic. they do not contain carbon they contain oxygen they are hydrophillic they are not polymers Phospholipids Question 44 18

Large_iological_Molecules_Presentation 2013 08 30.notebook 40 Lipids can be. 41 phospholipid is an example of a/an. hydrophobic hydrophobic molecule hydrophilic hydrophilic molecule E amphiphilic hydrophobic and amphiphilic hydrophilic and amphiphilic amphiphilic molecule hydrophobic and amphiphilic molecule Question 45 Question 46 Saturated Lipids Unsaturated Lipids and Fats Lipids Have the maximum number of hydrogen atoms possible Have no double bonds in their carbon chain They are solid at room temperature Have one or more double bonds. Oils are liquids at room temperature. When hydrogenated (by adding more hydrogen) they become solid and saturated. Saturated Lipids Unsaturated Lipids Fatty cid onding Structure 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 double bond Fatty cid onding Trans Fat 19

Large_iological_Molecules_Presentation 2013 08 30.notebook Trans Fat: Margarine 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 Health Hazards of Trans Fats 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. Margarine mphiphilic Lipids: Soaps and etergents Health Hazards Soaps and etergents 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 hydrophobic end of a soap or detergent is repelled by water, but attracted to other non polar molecules, like grease and oil. IRT REMOVE The water then goes down the drain, along with the oil or grease, leaving the surface clean. The hydrophilic end of the soap or detergent hydrogen bonds with water. detergent hydrophobic end hydrophilic end Soap Waxes IRT fabric being washed Soap Steroids Steroids are lipids with backbones which form rings. holesterol is an important steroid as are the male and female sex hormones, testosterone and estrogen. 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. Waxes Steriods 20

Large_iological_Molecules_Presentation 2013 08 30.notebook 42 Fatty acids with double bonds between some of their carbons are said to be: 43 Which of the following is not a lipid? saturated unsaturated triglycerides monoglycerides wax cellulose cholesterol triglyceride Question 47 Question 48 44 ellulose is a lipid found in cell membranes. True False 45 Which of the following is not one of the four major groups of molecules found in living organisms? glucose carbohydrates lipids E proteins nucleic acids Question 49 Question 50 Feb 26 1:55 PM 21