3.0 Introduction

1. Molecules Are Important to Biology
1. Many Molecules Are Very Small
2. Other Molecules Are Very Large fig 3.1
1. Called macromolecules
2. Four general types

3.1 Molecules are the building blocks of life

1. The Chemistry of Carbon
1. Organic Molecules Contain Carbon
1. Four electrons needed to fill outer orbital
1. Has four equidistant binding sites
2. Forms single, double and triple bonds with itself

2. Chains are linked together in a biological framework
1. Forms straight or branched chains or closed rings
2. Hydrogen, oxygen, nitrogen or other atoms added to chains

3. Hydrocarbons are constructed of only carbon and hydrogen
1. Example: Propane
2. Make good fuels

2. Functional Groups
1. Groups of elements attached to carbon framework fig 3.2
1. Example: Hydroxyl group is –OH
2. Have definite chemical properties
3. Most chemical reactions involve transfer of these groups

3. Biological Macromolecules
1. Large complex assemblies
1. Structural or informational function
2. Many are polymers, repeating units bonded together

2. Four classes: Carbohydrates, lipids, proteins, nucleic acids fig 3.3

4. Building Macromolecules
1. Dehydration synthesis (reaction) fig 3.4a
1. Molecule of water removed as subunits are linked
2. Requires input of energy to assemble
3. Anabolic reactions build macromolecules from subunits
4. Catalysis carried out by enzymes

2. Hydrolysis reaction fig 3.4b
1. Molecule of water added as subunits are broken apart
2. Catabolic reactions disassemble molecules to subunits, energy released

1. Kinds of Carbohydrates tbl 3.1
1. Variety of Forms
1. Some function in energy storage others are structural
2. Some are small and simple others are long polymers

2. Sugars Are Simple Carbohydrates
1. Contain C, H, O in 1:2:1 ratio
1. C–H bonds release energy when broken

2. Monosaccharides
   1. Contain as few as three carbon atoms
   2. Empirical formula C₆H₁₂O₆ or (CH₂O)₆
   3. May exist in straight chains that form rings in solution in water
   4. Primary six carbon sugar is glucose fig 3.5

3. Disaccharides
1. Double sugars include sucrose
2. Composed of two monosaccharides joined by covalent bond
3. Important in transport of sugars

4. Polysaccharides
1. Macromolecules composed of monosaccharide subunits
2. Starch is used by plants to store energy
3. Cellulose is a plant structural molecule, links hard to break

3. Sugar Isomers fig 3.6
1. Have same empirical formula
2. Atoms are arranged differently
1. Glucose and fructose are structural isomers
2. Glucose and galactose are stereoisomers

2. Linking Sugars Together
1. Transport Disaccharides fig 3.7
1. Protects sugar from being metabolized during transport
2. Are made of two monosaccharides linked together
1. Maltose = glucose + glucose
2. Sucrose = glucose + fructose
3. Lactose = glucose + galactose

2. Storage Polysaccharides fig 3.8
1. Insoluble polymers called polysaccharides
2. Starches are polysaccharides made from glucose
3. Amylose is simplest form in plants
1. Carbon 1 of glucose bonds to carbon 4 of next glucose
2. Chains of maltose that coil in water

4. Pectins are branched polysaccharides in plants
   1. Called amylopectin when based on amylose
   2. Branches formed by cross-links, short chain length between branches
   3. Results in mesh of linked glucose units

5. Glycogen is branched form in animals
   1. Long chain length
   2. Great number of branches

3. Nonfattening Sweets
1. Most sugars are "right-handed" hydroxyl is on right side
2. "Left-handed sugars can be made artificially
1. Cannot be broken down by enzymes for right-handed sugars
2. Called levo- or l-sugars
3. Not digested by body, cannot contribute to tooth decay

3. Structural Carbohydrates
1. Cellulose fig 3.9
1. Orientation of glucose subunits
1. In starch units are all alpha form glucose
2. In cellulose units are beta form glucose

2. Structural polysaccharide is component of plant cell walls
1. Chemically similar to amylose
2. Different bonds connect subunits
3. Cannot be degraded by enzyme that breaks amylose beta-glucose bonds
4. Undigestible by most organisms, human dietary fiber
5. Degraded by certain bacteria and protists

2. Chitin
1. Structural modification produces chitin fig 3.10
1. Present in insects and fungi
2. Adds nitrogen group to glucose units

2. Few organisms can digest this compound

1. Fats
1. Long term energy storage molecules tbl 3.1
1. Ratio of H to O is higher than carbohydrates
2. Are lipids that are insoluble due to nonpolar nature
1. Cannot form hydrogen bonds like water can
2. Fat molecules cluster together and exclude water

3. Oils and waxes are other kinds of lipids
4. Triacylglycerol (triglyceride) = glycerol + three fatty acids fig 3.11
1. Fatty acids can be different from one another
2. Fat rich diet may contribute to heart disease

2. Fatty Acids
1. Hydrocarbon Chains of Fatty Acids Vary
1. Saturated fatty acids fig 3.12
1. Internal carbons have maximum hydrogens
2. Single bonds between carbons
3. Present in hard animal fats

2. Unsaturated fatty acids
1. Internal carbons have fewer hydrogens
2. Double bonds between many carbons
3. Present in liquid plant oils
4. Polyunsaturated fats have more than one double bond

2. Fats as Food
1. Efficient energy storage molecules
1. Many C–H bonds, saturated have more than unsaturated
2. 9 kcal per gram fat, 4 kcal per gram carbohydrate

2. Animal fats are generally saturated, plants are unsaturated
1. Oils can be artificially hydrogenated to produce solid fats
2. Natural unsaturated fats are healthier than highly hydrogenated fats
3. Both saturated fats and artificially hydrogenated fats are unhealthy

3. Conversion of consumed carbon molecules
1. Glucose available for immediate use
2. Disaccharides transported within organism
3. Starch and fat storage reserves

3. Other Kinds of Lipids fig 3.13
1. Phospholipids
1. Comprise membranes
2. Composed of polar head and nonpolar tail
3. Form lipid bilayers fig 3.14
1. Polar head region faces outward
2. Nonpolar tails face inward

4. Steroids composed of four carbon rings

2. Terpenes
1. Form various long-chain pigments
2. Examples: Chlorophyll, retinal, rubber

3. Prostaglandins
1. Are modified fatty acids
2. Composed of two nonpolar tails attached to ring
3. Variety of biological functions, local chemical messengers

1. The Many Functions of Proteins tbl 3.1
1. Diverse Functions tbl 3.2
1. Enzyme catalysis
1. Facilitate biological reactions
2. Globular , three-dimensional shape

2. Defense
1. Also globular in shape, recognize foreign cells
2. Include cell surface receptors

3. Transport
1. Globular proteins that transport small molecules and ions
2. Examples: Hemoglobin, myoglobin, transferrin

4. Support fig 3.15
   1. Fibrous proteins are structural
   2. Include keratin, fibrin, collagen
   3. Most abundant protein in vertebrates

5. Motion
1. Muscle contraction due to sliding of actin and myosin filaments
2. Contractile proteins in cytoskeleton within cell

6. Regulation
1. Hormones are intercellular messengers
2. Cell surface receptors receive information

2. Amino Acids Are the Building Blocks of Protein
1. Complex, Versatile Molecules
1. Polymers of only 20 amino acids
2. Among first biological molecules to evolve

2. Amino Acid Structure
1. Amino, carboxyl, hydrogen bonded to central carbon
2. Identity conferred by variable R group
3. Five classes
1. Nonpolar
2. Polar, uncharged
3. Ionizable
4. Aromatic
5. Special function

4. Amino acids are linked together by peptide bonds fig 3.16

3. Proteins Are Chains of Amino Acids
1. Proteins composed of one or more polypeptides
2. Polypeptides are long chains of amino acids
3. Each protein has a unique, defined amino acid sequence
4. 20 common amino acids with characteristic side groups fig 3.17

3. The Shape of Globular Proteins
1. Overview of Protein Structure
1. Proteins are amino acid chains folded up into complex shapes
2. Examine three dimensional structure with X-ray diffraction
1. Myoglobin first one examined
2. All internal amino acids are nonpolar
3. Hydrophobic interactions shove nonpolar molecules inside
4. Polar and charged amino acids usually on surface of protein

2. Levels of Protein Structure
1. Possess six structural levels fig 3.18
1. Primary, secondary, tertiary, quaternary, structures
2. Motifs and domains

2. Primary structure
1. Specific amino acid sequence determined by gene's nucleotide sequence
2. Permits great diversity of proteins

3. Secondary structure
1. Side groups, –COOH and –NH groups of main chain form hydrogen bonds
2. Two patterns of H bonding
1. 1) Linking of two amino acids along chain forms alpha helix
2. 2) Many parallel links across two chains forms beta pleated sheet

4. Motifs
1. Sometimes called supersecondary structure
2. beta-alpha-beta creates fold or crease
3. "Russman fold" is an alpha-beta-alpha-beta motif
4. beta-barrel is a beta sheet folded into a tube
5. alpha-turn-alpha binds to DNA double helix

5. Tertiary structure
1. Protein's final folded shape, positions motifs and side groups
2. Spontaneous, driven by hydrophobic interactions with water
3. Nonpolar chains in close proximity exhibit van der Waal's forces
4. Allow very close fitting of nonpolar chains in protein interior
5. Single amino acid change can significantly disrupt fit

6. Domains
1. Exon-encoded, structurally independent globular unit
2. Several domains connected by single polypeptide chain
3. Each domain may have different function

7. Quaternary structure
1. Combination of two or more polypeptide subunits
2. Composes functional unit of a protein
3. Change in one amino acid can have profound effect - sickle cell anemia

4. How Proteins Fold
1. Nonpolar Proteins Play Key Role in Protein Folding
1. Folding not simple hydrophobic interaction
2. Sticky interior portions exposed during intermediate stages

2. Chaperone Proteins
1. Special proteins that help new proteins fold correctly fig 3.19
1. Identified in E.coli bacteria
2. If disabled, 30% of proteins fail to fold properly

2. More than 17 kinds of proteins act as molecular chaperones
1. Include heat shock proteins
2. High temperatures cause protein to unfold, heat shock chaperones help refold

3. Controversy regarding how chaperones work
1. First thought to provide protected environment
2. Now thought that they rescue proteins in wrongly folded state

3. Protein Folding and Disease
1. Cystic fibrosis membrane transport protein
1. Protein moves ions across cell membranes
2. Sometimes amino acid sequence is correct, protein fails to fold

2. May cause Alzheimer's disease protein clumping in brain tissue

5. How Proteins Unfold
1. Denaturation
1. Protein shape altered with changes in pH, temperature, ion concentration
2. Protein becomes biologically inactive
3. Enzymes function only within a narrow environmental range

2. Small Proteins May Return to Natural Shape fig 3.20
1. Large proteins rarely refold naturally
2. Distinguish denaturation from dissociation fig 3.21
1. Subunits may dissociate without denaturing folded proteins
2. Can readily reassume subunit quaternary structure

1. Information Molecules tbl 3.1
1. Cellular Information Storage Devices, the Hereditary Material
1. Deoxyribonucleic acid = DNA, master molecule
2. Ribonucleic acid = RNA, template copy

2. "Seeing" DNA
1. To small to be resolved by optical or electron microscopes
2. Visualized using scanning-tunneling microscope fig 3.22
3. Other microscopes work by bouncing light or electrons off object
4. Scanning-tunneling microscope place a probe on surface
1. Like feeling object with a hand
2. Probe advances in steps smaller than diameter of an atom

2. The Structure of Nucleic Acids
1. Nucleotides Polymerize Forming Nucleic Acids
1. Chemical components fig 3.23
1. Five-carbon ribose or deoxyribose sugar
2. Phosphate group
3. Organic nitrogen-containing base

2. Phosphodiester bonds join sugars
3. Nitrogen base attached to sugar and protrudes from chain
4. Two kinds of organic bases fig 3.24
1. Purines: Adenine (A), guanine (G)
2. Pyrimidines: Cytosine (C), thymine (T) (in DNA), uracil (U) (in RNA)
3. Adenine also found in ATP, NAD and FAD fig 3.25

2. DNA
1. Sequential nucleotides store hereditary information
2. DNA forms double chains fig 3.26
1. Helix is a spiral staircase shape
2. Two intertwined DNA molecules form a double helix
3. Hydrogen bonds between bases hold chains together as duplex

3. Base pairing is specific and complementary
1. Adenine with thymine (in DNA) or uracil (in RNA)
2. Guanine with cytosine (in DNA and RNA)

3. RNA
1. Chemical differences between RNA and DNA
1. RNA contains ribose sugar with hydroxyl at carbons 2 and 3
2. Uracil base in RNA, thymine in DNA

2. Single stranded helix under most circumstances

4. Which Came First, DNA or RNA
1. DNA stores information for protein synthesis
1. RNA is working copy of DNA master information
2. DNA protected by not being actively used to make protein

2. DNA evolved from RNA to protect the genetic information
3. Flow of genetic information: DNA ® RNA ® protein