Chapter 3. Biological Molecules Great and Small

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1 Chapter 3 Biological Molecules Great and Small Chapter Goal: Understanding how cells use small building blocks to build larger molecules and how some of those molecules then fold into 3-D shapes

2 Key Questions How do organisms use carbon atoms decorated with functional groups to build basic molecules of life? What are the categories of building block molecules? What reactions link and unlink building blocks? How are fatty acids, polysaccharides, nucleic acids and proteins formed?

3 Biological Molecules Size: either small (MW<300) or large (MW>10,000) Organic molecules based on hydrogen, carbon, nitrogen, oxygen, rarely phosphorus and sulfur Are built of subunits building blocks

4 Biological Molecules are Organic Compounds Common elements in living systems: C, H, O, N are the great majority atoms (96.3%) in living things. Important ions: Na, K, Mg, Ca, P, S, Cl, Trace ions and minerals: Zn, Cu, Mn, Fe, I, and others Element Symbol Percent of human body by weight Oxygen O Approximate percent of Earth s crust by weight Important Functions Necessary for cellular respiration, component of water Carbon C Backbone of organic molecules Hydrogen H Electron carrier, component of water and most organic molecules Nitrogen N 3.3 Trace Component of all proteins and nucleic acid Component of bones and teeth, trigger for many Calcium Ca cellular functions Phosphor Backbone of nucleic acids, important in energy P us transfer Principal positive ion in cells, important for nerve Potassium K function Sulfur S Component of most proteins Chlorine Cl Principal negative ion bathing cells Principal positive ion bathing cells, important in Sodium Na nerve function Magnesiu Critical component of many energy-transferring Mg

5 Subunits and Macromolecules Sugars Lipids Amino acids Nucleotides Polysaccharides Fats and cholesterol Proteins DNA and RNA

6 Carbon Carbon chains and rings are linked by single and double covalent bonds

7 Carbon Rings Carbon rings can be flat Carbon rings can be boat or chair

8 Chemical Interactions of Molecules Determined by: Shape Charge distribution Interactions with water Interactions with other molecules

9 Functional Groups Small groups of atoms Contribute to the chemical properties of a molecule Usually attached to the carbon backbone

10 Examples of Functional Groups -OH hydroxyl -C=O carbonyl -COOH carboxyl -NH 2 amine -SH sulfhydryl -PO 4 phosphate

11 Shapes of Biomolecules Lipids do not form chains of subunits Proteins, nucleic acids and carbohydrates can form long chains Carbohydrate chains may be branched

12 Linking Subunits to Make Macromolecules Macromolecule subunits are linked by removing water dehydration condensation

13 Breaking Macromolecules Subunits are broken apart by adding water to a bond hydrolysis

14 Macromolecules

15 Lipids Contain high levels of chemical energy Do not dissolve in water Have few polar functional groups Major component of biological membranes

16 The 6 Lipids Used in Cells

17 Fatty Acids Are amphipathic contain some polar groups Saturated (no double bonds) or unsaturated (some double bonds)

18 Health Effects Saturated fats increase cholesterol levels in the blood Unsaturated fats have less effect on cholesterol levels Omega-3 fatty acids (from fish and sea weed) inhibit inflammation response in blood vessels and joints

19

20 Forming Triglycerides Subunits Glycerol 3 fatty acids Linked by condensation reactions

21 Forming Phospholipids Subunits Glycerol 2 fatty acids Head with phosphate group Amphipathic Linked by condensation reactions

22 Phospholipids in Membranes Amphipathic structure causes formation of a bilayer Charged groups associate with water Hydrophobic tails clump together

23 Structure is 4 rings Steroids Based on cholesterol Functional groups determine biological activity

24 Carbohydrates Fundamental energy storage molecule Subunits are simple sugars 3 ~ 9 Carbons monosaccharides Ex. Glucose, fructose, ribose, deoxyribose Linked by dehydration condensation into disaccharide and polysaccharides glycosidic bond Disaccharide: sucrose (table sugar) Polysaccharide: starch, cellulose, glycogen,chitin

25 Formation of Polysaccharides 2 sugars link to form disaccharide Ex. sucrose Several sugars oligosaccharide Long chains of sugars polysaccharide Ex. Starch in bread Cellulose in wood and paper

26 Structure of Carbohydrates Chemical formula: (CH 2 O)n For each carbon: 1 oxygen 2 hydrogens Many hydroxyl groups make sugars hydrophilic Ribose and deoxyribose: building blocks for RNA and DNA

27 Carbohydrates and Energy Glucose (blood sugar) is the basis of most energy releasing reactions Short term energy mono- and disaccharides Long term energy storage glycogen in animals, starch in plants Sugar in coke (15 square sugars or 28g sugar/can)

28 Carbohydrates and Structure Glycogen Animal energy, branched Starch Plant energy, branched or unbranched Amyrose unbranched, amylopectin branched Cellulose Structural support for plant cells Glucose polysaccharide with bonds in straight orientation Chitin Exoskeleton of arthropods such as butterfly and crab Modified sugars in chains

29 Carbohydrates in Plants

30 Glycoproteins and Glycolipids Glycoproteins have short chains of sugars attached to proteins Glycolipids have short chains of sugars attached to lipids Both found on the exterior surface of cells Glycoproteins are signs that help cells to recognize one another and communicate, Glycoproteins attached to newly made proteins act as address labels to tell a cell where to ship new proteins

31 Polypeptides Protein: working molecules of a cell, carry out biological activities encoded by genes Classifications of Functions of Proteins: -Enzymes: catalysts that accelerate the rates of biological reactions. oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase -Regulatory proteins: sensors and switches, control protein activity and gene functions hormones, insulin, transcriptional factor, lac repressor -Transport proteins: control the flow of materials across cellular membrane. Mb & Hb (O 2 ), ion channel, serum albumin (FA: from adipose tissue to organs) -Storage proteins: as a reservoir of an essential nutrients. ovalbumin (egg white), casein ( 酪蛋白,milk), zeins (corn), ferritin (Fe 2+ ) -Motor proteins: cause motion, cell division, muscle contraction, cell motility. myosin, actin, tubulin, dynein/kinesin -Structural proteins: provide structural rigidity and protection to the cells and tissues. keratin, collagen, elastin, fibroin -Signaling proteins: transmit external signals to the cell interior. receptors, protein kinase/phosphatase, two component system -Protective or exploitive protein: play active role in cell defense, protection Ig (antibody), thrombin (blood-clotting protein), antifreeze protein, toxin

32 Polypeptides Structure Unbranched chains of amino acids Bend into unique shapes

33 Subunits of polypeptides 20 different types Structure: Amino group Carboxyl (acid) group R groups differ Amino Acids

34 Amino Acids

35 Formation of Polypeptides Linked by dehydration condensation Bonds are peptide bonds

36 Protein Shapes Globular irregular shapes, non-repeating amino acid sequence Hemoglobin Fibrous regular shapes, repeating sequences Keratin, collagen, elastin

37 Protein Structure 4 levels of folding Primary structure is sequence of amino acids

38 Protein Structure Secondary coils or folds of sections of protein Alpha helix Beta sheet Stabilized by hydrogen bonds Collagen helix: three polypeptide chains wound around each other

39 Protein Structure Tertiary 3-dimensional conformation of entire protein Stabilized by covalent, hydrogen and ionic bonds

40 Protein Structure Quaternary Multiple peptide chains fitted together to make 1 functional protein

41 Levels of Protein Folding

42 Protein Folding Some proteins fold spontaneously into their correct 3-dimensional shape Some proteins need chaperone proteins to fold correctly

43 Nucleic Acids Functions: Contain genetic information (DNA and RNA) Some nucleotides used for energy storage: ATP Some nucleotide used as signal transduction: camp, cgmp

44 Nucleic Acids Structure Subunits nucleotides 3 building blocks for each nucleotide: Sugar Phosphate Nitrogenous base

45 Nitrogenous Bases 2 types: Pyrimidines, single ring Purines, 2 rings Differ in functional groups attached to the rings

46 Sugars and Phosphates 5 carbon sugars Ribose in RNA (ribonucleic acid) Deoxyribose in DNA (deoxyribonucleic acid) Phosphate groups link nucleotides together: phosphodiester bond

47 Formation of Nucleic Acids Linked by dehydration condensation Bond is called a phosphodiester linkage

48 Nucleic Acid Structure

49 DNA Structure

50 Key Concepts 4 building blocks lipids, sugars, amino acids, nucleotides Functional groups determine chemistry Dehydration reactions link small molecules Protein shape is determined by R-groups

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