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The Molecules of Life BIO100 Biology Concepts Fall 2007.

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1 The Molecules of Life BIO100 Biology Concepts Fall 2007

2 Biology includes the study of life at many levels TRACING LIFE DOWN TO THE CHEMICAL LEVEL In order to understand life, we will start at the macroscopic level, the ecosystem, and work our way down to the microscopic level of cells Cells consist of enormous numbers of chemicals that give the cell the properties we recognize as life

3 Figure 2.1 Ecosystem African savanna Community All organisms in savanna Population Herd of zebras Organism Zebra Organ system Circulatory system Organ Heart Cell Heart muscle cell Tissue Heart muscle tissue Molecule DNA Atom Oxygen atom

4 Ecosystem Community Population ex. all humans in city, all termites in class Individual Organism Organ Systems ex. respiratory, reproductive, circulatory Organs ex. lungs, ovaries, heart Tissue ex. connective, nervous, muscular Cells ex. neuron, sarcomere, epithelial Organelles ex, nucleus, chloroplast, mitochondria Macromolecules ex. DNA, RNA, cellulose, lipids

5 Take any biological system apart and you eventually end up at the chemical level. SOME BASIC CHEMISTRY Cells ex. Prokaryotic, Eukaryotic Macromolecules ex. DNA, RNA, fat Molecules ex. H 2 O, HCl, H 2 SO 4, Atoms ex. C, H, O, N, Iodine C=carbon Subatomic particles: within nucleus (neutron & proton) around nucleus (electrons)

6 Matter is anything that occupies space and has mass Matter: Elements and Compounds Matter is found on the Earth in “3” physical states.  Solid  Liquid  Gas

7 Matter is composed of chemical elements.  Elements are substances that cannot be broken down into other substances  There are 92 naturally occurring elements on Earth

8 All the elements are listed in the periodic table. Atomic number Element symbol Mass number Figure 2.2

9 Twenty-five elements are essential to life.  Four of these make up about 96% of the weight of the human body H,O,N,C  Trace elements occur in smaller amounts Figure 2.3

10 Elements differ in the number of subatomic particles in their atoms  The number of protons, the atomic number, determines which element it is  An atom’s mass number is the sum of the number of protons and neutrons  Mass is a measure of the amount of matter in an object; protons and neutrons each have an atomic mass unit of 1

11 The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties Water’s Life-Supporting Properties  Water’s cohesive nature  Water’s ability to moderate temperature  Floating ice D=M/V, see p. 30  Versatility of water as a solvent.

12 The polarity of water results in weak electrical attractions between neighboring water molecules. These interactions are called hydrogen bonds and result in cohesion which accounts for surface tension (b) ()() Hydrogen bond ()() ()() ()() ()() ()() ()() ()() Figure 2.11b

13 Water molecules stick together as a result of hydrogen bonding The Cohesion of Water  This is called cohesion  Cohesion is vital for water transport in plants. Figure 2.12 Microscopic tubes

14 Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid  Hydrogen bonds give water an unusually high surface tension. Figure 2.13

15 Because of hydrogen bonding, water has a strong resistance to temperature change. How Water Moderates Temperature

16 Heat and temperature are related, but different  Heat is the amount of energy associated with the movement of the atoms and molecules in a body of matter  Temperature measures the intensity of heat Water can absorb and store large amounts of heat while only changing a few degrees in temperature.

17 When water molecules get cold, they move apart, forming ice The Biological Significance of Ice Floating  A chunk of ice has fewer molecules than an equal volume of liquid water, p. 30

18 The density of ice is lower than liquid water  This is why ice floats Figure 2.15 Hydrogen bond Liquid water Hydrogen bonds constantly break and re-form Ice Stable hydrogen bonds

19 Since ice floats, ponds, lakes, and even the oceans do not freeze solid  Marine life could not survive if bodies of water froze solid

20 A solution is a liquid consisting of two or more substances evenly mixed Water as the Solvent of Life  The dissolving agent is called the solvent, p. 30  The dissolved substance is called the solute Figure 2.16 Ion in solution Salt crystal

21 When water is the solvent, the result is called an aqueous solution. Water is a very common solvent.

22 Jesus Lizard (Basiliscus basiliscus) izard.shtml izard.shtml

23 Acid Acids, Bases, and pH  A chemical compound that donates H + ions to solutions. Acids are strong if pH near 1 and weak if pH near to 7. ex. HCl, H 2 SO 4 Base  A compound that accepts H + ions and removes them from solution. Strong bases have pH near 14, weak ones near 7.

24 Basic solution Neutral solution Acidic solution Oven cleaner Household bleach Household ammonia Milk of magnesia Seawater Human blood Pure water Urine Tomato juice Grapefruit juice Lemon juice; gastric juice pH scale To describe the acidity of a solution, we use the pH scale Figure 2.17

25 Buffers are substances that resist pH change  They accept H + ions when they are in excess  They donate H + ions when they are depleted Buffering is not foolproof  Example: acid precipitation. Figure 2.18

26 Macromolecules are large organic molecules. Macromolecules are large organic molecules. Most macromolecules are polymers Most macromolecules are polymers PolymerLarge molecules containing many repeating subunits covalently linked together. Polymer : Large molecules containing many repeating subunits covalently linked together. Monomer: Subunits (building blocks) of a polymer. Monomer : Subunits (building blocks) of a polymer. FYI:Poly = many, Di = two, Mono = one, meros = parts Mono = one, meros = parts Polymers(macromolecules) Polymers (macromolecules)

27 Construction (anabolic): joining subunits is via condensation (dehydration) reactions. Construction (anabolic): joining subunits is via condensation (dehydration) reactions. Deconstruction (catabolic): breaking subunits from each other is via hydrolysis reactions. Deconstruction (catabolic): breaking subunits from each other is via hydrolysis reactions. Construction & Deconstruction of Polymers

28 CONDENSATION REACTION (dehydration reaction) : Polymerization reaction that links monomers together via covalent bonding. CONDENSATION REACTION (dehydration reaction) : Polymerization reaction that links monomers together via covalent bonding. The chemical mechanism cells use for making polymers is similar for all macromolecules. The chemical mechanism cells use for making polymers is similar for all macromolecules.  One monomer provides a hydroxyl group and the other provides a hydrogen and together these form water.  Requires energy and is aided by enzymes. 4

29 Hydrolysis reaction The chemical mechanism cells use for breaking polymers is similar for all macromolecules.The chemical mechanism cells use for breaking polymers is similar for all macromolecules. The reaction that splits monomers in a polymer.Hydrolysis : The reaction that splits monomers in a polymer. Hydrolysis reactions dominate the digestive process, guided by specific enzymes. Hydrolysis reactions dominate the digestive process, guided by specific enzymes. 4

30 Polymers(macromolecules) Polymers (macromolecules) There are four categories of macromolecules: Carbohydrates Lipids Lipids Proteins Proteins Nucleic Acids Nucleic Acids

31 Organic molecules made up of sugars and their polymers (serve as fuel and a carbon source) Organic molecules made up of sugars and their polymers (serve as fuel and a carbon source). Monomers are simple sugars called monosaccharides. Monomers are simple sugars called monosaccharides. Also known as simple carbohydrates. Examples: fructose, glucose, galactose Examples: fructose, glucose, galactose Sugar Polymers are joined together by condensation reactions. Sugar Polymers are joined together by condensation reactions. Also known as complex carbohydrates. Examples: starches and fibers Carbohydrates Carbohydrates are classified based on the number and type of simple sugars they contain

32 Monosaccharidesimple sugar in which C,H,O ratio is 1:2:1 (CH 2 O). Monosaccharide: simple sugar in which C,H,O ratio is 1:2:1 (CH 2 O).  Example: Glucose is  Example: Glucose is C 6 H 12 O 6  Usually end in -ose Simple sugars are the main nutrients for cells. Simple sugars are the main nutrients for cells.  Glucose is the most common. Monosaccharides also function as the raw material (skeleton) for the synthesis of other monomers, including those of amino acids and fatty acids Monosaccharides also function as the raw material (skeleton) for the synthesis of other monomers, including those of amino acids and fatty acids Monosaccharides (Simple Sugars)

33 Disaccharide : a double sugar consisting of 2 monosaccharides joined by a glycosidiclinkage Disaccharide : a double sugar consisting of 2 monosaccharides joined by a glycosidic linkage. Glycosidic Linkage : Covalent bond formed by a condensation reaction between 2 monomers. Glycosidic Linkage : Covalent bond formed by a condensation reaction between 2 monomers. Disaccharides

34 Polysaccharides : macromolecules that are polymers of monosaccharides Polysaccharides : macromolecules that are polymers of monosaccharides. Formed by condensation reactions (mediated by enzymes) between lots of monomers. Formed by condensation reactions (mediated by enzymes) between lots of monomers. Polysaccharides Two very important biological functions Two very important biological functions: Energy Storage(starch and glycogen) Energy Storage (starch and glycogen) Structural Support(cellulose and chitin) Structural Support (cellulose and chitin)

35 Monomers are joined by an α 1-4 linkage between the glucose molecules. Monomers are joined by an α 1-4 linkage between the glucose molecules. Starch Starch : a glucose polysaccharide in plants. 1 4

36 Plants store starch within plastids, including chloroplasts. Plants store starch within plastids, including chloroplasts. Plants can store surplus glucose in starch and withdraw it when needed for energy or carbon. Plants can store surplus glucose in starch and withdraw it when needed for energy or carbon. Animals that feed on plants can also access this starch and break it down into glucose. Animals that feed on plants can also access this starch and break it down into glucose. Starch

37 Highly branched with α 1-4 and α 1-6 linkages between the glucose molecules. Highly branched with α 1-4 and α 1-6 linkages between the glucose molecules. ~1 day supply stored in muscle and liver cells. ~1 day supply stored in muscle and liver cells. Glycogen Glycogen : a glucose polysaccharide in animals.

38 Cellulose is a major component of the tough wall of plant cells. Cellulose is a major component of the tough wall of plant cells. Cellulose alpha 1-4 linkages between glucose that forms helical structures: starch alpha 1-4 linkages between glucose that forms helical structures: starch beta 1-4 linkages between glucose forms straight structures: cellulose beta 1-4 linkages between glucose forms straight structures: cellulose This allows hydrogen bonding between strands. This allows hydrogen bonding between strands.

39 Cellulose Cellulose : a glucose polysaccharide in plants. β -glucose α -glucose Cellulose is biologically inactive in humans. We don’t have the enzymes to break it down (Fiber).

40  Polymers and Monomers  Construction (dehydration synthesis) and deconstruction (hydrolysis)  Carbohydrates  Monosaccharides: define  Disaccharides: define  Polysaccharides: define  Starch  Glycogen  Cellulose Summary

41 Lipids : Macromolecules that are insoluble in water (hydrophobic). Lipids : Macromolecules that are insoluble in water (hydrophobic).  Because their structures are dominated by nonpolar covalent bonds. Lipids Three important groups of lipids : Fats (energy storage molecules) Phospholipids (cell membranes) Steroids (Hormones)

42 Fat : a macromolecule composed of glycerol (notice –ol) linked to a fatty acid Fat : a macromolecule composed of glycerol (notice –ol) linked to a fatty acid Fatty Acid : a carboxyl group attached to a long carbon skeleton, often 16 to 18 carbons long Fatty Acid : a carboxyl group attached to a long carbon skeleton, often 16 to 18 carbons long. Fats Glycerol’s 3 OH groups can each bond to a fatty acid Glycerol’s 3 OH groups can each bond to a fatty acid.

43 Triacylglycerol : A fat composed of 3 fatty acids bonded to 1 (one) glycerol. Triacylglycerol (Triglyceride) Glycerol Fatty Acids

44 Fats: A triglyceride Glycerol Fatty Acid

45 Fats are water insoluble (why?) Fats are water insoluble (why?) Fatty acids may vary in length (number of carbons) and in the number and locations of double bonds. Fatty acids may vary in length (number of carbons) and in the number and locations of double bonds. Characteristics of Fats Two main types of fats : Saturated (all C bonds taken by H) Saturated (all C bonds taken by H) Unsaturated (not all C bonds taken by H) Unsaturated (not all C bonds taken by H) H - C – C - H H C = C H H H H (C 2 H 6 ) (C 2 H 4 ) (Saturated) (Unsaturated)

46  NO double bonds between carbons  Maximum (saturated) number of hydrogens  Solid at room temp.  Mostly animal fats  Straight chains Saturated Fats

47  One or more double bonds between carbons  Liquid at room temperature temperature  Mostly plant fats fats  Tail “kinked” at double at double bond bond Unsaturated Fats

48 Long term fuel storage Long term fuel storage in adipose (fat) cells in adipose (fat) cells (more energy than carbos) (more energy than carbos) Cushion for vital organs Cushion for vital organs Insulation against Insulation against heat loss heat loss (whale blubber) (whale blubber) Function of Fats Adipose cells Blue whale

49 Most complex molecules known to exist Most complex molecules known to exist 100s of 1000s different kinds 100s of 1000s different kinds Variety of proteins: variety of life on earth. Variety of proteins: variety of life on earth. Polymers of amino acids (20 different kinds) Polymers of amino acids (20 different kinds) Roles (examples) Roles (examples) Proteins Structural Support (keratin)Structural Support (keratin) Storage of AA (albumin) Storage of AA (albumin) Transport (hemoglobin) Transport (hemoglobin) Signaling (insulin) Signaling (insulin) Stimuli (receptors)Stimuli (receptors) Movement (actin) Movement (actin) Immune (antibody) Immune (antibody) Enzyme (catalyst) Enzyme (catalyst)

50 Polypeptides : polymers of amino acids (monomers) arranged in a linear sequence and joined by peptide bonds Polypeptides : polymers of amino acids (monomers) arranged in a linear sequence and joined by peptide bonds Proteins : one or more polypeptide chains folded into specific conformations Proteins : one or more polypeptide chains folded into specific conformations Proteins

51 Amino Acids Amino Acids : Building blocks (monomers) of proteins. Amino Acids : Building blocks (monomers) of proteins.  A central carbon covalently attached to these groups: Hydrogen Hydrogen Carboxyl group Carboxyl group Amino group Amino group Variable “R” group Variable “R” group (20 different possibilities) (20 different possibilities)

52 Amino Acids

53 Peptide Bonds Amino acids are joined by covalent bonds: peptide bond formed by condensation reactionsAmino acids are joined by covalent bonds: peptide bond formed by condensation reactions

54 Protein Conformation Protein Conformation : 3D structure (shape) of a protein.Protein Conformation : 3D structure (shape) of a protein. Determined by the sequence of A.A.sDetermined by the sequence of A.A.s Determines protein functionDetermines protein function Formed by folding and coiling of the polypeptide chain (results from the different properties of amino acids)Formed by folding and coiling of the polypeptide chain (results from the different properties of amino acids)

55 Four Different Levels of Organization: Four Different Levels of Organization: Primary Primary Secondary Secondary Tertiary Tertiary Quarternary Quarternary Protein Conformation

56 Linear sequence of Amino Acids: Linear sequence of Amino Acids: Determined by genes (DNA sequence) Determined by genes (DNA sequence) Can be sequenced to determine the order of AAs Can be sequenced to determine the order of AAs Small changes can have large effects (sickle cell) Small changes can have large effects (sickle cell) Primary Structure

57 Formed by regular intervals of hydrogen bonds along the backbone. Formed by regular intervals of hydrogen bonds along the backbone. Coiling/Folding Coiling/Folding 2 structures: 2 structures:  Alpha Helix (coil)  Beta Sheet (fold) Secondary Structure

58 3-D shape 3-D shape Determined by “R” group interactions : Determined by “R” group interactions :  Hydrogen bonds  Ionic bonds  Hydrophobic interactions  Disulfide Bridges (strong covalent (strong covalent bonds) bonds) Tertiary Structure

59 Quarternary Structure Structures formed from two or more polypeptides Structures formed from two or more polypeptides Examples: Examples:  Collagen  Hemoglobin

60 Protein Conformation Summary

61 Polymers of nucleotides Polymers of nucleotides  Nucleotides are made from subunits Nitrogen base Nitrogen base Sugar Sugar Phosphate group Phosphate group Examples: Examples:  DNA  RNA  ATP Nucleic Acids

62 Deoxyribonucleic Acid (DNA) DNA is found in the nucleus of most cells and contains coded information (on genes) that programs all cell activity. DNA is found in the nucleus of most cells and contains coded information (on genes) that programs all cell activity. DNA is not directly involved in the day to day operations of the cell. DNA is not directly involved in the day to day operations of the cell. Proteins are responsible for implementing the instructions contained in DNA. Proteins are responsible for implementing the instructions contained in DNA. Contains the directions for its own replication. Contains the directions for its own replication. DNA passes an exact copy of itself to each subsequent generation of cells.DNA passes an exact copy of itself to each subsequent generation of cells. All cells in an organism contain the exact same set of instructions.All cells in an organism contain the exact same set of instructions.

63 Ribonucleic Acid (RNA) Involved in the actual synthesis of proteins encoded in DNA Involved in the actual synthesis of proteins encoded in DNA Three types : Three types : Messenger RNA (mRNA) Messenger RNA (mRNA) Carries encoded genetic messages (from DNA)Carries encoded genetic messages (from DNA) Transfer RNA (tRNA) Transfer RNA (tRNA) Transfers the Amino Acids to a forming protein Transfers the Amino Acids to a forming protein Ribosomal RNA (rRNA) Ribosomal RNA (rRNA) Involved in the actual synthesis of proteins (ribosome) Involved in the actual synthesis of proteins (ribosome)

64 Both molecules contain four of the five possible nucleotides (A,G,C, & T or U) linked together. Both molecules contain four of the five possible nucleotides (A,G,C, & T or U) linked together. RNA RNA  Single stranded  Contains Uracil rather than Thymine than Thymine  Unstable DNA DNA  Double stranded (helix  Double stranded (helix) Complimentary Nucletides pair up Nucletides pair up  A-T (2 H bonds)  C-G (3 H bonds)  Contains Thymine rather than Uracil rather than Uracil  Very stable Properties of RNA and DNA

65 Structure of Nucleic Acids

66 Nucleic Acids


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