SBI 4UY Biology Exam Review 1 PDF

SBI 4UY Exam Review 1 Biology Exam Review Exam Date: Tuesday, January 27, 2025 Unit 1: Biochemistry Macromolecules Carbohydrates -​ Carbohydrates include sugars and the polymers of sugars -​ The simplest carbohydrates are monosaccharides,...

SBI 4UY Exam Review 1 Biology Exam Review Exam Date: Tuesday, January 27, 2025 Unit 1: Biochemistry Macromolecules Carbohydrates -​ Carbohydrates include sugars and the polymers of sugars -​ The simplest carbohydrates are monosaccharides, or simple sugars -​ Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks -​ The ratio of elements in a monosaccharide is usually 1 C: 2 H: 1 O -​ Monosaccharides are classified by -​ The location of the carbonyl group (as aldose or ketose) -​ The number of carbons in the carbon skeleton -​ Sugars are linear when dry and form rings when aqueous -​ A disaccharide is formed when a dehydration reaction joins two monosaccharides -​ This covalent bond is called a glycosidic linkage -​ C6H12O6 + C6H12O6 → C12H22O11 + H2O -​ α-glucose + α-glucose → maltose + H2O -​ α-1,4 glycosidic linkage -​ α-glucose + galactose → lactose + H2O -​ β-1,4 glycosidic linkage -​ α-glucose + fructose → sucrose + H2O -​ α-1,2 glycosidic linkage -​ Polysaccharides, the polymers of sugars, have storage and structural roles -​ The architecture and function of a polysaccharide are determined by its sugar monomers and the positions of its glycosidic linkages -​ The polysaccharide cellulose is a major component of the tough wall of plant cells -​ Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ -​ The difference is based on two ring forms for glucose: alpha (α) and beta (β) -​ Starch (α configuration) is largely helical -​ α-1,4 glycosidic linkage -​ Cellulose molecules (β configuration) are straight and unbranched -​ β-1,4 glycosidic linkage  SBI 4UY Exam Review 2 -​ Starches: Amylose (unbranched), Amylopectin (Branched), Glycogen (Highly Branched) -​ Enzymes that digest starch by hydrolyzing α linkages can’t hydrolyze β linkages in cellulose -​ The cellulose in human food passes through the digestive tract as “insoluble fiber” Lipids -​ Not true polymers -​ Lipids consist mostly of hydrocarbon regions -​ The most biologically important lipids are fats, phospholipids, and steroids -​ Fats are constructed from two types of smaller molecules: glycerol and fatty acids -​ Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon -​ A fatty acid consists of a carboxyl group attached to a long carbon skeleton -​ Fat is nonpolar -​ three fatty acids are joined to glycerol by an ester linkage, creating a triglyceride -​ Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds -​ Unsaturated fatty acids have one or more double bonds -​ Saturated fats are solid at room temperature and unsaturated fats are liquid -​ Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen -​ Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds -​ These trans fats may contribute more than saturated fats to cardiovascular disease -​ In a phospholipid, two fatty acids and a phosphate group are attached to glycerol -​ The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head -​ When phospholipids are added to water, they self-assemble into double-layered sheets called bilayers -​ One tail is unsaturated and the other is saturated, increasing the fluidity of the membrane -​ Steroids are lipids characterized by a carbon skeleton consisting of four fused rings  SBI 4UY Exam Review 3 -​ Cholesterol, a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized -​ A high level of cholesterol in the blood may contribute to cardiovascular disease Proteins -​ Types of proteins: enzymatic, defensive, storage, transport, hormonal, receptor, motor and contractile, and structural -​ Enzymes are proteins that act as catalysts to reduce activation energy -​ Proteins are all constructed from the same set of 20 amino acids -​ Polypeptides are unbranched polymers built from these amino acids -​ A protein is a biologically functional molecule that consists of one or more polypeptides -​ Amino acids are organic molecules with amino and carboxyl groups -​ Amino acids differ in their properties due to differing side chains, called R groups -​ Amino acids are linked by covalent bonds called peptide bonds -​ Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus) -​ The sequence of amino acids determines a protein’s three-dimensional structure -​ A protein’s structure determines how it works -​ The primary structure of a protein is its sequence of amino acids -​ The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone -​ Typical secondary structures are a coil called an α helix and a folded structure called a β pleated sheet -​ Tertiary structure, the overall shape of a polypeptide, results from interactions between R groups, rather than interactions between backbone constituents -​ These interactions include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions -​ Strong covalent bonds called disulfide bridges may reinforce the protein’s structure -​ Quaternary structure results when two or more polypeptide chains form one macromolecule  SBI 4UY Exam Review 4 Functional groups -​ Functional groups are the components of organic molecules that are most commonly involved in chemical reactions -​ The number and arrangement of functional groups give each molecule its unique properties -​ The seven functional groups that are most important in the chemistry of life are the following: -​ Hydroxyl group -​ Carbonyl group -​ Carboxyl group -​ Amino group -​ Sulfhydryl group -​ Phosphate group -​ Methyl group Organic vs. Inorganic Compounds -​ Organic chemistry is the study of compounds that contain carbon, regardless of origin -​ Organic compounds range from simple molecules to colossal ones -​ The overall percentages of the major elements of life (C, H, O, N, S, and P) are quite uniform from one organism to another -​ Because of carbon’s ability to form four bonds, these building blocks can be used to make an inexhaustible variety of organic molecules -​ The great diversity of organisms on the planet is due to the versatility of carbon -​ With four valence electrons, carbon can form four covalent bonds with a variety of atoms -​ This makes large, complex molecules possible -​ In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape Isomers -​ Isomers are compounds with the same molecular formula but different structures and properties -​ Structural isomers have different covalent arrangements of their atoms -​ Cis-trans isomers (geometric isomers) have the same covalent bonds but  SBI 4UY Exam Review 5 differ in their spatial arrangements (particularly around double bonds) -​ Enantiomers (stereoisomers) are isomers that are mirror images of each other Inter and Intramolecular Bonds Covalent Bonds ​ A covalent bond is the sharing of a pair of valence electrons by two atoms ​ In a covalent bond, the shared electrons count as part of each atom’s valence shell ​ A molecule consists of two or more atoms held together by covalent bonds ​ A single covalent bond, or single bond, is the sharing of one pair of valence electrons ​ A double covalent bond, or double bond, is the sharing of two pairs of valence electrons ​ The notation used to represent atoms and bonding is called a structural formula ○​ For example, H—H ​ This can be abbreviated further with a molecular formula ○​ For example, H2 ​ Bonding capacity is called the atom’s valence ​ Covalent bonds can form between atoms of the same element or atoms of different elements ​ A compound is a combination of two or more different elements ​ Atoms in a molecule attract electrons to varying degrees ​ Electronegativity is an atom’s attraction for the electrons in a covalent bond ​ The more electronegative an atom is, the more strongly it pulls shared electrons toward itself ​ In a nonpolar covalent bond, the atoms share the electron equally ​ In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally ​ Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule Ionic Bonds ​ Atoms sometimes strip electrons from their bonding partners ​ An example is the transfer of an electron from sodium to chlorine ​ After the transfer of an electron, both atoms have charges ​ A charged atom (or molecule) is called an ion ​ A cation is a positively charged ion ​ An anion is a negatively charged ion ​ An ionic bond is an attraction between an anion and a cation ​ Compounds formed by ionic bonds are called ionic compounds, or salts ​ Salts, such as sodium chloride (table salt), are often found in nature as crystals  SBI 4UY Exam Review 6 Weak Chemical Interactions ​ Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules ​ Many large biological molecules are held in their functional form by weak bonds ​ The reversibility of weak bonds can be an advantage Hydrogen Bonds ​ A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom ​ In living cells, the electronegative partners are usually oxygen or nitrogen atoms Van der Waals Interactions (London Dispersion Force) ​ If electrons are not evenly distributed, they may accumulate by chance in one part of a molecule ​ Van der Waals interactions are attractions between molecules that are close together as a result of these charges ​ Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface Water Cohesion of Water Molecules ​ Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion ​ Cohesion helps the transport of water against gravity in plants ​ Adhesion is an attraction between different substances, for example, between water and plant cell walls ​ Surface tension is a measure of how difficult it is to break the surface of a liquid ​ Water has an unusually high surface tension due to hydrogen bonding between the molecules at the air-water interface and to the water below High Specific Heat and Ability to Moderate Temperature ​ Water absorbs heat from warmer air and releases stored heat to cooler air ​ Water can absorb or release a large amount of heat with only a slight change in its own temperature  SBI 4UY Exam Review 7 ​ The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1ºC ​ The specific heat of water is 1 cal/(g ºC) ​ Water resists changing its temperature because of its high specific heat ​ Water’s high specific heat can be traced to hydrogen bonding ○​ Heat is absorbed when hydrogen bonds break ○​ Heat is released when hydrogen bonds form ​ The high specific heat of water minimizes temperature fluctuations to within limits that permit life ​ Evaporation (or vaporization) is transformation of a substance from liquid to gas ​ Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas ​ As a liquid evaporates, its remaining surface cools, a process called evaporative cooling ​ Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water Expansion upon Freezing ​ Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense than water ​ Water reaches its greatest density at 4ºC ​ If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth ​ Many scientists are worried that global warming is having a profound effect on icy environments around the globe ​ The rate at which glaciers and Arctic sea ice are disappearing poses an extreme challenge to animals that depend on ice for their survival Universal Solvent ​ A solution is a liquid that is a completely homogeneous mixture of substances ​ The solvent is the dissolving agent of a solution ​ The solute is the substance that is dissolved ​ An aqueous solution is one in which water is the solvent ​ Water is a versatile solvent due to its polarity ​ When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell ​ Water can also dissolve compounds made of nonionic polar molecules ​ Even large polar molecules such as proteins can dissolve in water if they have ionic and polar regions ​ A hydrophilic substance is one that has an affinity for water ​ A hydrophobic substance is one that does not have an affinity for water ​ Oil molecules are hydrophobic because they have relatively nonpolar bonds  SBI 4UY Exam Review 8 ​ Most chemical reactions in organisms involve solutes dissolved in water ​ When carrying out experiments, we use mass to calculate the number of solute molecules in an aqueous solution Unit 2: Metabolic Processes Exergonic vs Endergonic Reactions Free-Energy Change, ΔG -​ A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell -​ The change in free energy (ΔG) during a process is related to the change in enthalpy -​ ΔG is negative for all spontaneous processes; processes with zero or positive ΔG are never spontaneous -​ Spontaneous processes can be harnessed to perform work Free Energy, Stability, and Equilibrium -​ Free energy is a measure of a system’s instability, its tendency to change to a more stable state -​ During a spontaneous change, free energy decreases and the stability of a system increases -​ Equilibrium is a state of maximum stability -​ A process is spontaneous and can perform work only when it is moving toward equilibrium Exergonic and Endergonic Reactions in Metabolism -​ The concept of free energy can be applied to the chemistry of life’s processes -​ An exergonic reaction proceeds with a net release of free energy and is spontaneous -​ An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous Equilibrium and Metabolism -​ Reactions in a closed system eventually reach equilibrium and can then do no work -​ Cells are not in equilibrium; they are open systems experiencing a constant flow of materials -​ A defining feature of life is that metabolism is never at equilibrium  SBI 4UY Exam Review 9 -​ A catabolic pathway in a cell releases free energy in a series of reactions Thermodynamics Organization of the Chemistry of Life into Metabolic Pathways -​ A metabolic pathway begins with a specific molecule and ends with a product -​ Each step is catalyzed by a specific enzyme -​ Catabolic pathways release energy by breaking down complex molecules into simpler compounds -​ Anabolic pathways consume energy to build complex molecules from simpler ones The Laws of Energy Transformation -​ Thermodynamics is the study of energy transformations -​ An isolated system is unable to exchange energy or matter with its surroundings -​ In an open system, energy and matter can be transferred between the system and its surroundings -​ Organisms are open systems The First Law of Thermodynamics -​ According to the first law of thermodynamics, the energy of the universe is constant -​ Energy can be transferred and transformed, but it cannot be created or destroyed -​ The first law is also called the principle of conservation of energy The Second Law of Thermodynamics -​ During every energy transfer or transformation, some energy is unusable and is often lost as heat -​ According to the second law of thermodynamics, -​ Every energy transfer or transformation increases the entropy of the universe -​ Entropy is a measure of molecular disorder, or randomness -​ Living cells unavoidably convert organized forms of energy to heat, a more disordered form of energy -​ Spontaneous processes occur without energy input; they can happen quickly or slowly -​ For a process to occur spontaneously, it must increase the entropy of the universe -​ Processes that decrease entropy are nonspontaneous; they will occur only if energy is provided -​ Entropy (disorder) may decrease in a particular system, such as an organism, as long as the total entropy of the system and surroundings increases  SBI 4UY Exam Review 10 Enzymes: Structure and Function -​ A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction -​ An enzyme is a catalytic protein How Enzymes Speed Up Reactions -​ The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA) -​ In catalysis, enzymes or other catalysts speed up specific reactions by lowering the EA barrier -​ Enzymes do not affect the change in free energy (ΔG); instead, they hasten reactions that would occur eventually Substrate Specificity of Enzymes -​ The reactant that an enzyme acts on is called the enzyme’s substrate -​ The enzyme binds to its substrate, forming an enzyme-substrate complex -​ While bound, the activity of the enzyme converts substrate to product -​ The reaction catalyzed by each enzyme is very specific -​ The active site is the region on the enzyme where the substrate binds -​ Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction Catalysis in the Enzyme’s Active Site -​ In an enzymatic reaction, the substrate binds to the active site of the enzyme -​ Enzymes are extremely fast acting and emerge from reactions in their original form -​ Very small amounts of enzyme can have huge metabolic effects because they are used repeatedly in catalytic cycles -​ The active site can lower an EA barrier by -​ orienting substrates correctly -​ straining substrate bonds -​ providing a favorable microenvironment -​ covalently bonding to the substrate -​ The rate of an enzyme-catalyzed reaction can be sped up by increasing substrate concentration -​ When all enzyme molecules have their active sites engaged, the enzyme is saturated -​ If the enzyme is saturated, the reaction rate can only be sped up by adding more enzyme  SBI 4UY Exam Review 11 Effects of Temperature and pH -​ Each enzyme has an optimal temperature in which it can function -​ Each enzyme has an optimal pH in which it can function -​ Optimal conditions favor the most active shape for the enzyme molecule Cofactors -​ Cofactors are non protein enzyme helpers -​ Cofactors may be inorganic (such as a metal in ionic form) or organic -​ An organic cofactor is called a coenzyme -​ Coenzymes include vitamins Enzyme Inhibitors -​ Competitive inhibitors bind to the active site of an enzyme, competing with the substrate -​ Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective Allosteric Regulation of Enzymes -​ Allosteric regulation may either inhibit or stimulate an enzyme’s activity -​ Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site Allosteric Activation and Inhibition -​ Most allosterically regulated enzymes are made from polypeptide subunits, each with its own active site -​ The enzyme complex has active and inactive forms -​ The binding of an activator stabilizes the active form of the enzyme -​ The binding of an inhibitor stabilizes the inactive form of the enzyme -​ Cooperativity is a form of allosteric regulation that can amplify enzyme activity -​ One substrate molecule primes an enzyme to act on additional substrate molecules more readily -​ Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site Feedback Inhibition -​ In feedback inhibition, the end product of a metabolic pathway shuts down the pathway  SBI 4UY Exam Review 12 -​ Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed Cellular Respiration -​ Overall Equation: C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + Energy -​ Electron Carriers: -​ NADH (reduced) → NAD+ (oxidized) + 2e- -​ FADH2 (reduced) → FAD (oxidized) + 2e- Glycolysis Pyruvate Citric Acid Cycle ETC/ Oxidative Net Oxidation Phosphorylation ATP -2 + 4 = 2 -2 +2 +34 36 NADH +2 +2 +6 -10 FADH2 +2 -2 Structure of the Mitochondria Glycolysis -​ Occurs in the cytosol -​ Glucose → 2 Glycerol-3-phosphate → 2 Pyruvate -​ Energy Investment and Energy Payoff phases -​ Net gain of 2 ATP and 2 NADH Pyruvate Oxidation -​ Occurs across the mitochondrial membrane -​ 2 Pyruvate → 2 Acetyl Coenzyme A + 2 CO2 -​ Net loss of 2 ATP and gain of 2 NADH  SBI 4UY Exam Review 13 Citric Acid Cycle -​ Also called Krebs Cycle -​ Occurs in the mitochondrial matrix -​ Pyruvate + Oxaloacetate → Citric Acid → Oxaloacetate + 2 CO2 -​ Net gain of 3 NADH, 1 FADH2, and 1 ATP per cycle Electron Transport Chain and Oxidative Phosphorylation -​ Occurs along the inner mitochondrial membrane -​ NADH and FADH2 are oxidized, resulting in a high concentration of protons in the intermembrane space -​ This creates a proton motive force as protons move from high to low concentration -​ The protons re enter the matrix through ATP synthase, producing ATP via chemiosmosis -​ 1 NADH → 3 ATP -​ 1 FADH2 → 2 ATP -​ Oxygen is the final electron acceptor​ Regulation of Cellular Respiration via Feedback Mechanisms -​ If ATP concentration begins to drop, respiration speeds up; when there is plenty of ATP, respiration slows down -​ AMP stimulate phosphofructokinase; ATP and citrate inhibit phosphofructokinase Alternate Pathways -​ If glucose is not available, the body can perform cellular respiration with other organic molecules -​ Fatty acids are broken down via beta oxidation and enter as acetyl-CoA -​ every two carbons becomes one acetyl-CoA -​ Glycerol enters as a single molecule of G3P -​ Different amino acids enter at different points  SBI 4UY Exam Review 14 Fermentation -​ Fermentation consists of glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis -​ In alcohol fermentation, pyruvate is converted to ethanol in two steps -​ The first step releases CO2 from pyruvate -​ The second step produces NAD+ and ethanol -​ Alcohol fermentation by yeast is used in brewing, winemaking, and baking -​ In lactic acid fermentation, pyruvate is reduced by NADH, forming NAD+ and lactate as end products, with no release of CO2 -​ Lactic acid fermentation by some fungi and bacteria is used to make cheese and yogurt -​ Human muscle cells use lactic acid fermentation to generate ATP during strenuous exercise when O2 is scarce -​ Obligate anaerobes carry out fermentation or anaerobic respiration and cannot survive in the presence of O2 -​ Yeast and many bacteria are facultative anaerobes, meaning that they can survive using either fermentation or cellular respiration Photosynthesis -​ Overall equation: 6 CO2 + 6 H2O + Energy → C6H12O6 + 6 O2 -​ The overall chemical change during photosynthesis is the reverse of the one that occurs during cellular respiration -​ Electron carrier: NADPH (reduced) → NADP+ (oxidized) + 2e- Structure of the Chloroplast  SBI 4UY Exam Review 15 -​ Leaves are the major locations of photosynthesis in plants -​ Chloroplasts are found mainly in cells of the mesophyll, the interior tissue of the leaf -​ Each mesophyll cell contains 30–40 chloroplasts -​ CO2 enters and O2 exits the leaf through microscopic pores called stomata -​ A chloroplast has an envelope of two membranes surrounding a dense fluid called the stroma -​ Thylakoids are connected sacs in the chloroplast that compose a third membrane system -​ Thylakoids may be stacked in columns called grana -​ Chlorophyll, the pigment that gives leaves their green color, resides in the thylakoid membranes Light Reactions -​ Light is electromagnetic energy, also called electromagnetic radiation -​ Light behaves as both a particle (called a photon) and a wave -​ Visible light consists of wavelengths (380 nm to 750 nm) that produce colors we can see -​ Pigments are substances that absorb visible light -​ Different pigments absorb different wavelengths -​ Wavelengths that are not absorbed are reflected or transmitted -​ Leaves appear green because chlorophyll reflects and transmits green light -​ There are three types of pigments in chloroplasts: -​ Chlorophyll a, the key light-capturing pigment -​ Chlorophyll b, an accessory pigment -​ Carotenoids, a separate group of accessory pigments -​ The absorption spectrum of chlorophyll a suggests that violet-blue and red light work best for photosynthesis -​ The difference in the absorption spectrum between chlorophyll a and b is due to a slight structural difference between the pigment molecules -​ When a pigment absorbs light, it goes from a ground state to an excited state, which is unstable -​ When excited electrons fall back to the ground state, excess energy is released -​ In isolation, some pigments also emit light, an afterglow called fluorescence -​ A photosystem consists of a reaction-center complex surrounded by light-harvesting complexes  SBI 4UY Exam Review 16 -​ The reaction-center complex is an association of proteins holding a special pair of chlorophyll a molecules and a primary electron acceptor -​ The light-harvesting complex consists of pigment molecules bound to proteins -​ Light-harvesting complexes transfer the energy of photons to the chlorophyll a molecules in the reaction-center complex -​ These chlorophyll a molecules are special because they can transfer an excited electron to a different molecule -​ A primary electron acceptor in the reaction center accepts excited electrons and is reduced as a result -​ Solar-powered transfer of an electron from a chlorophyll a molecule to the primary electron acceptor is the first step of the light reactions -​ There are two types of photosystems: Photosystem II (PSII) and Photosystem I (PSI) -​ Their reaction centers are called P680 and P700 respectively -​ During the light reactions, there are two possible routes for electron flow: cyclic and linear -​ The light reactions occur across the thylakoid membrane Linear Electron Flow -​ Linear electron flow, the primary pathway, involves both photosystems and produces ATP and NADPH using light energy 1.​ A photon hits a pigment in a light-harvesting complex of PSII, and its energy is passed among pigment molecules until it excites P680 2.​ An excited electron from P680 is transferred to the primary electron acceptor (we now call it P680+) 3.​ H2O is split by enzymes, and the electrons are transferred from the hydrogen atoms to P680+, thus reducing it to P680 a.​ P680+ is the strongest known biological oxidizing agent b.​ The H+ are released into the thylakoid space c.​ O2 is released as a by-product of this reaction 4.​ Each electron “falls” down an electron transport chain from the primary electron acceptor of PSII to PSI. Energy released by the fall drives the creation of a proton gradient across the thylakoid membrane  SBI 4UY Exam Review 17 a.​ Cytochrome b6f catalyzes the transfer of electrons from plastoquinone to plastocyanin, while pumping protons from the stroma into the thylakoid lumen 5.​ Potential energy stored in the proton gradient drives production of ATP by chemiosmosis 6.​ In PSI (like PSII), transferred light energy excites P700, which loses an electron to the primary electron acceptor a.​ P700+ (P700 that is missing an electron) accepts an electron passed down from PSII via the electron transport chain 7.​ Each electron “falls” down an electron transport chain from the primary electron acceptor of PSI to the protein ferredoxin (Fd) 8.​ NADP+ reductase catalyzes the transfer of electrons to NADP+, reducing it to NADPH a.​ The electrons of NADPH are available for the reactions of the Calvin cycle b.​ This process also removes an H+ from the stroma Cyclic Electron Flow -​ In cyclic electron flow, electrons cycle back from Fd to the PSI reaction center via a plastocyanin molecule (Pc) -​ Cyclic electron flow uses only photosystem I and produces ATP, but not NADPH -​ No oxygen is released -​ Cyclic electron flow is thought to have evolved before linear electron flow Calvin Cycle -​ The Calvin cycle is anabolic; it builds sugar from smaller molecules by using ATP and the reducing power of electrons carried by NADPH -​ Takes place in the stroma -​ Carbon enters the cycle as CO2 and leaves as glyceraldehyde 3-phosphate (G3P)  SBI 4UY Exam Review 18 -​ For net synthesis of one G3P, the cycle must take place three times, fixing three molecules of CO2 -​ The Calvin cycle has three phases: -​ Carbon fixation (catalyzed by rubisco) -​ Reduction -​ Regeneration of the CO2 acceptor (RuBP) -​ 3 CO2 + 3 RuBP → 6 G3P → 1 G3P + 3 RuBP -​ Reduction uses 6 ATP and 6 NADPH -​ RuBP Regeneration uses another 3 ATP Photorespiration -​ Dehydration is a problem for plants, sometimes requiring trade-offs with other metabolic processes, especially photosynthesis -​ On hot, dry days, plants close stomata, which conserves H2O but also limits photosynthesis -​ The closing of stomata reduces access to CO2 and causes O2 to build up -​ These conditions favor an apparently wasteful process called photorespiration -​ In most plants (C3 plants), initial fixation of CO2, via rubisco, forms a three-carbon compound (3-phosphoglycerate) -​ In photorespiration, rubisco adds O2 instead of CO2 in the Calvin cycle, producing a two-carbon compound -​ Photorespiration consumes O2 and organic fuel and releases CO2 without producing ATP or sugar C4 Plants -​ C4 plants minimize the cost of photorespiration by incorporating CO2 into four-carbon compounds -​ There are two distinct types of cells in the leaves of C4 plants: -​ Bundle-sheath cells are arranged in tightly packed sheaths around the veins of the leaf -​ Mesophyll cells are loosely packed between the bundle sheath and the leaf surface -​ Sugar production in C4 plants occurs in a three-step process: 1.​ The production of the four-carbon precursors (such as malate) is catalyzed by the enzyme PEP carboxylase in the mesophyll cells by fixing CO2 to PEP (3C)  SBI 4UY Exam Review 19 -​ PEP carboxylase has a higher affinity for CO2 than rubisco does; it can fix CO2 even when CO2 concentrations are low 2.​ These four-carbon compounds are exported to bundle-sheath cells 3.​ Within the bundle-sheath cells, they release CO2 that is then used in the Calvin cycle -​ C4 photosynthesis uses less water and resources than C3 photosynthesis -​ Scientists have genetically modified rice, a C3 plant, to carry out C4 photosynthesis -​ Other examples of C4 plants include corn and sugarcane CAM Plants -​ Some plants, including succulents, use crassulacean acid metabolism (CAM) to fix carbon -​ CAM plants open their stomata at night, incorporating CO2 into organic acids that are stored in the vacuoles -​ Stomata close during the day, and CO2 is released from organic acids and used in the Calvin cycle -​ The CAM pathway is similar to the C4 pathway in that they both incorporate CO2 into organic intermediates before it enters the Calvin cycle -​ C4 plants separate the steps spatially while CAM plants separate the steps temporally Unit 3: Genetics and Biotechnology DNA Structure and Function -​ Frederick Griffith discovered transformation by working with pathogenic and nonpathogenic strains of a bacteria -​ Information was transferred from heat-treated pathogenic bacteria to live nonpathogenic bacteria -​ Later work by Oswald Avery, Maclyn McCarty, and Colin MacLeod identified the transforming substance as DNA -​ Alfred Hershey and Martha Chase showed that DNA is the genetic material by working with bacteriophages -​ Using radioactive isotopes (phosphorus and sulfur), they that DNA was part of the virus that was being injected into the bacterium -​ DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group -​ The nitrogenous bases can be adenine (A), thymine (T), guanine (G), or cytosine (C)  SBI 4UY Exam Review 20 -​ Chargaff’s rules: -​ The base composition of DNA varies between species -​ In any species the number of A and T bases is equal and the number of G and C bases is equal -​ After DNA was accepted as the genetic material, the challenge was to determine how its structure accounts for its role in heredity -​ Maurice Wilkins and Rosalind Franklin were using a technique called X-ray crystallography to study molecular structure -​ They deduced that the structure of DNA was a double helix -​ Watson and Crick built models of the helical structure of DNA, deducing that the backbones must be antiparallel -​ Based on these models they also discovered that pairing a purine (A or G) with a pyrimidine (C or T) resulted in a uniform width consistent with the X-ray data -​ They determined that adenine (A) paired only with thymine (T), and guanine (G) paired only with cytosine (C) -​ Purines have two rings, pyrimidines have one -​ The Watson-Crick model explains Chargaff’s rules: in any organism the amount of A = T, and the amount of G = C -​ There are three hydrogen bonds between G and C and two hydrogen bonds between A and T -​ The sequence of these four nucleotides is what allows DNA to code for every aspect of life DNA Packaging -​ The bacterial chromosome is a double-stranded, circular DNA molecule associated with a small amount of protein -​ Eukaryotic chromosomes have linear DNA molecules associated with a large amount -​ of protein -​ In a bacterium, the DNA is “supercoiled” and found in a region of the cell called the nucleoid -​ In the eukaryotic cell, DNA is precisely combined with proteins in a complex called chromatin -​ Chromosomes fit into the nucleus through an elaborate, multilevel system of packing -​ Proteins called histones are responsible for the first level of packing in chromatin  SBI 4UY Exam Review 21 -​ Unfolded chromatin resembles beads on a string, with each “bead” being a nucleosome, the basic unit of DNA packaging -​ They are composed of two each of the four basic histone types, with DNA wrapped twice around the core of the eight histones -​ The N-termini (“tails”) of the histones protrude from the nucleosome -​ Nucleosomes, and especially their histone tails, are involved in the regulation of gene expression -​ Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis -​ Loosely packed chromatin is called euchromatin -​ During interphase a few regions of chromatin (centromeres and telomeres) are highly condensed into heterochromatin -​ Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions DNA Replication -​ The relationship between structure and function is manifest in the double helix -​ Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replication -​ In DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules -​ Watson and Crick’s semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand -​ Competing models were the conservative model (the two parent strands rejoin) and the dispersive model (each strand is a mix of old and new) -​ Experiments by Matthew Meselson and Franklin Stahl supported the semiconservative model -​ Replication begins at particular sites called origins of replication, where the two DNA strands are separated, opening up a replication “bubble” -​ There is multiple origins of replication in eukaryotic cells and only one in prokaryotes -​ Replication proceeds in both directions from each origin, until the entire molecule is copied  SBI 4UY Exam Review 22 -​ At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating -​ Helicases are enzymes that untwist the double helix at the replication forks -​ Single-strand binding proteins (SSBs) bind to and stabilize single-stranded DNA -​ Topoisomerase relieves the strain of twisting of the double helix by breaking, swiveling, and rejoining DNA strands -​ Enzymes called DNA polymerases catalyze the synthesis of new DNA at a replication fork -​ Most DNA polymerases require a primer and a DNA template strand -​ Primase synthesizes RNA primers, which are short strands of RNA -​ Primase can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template -​ The primer is short (5–10 nucleotides long), and the 3′ end serves as the starting point for the new DNA strand -​ Each nucleotide that is added to a growing DNA strand is a deoxyribonucleoside triphosphate (dNTP) -​ As each monomer joins the DNA strand, via a dehydration reaction, it loses two phosphate groups as a molecule of pyrophosphate -​ The antiparallel structure of the double helix affects replication -​ DNA polymerases add nucleotides only to the free 3′ end of a growing strand; therefore, a new DNA strand can elongate only in the 5′ to 3′ direction -​ Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork -​ To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork -​ The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase -​ DNA Polymerase I converts the RNA primers to DNA -​ DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides -​ In mismatch repair of DNA, repair enzymes correct errors in base pairing -​ In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA -​ Ligase rejoins the newly synthesized DNA to the rest of the strand -​ The error rate after proofreading and repair is low but not zero -​ Sequence changes may become permanent and can be passed on to the next generation  SBI 4UY Exam Review 23 -​ These changes (mutations) are the source of the genetic variation upon which natural selection operates and are ultimately responsible for the appearance of new species -​ Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes -​ The usual replication machinery provides no way to complete the 5′ ends, so repeated rounds of replication produce shorter DNA molecules with uneven ends -​ This is not a problem for prokaryotes, most of which have circular chromosomes -​ Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends called telomeres -​ Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules -​ It has been proposed that the shortening of telomeres is connected to aging -​ If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce -​ An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells -​ The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions Gene Expression -​ Central dogma: DNA is transcribed into RNA which is translated into polypeptide Transcription -​ Transcription is the first stage of gene expression -​ RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and joins together the RNA nucleotides -​ The RNA is complementary to the DNA template strand -​ RNA polymerase does not need any primer -​ RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine -​ The DNA sequence where RNA polymerase attaches is called the promoter -​ In bacteria, the sequence signaling the end of transcription is called the terminator -​ The stretch of DNA that is transcribed is called a transcription unit -​ The three stages of transcription: -​ Initiation -​ Elongation -​ Termination  SBI 4UY Exam Review 24 -​ Promoters signal the transcription start point and usually extend several dozen nucleotide pairs upstream of the start point -​ Transcription factors mediate the binding of RNA polymerase and the initiation of transcription -​ The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex -​ A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes -​ The sigma factor aids in RNA synthesis in prokaryotes -​ During elongation, RNA polymerase synthesizes the mRNA from 5’ to 3’ -​ The mechanisms of termination are different in bacteria and eukaryotes -​ In bacteria, the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification -​ In eukaryotes, RNA polymerase transcribes the polyadenylation signal sequence and the RNA transcript is released shortly after Post-Transcriptional Modification -​ Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm -​ Each end of a pre-mRNA molecule is modified in a particular way -​ The 5′ end receives a modified guanine 5′ cap -​ The 3′ end gets a poly-A tail -​ These modifications share several functions -​ They seem to facilitate the export of mRNA to the cytoplasm -​ They protect mRNA from hydrolytic enzymes -​ They help ribosomes attach to the 5′ end -​ Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions -​ These noncoding regions are called intervening sequences, or introns -​ The other regions are called exons because they are eventually expressed, usually translated into amino acid sequences -​ RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence -​ In some cases, RNA splicing is carried out by spliceosomes -​ Spliceosomes consist of a variety of proteins and several small RNAs that recognize the splice sites -​ The RNAs of the spliceosome also catalyze the splicing reaction -​ Ribozymes are catalytic RNA molecules that function as enzymes and can splice RNA  SBI 4UY Exam Review 25 -​ The discovery of ribozymes rendered obsolete the belief that all biological catalysts were proteins -​ Three properties of RNA enable it to function as an enzyme -​ It can form a three-dimensional structure because of its ability to base-pair with itself -​ Some bases in RNA contain functional groups that may participate in catalysis -​ RNA may hydrogen-bond with other nucleic acid molecules -​ Some introns contain sequences that may regulate gene expression -​ Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing -​ This is called alternative RNA splicing -​ Consequently, the number of different proteins an organism can produce is much greater than its number of genes -​ Proteins often have a modular architecture consisting of discrete regions called domains -​ In many cases, different exons code for the different domains in a protein -​ Exon shuffling may result in the evolution of new proteins Translation (Protein Synthesis) -​ Genetic information flows from mRNA to protein through the process of translation -​ A cell translates an mRNA message into protein with the help of transfer RNA (tRNA) -​ tRNAs transfer amino acids to the growing polypeptide in a ribosome -​ Translation is a complex process in terms of its biochemistry and mechanics -​ Each tRNA molecule enables translation of a given mRNA codon (base triplets) into a certain amino acid -​ Each carries a specific amino acid on one end -​ Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA -​ Which protein each codon codes for is determined by the universal genetic code -​ Because of hydrogen bonds, tRNA actually twists and folds into a three-dimensional molecule -​ The protruding 3' end acts as an attachment site for an amino acid -​ Accurate translation requires two steps -​ First: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase -​ Second: a correct match between the tRNA anticodon and an mRNA codon -​ Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon -​ Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis  SBI 4UY Exam Review 26 -​ The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA) -​ Bacterial and eukaryotic ribosomes are somewhat similar but have significant differences -​ A ribosome has three binding sites for tRNA -​ The P site holds the tRNA that carries the growing polypeptide chain -​ The A site holds the tRNA that carries the next amino acid to be added to the chain -​ The E site is the exit site, where discharged tRNAs leave the ribosome -​ The three stages of translation: -​ Initiation -​ Elongation -​ Termination -​ The start codon (AUG) signals the start of translation -​ First, a small ribosomal subunit binds with mRNA and a special initiator tRNA -​ Then the small subunit moves along the mRNA until it reaches the start codon -​ Proteins called initiation factors bring in the large subunit that completes the translation initiation complex -​ During elongation, amino acids are added one by one to the C-terminus of the growing chain -​ Each addition involves proteins called elongation factors -​ Elongation occurs in three steps: codon recognition, peptide bond formation, and translocation -​ Energy expenditure occurs in the first and third steps -​ Translation proceeds along the mRNA in a 5′ → 3′ direction -​ The ribosome and mRNA move relative to each other, codon by codon -​ Elongation continues until a stop codon in the mRNA reaches the A site of the ribosome -​ The A site accepts a protein called a release factor -​ The release factor causes the addition of a water molecule instead of an amino acid -​ This reaction releases the polypeptide, and the translation assembly comes apart -​ Ribosomes can either be free or bound to the rough ER -​ Free ribosomes mostly synthesize proteins that function in the cytosol -​ Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell -​ Ribosomes are identical and can switch from free to bound  SBI 4UY Exam Review 27 -​ Multiple ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or polysome) -​ Polyribosomes enable a cell to make many copies of a polypeptide very quickly -​ A bacterial cell ensures a streamlined process by coupling transcription and translation -​ In this case the newly made protein can quickly diffuse to its site of function -​ In eukaryotes, the nuclear envelope separates the processes of transcription and translation -​ RNA undergoes processing before leaving the nucleus -​ A protein’s primary structure is determined by a gene, and primary structure in turn determines shape -​ Post-translational modifications may be required before the protein can begin doing its particular job in the cell Mutations -​ Mutations are changes in the genetic information of a cell -​ Point mutations are changes in just one nucleotide pair of a gene -​ The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein -​ Point mutations within a gene can be divided into two general categories: -​ Single nucleotide-pair substitutions -​ Nucleotide-pair insertions or deletions -​ A nucleotide-pair substitution replaces one nucleotide and its partner with another pair of nucleotides -​ Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code -​ Missense mutations still code for an amino acid, but not the correct amino acid -​ Nonsense mutations change an amino acid codon into a stop codon; most lead to a nonfunctional protein -​ Insertions and deletions are additions or losses of nucleotide pairs in a gene -​ These mutations have a disastrous effect on the resulting protein more often than substitutions do -​ Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation -​ Spontaneous mutations can occur during errors in DNA replication, recombination, or repair -​ Mutagens are physical or chemical agents that can cause mutations -​ Chemical mutagens fall into a variety of categories  SBI 4UY Exam Review 28 Regulation of Gene Expression -​ Almost all the cells in an organism contain an identical genome -​ Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome Lac and Trp Operons -​ One mechanism for control of gene expression in bacteria is the operon model -​ An operon is a cluster of functionally related genes that can be coordinately controlled by a single “on-off switch” -​ The switch is a segment of DNA called an operator, usually positioned within the promoter -​ An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control -​ The operon can be switched off by a protein repressor -​ The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase -​ The repressor is the product of a separate regulatory gene, located some distance from the operon itself -​ The repressor can be in an active or inactive form, depending on the presence of other molecules -​ A corepressor is a molecule that cooperates with a repressor protein to switch an operon off -​ For example, E. coli can synthesize the amino acid tryptophan when it has insufficient tryptophan -​ A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription -​ The trp operon is a repressible operon -​ By default, the trp operon is on and the genes for tryptophan synthesis are transcribed -​ When tryptophan is present, it binds to the trp repressor protein, which turns the operon off -​ The repressor is active only in the presence of its corepressor tryptophan; thus the trp operon is turned off (repressed) if tryptophan levels are high -​ An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription  SBI 4UY Exam Review 29 -​ The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose -​ By itself, the lac repressor is active and switches the lac operon off -​ A molecule called an inducer inactivates the repressor to turn the lac operon on -​ In the case of the lac operon, the inducer is allolactose, an isomer of lactose -​ Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal -​ Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product -​ Regulation of both the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor Regulation of Chromatin Structure -​ The structural organization of chromatin helps regulate gene expression in several ways -​ Genes within highly packed heterochromatin are usually not expressed -​ Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression -​ In histone acetylation, acetyl groups are attached to an amino acid in a histone tail -​ This appears to open up the chromatin structure, thereby promoting the initiation of transcription -​ The addition of methyl groups (methylation) can condense chromatin and reduce transcription -​ DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription -​ Although the chromatin modifications just discussed do not alter DNA sequence, they may be passed to future generations of cells -​ The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance Biotechnology DNA Sequencing and Gel Electrophoresis -​ Researchers can exploit the principle of complementary base pairing to determine the complete nucleotide sequence of a DNA molecule, a process called DNA sequencing. -​ The DNA is first cut into fragments, and then each fragment is sequenced.  SBI 4UY Exam Review 30 -​ Dideoxynucleotides (ddNTP) are chain-elongating inhibitors of DNA polymerase, used in the Sanger method for DNA sequencing. -​ Because they do not have a hydroxyl group on their 3’ carbon, another nucleotide cannot be added after a ddNTP, resulting in the termination of DNA replication. -​ Four samples are prepared, one with each ddNTP, creating many strands of replicated DNA with distinct lengths -​ By analyzing the lengths of DNA found in each sample, we can determine the sequence of nucleotides in the original DNA molecule -​ This can be done using a process called gel electrophoresis, wherein each sample is placed in a well at the end of a surface of gel -​ At one end there is a negative cathode and at the opposite there is a positive cathode -​ Because DNA is negatively charged, the molecules move towards the positively charged end -​ Smaller strands of DNA move more quickly through the gel, creating distinct bands along the gel that indicate the relative lengths of the DNA molecules -​ This allows us to read bands on the gel from top to bottom as the DNA sequence from 5’ to 3’ -​ The strand sequenced here is complementary to the original strand of DNA Polymerase Chain Reaction (PCR) -​ The polymerase chain reaction, PCR, can produce many copies of a specific target segment of DNA -​ A three-step cycle—denaturation, annealing, and extension—brings about a chain reaction that produces an exponentially growing population of identical DNA molecules -​ The key to PCR is an unusual, heat-stable DNA polymerase called Taq polymerase -​ PCR uses a pair of DNA primers specific for the sequence to be amplified, PCR primers are designed to hybridize only to sequences at opposite ends of the target sequences. -​ The number of replicated DNA strands can be determined using the formula 2n, where n is the number of cycles -​ DNA molecules that match the target sequence do not begin appearing until the third cycle  SBI 4UY Exam Review 31 Recombinant DNA and Restriction Enzymes -​ To work directly with specific genes, scientists prepare well-defined DNA segments in multiple identical copies by a process called DNA cloning -​ Plasmids are small, circular DNA molecules that replicate separately from the bacterial chromosome -​ Researchers can insert DNA into a plasmid to produce a recombinant DNA molecule, which contains DNA from two different sources -​ Reproduction of a recombinant plasmid in a bacterial cell results in cloning of the plasmid including the foreign DNA -​ This production of multiple copies of a single gene is a type of DNA cloning called gene cloning -​ A plasmid used to clone a foreign gene is called a cloning vector -​ Bacterial plasmids are widely used as cloning vectors because they are readily obtained, easily manipulated, and easily introduced into bacterial cells, and once in the bacteria they multiply rapidly -​ Gene cloning is useful for amplifying genes to produce a protein product for research, medical, or other purposes -​ Bacterial restriction enzymes cut DNA molecules at specific DNA sequences called restriction sites -​ A restriction enzyme usually makes many cuts, yielding restriction fragments -​ The most useful restriction enzymes cut DNA in a staggered way, producing fragments with at least one single-stranded end called a sticky end -​ Sticky ends can bond with complementary sticky ends of other fragments -​ DNA ligase is an enzyme that seals the bonds between restriction fragments -​ This allows researchers to join two DNA fragments from different sources -​ Getting a cloned eukaryotic gene to function in bacterial host cells can be difficult because certain aspects of gene expression are different in eukaryotes and bacteria. -​ To overcome differences in promoters and other DNA control sequences, scientists usually employ an expression vector, a cloning vector that contains a highly active bacterial promoter just upstream of a restriction site where the eukaryotic gene can be inserted in the correct reading frame. -​ The bacterial host cell will recognize the promoter and proceed to express the foreign gene now linked to that promoter. -​ Such expression vectors allow the synthesis of many eukaryotic proteins in bacterial cells  SBI 4UY Exam Review 32 Unit 4: Homeostasis The Immune System -​ Pathogens, agents that cause disease, infect a wide range of animals, including humans -​ Dedicated cells of the immune system interact with and destroy pathogens -​ First lines of defense help prevent pathogens from gaining entry to the body -​ Within the body, two types of molecular recognition allow detection of nonself molecules, particles, and cells -​ All animals have innate immunity, a defense active immediately upon infection -​ Innate immunity includes barrier defenses -​ Vertebrates also have adaptive immunity -​ The adaptive immune response is activated after the innate response and develops more slowly Innate Immunity -​ Innate immunity include barrier defenses, phagocytosis, and antimicrobial peptides -​ Additional defenses unique to vertebrates are natural killer cells, interferons, and the inflammatory response -​ Barrier defenses include the skin and mucous membranes of the respiratory, urinary, and reproductive tracts -​ Mucus traps and allows for the removal of microbes -​ Many body fluids including saliva, mucus, and tears are hostile to many microbes -​ The low pH of skin and the digestive system prevents growth of many bacteria -​ Innate immune cells in mammals detect, devour, and destroy invading pathogens -​ These cells recognize groups of pathogens using TLRs, or Toll-like receptors -​ TLRs recognize fragments of molecules characteristic of a set of pathogens -​ There are two main types of phagocytic cells, which engulf and destroy pathogens, in the mammalian body: -​ Neutrophils circulate in the blood -​ Macrophages migrate through the body or reside permanently in organs and tissues -​ There are two additional types of phagocytic cells: -​ Dendritic cells stimulate development of adaptive immunity -​ Eosinophils discharge destructive enzymes against parasites  SBI 4UY Exam Review 33 -​ Cellular innate defenses in vertebrates also involve natural killer cells -​ These circulate through the body and detect abnormal cells -​ They release chemicals leading to cell death, inhibiting the spread of virally infected or cancerous cells -​ Many cellular innate defenses involve the lymphatic system -​ Peptides and proteins function in innate defense by attacking pathogens or impeding their reproduction -​ Interferon proteins provide innate defense, interfering with viruses and helping activate macrophages -​ About 30 proteins make up the complement system, which causes lysis of invading cells and helps trigger inflammation -​ The inflammatory response, such as pain and swelling, is brought about by molecules released upon injury or infection -​ Mast cells, immune cells found in connective tissue, release histamine, which triggers blood vessels to dilate and become more permeable -​ Activated complement proteins promote further release of histamine, attracting more phagocytic cells -​ Enhanced blood flow to the site helps deliver antimicrobial peptides -​ The result is an accumulation of pus, a fluid rich in white blood cells, dead pathogens, and cell debris from damaged tissues Adaptive Immunity -​ The adaptive response relies on two types of lymphocytes, or white blood cells -​ Lymphocytes that mature in the thymus, above the heart, are called T cells, and those that mature in bone marrow are called B cells -​ Antigens are substances that can elicit a response from a B or T cell -​ T or B cells bind to antigens via antigen receptors specific to part of one molecule of that pathogen -​ The small, accessible part of an antigen that binds to an antigen receptor is called an epitope  SBI 4UY Exam Review 34 -​ Each individual B or T cell is specialized to recognize a specific type of molecule -​ The antigen receptors of B cells and T cells have similar components, but they encounter antigens in different ways -​ Each B cell antigen receptor is a Y-shaped molecule with two identical heavy chains and two identical light chains -​ The constant (C) regions of the chains vary little among B cells, whereas the variable (V) regions differ greatly -​ The variable regions provide antigen specificity -​ For a T cell, the antigen receptor consists of two different polypeptide chains, an ⍺ chain and a β chain, linked by a disulfide bridge -​ At the outer tip of the molecule, the variable (V) regions of the α and β chains together form a single antigen-binding site -​ The remainder of the molecule is made up of the constant (C) regions. -​ Whereas the antigen receptors of B cells bind to epitopes of intact antigens protruding from pathogens or circulating free in body fluids, antigen receptors of T cells bind only to fragments of antigens that are displayed, or presented, on the surface of host cells. -​ The host protein that displays the antigen fragment on the cell surface is called a major histocompatibility complex (MHC) molecule. -​ By displaying antigen fragments, MHC molecules are essential for antigen recognition by T cells. -​ The adaptive immune system has four major characteristics: -​ Immense diversity of lymphocytes and receptors -​ Self-tolerance: lack of reactivity against an animal’s own molecules and cells -​ B and T cells proliferate after activation -​ Immunological memory -​ Antigen receptors are generated by random rearrangement of DNA -​ As lymphocytes mature in bone marrow or the thymus, they are tested for self-reactivity -​ Some B and T cells with receptors specific for the body’s own molecules are destroyed by apoptosis, or programmed cell death -​ The remainder are rendered nonfunctional -​ In the body there are few lymphocytes with antigen receptors for any particular epitope -​ In the lymph nodes, an antigen is exposed to a steady stream of lymphocytes until a match is made -​ This binding of a mature lymphocyte to an antigen initiates events that activate the lymphocyte  SBI 4UY Exam Review 35 -​ Once activated, a B or T cell undergoes multiple cell divisions (clonal selection) to produce a clone of identical cells -​ Some cells from the clone become effector cells that act immediately against the antigen -​ For B cells, the effector forms are plasma B cells, which secrete antibodies. -​ For T cells, the effector forms are helper T cells and cytotoxic T cells -​ The remaining cells in the clone become long-lived memory cells that can give rise to effector cells if the same antigen is encountered again -​ The process is called clonal selection because an encounter with an antigen selects which lymphocyte will divide to produce a clonal population of thousands of cells specific for a particular epitope -​ Cells that have antigen receptors specific for other antigens do not respond -​ Immunological memory is responsible for long-term protections against diseases -​ The first exposure to a specific antigen represents the primary immune response -​ The secondary immune response relies on the reservoir of T and B memory cells generated upon initial exposure to an antigen -​ Because these cells are long-lived, they provide the basis for immunological memory, which can span many decades (Most effector cells have much shorter life spans) -​ If an antigen is encountered again, memory cells specific for that antigen enable the rapid formation of clones of thousands of effector cells also specific for that antigen, thus generating a greatly enhanced immune defense -​ The defenses provided by B and T lymphocytes can be divided into humoral and cell-mediated immune responses -​ The humoral immune response occurs in the blood and lymph (once called body humors, or fluids) -​ In this response, antibodies help neutralize or eliminate toxins and pathogens in body fluids. -​ In the cell-mediated immune response, cytotoxic T cells destroy infected host cells -​ Helper T cells activate the humoral and cell-mediated immune responses -​ Before this can happen, however, two conditions must be met -​ First, a foreign molecule must be present that can bind specifically to the antigen receptor of the helper T cell. -​ Second, this antigen must be displayed on the surface of an antigen-presenting cell. An antigen-presenting cell can be a dendritic cell, macrophage, or B cell. -​ Helper T cells release Interleukin I (cytokine) leading to the release of Interleukin II -​ Antigen presentation by a dendritic cell or macrophage activates a helper T cell, which proliferates, forming a clone of activated cells -​ In contrast, B cells present antigens to already activated helper T cells, which in turn activate the B cells themselves -​ Activated helper T cells also help stimulate cytotoxic T cells  SBI 4UY Exam Review 36 Humoral Immune Response -​ Stimulated by both an antigen and cytokines, the B cell proliferates and differentiates into memory B cells and antibody secreting plasma cells -​ B cell activation leads to a robust humoral immune response: A single activated B cell gives rise to thousands of identical plasma cells -​ These plasma cells stop expressing a membrane-bound antigen receptor and begin producing and secreting antibodies -​ These secreted antibodies defend against extracellular pathogens in blood and lymph by binding to antigens, thereby neutralizing pathogens or making them better targets for phagocytic cells and complement proteins -​ Antibodies do not directly kill pathogens, but by binding to antigens, they interfere with pathogen activity or mark pathogens in various ways for inactivation or destruction. -​ The bound antibodies prevent infection of a host cell, thus neutralizing the virus -​ In opsonization, antibodies that are bound to antigens on bacteria do not block infection, but instead present a readily recognized structure for macrophages or neutrophils thereby promoting phagocytosis -​ When antibodies facilitate phagocytosis, as in opsonization, they also help fine-tune the humoral immune response. -​ Recall that phagocytosis enables macrophages and dendritic cells to present antigens to and stimulate helper T cells, which in turn stimulate the very B cells whose antibodies contribute to phagocytosis -​ This positive feedback between innate and adaptive immunity contributes to a coordinated, effective response to infection Cell-mediated Immune Response -​ Cytotoxic T cells use toxic proteins to kill cells infected by viruses or other intracellular pathogens -​ Cytotoxic T cells recognize fragments of foreign proteins produced by infected cells -​ The activated cytotoxic T cell secretes proteins that disrupt the membranes of target cells and trigger apoptosis -​ They defend against intracellular pathogens and certain cancers by binding to and lysing the infected cells Osmoregulation and Excretion Osmosis -​ Osmoregulation is based largely on balancing the uptake and loss of water and solutes -​ The driving force for movement of water and solutes is a concentration gradient of one or more solutes across the plasma membrane  SBI 4UY Exam Review 37 -​ Water enters and leaves cells by osmosis -​ Osmolarity, the solute concentration of a solution, determines the movement of water across a selectively permeable membrane -​ If two solutions are isoosmotic, water molecules will cross the membrane at equal rates in both directions -​ If two solutions differ in osmolarity, the net flow of water is from the hypoosmotic (less concentrated) to the hyperosmotic (more concentrated) solution -​ Animals can maintain water balance in one of two ways -​ Osmoconformers are isoosmotic with their surroundings and do not regulate their osmolarity -​ Ie. marine invertebrates -​ Osmoregulators expend energy to control water uptake and loss in a hyperosmotic or hypoosmotic environment -​ Ie. marine vertebrates Structure of Kidneys -​ Kidneys, are the excretory organs of vertebrates, function in both excretion and osmoregulation -​ The numerous tubules of kidneys are highly organized -​ The vertebrate excretory system also includes ducts and other structures that carry urine from the tubules out of the kidney and out of the body Nephrons and Urine Production -​ Excretory systems regulate solute movement between internal fluids and the external environment -​ Most excretory systems produce urine by refining a filtrate derived from body fluids -​ Key functions of most excretory systems -​ Filtration: Filtering of body fluids -​ Reabsorption: Reclaiming valuable solutes -​ Secretion: Adding nonessential solutes and wastes to the filtrate -​ Excretion: Processed filtrate containing nitrogenous wastes is released from the body -​ The filtrate produced in Bowman’s capsule contains salts, glucose, amino acids, vitamins, nitrogenous wastes, and other small molecules -​ Proximal Tubule:  SBI 4UY Exam Review 38 -​ Reabsorption of ions, water, and nutrients takes place in the proximal tubule -​ Molecules are transported actively and passively from the filtrate into the interstitial fluid and then capillaries -​ As the filtrate passes through the proximal tubule, materials to be excreted become concentrated -​ Some toxic materials are actively secreted into the filtrate -​ Descending Limb of the Loop of Henle: -​ Reabsorption of water continues through channels formed by aquaporin proteins -​ Movement is driven by the high osmolarity of the interstitial fluid, which is hyperosmotic to the filtrate -​ The filtrate becomes increasingly concentrated -​ Ascending Limb of the Loop of Henle: -​ In the ascending limb of the loop of Henle, salt but not water is able to diffuse from the tubule into the interstitial fluid -​ The filtrate becomes increasingly dilute -​ Distal Tubule: -​ The distal tubule regulates the K+ and NaCl concentrations of body fluids -​ The controlled movement of ions (H+ and HCO3–) contributes to pH regulation -​ Collecting Duct: -​ The collecting duct carries filtrate through the medulla to the renal pelvis -​ One of the most important tasks is reabsorption of solutes and water -​ Urine is hyperosmotic to body fluids Antidiuretic Hormone -​ Antidiuretic hormone, ADH, is also called vasopressin -​ ADH molecules released from the posterior pituitary bind to and activate membrane receptors on collecting duct cells -​ This initiates a signal cascade leading to insertion of aquaporin proteins into the membrane lining the collection duct -​ The increase in water recapture reduces urine volume -​ Osmoreceptor cells in the hypothalamus monitor blood osmolarity and regulate release of ADH from the posterior pituitary  SBI 4UY Exam Review 39 -​ When osmolarity rises above its set point, ADH release into the bloodstream increases -​ When osmolarity drops below a set point, it causes a reduction in ADH secretion -​ Alcohol is a diuretic, as it inhibits the release of ADH Renin-Angiotensin-Aldosterone System (RAAS) -​ The renin-angiotensin-aldosterone system (RAAS) is part of a complex feedback circuit that functions in homeostasis -​ A drop in blood pressure near the glomerulus causes the juxtaglomerular apparatus (JGA) to release the enzyme renin -​ Renin travels through the bloodstream to the liver where it breaks down angiotensinogen to angiotensin I -​ ACE then converts angiotensin I to angiotensin II -​ Angiotensin II raises blood pressure and decreases blood flow to the kidneys -​ It also stimulates the release of the hormone aldosterone, which increases blood volume and pressure