What, no notes today?

Transcription

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2 What, no notes today?

3 2. Carbon atoms are the most versatile building blocks of molecules With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second shell. Carbon has little tendency to form ionic bonds by losing or gaining 4 electrons. Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds. This tetravalence by carbon makes large, complex molecules possible. The complex chemistry of life requires complex molecules.

4 Isomers are compounds that have the same molecular formula but different structures and therefore different chemical properties. For example, butane and isobutane have the same molecular formula C 4 H 10, but butane has a straight skeleton and isobutane has a branched skeleton. The two butanes are structural isomers, molecules with the same molecular formula but differ in the covalent arrangement of atoms. Fig. 4.6a

5 Enantiomers are molecules that are mirror images of each other Enantiomers are possible if there are four different atoms or groups of atoms bonded to a carbon. If this is true, it is possible to arrange the four groups in space in two different ways that are mirror images. They are like left-handed and right-handed versions. Usually one is biologically active, the other inactive. Fig. 4.6c

6 Even the subtle structural differences in two enantiomers have important functional significance because of emergent properties from the specific arrangements of atoms. One enantiomer of the drug thalidomide reduced morning sickness,but the other isomer caused severe birth defects. Here s the story. 14 min. This is a great examples of the structure/function theme at a molecular level. Fig. 4.7

7 Laboratory tests after the thalidomide disaster showed that in some animals the 'S' enantiomer was teratogenic (caused changes but not DNA mutations) but the 'R' isomer was an effective sedative. It is now known that even if only one isomer (the good one) is administered at the ph in the body, it can cause racemizing, which means that both enantiomers are formed in a roughly equal mix in the blood. So, even if a drug of only the 'R' isomer had been created, the disaster would not have been averted.

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9 Explain the connection between the sequence and the subcomponents of a biological polymer and its properties. [LO 4.1, SP 7.1] Refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. [LO 4.2, SP 1.3] Use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule. [LO 4.3, SP 6.1, SP 6.4]

10 The basic structure of testosterone (male hormone) and estradiol (female hormone) is identical. Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings. These then interact with different targets in the body. Fig. 4.8

11 In a hydroxyl group (-OH), a hydrogen atom forms a polar covalent bond with an oxygen which forms a polar covalent bond to the carbon skeleton. Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol.

12 A carboxyl group (-COOH) consists of a carbon atom with a double bond with an oxygen atom and a single bond to a hydroxyl group. Compounds with carboxyl groups are acids.

13 An amino group (-NH 2 ) consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. Organic compounds with amino groups are amines. The amino group acts as a base because ammonia can pick up a hydrogen ion (H + ) from the solution. Amino acids, the building blocks of proteins, have amino and carboxyl groups.

14 A phosphate group (-OPO 3 2- ) consists of phosphorus bound to four oxygen atoms (three with single bonds and one with a double bond). One function of phosphate groups is to transfer energy between organic molecules.

15 So what happens to your lunch? We are going to frame this section based on your lunch. You can find a million diet advice sources. Here s a good common sense one. mple-rules-for-healthyeating.html?emc=eta1&_r=0&abt=0002&abg= 0 I would add one thing Watch the sugar!

16 1. Most macromolecules are polymers Three of the four classes of macromolecules form chainlike molecules called polymers. Polymers consist of many similar or identical building blocks linked by covalent bonds. The repeated units are small molecules called monomers. Some monomers have other functions of their own.

17 The chemical mechanisms that cells use to make and break polymers are similar for all classes of macromolecules. Monomers are connected by covalent bonds via a condensation (or dehydration synthesis) reaction. One monomer provides a hydroxyl group, and the other provides a hydrogen and together these form water. This process requires energy and is aided by enzymes. Fig. 5.2a

18 4.A.1.a Compare the synthesis and decomposition of biological macromolecules.

19 The covalent bonds connecting monomers in a polymer are disassembled by hydrolysis. In hydrolysis as the covalent bond is broken a hydrogen atom and hydroxyl group from a split water molecule attaches where the covalent bond used to be. Hydrolysis reactions dominate the digestive process, guided by specific enzymes. Fig. 5.2b

20 Explain the connection between the sequence and the subcomponents of a biological polymer and its properties. [LO 4.1, SP 7.1] Refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. [LO 4.2, SP 1.3] Use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule. [LO 4.3, SP 6.1, SP 6.4]

21 Untested: The molecular structure of specific nucleotides is beyond the scope of the course and the AP Exam. The molecular structure of specific amino acids is beyond the scope of the course and the AP Exam. The molecular structure of specific lipids is beyond the scope of the course and the AP Exam. The molecular structure of specific carbohydrate polymers is beyond the scope of the course and the AP Exam.

22 Introduction Carbohydrates include both sugars and polymers. The simplest carbohydrates are monosaccharides or simple sugars. Disaccharides, double sugars, consist of two monosaccharides joined by a condensation reaction. Polysaccharides are polymers of monosaccharides.

23 1. Sugars, the smallest carbohydrates serve as a source of fuel and carbon sources Monosaccharides generally have molecular formulas that are some multiple of CH 2 O. Glucose has the formula C 6 H 12 O 6, but so does fructose and galactose, They are isomers. Be able to list them. Most names for sugars end in -ose. Monosaccharides differ in the number of carbons. Glucose and other six carbon sugars are hexoses. Five carbon backbones are pentoses like ribose.

24 Monosaccharides, particularly glucose, are a major fuel for cellular work. It also functions as the main transport sugar in vertebrates. While often drawn as a linear skeleton, in aqueous solutions monosaccharides form rings. Fig. 5.4

25 Girls are made of sugar and spice, so the saying goes??? Very scary, that. Turns out fructose is quite a bad guy. Found as part of table sugar and high fructose corn syrup (check your food labels), it is broken down only by the liver, which turns much of it to fat if there is too much to begin with, like there will be in a sugary diet. Glucose, on the other hand, is broken down by all cells, so turning it to fat is less likely. Back to the liver, this fat causes it to become resistant to insulin, a protein hormone that is released to help get sugar into cells. Insulin resistance is the main problem in diabetes (type 2), obesity, heart disease and some cancers. Every human group ever studied has shown a positive correlation between sugar consumption and these conditions. Stay away from sweets, especially sodas!!!

26 Two monosaccharides can join to form a dissaccharide via dehydration synthesis. Maltose, malt sugar, is formed by joining two glucose molecules. Lactose is glucose and galactose. It is milk sugar. Sucrose is glucose and fructose. Fig. 5.5a

27 Sucrose, table sugar, is the major transport form of sugars in plants. Fig. 5.5

28 2. Polysaccharides, the polymers of sugars, have storage and structural roles Polysaccharides, aka complex carbohydrates, are polymers of hundreds to thousands of monosaccharides joined by condensation. One function of polysaccharides is as an energy storage macromolecule that is hydrolyzed as needed. These are what we call starches. Other polysaccharides serve a structural function as building materials for the cell or whole organism.

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30 Starch is a storage polysaccharide composed entirely of glucose monomers. One non-branched form of starch, amylose, forms a helix. When they crystalize they become resistant to digestion and good for your gut microbes! Branched forms, like amylopectin, are more complex. Fig. 5.6a

31 Animals also store glucose in a polysaccharide called glycogen. Still all glucose monomers. Glycogen is highly branched, like amylopectin. Humans and other vertebrates store glycogen in the liver and muscles, but only have about a one day supply. Fig. 5.6b Insert Fig. 5.6b - glycogen

32 So do other carbs affect blood sugar? Yes they do. They hydrolyze quickly in the mouth and small intestine to release glucose into the blood stream. Some hydrolyze faster than others (why?), and this is indicated by what is called their glycemic index. Resistant starches, like in oats, green bananas, and cooled potatoes, are those that don t break down so fast and so are good for your gut bugs! 00_foods

33 While polysaccharides can be built from a variety of monosaccharides, glucose is the primary monomer used in polysaccharides. One key difference among polysaccharides develops from 2 possible ring structure of glucose. These two ring forms differ in whether the hydroxyl group attached to the number 1 carbon is fixed above (beta glucose) or below (alpha glucose) the ring plane. Fig. 5.7a

34 Starch is a polysaccharide of alpha glucose monomers. Fig. 5.7

35 Structural polysaccharides form strong building materials. Cellulose makes up the cell wall of plant cells. Be able to list starch, glycogen and cellulose. Cellulose is also a polymer of glucose monomers, but using beta rings. Fig. 5.7c

36 While polymers built with alpha glucose form helical structures, polymers built with beta glucose form straight structures. This allows H atoms on one strand to form hydrogen bonds with OH groups on other strands. Groups of polymers form strong strands, microfibrils, that are basic building material for plants and animals. This is a great example of your favorite theme.

37 Fig. 5.8

38 Another good thing about fiber. There are good and bad guys in our gut, collectively referred to as our microbiome. The good guys help in one simple way by outnumbering the bad guys. In general, the good guys can eat fiber and resistant starches, the bad guys can t. So if you feed your good guys they will keep outnumbering the bad guys, and that is good for you Retrogradation is a process by which amylose and amylopectin, normally broken down very quickly to make blood sugar shoot up, get bonded together when things like potato or pasta dries and cools. This makes them harder to digest so they make it past the small intestine into the colon and feed the good guys!

39 4.A.1.a.4 Why is starch easily digested by animals, while cellulose isn t? 4.A.1.a how does the structure of <polysaccharides, proteins, nucleic acids> influence the function of those molecules?

40 Another important structural polysaccharide is chitin, used in the exoskeletons of arthropods (including insects, spiders, and crustaceans). Chitin is similar to cellulose, except that it contains a nitrogen-containing group on each glucose. Pure chitin is leathery, but the addition of calcium carbonate hardens the chitin. Chitin also forms the structural support for the cell walls of many fungi. Fig. 5.9

41 Introduction Lipids as a group are an exception among macromolecules because the group does not include polymers. The unifying feature of lipids is that they all have little or no affinity for water. This is because their structures are dominated by nonpolar covalent bonds. Lipids are highly diverse in form and function.

42 Glycerol consists of a three carbon skeleton with a hydroxyl group attached to each. A fatty acid consists of a carboxyl group attached to a long carbon skeleton, often 16 to 18 carbons long. Fig. 5.10a

43 The many nonpolar C-H bonds in the long hydrocarbon skeleton make fats hydrophobic. In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triglyceride. Fig. 5.10b

44 Fish: Healthy or Hazardous? The long chain unsaturated fats in Omega 3 oils found in fish can actually lower blood cholesterol, but they also may contain harmful mercury. Always be careful where fish are involved.

45 The major function of fats is energy storage. A gram of fat stores more than twice as much energy as a gram of a polysaccharide (9C/g vs. 4C/g) Plants use starch for energy storage when mobility is not a concern but use oils when dispersal and packing is important, as in seeds. Humans and other mammals store fats as long-term energy reserves in adipose cells. Fat also functions to cushion vital organs. A layer of fats can also function as insulation. This subcutaneous layer is especially thick in whales, seals, and most other marine mammals.

46 4.A.1.a.3 Explain how the structure of lipids determines the polarity of the molecule. 4.A.1.a.3 If the chemistry of water occurs in aqueous solution, why are lipids useful in biological systems?

47 2. Phospholipids are major components of cell membranes Phospholipids have two fatty acids attached to glycerol and a phosphate group at the third position. The phosphate group carries a negative charge.

48 The interaction of phospholipids with water is complex. The fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head. Fig. 5.12

49 3. Steroids are lipids that include cholesterol and certain hormones Steroids have a carbon skeleton consisting of four fused carbon rings, very different than triglycerides. Different steroids are created by varying functional groups attached to the rings. Fig. 5.14

50 Cholesterol, an important steroid, is a component in animal cell membranes. Cholesterol is also the precursor from which all other steroids are synthesized. Many of these other steroids are hormones, including the vertebrate sex hormones. Sunshine helps convert cholesterol in your skin to vitamin D. While cholesterol is clearly an essential molecule, high levels of cholesterol in the blood may contribute to cardiovascular disease.

51 Introduction Proteins are instrumental in about everything that an organism does. These functions include catalyzing reactions, structural support, storage, transport of other substances, intercellular signaling, movement, and defense against foreign substances. Protein enzymes are of overwhelming importance in a cell and regulate metabolism by selectively accelerating chemical reactions. Humans have tens of thousands of different proteins, each with their own structure and function.

52 4.A.1.a how does the structure of <polysaccharides, proteins, nucleic acids> influence the function of those molecules? 4.A.1.a.2 Explain how the sequence of amino acids in a protein determines each level of that protein s structure. 4.A.1.a.2 Explain how the conditions of the environment that a protein is in affect the structure and function of that protein.

53 All protein polymers are constructed from the same set of 20 monomers, called amino acids. Polymers of proteins are called polypeptides. A protein consists of one or more polypeptides folded and coiled into a specific shape, generally either fibrous or globular. See what you remember from the 9 th grade watch this. 4 min., or this, 6 min. with a bit more detail.

54 1. A polypeptide is a polymer of amino acids connected in a specific sequence Amino acids consist of four components attached to a central carbon, the alpha carbon. These components include a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or side chain). Differences in R groups produce the 20 different amino acids.

55 One group of amino acids has hydrophobic R groups. Don t try to memorize these, just get the general idea of differences in R groups. What if one of these was substituted for another in a protein?

56 The last group of amino acids includes those with functional groups that are charged (ionized) at cellular ph. Some R groups are bases, others are acids. Fig. 5.15c

57 Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. The resulting covalent bond is called a peptide bond. Fig. 5.16

58 2. A protein s function depends on its specific conformation (that means shape) A protein consists of one or more polypeptides that have been precisely folded and coiled into a unique shape, again, generally fibrous or globular. It is the order of amino acids that determines what the three-dimensional conformation will be. Fig. 5.17

59 A protein s specific structure determines its function. In almost every case, the function depends on its ability to recognize and bind to some other molecule like two pieces of a puzzle. For example, antibodies bind to particular foreign substances that fit their binding sites. Enzymes recognize and bind to specific substrates, facilitating a chemical reaction. Neurotransmitters pass signals from one cell to another by binding to receptor sites on proteins in the membrane of the receiving cell.

60 More protein functions Structural proteins: Collagen, Keratin, Silk Transport proteins: membrane pumps (e.g.- Na/K Pump), hemoglobin Hormones: insulin, HGH Movement: actin and myosin, tubulin Proteins in the news: gluten and casein

61 The folding of a protein from a chain of amino acids occurs spontaneously, but with the help of other proteins called Chaperonins. We ll come back to them later. Three levels of structure: primary, secondary, and tertiary structure, are used to organize the folding within a single polypeptide. Quaternary structure arises when two or more polypeptides join to form a protein.

62 The primary structure of a protein is its unique sequence of amino acids. Lysozyme, an enzyme that attacks bacteria, consists on a polypeptide chain of 129 amino acids. The precise primary structure of a protein is determined by inherited genetic information. Primary structure will then determine how it folds after it is formed. Fig. 5.18

63 Even a slight change in primary structure can affect a protein s shape and ability to function. Here s the classic example: In individuals with sickle cell disease, abnormal hemoglobins, oxygen-carrying proteins, develop because of a single amino acid substitution. These abnormal hemoglobins crystallize, deforming the red blood cells and leading to clogs in tiny blood vessels.

64 Fig. 5.19

65 The secondary structure of a protein results from hydrogen bonds at regular intervals along the polypeptide backbone. Typical shapes that develop from secondary structure are coils (an alpha helix) or folds (beta pleated sheets). Both give the molecule structural support. Link to animation. Fig. 5.20

66 Linus Pauling One of only a few to have won two Nobel Prizes in science - the first was for his discovery of the alpha helical nature of many proteins. Pauling did his work at Cal-Tech

67 Tertiary structure refers to irregular shapes determined by a variety of interactions among R groups and between R groups and the polypeptide backbone, including disulfide bridges. Link to animation. 1 min.

68 Tertiary Structure These irregular foldings are due to many different types of bonds between R groups. The H bonds which determine secondary structure are not between R groups.

69 Quaternary structure results from the aggregation of two or more polypeptide subunits. Collagen is a fibrous protein of three polypeptides that are supercoiled like a rope. Collagen and silk are fibrous. This provides the structural strength for their role in connective tissue. Hemoglobin is a globular protein with two copies of two kinds of polypeptides. Hemoglobin and insulin are globular. Fig. 5.23

70 Here s gluten. What is it found in? Why have you heard of it?

71 Here s some gluten tidbits In baking, fats interfere with gluten development process. Cookies are more crumbly than bread because they've got more fat in them. What happens is that the fat molecules surround and literally shorten the strands of gluten so that they can't stretch out as much. That's where we get the name "shortening" as well as shortbread cookies. Kneading dough and tossing pizza dough gives the chains more time to form, so they stick together better. Pizza and bagels lots of gluten.

72 A protein s shape, and therefore its function, can change in response to the physical and chemical conditions. Alterations in ph, salt concentration, temperature, or other factors can unravel or denature a protein. These forces disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain the protein s shape. Some proteins can return to their functional shape after denaturation, but others cannot, especially in the crowded environment of the cell. A cooked egg is an example of a denatured protein.

73 4.A.1.a.2 Explain how the conditions of the environment that a protein is in affect the structure and function of that protein.