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BIOLOGICAL MOLECULES
This chapter discusses biological molecules and carbon chemistry. Carbon atoms can form up to four bonds and are versatile building blocks of organic molecules. Organic molecules contain carbon and often have functional groups that determine properties like polarity and reactivity. Lipids are nonpolar and include fats and fatty acids. Fats are made of glycerol bonded to three fatty acids, releasing water. This forms triglycerides, the main energy storage molecules in animals.
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BIOLOGICAL MOLECULES
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- 2. Chapter 3 2 Why Is Carbon So Important? Organic vs. Inorganic in Chemistry • Organic refers to molecules containing a carbon skeleton • Inorganic refers to carbon dioxide and all molecules without carbon
- 3. Chapter 3 3 Why Is Carbon So Important? Carbon atoms are versatile and can form up to four bonds (single, double, or triple) in rings and chains Bonds are very high in energy (strongest substance on Earth = pure carbon = …?) Functional groups in organic molecules confer chemical reactivity and other characteristics…
- 4. Chapter 3 4 Example Groups, I • Polar / Nonpolar • Dehyd. Synth / Hydrogen Hydrolysis H • Almost all biochemicals • Polar • Dehyd. Synth / Hydroxyl Hydrolysis OH • Sugars
- 5. Chapter 3 5 Example Groups, II • Polar & acidic Carboxyl (Carboxylic • Peptide bonds acid) COOH • Fats; amino acids • Polar & basic Amine • Peptide bonds or Amino • Amino acids; NH2 proteins
- 6. Example Chapter 3 6 Groups, III • Acidic & polar • Energetic bonds; Phosphate Links nucleotides • DNA; ATP; H2PO4 Phospholipids • Nonpolar • Hydrophobic Methyl • Many, especially CH4 lipids
- 7. Chapter 3 7 Joining Monomers Together Builds bigger molecules H from one joins OH from another Forms water (condensation) – the molecule loses water “DEHYDRATION” Loose bonds of remaining molecules join “SYNTHESIS” of starch
- 8. Chapter 3 8 Splitting Polymers Apart Opposite of condensation "Splitting (lysis) with water (hydro-)" Molecule broken in two Water is split (“HYDROLYSIS”) –H+ goes to one; –OH- goes to other Digestion
- 9. Chapter 3 9 Dehydration / Hydrolysis Dehydration Synthesis Hydrolysis
- 10. 1. Carbohydrates Chapter 3 10 Monosaccharides “Mono-” means “one” Simple sugars — glucose, fructose HOCH2 H Usually with 5 or 6 carbons O H H • 5-carbon sugars are pentoses HO OH • 6-carbon sugars are hexoses • etc. CH OH HO H 2 Deoxyribose Soluble in water HO O OH H Taste sweet H OH H H Galactose H HO
- 11. 1. Carbohydrates Chapter 3 11 Oligosaccharides “Oligo-” means “few” Few monosaccharides joined together Sucrose is disaccharide of glucose & fructose Often combined with other molecules Sometimes used for cell I.D. CH2OH CH2OH HOCH2 H HOCH2 O H O H OH H OH H + H HO H H HO OH H CH2OH OH H O HO OH HO HO CH2OH H HO HO H H HO HOH HO H Glucose + Fructose Sucrose & Water
- 12. 1. Carbohydrates Chapter 3 12 Plant Starch (Amylose) Actually forms CH2OH CH H OH CH 2O O 2 O O CH a spiral O O OH 2 OH H2 O OH C O OH O O OH OH 2 OH Glucose OH O OH O O CH CH2OH CH2OH CH2OH CH2OH CH2OH O O O O O O O O O O OH OH OH OH OH Polymerization of glucose to form starch
- 13. 1. Carbohydrates Chapter 3 13 Starch CH2OH CH2OH CH2OH O O O O O OH OH OH CH2OH CH2OH CH2OH CH2 O O O O O O O O OH OH OH OH
- 14. Cellulose Chapter 3 14 CH2OH HO CH2OH HO CH2OH O O O O O O O O O O OH CH2OH OH CH2OH OH CH2OH HO CH2OH HO CH2OH O O O O O O O O O O OH CH2OH OH CH2OH OH CH2OH HO CH2OH HO CH2OH O O O O O O O O O O OH CH2OH OH CH2OH OH
- 15. 1. Carbohydrates Chapter 3 15 Cellulose Structure & Function
- 16. 1. Carbohydrates Chapter 3 16 Chitin Like cellulose, but with nitrogen Arthropods’ exoskeletons, fungal cell walls Strong, very resistant to digestion CH3 CH3 O C O C CH2OH N H CH2OH N H CH2OH O O O O O O O O O O N H CH2OH N H CH2OH N H O C O C O C CH3 CH3 CH3
- 17. 1. Carbohydrates Chapter 3 17 Chitin
- 18. Lipids - 2ndof 4 Classes Chapter 3 18 of Organic Compounds Slippery-oils Nonpolar; mostly C & H, little bit of O Heterogeneous group • Other classes more homogeneous • Unified by insolubility in water Fatty-acid types: Oils & waxes Nonfatty-acid types: steroids
- 19. 2. Lipids Chapter 3 19 Fat Molecules Triglycerides from beef, vegetable oils Three fatty acids and a glycerol • Glycerol has 3 carbons • Each with an –OH group Each fatty acid has a COOH These condense to form triglyceride and H2O
- 20. 2. Lipids Chapter 3 20 Fatty Acids Determines properties of fat Hydrocarbon chain with a COOH Most fats = 3 FAs + glycerol • Glycerol: 3-carbon alcohol • 3 OHs attract the COOH of FAs
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- 22. Triglyceride Chapter 3 22 (Fat) Formation Triglyceride H H H H H H Glycerol HC C CH HC C CH OH OH OH O O O Remove C O C O C O OH OH OH These C O C O C O HC H C O HC H C O HC H C O Waters HC H HC H HC H HC H HC H HC H HC H HC H HC H HC H HC H HC H HC H HC H HC H HC H HC H HC H Add 3 HC H HC H HC H H HC H H HC H H HC H Fatty H H H H H H HOH HOH HOH Acids 3 Waters
- 23. 2. Lipids Chapter 3 23 Fatty Acid Types Saturated - No C=C double bonds animal fat, solid @ room temp, “bad” fats Unsaturated - One or more C=C double bonds plants & fish, liquids oils, “good” fats
- 24. 2. Lipids Chapter 3 24 Phospholipids Phospholipids - mostly in cell membranes 1 glycerol, 2 FAs, & 1 polar phosphate group • Like a triglyceride... • 1 FA swapped for polar, phosphate group Soap-like properties Likes to get between polar and nonpolar materials
- 25. 2. Lipids Chapter 3 25 Phospholipids Polar Glycerol Fatty Acid Tails Head Hydrophilic Hydrophobic
- 26. 2. Lipids Chapter 3 26 Steroids Complex ring forms Some hormones Cholesterol • Natural substance • Found in membranes • Gives membranes natural flexibility
- 27. 2. Lipids Chapter 3 27 Steroids Cholesterol Estradiol Testosterone
- 28. Proteins - 3rdof 4 Classes Chapter 3 28 of Organic Compounds Proteins are amino acid polymers Many roles in the cell… • Enzymes • Hormones • Structure (muscle, hair, nails)
- 29. 3. Proteins Chapter 3 29 Amino Acids Small molecules — 20 kinds • 1 amino group • 1 carboxyl group • 1 "R" group Joined by peptide bonds to form polypeptide Different sequence makes different protein
- 30. Generic Amino Chapter 3 30 Acid: 20 Different “R” Groups Amine Carboxylic Acid Group Group R “Alpha” The “R” Group Carbon Placeholder
- 31. Amino Acids: Chapter 3 31 Glutamic Acid Structure Amine Carboxylic Acid Group Group “Alpha” Carbon Glutamic Acid “R” Group
- 32. 3. Proteins Chapter 3 32 Amino Acids: Leucine Structure Amine Carboxylic Acid Group Group Leucine “R” Group
- 33. 3. Proteins Chapter 3 33 Amino Acids: Cysteine Structure Amine Carboxylic Acid Group Group Cysteine “R” Group
- 34. 3. Proteins Chapter 3 34 Structural Proteins Horn Hair Spiderweb
- 35. 3. Proteins Chapter 3 35 Peptide Bond Formation Phenylalanine Leucine By Condensation between COOH & NH2
- 36. Peptide Bond: Chapter 3 36 Phenylalanine-Leucine Dipeptide The Peptide Bond Water
- 37. 3. Proteins Chapter 3 37 Levels of Protein Structure Like describing a knot by starting with the strands of the rope • Primary: The amino acid sequence • Secondary: Coiling or folding • Tertiary: folding, kinking, twisting entire structure • Quaternary: Two or more chains together
- 38. Illustration of Chapter 3 38 Protein Structure Primary Tertiary (Sequence) (Bending) Quaternary (Layering) Secondary (Coiling)
- 39. 3. Proteins Chapter 3 39 Pleated Sheets Hydrogen “Right-side up” AAs Bonds “Flipped” AAs
- 40. Nucleic Acids: 4thClass Chapter 3 40 of Organic Compound Nucleic acids are nucleotide polymers Genetics & cell control DNA: Genes RNA: Manages protein synthesis
- 41. 4. Nucleic Acids Chapter 3 41 Nucleotides 5-carbon sugar, a PO3, and a nitrogenous base Not only serve to make RNA & DNA Some are energy carriers (ATP, NAD) Some are chemical messengers (cAMP)
- 42. 4. Nucleic Acids Chapter 3 42 Nucleotide Structure: 3 Parts NH 2 Phosphate Group N C C OH N HC N C CH HO P O CH2 O N O Deoxyribose Nitrogenous H or H Base (1 of 5) H Ribose H OH H Pentose Sugar
- 43. 4. Nucleic Acids Chapter 3 43 Nucleic Acid Molecule Nucleotides can be joined together into a chain Result is a nucleic acid Nucleotide polymer DNA, RNA Connected by “sugar- phosphate” backbone
- 44. Cyclic AMP: Chapter 3 44 (Adenosine Monophosphate) NH2 Used for intracellular N C C N communication HC N C CH O CH2 O N Ribose H H H H O P O OH OH
- 45. 4. Nucleic Acids Chapter 3 45 ATP: (Adenosine Triphosphate) Used for energy transfer NH2 from one molecule to another N C C OH OH OH N HC N C CH HO P O P O P O CH2 O N Deoxyribose O O O H or H H Ribose H OH H
- 46. 4. Nucleic Acids Chapter 3 46 Coenzyme Structure NH2 N C C OH N HC N C CH HO P O CH2 O N Deoxyribose O H or H H Ribose H OH H
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Editor's Notes
- #5 1. Hydrogen “group”: In: Almost all biochemicals Polar/nonpolar 2. Hydroxyl group: Polar Sugars
- #6 1. Carboxyl group: In: Fats & Oils, amino acids Polar, and conveys acidity 2. Amine group: Polar, and conveys alkalinity (base) Amino acids, which form proteins
- #7 1. Phosphate Group: Polar, and conveys acidity Membranes; high energy bonds for energy storage (ATP); DNA & RNA. 2. Methyl group: In: Waxes, Fats & Oils Nonpolar and hydrophobic (hates water)
- #8 Condensation Reactions: Most of the reactions that combine smaller molecules to make larger molecules are of this general type. Enzymes detach a hydrogen from one of the molecules and a hydroxyl from the other and then join the two broken bonds together. The -H + from one combines with the -OH - from another. Forms water (therefore the source of the term "condensation"). Loose bonds of remaining molecules join. Example-synthesis of starch from glucose units (p39).
- #9 Condensation reactions are so called because a water molecule is a byproduct of the joining reaction of two other molecules. Sucrose C 12 H 22 O 11 is a disaccharide produced by the condensation of glucose C 6 H 12 O 6 and fructose C 6 H 12 O 6 Note that the formula for sucrose has one less oxygen and two less hydrogens than you get by adding up the numbers for glucose and fructose These missing atoms are combined to form water
- #11 Monosaccharides are simple sugars. Glucose (blood sugar or corn sugar). Fructose (fruit sugar). Usually with 5 or six carbons. 3-carbon sugars are trioses. 5-carbon sugars are pentoses. 6-carbon sugars are hexoses; etc. Soluble in water. Taste sweet.
- #12 Oligosaccharides (“oligo-” means few or scant). Several monosaccharides joined together. Sucrose (table sugar) is disaccharide of one glucose and one fructose (Fig 3-1, p39). Often combined with other molecules. Many larger molecules have oligosaccharides attached for various purposes. Sometimes used for cell ID. The cell membrane has many proteins in it, some of which have attached oligosaccharides projecting away from the cell. Sometimes these are used as chemical labels for cell type.
- #13 Plant starch comes in many forms, but most are straight-chain (unbranched) polymers of glucose. The CH 2 OH groups bump into each other forcing the chain into a spiral.
- #15 Note that the bonds connecting the glucoses in cellulose are alternating up and down, unlike in starch. The chains are crosslinked with hydrogen bonds.
- #17 The hard outer covering of arthropods, like beetles, is composed mostly of chitin. It is very resistant to degradation and digestion. Only a few animals can digest chitin, among them, some insectivorous birds.
- #19 Lipids-The second of four major classes of biochemical compounds. Nonpolar molecules of mostly Carbon & Hydrogen. Heterogeneous group. This means varied and diversified. The other three classes of biochemical compounds (carbos, proteins and nucleic acids) are structurally and chemically homogeneous (all based on the same chemical family within the class). But lipids are characterized by properties not related to structure or chemical family. Lipids are classed together on the basis of being mostly nonpolar hydrocarbons. Two broad chemical classes of lipids. Fatty-acid types: Oils & waxes. Nonfatty-acid types: steroids.
- #20 The so-called ”true fats" are "triglycerides." Found in beef fat, lard, and vegetable oils. Also makes up beer bellies. Contain three fatty acid molecules attached to a glycerol molecule. Glycerol is a 3-carbon alcohol with 3 -OH groups( Fig 2.21b p32). Each fatty acid is a long chain hydrocarbon with a COOH (carboxylic acid group) on one end (Fig 2.21a p32). Each acid group condenses with one -OH group to form triglyceride and 3H 2 O (Fig. 2.21b p29).
- #21 Long hydrocarbon chain with COOH at one end. Combine with glycerol to make most fats & oils. Glycerol is a three-carbon alcohol with a —OH on each carbon. These —OH groups will readily combine with the acidic —COOH group on the end of a fatty acid. "Saturated" - No carbon=carbon double bonds. No double bonds between carbons in the fatty acid like in stearic acid (Fig 2.21a, p32). These fatty acids are mostly from animal sources. "Unsaturated" - One or more carbon=carbon double bonds like oleic and linoleic acids (Fig 2.21a, p32). These fatty acids are often from plant sources, especially if polyunsaturated (two or more double bonds, like linoleic acid).
- #23 This shows how water is removed from three fatty acids and glycerol to make a fat and water.
- #25 One glycerol, 2 fatty acids, & 1 polar group. This is much like a triglyceride Except that one of the three fatty acids of the triglyceride has been taken off and swapped for some sort of "polar group" containing phosphate (Fig 2.23a, p33). Soapy properties Soap gets its properties from having a polar region and a nonpolar region in the same molecule. The polar group of a phospholipid likes water, but the two fatty acids on the same molecule hate water. Phospholipids like to get in between polar and nonpolar materials. Biological membranes. The cell membrane and other structures in the cell are covered with a double layer of phospholipid molecules. The fatty acids in each layer face each other on the inside of the double layer (p42). The polar groups face outward toward the water.
- #27 Complex ring forms Some hormones, especially those produced by the adrenal gland and sex hormones. Cholesterol Natural substance; not necessarily bad for you. Found in membranes in between the fatty acid tails of phospholipids. Athletes beware of androgenics ! Dangerous chemicals. Please reconsider your value system if you use these. If you use them, you WILL regret it!
- #29 Composed of many amino acid units. A polymer of amino acids. "Polymer" is a generic term for a large molecule consisting of many repeating units connected together. Other examples of polymers are cellulose and starch, both of which are glucose polymers. Many roles in cell. Enzymes. Biological catalysts that control all the biochemical reactions in metabolism. Hormones. Chemicals that are released into the blood by one cell and are designed to influence another cell some distance away. Structure. The framework of many subcellular structures are based on a protein grid work.
- #30 Small molecules-20 kinds of amino acids in proteins. 1 amino group (NH 2 ). 1 carboxyl group (COOH). 1 "R" group (Fig 2.24, p34). The “R” stands for radicle. It’s a place holder for a fragment of the molecule. This is essentially the only part of an amino acid that varies from to another of the twenty types of amino acids. So, there are twenty different “R” groups that distinguish the twenty amino acids. Joined together by special linkage called "peptide bonds" to form a polypeptide. Different sequences of amino acids make different proteins with different characteristics.
- #31 See p 34
- #32 See p 34
- #36 Here we position two amino acids close together so that the amine group of one is close to the carboxyl group of the other. Note that a -H is hanging out from one, and a -OH from the other. These will be broken off (by an enzyme) to form water. The remaining bonds of the two amino acids will be connected to form a dipeptide (two amino acids joined by a peptide linkage).
- #38 This is just a way of classifying what we know about the structure of proteins. Primary: The amino acid sequence. This is simply a list of the actual sequence of amino acids in the "backbone" of the protein. You just start at one end and read off the names of the amino acids in sequence and you have described the primary sequence. See Fig 2.26 on p 35 Secondary: Coiling of the chain. The "R" groups get in each other's way and force a twisting of the chain into a coil. See Fig 2.26 on p 35 Tertiary: Coiling of the coil. Like if you were to take a screen door spring and tie it in a super knot. See Fig 2.27a on p 36. Both the secondary and tertiary structure are affected by the primary structure. Changing only one of the amino acids for another may radically affect the tertiary structure and therefore the properties of the protein. Quaternary: Two or more chains together. Not all proteins have this level. It only applies to proteins composed of two or more separate polypeptides glued together. It refers to how the individual polypeptides are attached. See Fig 2.27b on p 36.
- #39 Depending on the sequence of amino acids, the polypeptide chain can either form a spiral like the tube on the left, or a pleated sheet like on the right. Some proteins have a spiral section followed by a sheet section, etc. Fig 2.26, p35.
- #41 Nucleotide polymers. Nucleotide subunits connected end to end. Genetics & cell control. Sequence of nucleotides determines genetic information. Also determines the nature of proteins produced when gene is expressed. DNA: Genes. RNA: Manages synthesis. DNA contains genetic information. RNA carries out instructions in genes.
- #42 Consist of 5-carbon sugar, a PO 3 , and a nitrogenous base. The sugar is usually either ribose or deoxyribose;. The nitrogenous base (containing nitrogen) is adenine, cytosine, thymine, guanine, or uracil. Nucleotides not only serve to make RNA & DNA. Some are energy carriers (ATP, NAD) NAD carries high energy electrons from one place to another. ATP provides the energy necessary to get two reluctant molecules to react. Some are chemical messengers (cAMP)
- #43 This is a model of the molecule described on the previous slide. See p37.
- #44 These nucleotides have joined together to form a nulceic acid chain. The zig-zag phosphate-sugar-phosphate is called the backbone of the molecule. The nitrogenous bases hang out to the side. Note the hydrogen bonding sites on the bases. These will be used to pair this chain up beside another.
- #45 This is a model of the molecule described on the previous slide. See p37.
- #46 This is a model of the molecule described on the previous slide. See p37.
- #47 This is a model of the molecule described on the previous slide. See p37.