CARBON AND THE MOLECULAR DIVERSITY OF LIFE CHAPTER 4

ISOMERS FUNCTIONAL GROUPS Compounds with the same chemical formula but different structures FUNCTIONAL GROUPS See diagram of functional groups

Figure 4.6 Three types of isomers

Figure 4.6ax Structural isomers

Table 4.1 Functional Groups of Organic Compounds

Figure 4.8 A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones

Figure 4.8x1 Estrone and testosterone

THE STRUCTURE AND FUNCTION OF MACROMOLECULES CHAPTER 5

SYNTHESIS AND BREAKDOWN Dehydration synthesis (condensation reaction) – removal of water to join 2 compounds Hydrolysis – addition of water to break a bond between 2 compounds

Figure 5.2 The synthesis and breakdown of polymers

CARBOHYDRATES Monosaccharides Examples: glucose, fructose, and galactose One sugar Disaccharides Examples: Lactose, sucrose and maltose Two sugars Joined by glycosidic linkage via dehydration synthesis Polysaccharides Examples: starch, glycogen, and cellulose Many sugars

Figure 5.3 The structure and classification of some monosaccharides

Figure 5.4 Linear and ring forms of glucose

Figure 5.5 Examples of disaccharide synthesis

Figure 5.6 Storage polysaccharides

Figure 5.7a Starch and cellulose structures

Figure 5.7b,c Starch and cellulose structures

Figure 5.8 The arrangement of cellulose in plant cell walls

Figure 5.x1 Cellulose digestion: termite and Trichonympha

Figure 5.x2 Cellulose digestion: cow

Figure 5.9 Chitin, a structural polysaccharide: exoskeleton and surgical thread

LIPIDS Little or no affinity for water (hydrophobic) Examples: Fat, phospholipids, and steroids Fats – composed of glycerol (an alcohol) and fatty acids Saturated – no double bonds in carbon chain Unsaturated – at least one double bond in carbon chain

Figure 5.11 Examples of saturated and unsaturated fats and fatty acids

Figure 5.11x Saturated and unsaturated fats and fatty acids: butter and oil

Figure 5.12 The structure of a phospholipid

Figure 5.13 Two structures formed by self-assembly of phospholipids in aqueous environments   

Figure 5.10 The synthesis and structure of a fat, or triacylglycerol

Figure 5.14 Cholesterol, a steroid

Figure 5.14x Cholesterol    

Table 5.1 An Overview of Protein Functions

PROTEIN Polypeptide – polymer of amino acids There are 20 different amino acids differing only by the R group

Figure 5.15 The 20 amino acids of proteins: nonpolar

Figure 5.15 The 20 amino acids of proteins: polar and electrically charged

Figure 5.16 Making a polypeptide chain

FOUR LEVELS OF PROTEIN STRUCTURE Primary – sequences of amino acids Secondary – hydrogen bonds cause coils and folds Pleated sheet and alpha helix Tertiary – irregular contortions due to various weak bonds: Hydrophobic interactions Disulfide bridges Ionic bonds Van der Waals interactions Quaternary – two or more polypeptide chains aggregated into one functional macromolecule Examples: collagen and hemoglobin

Figure 5.18 The primary structure of a protein

Figure 5.19 A single amino acid substitution in a protein causes sickle-cell disease

Figure 5.19x Sickled cells

Figure 5.20 The secondary structure of a protein

Figure 5.22 Examples of interactions contributing to the tertiary structure of a protein

Figure 5.23 The quaternary structure of proteins

Figure 5.24 Review: the four levels of protein structure

Figure 5.25 Denaturation and renaturation of a protein

Figure 5.21 Spider silk: a structural protein

Figure 5.21x Silk drawn from the spinnerets at the rear of a spider

NUCLEIC ACIDS Examples: DNA and RNA We will discuss these in great detail later in the semester! 

Figure 5.29 The components of nucleic acids

Figure 5.30 The DNA double helix and its replication

AN INTRODUCTION TO METABOLISM CHAPTER 8

Figure 6.2 Transformations between kinetic and potential energy

Figure 6.2x1 Kinetic and potential energy: dam

Figure 6.2x2 Kinetic and potential energy: cheetah at rest and running

THERMODYNAMICS First Law of Thermodynamics – energy can be transferred and transformed, but not created nor destroyed Second Law of Thermodynamics – every energy transfer or transformation makes the universe more disordered (have more entropy)

Entropy – measure of disorder or randomness Most energy transformations involve at least some energy be changed to heat Heat is the lowest form of energy Biological order has increased over time Second law requires only that processes increase the entropy of the universe Organisms may decrease entropy but entire universe must increase entropy

Figure 6.4 Order as a characteristic of life

Free energy (G) – energy available to do work when temperature is uniform throughout system G = H – TS H = system’s total energy (enthalpy) T = temp in Kelvin (° C + 273) S = entropy

∆ G = G final state – G starting state ∆ G = ∆ H - T∆ S For a spontaneous reaction: ∆ G = negative So must: give up energy (decrease H) and/or give up order (increase S) ∆ G = 0 at equilibrium Free energy increases if move away from equilibrium and decreases if move toward equilibrium

Figure 6.5 The relationship of free energy to stability, work capacity, and spontaneous change

Exergonic ∆ G = negative Spontaneous Net release of energy Endergonic ∆ G = positive NOT spontaneous Stores free energy in molecules

Figure 6.6 Energy changes in exergonic and endergonic reactions

Cells at equilibrium are dead! Cells can keep disequilibrium by having products of one reaction not accumulate but instead become reactants of another reaction Energy coupling – an exergoinc reaction drives an endergoinc reaction

Figure 6.7 Disequilibrium and work in closed and open systems

ATP = ADENOSINE TRIPHOSPHATE ATP + H2O ADP + Pi ∆ G = -7.3kcal/mol ADP = adenosine diphosphate Normally the phosphate is bonded to an intermediate compound which is then considered phosphorylated The reverse reaction is endergonic and requires +7.3 kcal/mol to make ATP from ADP

Figure 6.8 The structure and hydrolysis of ATP

Figure 6.9 Energy coupling by phosphate transfer

Figure 6.10 The ATP cycle

ENZYMES Catalytic proteins or enzymes – change the rate of reaction without being consumed by the reaction Activation energy (EA) – energy needed to start a reaction Energy needed to contort the reactants so the bonds can change Enzymes lower activation energy by enabling reactants to absorb enough energy to reach transition state at moderate temps

Enzymes are substrate specific Substrate – the reactant on which an enzyme works Active site – area on enzyme where substrate fits Induced fit – model of enzyme activity

Figure 6.12 Energy profile of an exergonic reaction

Figure 6.14 The induced fit between an enzyme and its substrate

Figure 6.15 The catalytic cycle of an enzyme

Effects of pH and Temp Optimal temperatures and pH ranges exist for enzymes

Figure 6.16 Environmental factors affecting enzyme activity

Cofactors – non-protein helpers that bind to active site or substrate (zinc, iron) Coenzymes – cofactors that are organic (vitamins) Enzyme Inhibitors – reduce enzyme activity Competitive inhibitors – block substrate from entering active site Reversible Overcome by adding more substrate Noncompetitive inhibitors – bind to another part of enzyme thereby changing the enzyme’s shape making it inactive Irreversible Examples: DDT, sarin gas, and penicillin

Figure 6.17 Inhibition of enzyme activity

Allosteric regulation Allosteric sites – receptors on enzymes (not the active site) that may either inhibit or stimulate enzyme activity Feedback inhibition End product of a pathway acts as a inhibitor of an enzyme within the pathway Cooperativity – an enzyme with multiple subunits where binding to one active site causes shape changes to rest of subunits which in turn activates those subunits

Figure 6.18 Allosteric regulation of enzyme activity

Figure 6.19 Feedback inhibition

Figure 6.20 Cooperativity