Bio 1107: Exam 2

Figure 7.4: Three Stages of Cellular Respiration

-> (1) glycolysis; (2) pyruvate oxidation and the citric acid cycle; and (3) oxidative phosphorylation, which includes the electron transfer system and chemiosmosis.

Figure 6.2: Energy from the Sun

-> Energy flow from the Sun to photosynthetic organisms (here, colonies of the green alga Volvox), which capture the kinetic radiant energy of sunlight and convert it to potential chemical energy in the form of complex organic molecules.

Figure 6.4: Exergonic and Endergonic Reactions

-> Exergonic (A) and endergonic (B) reactions. An endergonic reaction proceeds only if energy is supplied by an exergonic reaction.

Figure 6.13: Competitive and Noncompetitive Inhibitors

-> How competitive (A) and noncompetitive (B) inhibitors reduce enzyme activity.

Figure 14.11: DNA Polymerase and Sliding Clamp

-> (A) Stylized drawing of a bacterial DNA polymerase. The enzyme viewed from the side resembles a human right hand. The polymerization reaction site lies on the palm. When the incoming nucleotide is added, the thumb and fingers close over the site to facilitate the reaction. (B) How DNA polymerase is shown in subsequent figures of DNA replication. The figure also shows a sliding DNA clamp tethering the DNA polymerase to the template strand.

Figure 3.27: Double

-> (A)Arrangement of sugars, phosphate groups, and bases in the DNA double helix. The dotted lines between the bases designate hydrogen bonds. (B)Space-filling model of the DNA double helix. The paired bases, which lie in flat planes, are seen edge-on in this view.)

Figure 14.6: DNA Double Helix

-> (A)Space-filling model. (B)Schematic drawing. (C)Chemical structure drawing. Arrows and labeling of the ends show that the two polynucleotide chains of the double helix are antiparallel—that is, they have opposite polarity in that they run in opposite directions. In the space-filling model at the top, the spaces occupied by atoms are indicated by spheres. There are 10 base pairs per turn of the helix; only 8 base pairs are visible because the other 2 are obscured where the backbones pass over each other.

Figure 14.5: X-Ray Diffraction of DNA

-> (A)The X-ray diffraction method to study DNA. (B)The diffraction pattern Rosalind Franklin obtained. The X-shaped pattern of spots (dashed lines) was correctly interpreted by Franklin to indicate that DNA has a helical structure similar to a spiral staircase.

Figure 15.11: Aminoacylation (also known as charging): the addition of an amino acid to a tRNA. (1)

-> 1. ATP and the amino acid bind to the aminoacyl-tRNA synthetase. The enzyme catalyzes the joining of the amino acid to AMP, with the release of two phosphates.

Figure 15.15: Translation elongation (2)

-> 2. Peptidyl transferase, an enzyme in the large ribosomal subunit, cleaves the amino acid (here the initiator methionine) from the tRNA in the P site and forms a peptide bond between it and the amino acid on the tRNA in the A site. When the reaction is complete, the polypeptide chain is attached to the A site tRNA, and an "empty" tRNA (a tRNA with no amino acid attached) is in the P site.

Figure 15.11: Aminoacylation (also known as charging): the addition of an amino acid to a tRNA. (2)

-> 2. The correct tRNA binds to the enzyme.

Figure 15.11: Aminoacylation (also known as charging): the addition of an amino acid to a tRNA. (3)

-> 3. The enzyme transfers the amino acid from AA-AMP to the tRNA, forming AA-tRNA. AMP is released.

Figure 15.15: Translation elongation (3)

-> 3. The ribosome translocates (moves) along the mRNA to the next codon, using energy from TP hydrolysis. During translocation, the two tRNAs remain bound to their respective codons, so this step positions the peptidyl-tRNA (the tRNA with the growing polypeptide) in the P site, and generates a new vacant A site. The empty tRNA that was in the P site is now in the E site.

Figure 15.7: mRNA Splicing (cont'd.)

-> 3. The spliceosome cleaves the pre-mRNA at the junction between the 3' end of exon 1 and the 5' end of the intron. The intron is looped back to bond with itself near its 3' end. -> 4. The spliceosome cleaves the pre-mRNA at the junction between the 3' end of the intron and exon 2, releasing the intron and joining together the two exons. The released intron, called a lariat structure because of its shape, is degraded by enzymes, and the released snRNPs are used in other mRNA splicing reactions.

Figure 15.11: Aminoacylation (also known as charging): the addition of an amino acid to a tRNA. (4)

-> 4. AA-tRNA is released from the enzyme, and the enzyme is ready to enter another reaction series.

Figure 7.5: Substrate-level Phosphorylation

-> A phosphate group is transferred from a high-energy donor directly to ADP, forming ATP.

Figure 15.15: Translation elongation (1)

-> A protein elongation factor (EF) complexes with the aminoacyl-tRNA to bring it to the ribosome, and another EF is needed for ribosome translocation. For simplicity, the EFs are not shown in the figure. -> 1. An aminoacyl-tRNA binds to the codon in the A site; TP is hydrolyzed in this step.

Figure 14.20: Telomere Repeat

-> Addition of a telomere repeat to the 39 end of a eukaryotic linear chromosome by telomerase. - 1. End of a chromosome showing the primer used for new DNA synthesis (red) still in place. -> 2. Chromosome end after primer removal. -> 3. Telomerase binds to the single-stranded 3' end of the chromosome by complementary base pairing between the RNA of telomerase and the telomere repeat. -> 4. Telomerase synthesizes new telomere DNA using telomerase RNA as the template. -> 5. The longer (top) strand is replicated by primase and DNA polymerase, and then the primer is removed, leaving a new 5' end to the bottom strand of the chromosome.

Figure 6.10: An Enzyme and its Substrate

-> Combination of an enzyme, hexokinase (in blue), with its substrate, glucose (in yellow). Hexokinase catalyzes the phosphorylation of glucose to form glucose-6-phosphate. The phosphate group that is transferred to glucose is not shown. Note how the enzyme undergoes a conformational change (an induced fit), closing the active site more tightly as it binds the substrate.

Figure 14.11: DNA Polymerase

-> DNA polymerase structure. + (A) Stylized drawing of a bacterial DNA polymerase. The enzyme viewed from the side resembles a human right hand. The polymerization reaction site lies on the palm. When the incoming nucleotide is added, the thumb and fingers close over the site to facilitate the reaction. (B) How DNA polymerase is shown in subsequent figures of DNA replication. The figure also shows a sliding DNA clamp tethering the DNA polymerase to the template strand

Figure 6.12: Enzyme Concentration

-> Effect of increasing enzyme concentration (A) or substrate concentration (B) on the rate of an enzyme-catalyzed reaction.

Figure 15.19: Frameshift Mutation (cont'd.)

-> Effects of base-pair mutations in protein-coding genes on the amino acid sequence of the encoded polypeptide.

Figure 6.6: Energy Coupling Using ATP

-> Energy coupling using ATP in the synthesis of glutamine from glutamic acid and ammonia.

Figure 15.10: tRNA Structure

-> In A, the red dots show sites where bases are chemically modified into other forms; chemical modification of certain bases is typical of tRNAs. This yeast alanine tRNA has the purine inosine (I) in the anticodon which has relatively loose base-pairing ability, allowing this single tRNA to pair with each of three alanine codons 59-GCU-39, 59-GCC-39, and 59-GCA-39. This tRNA also has the unusual base pair G-U. Unusual base pairs, allowed by the greater flexibility of short RNA chains, are common in tRNAs. The amino acid, in this case alanine, binds to the 39end of a tRNA molecule.

Figure 5.11 A

-> In glycolysis, each six-carbon glucose molecule is converted into two molecules of pyruvate. The next two stages of cellular respiration require oxygen. The Krebs cycle (bottom left) releases carbon dioxide and generates high-energy molecules. Oxidative phosphorylation (bottom right), the last stage in cellular respiration, produces more ATP than any other metabolic pathway.

Figure 7.6: Membranes and Compartments of a Mitochondrion

-> Label lines that end in a dot indicate a compartment enclosed by the membranes.

Figure 5.10:

-> Mitochondria are the site of cellular respiration in eukaryotes

Figure 5.10: Cellular Respiration in Eukaryotes

-> Mitochondria are the site of cellular respiration in eukaryotes

Figure 6.3: Equilibrium Point of a Reaction

-> No matter what quantities of glucose-1-phosphate and glucose-6-phosphate are dissolved in water, when equilibrium is reached, there is 95% glucose-6-phosphate (product) and 5% glucose-1-phosphate (reactant). At equilibrium, the number of reactant molecules being converted to product molecules equals the number of product molecules being converted back to reactant molecules. The reaction at the equilibrium point is reversible; it may be made to run to the right (forward) by adding more reactants, or to the left (reverse) by adding more products.

Figure 3.24: Nucleotide Structure

-> Nucleotide structure

Figure 3.24: Part 2

-> Other nucleotides: + Containing guanine: Guanosine or deoxyguanosine monophosphate, diphosphate, or triphosphate + Containing cytosine: Cytidine or deoxycytidine monophosphate, diphosphate, or triphosphate + Containing thymine: Thymidine monophosphate, diphosphate, or triphosphate + Containing uracil: Uridine monophosphate, diphosphate, or triphosphate

Figure 7.7: Overall Reaction of Glycolysis

-> Overall reactions of glycolysis, which occur in the cytosol. Glycolysis splits glucose (six carbons) into pyruvate (three carbons) and yields ATP and NADH.

Figure 7.9: Pyruvate Oxidation and the Citric Acid Cycle

-> Overall reactions of pyruvate oxidation and the citric acid cycle, which occur in the mitochondrial matrix. Pyruvate (three carbons) is oxidized to an acetyl group (two carbons) and CO2. NAD1 accepts two electrons and one proton removed in the oxidation. The acetyl group, carried by CoA, is the fuel for the citric acid cycle. Each turn of the citric acid cycle oxidizes an acetyl group of acetyl-CoA to 2 CO2. Acetyl-CoA, NAD1, FAD, ADP, and Pi enter the cycle; CoA, NADH, FADH2, ATP, and CO2 are released as products.

Figure 7.11: Oxidative Phosphorylation

-> Oxidative phosphorylation: the mitochondrial electron transfer system and chemiosmosis. Oxidative phosphorylation involves the electron transfer system (steps 1-6), and chemiosmosis by ATP synthase (steps 7-9). Blue arrows indicate electron flow; red arrows indicate H+ movement.

Figure 15.16: Polysomes

-> Polysomes, consisting of a series of ribosomes reading the same mRNA

Figure 15.13: Initiation of Translation

-> Protein initiation factors (IFs) participate in the event but, for simplicity, they are not shown in the figure. The IFs are released when the large ribosomal subunit binds and GTP is hydrolyzed.

Figure 3.25: Nitrogenous Bases

-> Pyrimidine and purine bases of nucleotides and nucleic acids. Red arrows indicate where the bases link to ribose or deoxyribose sugars in the formation of nucleotides.

Figure 14.10

-> Reaction assembling a complementary DNA chain in the 5'→3' direction on a template DNA strand, showing the phosphodiester bond formed when the DNA polymerase enzyme adds each deoxyribonucleotide to the chain. -> 1 DNA polymerase forms a complementary base pair between a deoxyribonucleoside triphosphate with an A base (dATP) from the surrounding solution with the next, T, nucleotide of the template strand. -> 2 DNA polymerase catalyzes the formation of a phosphodiester bond involving the 3 '-OH group at the end of the new chain and the innermost of the three phosphate groups of the dATP. The other two phosphates are released as a pyrophosphate molecule. The new chain has been lengthened by one nucleotide. The process continues, with DNA polymerase adding complementary nucleotides one by one to the growing DNA chain.

Figure 7.8: Reactions of Glycolysis (1)

-> Reactions of glycolysis. Because two molecules of G3P are produced in reaction 5, all the reactions from 6 to 10 are doubled (not shown). The names of the enzymes that catalyze each reaction are in rust.

Figure 7.10: The Citric Acid Cycle

-> Reactions of the citric acid cycle. Acetyl-CoA, NAD1, FAD, ADP, and Pi enter the cycle; CoA, NADH, FADH2, ATP, and CO2 are released as products. The CoA released in reaction 1 can cycle back for another turn of pyruvate oxidation. Enzyme names are in rust.

Figure 15.6: Processing Eukaryotic Pre-mRNA

-> Relationship between a eukaryotic protein-coding gene, the pre-mRNA transcribed from it, and the mRNA processed from the pre-mRNA

Figure 7.2

-> Relative loss and gain of electrons in a redox reaction, the burning of methane (natural gas) in oxygen. Compare the positions of the electrons in the covalent bonds of reactants and products In this redox reaction, methane is oxidized because the carbon atom has partially lost its shared electrons, and oxygen is reduced because the oxygen atoms have partially gained electrons.

Figure 14.19: Multiple Origins of Replication

-> Replication from multiple origins in the linear chromosomes of eukaryotes.

Figure 14.14: Replication at a Replication Fork

-> Replication of antiparallel template strands at a replication fork. Synthesis of the new DNA strand on the top template strand is continuous. Synthesis on the new DNA strand on the bottom template strand is discontinuous—short lengths of DNA are made which are then joined into a continuous chain. The overall effect is synthesis of both strands in the direction of replication fork movement.

Figure 15.12: Ribosome Structure

-> Ribosomal structure

Figure 14.8: DNA Replication Models

-> Semiconservative (A), conservative (B), and dispersive (C) models for DNA replication.

Figure 15.17: Simultaneous Transcription and Translation

-> Simultaneous transcription and translation in progress in an electron microscope preparation extracted from E. coli. X57,000

Figure 7.14: Summary of ATP Production

-> Summary of ATP production from the complete oxidation of a molecule of glucose. The total of 32 ATP assumes that electrons carried from glycolysis by NADH are transferred to NAD+ inside mitochondria. If the electrons from glycolysis are instead transferred to FAD inside mitochondria, total production will be 30 ATP.

Figure 14.17: Replication Bubble

-> Synthesis of leading and lagging strands in the two replication forks of a replication bubble formed at an origin of replication.

Figure 6.7: The ATP/ADP Cycle

-> The ATP/ADP cycle that couples reactions releasing free energy and reactions requiring free energy.

Figure 3.28: DNA Base Pairs

-> The DNA base pairs A-T (adenine-thymine) and G-C (guanine-cytosine), as seen from one end of a DNA molecule.Dotted lines between the bases designate hydrogen bonds.

Figure 7.13: H+ Gradient Powers ATP Synthesis

-> The Racker and Stoeckenius experiment demonstrating that an H+ gradient powers ATP synthesis by ATP synthase.

Figure 6.11: Catalytic Cycle of Enzymes

-> The catalytic cycle of enzymes

Figure 14.15: Molecular model of DNA replication

-> The drawings simplify the process. In reality, the enzymes assemble at the fork, replicating both strands from that position as the template strands fold and pass through the assembly. -> 1 DNA helicase unwinds the DNA. Primases synthesize short RNA primers in the 5'→3' direction—in the direction of unwinding on the leading strand template, and in the opposite direction on the lagging strand template. Topoisomerase prevents twisting ahead of the replication fork as the DNA unwinds. -> 2 DNA polymerase III adds DNA nucleotides to the RNA primer, continuing the 5'→3' direction of synthesis.

Figure 14.1

-> The four deoxyribonucleotide subunits of DNA, linked into a polynucleotide chain. The sugar-phosphate backbone of the chain is highlighted in gray. The connection between adjacent deoxyribose sugars is a phosphodiester bond. The polynucleotide chain has polarity; at one end, the 5' end, a phosphate group is bound to the 5' carbon of a deoxyribose sugar, whereas at the other end, the 3' end, a hydroxyl group is bound to the 3' carbon of a deoxyribose sugar.

Figure 6.9: Enzymes Reduce Activation Energy

-> The reduction allows biological reactions to proceed rapidly at the relatively low temperatures that can be tolerated by living organisms.

Figure 14.12: Helicase, SSBs, and Topoisomerase

-> The roles of DNA helicase, single-stranded binding proteins (SSBs), and topoisomerase in DNA replication.

Figure 15.2: Prokaryote and Eukaryote Transcription and Translation

-> Transcription and translation in: (A)prokaryotes; and (B) eukaryotes. In prokaryotes, RNA polymerase synthesizes an mRNA molecule that is ready for translation on ribosomes. In eukaryotes, RNA polymerase synthesizes a precursor-mRNA (pre-mRNA molecule) that is processed to produce a translatable mRNA. That mRNA exits the nucleus through a nuclear pore and is translated on ribosomes in the cytoplasm.

Figure 15.5 (part 2)

-> Transcription has three stages: initiation, elongation, and termination. RNA polymerase moves along the gene, separating the two DNA strands to allow RNA synthesis in the 5'->3' direction using the 3'->5' strand as template.

Figure 15.5: Transcription of a Eukaryotic Protein-Coding Gene

-> Transcription of a Eukaryotic Protein-Coding Gene Transcription has three stages: initiation, elongation, and termination. RNA polymerase moves along the gene, separating the two DNA strands to allow RNA synthesis in the 5'->3' direction using the 3'->5' strand as template

Figure 15.15: Termination of Translation

-> Translation termination

Figure 14.7: Semiconservative Replication

-> Watson and Crick's model for DNA replication. The original DNA molecule is shown in gray. A new polynucleotide chain (red) is assembled on each original chain as the two chains unwind. The template and complementary copy chains remain wound together when replication is complete, producing molecules that are half old and half new. The model is known as the semiconservative model for DNA replication.

Figure 7.3: NAD+

-> When a fuel molecule is oxidized, releasing two hydrogen atoms, NAD+, the oxidized form of the carrier, accepts a proton (H+) and two electrons and is transformed into NADH, the reduced form of the carrier. The nitrogenous base (blue) of NAD that adds and releases electrons and protons is nicotinamide, which is derived from the vitamin niacin (nicotinic acid).

Figure 15.15: Translation elongation (4)

->4. When translocation is complete, the empty tRNA in the E site is released. With the A site vacant and the peptidyl-tRNA in the P site, the ribosome repeats the elongation cycle. In each cycle, the growing polypeptide chain is transferred from the P site tRNA to the amino acid on the A site tRNA.

Figure 6.5: ATP

->ATP, the primary molecule that couples energy requiring reactions to energy-releasing reactions in living organisms. ( Pi is the symbol used in this book for inorganic phosphate.)

Learning Objective 31: Describe the importance of enzymes in metabolic pathways

Class 10 PPT Slides: -> 24: Enzymes/catalysts + Enzymes decrease activation energy of a reaction system. - By decreasing activation energy an enzyme can increase the speed of a reaction. + heat has a similar effect, but you can not heat only one system, therefore heat can lead to damage (denaturation). -> 25: What enzymes don't do + Do NOT supply free energy + Can't make an endergonic reaction exergonic - ATP hydrolysis can be coupled to an endergonic reaction to make it proceed spontaneously but, alone, an enzyme cannot. - Enzymes do NOT change the ΔG of a reaction. + Enzymes are reusable - Although anything that would affect protein conformation would also affect enzymes + Enzymes sometimes require a cofactor Cengage Chapter 6 Slides: -> 35: 6.4 Role of Enzymes in Biological Reactions + Even when a reaction is spontaneous (negative ΔG), the reaction will not start unless a small amount of activation energy (Ea) is added - Activation energy makes bonds unstable and ready to be broken (the transition state) -> 36: Figure 6.8 -> 37: Enzymes + A catalyst is a chemical agent that accelerates (catalyzes) the rate of a reaction without being changed by the reaction - The most common biological catalysts are proteins called enzymes, which increase the rate of reaction by lowering the activation energy of the reaction - Enzymes do not alter the ΔG of the reaction = The free energy stays the same; the difference is in the path the reaction takes -> 38: Figure 6.9 -> 39: Enzymes (cont'd.) + The 3-D structure of a protein (its conformation) determines its function - each enzyme has a specific protein structure that catalyzes a specific reaction - Cells have thousands of different enzymes, found in different areas inside and outside of the cell - The name of an enzyme typically refers to its substrate or type of reaction, and ends in -ase (e.g., proteinases) -> 40: Enzymatic Reactions + In enzymatic reactions, an enzyme combines briefly with reacting molecules and is released unchanged when the reaction is complete - The reactant that an enzyme acts on is called the substrate - Each type of enzyme catalyzes the reaction of a single type of substrate molecule or group of closely related molecules (enzyme specificity) -> 41: Figure 6.10 -> 42: Enzymatic Reactions (cont'd.) + The substrate interacts with a small pocket or groove in the enzyme molecule, called the active site - When the substrate binds at the active site, both enzyme and substrate molecules are distorted - this makes the chemical bonds in the substrate ready for reaction (induced fit) = Once an enzyme-substrate complex is formed, catalysis occurs - the substrate is converted into one or more products -> 43: Figure 6.11 -> 44: Cofactors and Coenzymes + Many enzymes require a cofactor, a nonprotein group that binds to the enzyme, for catalytic activity. - Some are metallic ions, including iron, copper, magnesium, zinc, and manganese. + Other cofactors are small organic molecules (coenzymes) which are often derived from vitamins - Some coenzymes bind loosely to enzymes - Others (prosthetic groups) bind tightly -> 45: Enzymes Stabilize the Transition State + Enzymes stabilize the transition state through three major mechanisms - Bringing the reacting molecules together - Exposing the reactant molecules to altered charge environments that promote catalysis - Changing the shape of the substrate molecules -> 46: Study Break 6.4 + 1.How do enzymes increase the rates of the reaction they catalyze? + 2.Can enzymes alter the ΔG of a reaction? -> 47: 6.5 Factors That Affect Enzyme Activity + Changes in concentration of substrate and other molecules that bind to enzymes can alter enzyme activity + Control mechanisms modify enzyme activity, adjusting reaction rates to meet a cell's requirements for chemical products + Changes in temperature and pH can have a significant effect on enzyme activity -> 48: Enzyme and Substrate Concentrations + When excess substrate is present the rate of catalysis is proportional to the amount of enzyme. - When enzyme concentration is kept constant and the amount of substrate increases the rate of catalysis increases as well until enzymes are cycling as rapidly as possible. + Once enzymes reach saturation, more substrate being added has no effect on rate of catalysis -> 49: Figure 6.12 -> 50: Enzyme Inhibitors + : non substrate molecules that bind to an enzyme and decrease its activity - Competitive: Inhibitors bind to the active site, blocking access for the normal substrate - slowing or stopping the reaction - Noncompetitive: Inhibitors bind at a location other than the active site - reducing the ability of the active site to bind substrate -> 51: Figure 6.13 Class 10 Handout:

Learning Objective 29: Recognize the energy content of a reacting system's reactants/substrates and products. Differentiate between anabolic and catabolic, exergonic and endergonic, and spontaneous and non-spontaneous reactions

Class 10 PPT Slides: -> 10: Energy content in Reacting systems + System: The object being studied + Open system: exchange matter and energy with their surroundings -> 11: Rules about energy in reacting systems + Conservation of energy - You can transfer and transform energy however it can't be created or destroyed = This is referred to as the 1st law of thermodynamics -> 12: Rules about energy in reacting systems + Entropy= disorder - As changes occur during a chemical reaction, entropy increases. = Second law of thermodynamics - The total disorder of a reacting system increases - If parts of a reacting system get more ordered (ex: bigger, more complex molecule), somewhere else in the system, something is getting even more disordered. -> 13: Spontaneous vs non-spontaneous reactions + In order to determine whether a reaction will be ender or exergonic you have to look at the enthalpy and entropy. - Enthalpy - if the REACTANTS have more potential energy than the products, the reaction may be spontaneous. - Entropy - if the PRODUCTS have more entropy than the reactants, the reaction may be spontaneous. = These two factors are related in the formula for FREE ENERGY -> 14: Spontaneous vs nonspontaneous reactions (pt. 2) + Delta= change + ΔG=ΔH−TΔS - Equation for change in free energy between a reactions start and finish - The change in free energy of a reaction = the change in ENTHALPY (potential energy) minus Temp* (change in ENTROPY) + If ΔG is negative then that means a reaction is spontaneous because free energy has decreased + If ΔG is positive then a reaction is nonspontaneous and free energy is increasing -> 15: CLARIFYING SPONTANEOUS + Spontaneous means that the reactants have more free energy than the products, and a reaction can occur without additional energy or fuel. - Spontaneous does NOT mean quick -> 16: Spontaneous/non-spontaneous, exergonic/endergonic + Exergonic= spontaneous - decrease in free energy + Endergonic= nonspontaneous - increase in free energy -> 17: Catabolic/Anabolic + Metabolism: The chemical reactions of a living thing + Catabolic reactions: Something is being broken down (chemical energy is released) + Anabolic reactions: Something is being built (energy is expended) - Biosynthetic reaction - Biosynthetic reaction: Multistep, enzyme catalyzed reaction where substrates are converted into more complex products. Cengage Chapter 6 Slides: -> 8: First Law of Thermodynamics (the principle of the conservation of energy) + Energy can be transformed from one form to another, or transferred from one place to another, but it cannot be created or destroyed - Total amount of energy remains constant -> 9: Energy Flow from the Sun + For most organisms, the ultimate source of energy is the sun - plants capture kinetic energy of light and convert it to the chemical potential energy of complex organic molecules. - that energy is stored in sugars (and other organic compounds) and is used for growth, reproduction, and other processes of living organisms. + Eventually the solar energy plants utilized is completely converted into heat energy and is released (as it is largely unusable for living organisms). -> 10: Figure 6.2 -> 11: Second Law of Thermodynamics + The total disorder (entropy) of a system and its surroundings always increases (although the total energy in the universe does not change). - Living organisms seem to decrease in entropy as they grow - but when nutrients and waste products are considered, total energy remains constant and entropy increases -> 12: Study break + 1.What are kinetic energy and potential energy? + 2.In thermodynamics, what is meant by an isolated system, a closed system, and an open system? -> 13: Free Energy and Spontaneous Reactions + A spontaneous reaction is a chemical or physical reaction that will occur without an input of energy. - Two factors related to the first and second laws of thermodynamics must be considered to determine whether a reaction is spontaneous: (1) the change in energy content of a system, and (2) its change in entropy -> 14: Energy Content and Entropy + Reactions tend to be spontaneous if the products have less potential energy then the reactants. - Potential energy in a system is its enthalpy (H) + Reactions that release energy are exothermic - the products have less potential energy than the reactants. + Reactions that absorb energy are endothermic - the products have more potential energy than the reactants. -> 15: Energy Content and Entropy (cont'd.) + Reactions tend to be spontaneous when the products are less ordered (more random) than the reactants. - Entropy increases after each reaction + Reactions tend to occur spontaneously if the entropy of the products is greater than the entropy of the reactants -> 16: Change in Free Energy + The portion of a system's energy that is available to do work is called free energy (G) + The change in free energy, ΔG can be calculated for any chemical reaction from the formula: - ΔG = ΔH - TΔS + ΔH is the change in enthalpy + T is the absolute temperature in degrees Kelvin (K) + ΔS is the change in entropy -> 17: Change in Free Energy (cont'd.) + For a reaction to be spontaneous, ΔG must be negative. + In some processes, such as the combustion of methane, the large loss of potential energy, negative enthalpy (ΔH), dominates in making a reaction spontaneous + In other reactions, such as the melting of ice at room temperature, a decrease in order (ΔS increases) dominates -> 18: Equilibrium Point + In many spontaneous biological reactions reactants may not convert completely to products even though the reactions have a negative ΔG + The reactions run in the direction of completion (toward reactants or toward products) until they reach the equilibrium point - a state of balance between the opposing factors pushing the reaction in either direction - balanced reactions -> 19: Equilibrium Point (cont'd.) + As a system moves toward equilibrium, its free energy becomes progressively lower and reaches its lowest point when the system achieves equilibrium (ΔG = 0) + To move away from equilibrium requires free energy and thus will not be spontaneous + The more negative the ΔG, the further toward completion the reaction will move before equilibrium is established -> 20: Figure 6.3 -> 21: Reversible Reactions + Many reactions have a ΔG that is near zero and are readily reversible by adjusting the concentration of products and reactants slightly. + Reversible reactions are written with a double arrow: - A + B ↔ C + D reactants products -> 22: Reactions in Living Organisms + Many reactions in living organisms never reach equilibrium because living systems are open - the supply of reactants is constant and products do not accumulate. - The ΔG of life is always negative - organisms constantly take in energy-rich molecules and use them to do work + Organisms reach equilibrium, ΔG = 0, only when they die -> 23: Exergonic and Endergonic Reactions + Exergonic reaction - Reaction that releases free energy - ΔG is negative because the products contain less free energy than the reactants + Endergonic reaction - Reactants must gain free energy from the surroundings to form the products - ΔG is positive because the products contain more free energy than the reactants -> 24: Figure 6.4 -> 25: Metabolic Pathways + A metabolic pathway is a series of reactions in which the products of one reaction are used immediately as the reactants for the next reaction in the series. + In a catabolic pathway (or a single catabolic reaction) energy is released by the breakdown of complex molecules to simpler compounds; overall ΔG is negative. + In an anabolic pathway (or an anabolic reaction or biosynthetic reaction), energy is used to build complicated molecules from simpler ones; overall ΔG is positive. -> 26: STUDY BREAK 6.2 + 1.What two factors must be taken into account to determine if a reaction will proceed spontaneously? + 2.What is the relation between ΔG and the concentrations of reactants and products at the equilibrium point of a reaction? + 3.Distinguish between exergonic and endergonic reactions, and between catabolic and anabolic reactions. How are the two categories of reactions related? Class 10 Handout:

Learning Objective 30: Detail the role of ATP in a cell

Class 10 PPT Slides: -> 20: ATP + ATP- Adenosine triphosphate + ADP- Adenosine diphosphate + AMP- Adenosine monophosphate -> 21: Atp's role in the cell + ATP + H2O -> ADP + Pi + Change in G= -7.3 Kcal/Mol -> 22: Atp's role in the cell + You can couple the energy released by the exergonic hydrolysis of ATP to other cellular processes through phosphorylation + ATP is used by the cell to do work that would otherwise be impossible. Cengage Chapter 6 Slides: -> 27: 6.3 Adenosine Triphosphate (ATP): Energy Currency of the Cell + ATP: Consists of five- carbon ribose, nitrogenous base, and a chain of three phosphate groups + Negative charges repel each other- bonding arrangement is unstable + Removal of one or two phosphate groups is spontaneous and releases large amounts of free energy -> 28: Hydrolysis of ATP + Breakdown of ATP is a hydrolysis reaction - Results in the formation of ADP and a molecule of inorganic phosphate. + ADP can be broken down to AMP -> 29: Figure 6.5 -> 30: Energy Coupling + Energy coupling: When ATP is hydrolyzed the terminal phosphate group is transferred to the reactant molecule involved in an endergonic reaction. + The addition of a phosphate group to a molecule is called phosphorylation. + Energy coupling requires an enzyme with a specific site that binds both ATP and the reactant molecule to bring the ATP and reactant molecule into close association -> 31: Figure 6.6 -> 32: Regeneration of ATP + ATP synthesis from ADP and Pi is an endergonic reaction that uses energy from the exergonic breakdown of carbohydrates, proteins, and fats (food) + The continual hydrolysis and resynthesis of ATP is called the ATP/ADP cycle - Approximately 10 million ATP molecules are hydrolyzed and resynthesized each second in a typical cell -> 33: Figure 6.7 -> 34: Study break 6.3 + 1.How does the structure of the ATP molecule store and release energy? + 2.How are coupled reactions important to cell function? How is ATP involved in coupled reactions? Class 10 Handout:

Learning Objective 28: Explain and provide examples of kinetic and potential energy

Class 10 PPT Slides: -> 8: Kinetic and Potential Energy + Kinetic- Energy something has as result of movement + Potential- Energy something has as a result of location/ position + Molecules have both types of energy (provided they are not at absolute o)- kinetic comes from the movement of the atoms and potential comes from arrangement of atoms and bonds. Cengage Chapter 6 Slides: -> 4: 6.1 Energy, Life, and Laws of Thermodynamics + Energy: the capacity to do work + Different forms of Energy: Heat, Chemical, Mechanical, Electrical, Radiant (light, gamma rays, and x-rays) + Energy can be converted from one form to another- Eg. photosynthesis transforms radiant light energy into chemical energy (ATP) -> 5: Kinetic Energy and Potential Energy + All energy can exist in two forms- kinetic and potential + Kinetic energy: Energy of an object in motion + Potential energy: Stored energy Worksheet 10: -> Define energy: -> Two forms of energy: kinetic, and potential -> First law of thermodynamics: -> Second law of thermodynamics: -> What is the role of cellular respiration: -> Anabolism -> Catabolism -> Spontaneous reactions: -> Non-spontaneous reactions: -> Endergonic -> Exergonic -> Energy carriers -> ATP -> ADP -> ΔG -> Activation energy -> Two roles of enzymes -> Reaction coupling

Learning Objective 32: Describe the common components of all cells and the specific structural features of eukaryotic cells.

Class 11 PPT Slides: -> 11: Background on cells + Cells = basic unit of life + Tissues = combos of cells with common function + Several tissues together = organ + Organs working cooperatively = organ system + The whole shebang, all the organ systems working together in 1 flesh sack = the organism -> 12: Cells have 4 common components + Plasma membrane (fluid mosaic, barrier, proteins are embedded) + Cytoplasm + DNA (genetic material for all cells) + Ribosomes - RNA + protein, used for protein synthesis -> 13: Prokaryotes and Eukaryotes + Prokaryotes - lack membrane-enclosed internal compartments (eg. nucleus) + Most have a cell wall containing peptidoglycan + Prokaryotes are believed to be much like the first cells + Organisms in the domains Archaea & Bacteria are prokaryotes -> 14: Eukaryotes + Membrane bound organelles! - Nucleus - Mitochondria - Endoplasmic reticulum and golgi apparatus - Bigger! - We are eukaryotic organisms, as are plants. -> 15: Eukaryotic cells have mitochondria + Site for conversion of stored energy (macromolecule molecular bonds - which types??) to more useful form (ATP) + Inner membrane is folded - Folds are called cristae - Area enclosed is the mitochondrial matrix - Area between inner and outer membrane is the intermembrane space Cengage Chapter 7 Slides: -> 4: Mitochondria and ATP + ATP forms in mitochondria as part of the reactions of cellular respiration + Cellular respiration - Collection of metabolic reactions that breaks down food molecules to produce energy in the form of ATP. Class 11 Handout:

Learning Objective 27: Understand the orientation of nucleotides in the DNA double helix, including complementary base pairing.

Class 8 PPT Slides: -> 14: The DNA double helix + Two strands of DNA nucleotides interact to form the recognizable double helix + The backbones/exterior of the helix = the five carbon sugar-phosphate group held together by a phosphodiester bond (see slide 13) + The two strands are held together by hydrogen bonds between nitrogenous bases. -> 15: Double helix + Facilitates its replication. The helix can be opened and 1 strand used as a template for the other. + Note 5' and 3' ends of the molecule -> 16: 5'-3' orientation of DNA strands + Each of the 5 carbons in deoxyribose or ribose has a number. The strand's ends are distinguishable by whether the exposed tail of the strand is on the 5' or 3' side of the sugar. -> 17: Complementary base pairing in the DNA double helix + Antiparallel orientation + A:T + C: G Cengage Chapter 3 Slides: -> 98: The DNA Molecule + The DNA molecule is a double helix (double-stranded) consisting of two nucleotide chains wrapped around each other in a spiral that resembles a twisted ladder + The sides of the ladder are the sugar-phosphate backbones of the two chains - The rungs of the ladder are nitrogenous bases which extend inward from the sugars toward the center of the helix -> 99: Figure 3.27 -> 100: DNA Base Pairs + The two nucleotide chains of a DNA double helix are held together by hydrogen bonds between the base pairs + A base pair consists of one purine and one pyrimidine + Adenine pairs only with thymine (A-T), forming two stabilizing hydrogen bonds + Guanine pairs only with cytosine (G-C), forming three hydrogen bonds -> 101: Figure 3.28 -> 102: Complementary Base Pairing + Formation of A-T and G-C pairs allows the sequence of one nucleotide chain to determine the sequence of its partner in the double helix + The nucleotide sequence of one chain is said to be complementary to the nucleotide sequence of the other chain + In DNA replication, one nucleotide chain is used as a template for the assembly of a complementary chain according to the A-T and G-C base-pairing rules -> Fig. 3.29

Learning Objective 33: Describe the role of oxidation and reduction in the flow of energy from sunlight to ATP

Class 11 PPT Slides: -> 17: Energy flow/electron flow + Life and its systems are driven by a cycle of electron flow that is powered by light in photosynthesis and oxidation in cellular respiration. -> 18: Energy flow/electron flow + Redox reactions = oxidation and reduction + Oxidation = LOSS of electrons, becoming more +, loss of a full H + Reduction = GAIN of electrons, becoming more -, gain of a full H - OIL RIG = Oxidation Is Loss, Reduction Is Gain - The process of getting energy from glucose àATP involves transferring electrons = From glucose to oxygen =Glucose is oxidized and O2 is reduced -> 19: Cellular Respiration in Eukaryotes + Figure 5.10 -> 20: Electron transfer + Throughout the process of oxidizing glucose to get energy, dehydrogenases move electrons to carriers - What type of molecule do you think a dehydrogenase is? Enzyme = Example of electron carriers: nicotinamide adenine dinucleotide (NAD) Cengage Chapter 7 Slides: -> 9: Oxidation and Reduction Reactions + Oxidation - The removal of electrons from a substance - The substance from which the electrons are removed (the electron donor) is oxidized + Reduction - The addition of electrons to a substance - The substance that receives the electrons (the electron acceptor) is reduced -> 10: Redox Reactions + Oxidation and reduction reactions are always coupled + Redox reactions - Reactions that remove electrons from a donor molecule and simultaneously add them to an acceptor molecule -> 11: Redox Reaction (cont'd.) + In redox reactions, electrons release some of their energy as they pass from a donor molecule to an acceptor molecule + This free energy is available for cellular work, such as ATP synthesis + Molecules that accept electrons may also combine with protons (H+), as oxygen does when it is reduced to form water -> 12: Electron Sharing + The gain or loss of an electron in a redox reaction is not always complete + Sometimes only the degree of electron sharing in covalent bonds changes (a relative loss or gain of electrons) - Example: When methane burns, carbon loses a relative share of electrons, and oxygen gains a share -> 13: Figure 7.2 -> 14: Electron Flow from Fuel to Final Electron Acceptors + During photosynthesis, electrons from water are pushed to very high energy levels and stored (along with H+) in sugar molecules. + Cellular respiration releases energy from electrons as they pass among acceptor molecules to a final acceptor (oxygen) + Total energy obtained depends on the difference between the high energy level in fuel and the lower energy level in the final acceptor -> 15: Summary: Cellular Respiration + Cellular respiration includes reactions that transfer electrons from organic molecules (such as glucose) to oxygen, and reactions that make ATP + C6H12O6 + 6 O2 + 32 ADP + 32 Pi → 6 H2O 6 CO2 + 32 ATP -> 16: Electron Carriers + Dehydrogenase enzymes facilitate transfer of electrons from a fuel molecule to a molecule that acts as an electron carrier + The most common electron carrier is the coenzyme nicotinamide adenine dinucleotide (NAD+) + In cellular respiration, dehydrogenases transfer two electrons and one proton to NAD+ (the oxidized form), resulting in its complete reduction to NADH (the reduced form) -> 17: Figure 7.3 -> Fig. 7.1 Class 11 handout

Learning Objective 34: Explain the 3 steps of cellular respiration, including the 2 methods for making ATP.

Class 11 PPT Slides: -> 22: Cellular Respiration in Eukaryotes: glycolysis, pyruvate processing + CAC, and oxidative phosphorylation + Figure 5.10 + Cytoplasm: - Glycolysis + Mitochondria: - Citric Acid Cycle - Oxidative Phosphorylation - Electron Transport Chain - ATP Synthesis -> 23: Cellular Respiration Overview + Figure -> 24: 3 steps of cellular respiration + Cellular respiration is a set of four processes: - 1. Glycolysis—A six-carbon glucose is broken down into two three-carbon pyruvate - 2. Oxidation of Pyruvate and the Citric Acid Cycle—Each pyruvate is oxidized to CO2 - 3. Oxidative phosphorylation (ETC, and ATP synthesis) — Electrons move through a transport chain and their energy is used to set up a proton gradient, which is used to make ATP Cengage Chapter 7 Slides: -> 18: Three Stages of Cellular Respiration + Glycolysis: - Enzymes break a 6-carbon molecule of glucose into two 3-carbon molecules of pyruvate - Some ATP is synthesized by substrate-level phosphorylation - an enzyme-catalyzed reaction that transfers a phosphate group from a substrate to ADP -> 19: Three Stages of Cellular Respiration + Pyruvate Oxidation - Enzymes convert the 3-carbon pyruvate into a 2-carbon acetyl group, which enters the citric acid cycle and is completely oxidized to carbon dioxide - Some ATP is synthesized during the citric acid cycle -> 20: Three Stages of Cellular Respiration + Oxidative phosphorylation - High-energy electrons are delivered to oxygen by a sequence of electron carriers in the electron transfer system - Free energy released by electron flow generates an H+ gradient by chemiosmosis - ATP synthase uses the H+ gradient as the energy source to make ATP -> 21: Figure 7.4 -> 22: Figure 7.5 -> 23: Where Cellular Respiration Takes Place + Reaction locations: - Glycolysis - in the cytosol - Pyruvate oxidation and citric acid cycle - in the mitochondrial matrix - Electron transfer system and ATP synthase enzymes - in the inner mitochondrial membrane -> 24: Figure 7.6 -> 25: Study break 7.1 + 1.Distinguish between oxidation and reduction. + 2.Distinguish between cellular respiration and oxidative phosphorylation. -> Fig 7.4 Class 11 handout

Learning Objective 35: Understand the input and output of glycolysis and the energy-requiring and energy-producing steps of the process.

Class 11 PPT Slides: -> 28: Cellular Respiration Is Highly Efficient in Eukaryotes: Glycolysis + Glycolysis: the first stage of cellular respiration - Occurs in the cytoplasm of the cell - Is an anaerobic process (does not require oxygen) - Splits sugars making a three-carbon compound called pyruvate = For each glucose molecule that is split, the products are: + Two molecules of ATP + Two molecules of NADH Cengage Chapter 7 Slides: -> 26: 7.2 Glycolysis: Splitting Sugar in Half + Glycolysis (Embden-Meyerhof pathway) breaks 6-carbon glucose into two molecules of 3-carbon pyruvate (pyruvic acid) in 10 sequential enzyme-catalyzed reactions + Glycolysis takes place in the cytosol of all organisms -> 27: Energy Flow in Glycolysis + The initial steps of glycolysis require energy - 2 ATP are hydrolyzed + 4 ATP are produced by substrate-level phosphorylation, for a net gain of 2 ATP + The electron carrier NAD+ is reduced to NADH, which carries 2 electrons and a proton (H+) removed from fuel molecules -> 28: Summary: Glycolysis + Reactions 1-5 generate 2 molecules of G3P using 2 ATP; reactions 6-10 convert G3P to pyruvate, producing 4 ATP and 2 NADH -> 29: Figure 7.7 -> 30: Figure 7.8: Part 1 -> 31: Figure 7.8: Part 2 -> 32: STUDY BREAK 7.2 + 1.What are the energy-requiring and energy-releasing steps of glycolysis? + 2.What is the redox reaction in glycolysis? + 3.How is ATP synthesized in glycolysis? -> Fig 7.7 Class 11 handout -> https://www.youtube.com/watch?time_continue=8&v=o6Fdq103cNo&feature=emb_logo, https://www.youtube.com/watch?v=8qij1m7XUhk -

Learning Objective 36: Understand the input and output of pyruvate oxidation and the citric acid cycle.

Class 12 PPT Slides: -> 10: Pyruvate oxidation and the CAC + Glycolysis (in the cytosol) creates 2 pyruvate molecules of glucose each of which contains 3C. + That pyruvate is then transported into the mitochondrial matrix + Pyruvate oxidation and the citric acid cycle involve a sequence of enzyme driven reactions - Input: Pyruvate Output: CO2 Reduces NADH and FADH2 which are brought to the inner mitochondrial matrix. -> 11: Pyruvate oxidation + Pyruvate are oxidized to acetyl coA + In the process of pyruvate oxidation, electrons are loaded onto NAD+ -> 12: Acetyl-Co-A enters the citric acid cycle + Citric acid cycle = Krebs cycle = tricarboxylic acid cycle + In the citric acid cycle, 2 acetyl Co-A will be processed. Let's just track 1 for now. - reactants: 1 Acetyl CoA+ 3 NAD+ 1 FAD+ ADP+ Pi+H20 - Products: 2 CO2, 3 NADH, 1 FADH, 1 ATP, 3 H, 1 CoA = ATP here is made by substrate level phosphorylation. -> 13: Substrate level phosphorylation + In the process of oxidizing acetyl CoA, ATP is produced through substrate level phosphorylation -> 14: Input/output for "1-turn" of TCA cycle + By the end of TCA cycle, we have fully oxidized glucose to carbon dioxide and loaded up electron carriers Cengage Chapter 7 Slides: -> 33: 7.3 Pyruvate Oxidation and the Citric Acid Cycle + Active transport moves pyruvate into the mitochondrial matrix where pyruvate oxidation and the citric acid cycle take place + Oxidation of pyruvate generates CO2, acetyl-coenzyme A (acetyl-CoA), and NADH + The acetyl group of acetyl-CoA enters the citric acid cycle -> 34: Summary: Pyruvate Oxidation + Pyruvate oxidation (pyruvic acid oxidation) removes CO2 from pyruvate and oxidizes the remaining 2-carbon fragment to an acetyl group (CH3CO) which is carried by acetyl-CoA to the citric acid cycle -> 35: Figure 7.9 -> 36: Overview: The Citric Acid Cycle + In the citric acid cycle, carbon products of pyruvate oxidation are oxidized to CO2 + All available electrons are transferred to 3 NAD+ (NADH) and 1 FAD (FADH2) + Each turn of the citric acid cycle produces 1 ATP by substrate-level phosphorylation -> 37: Summary: The Citric Acid Cycle + The eight reactions of the citric acid cycle (tricarboxylic acid cycle or Krebs cycle) oxidize acetyl groups completely to CO2 , generate 3 NADH and 1 FADH2, and synthesize 1 ATP by substrate-level phosphorylation -> 38: Figure 7.10 -> 7.9 -> 7.10

Learning Objective 24: Understand the general functions of DNA and RNA

Class 8 PPT Slides: -> 5: DNA and RNA + DNA - deoxyribonucleic acid + Made of deoxyribonucleotides + RNA - ribonucleic acid + Made of ribonucleotides + Nucleotides, the components of DNA and RNA, userve as the building blocks of nucleic acids + Two of them (ATP and GTP) - chemical energy, regulate and adjust cellular activity, play important roles in biochemical reactions, etc. -> 6: DNA and RNA + DNA - stores hereditary information for all cells and many viruses + RNA - - hereditary information storage for another group of viruses - The code for moving between the language of DNA and the language of amino acids/proteins - Part of the sites where proteins are made within cells (those sites are called ribosomes, and in addition to RNA, they contain protein) - A type of RNA is responsible for bringing amino acids to ribosomes Cengage Chapter 3 Slides: -> 88: 3.5 Nucleotides and Nucleic Acids + Nucleic acids are macromolecules assembled from repeating monomers called nucleotides - DNA (deoxyribonucleic acid) stores hereditary information responsible for inherited traits in all eukaryotes and prokaryotes and in a large group of viruses - RNA (ribonucleic acid) is the hereditary molecule of another large group of viruses - three major types of RNA are involved in protein synthesis -> 89: Nucleotides + A nucleotide, the monomer of nucleic acids, consists of three parts linked together by covalent bonds: - A nitrogenous base formed from rings of carbon and nitrogen atoms - A five-carbon, ring-shaped sugar - One to three phosphate groups Cengage Chapter 14 Slides: -> 7: 14.2 DNA Structure + DNA contains four different nucleotides: - Adenine (A) and guanine (G) are purines Built from a pair of fused carbon-nitrogen rings - Thymine (T) and cytosine (C) are pyrimidines Built from a single carbon-nitrogen ring -> 8: Chargaff's Rules + A must pair with T and C must pair with G + Discovered Nitrogenous bases in DNA occur in different ratios - amount of purines equals the amount of pyrimidines. -> 9: The Polynucleotide Chain + DNA nucleotides are joined to form a polynucleotide chain + Deoxyribose sugars are linked by phosphate groups in an alternating pattern forming a sugar-phosphate backbone. - each phosphodiester bond links the 3' of one sugar to the 5' of another. -> 10: Polarity + DNA has polarity - one end is a hydroxyl group (bound to a 3' sugar) and the other is a phosphate bound to the 5' end of a sugar. -> 11: Four Subunits of DNA + Phosphodiester bonds connect adjacent deoxyribose sugars of the four subunits of DNA + The polynucleotide chain has polarity - Figure 14.4 -> 12: Molecular Structure + Maurice Wilkins and Rosalind Franklin, of King's College, London, each used X-ray diffraction to study DNA structure - Franklin interpreted an X-shaped distribution of spots in the diffraction pattern to mean that DNA has a helical structure + X-ray diffraction: - An X-ray beam is directed at a molecule in the form of a regular solid (ideally a crystal) - Positions of atoms in the molecule are deduced from diffraction patterns produced on photographic film -> 13: Figure 14.5 -> 14: The DNA Model + Watson and Crick constructed a double-helix model for DNA - Two polynucleotide chains twist around each other, like a double-spiral staircase - The two chains are antiparallel (opposite polarity) - Pairs of bases fill the central space + This arrangement satisfied both Franklin's X-ray data and Chargaff's chemical analysis3.5 Nucleotides and Nucleic Acids

Learning Objective 25: Explain the three components of nucleotides, including the differences between purines and pyrimidines.

Class 8 PPT Slides: -> 8: The structure of nucleotides + Can be 1-3 phosphate groups + Nitrogenous bases are formed by rings of C and N, can accept protons. + Two types: - Purines - 2 rings - Pyrimidines - 1 ring - "pure as gold" - the purines are A and G, the others are pyrimidines -> 9: Nucleotides + Difference between a nucleotide and a nucleoside-> Nucleotide (5 C sugar, nitrogenous base, phosphate group), Nucleoside ( 5 C sugar, nitrogenous base) + Difference between ribose and deoxyribose. Ribose has an OH group rather than an H (like deoxyribose) on the 2' C. Cengage Chapter 3 Slides: -> 90: Figure 3.24 -> 91: Figure 3.24: Nucleotide Structure -> 92: Two Types of Nitrogenous Bases + Pyrimidines - Nitrogenous bases with one carbon-nitrogen ring - Uracil (U), thymine (T), and cytosine (C) + Purines - Nitrogenous bases with two carbon-nitrogen rings - Adenine (A) and guanine (G) -> 93: Figure 3.25 -> 94: Ring-shaped Sugars + Nitrogenous bases link covalently to a five-carbon sugar: - Deoxyribose in DNA deoxyribonucleotides - Ribose in RNA ribonucleotides + The two sugars differ only in the chemical group bound to the 2′ carbon (—H in deoxyribose, —OH in ribose) + In unlinked nucleotides: 1, 2, or 3 phosphate groups bond to the ribose or deoxyribose sugar at the 5′ carbon -> 95: Nucleosides and Nucleotide Phosphates + A structure containing only a nitrogenous base and a five-carbon sugar is a nucleoside + A nucleotide is a nucleoside phosphate + Examples: - Adenosine monophosphate (AMP) - Adenosine diphosphate (ADP) - Adenosine triphosphate (ATP) -> 96: DNA and RNA + DNA and RNA consist of polynucleotide chains, with one nucleotide linked to the next by a phosphodiester bond + One nucleotide is linked to the next by a bridging phosphate group between the 5′ carbon of one sugar and the 3′ carbon of the next sugar - Alternating sugar and phosphate groups forms the backbone of a nucleic acid chain Cengage Chapter 14 Slides: -> 15: Figure 14.6 -> 16: Base Pairs + A purine pairs with a pyrimidine and fills exactly the space between the two strands. - The purine-pyrimidine base pairs in Watson and Crick's model (A-T and G-C) are stabilized by hydrogen bonds - two between A and T and three between G and C. - C cannot pair with A, and G cannot pair with T, because of the hydrogen bonding requirements -> 17: Complementary Strands + The two strands of a DNA molecule are complementary to each other - Complementary base pairing: = wherever a T is present the matching nucleotide must be an A and visa versa = wherever a C is present the corresponding nucleotide must be a G and visa versa -> 18: Hereditary Material + Watson and Crick recognized that genetic information is coded into DNA by the linear sequence of the four nucleotides - Combining the nucleotides into groups allows an essentially infinite number of different sequences to be "written" - Watson, Crick, and Wilkins shared a Nobel Prize for their discovery in 1962 - Franklin died of cancer at age 38 in 1958 -> 19: Study Break 14.2 + 1.Which bases in DNA are purines? Which are pyrimidines? + 2.What bonds form between complementary base pairs? Between a base and the deoxyribose sugar? + 3.Which features of the DNA molecule did Watson and Crick describe? + 4.The percentage of A in a double-stranded DNA molecule is 20. What is the percentage of C in that DNA molecule? -> Fig 3.24

Learning Objective 37: Describe the structure and function (in terms of electrons and H+) of the electron transfer system.

Class 12 PPT Slides: -> 16: Oxidative phosphorylation starts with the electron transfer system / ETC + Oxidative phosphorylation: 3rd stage of cellular respiration + Occurs in the inner mitochondrial matrix + Aerobic process + Passes hydrogen and e- from e- carriers through the chain towards the final acceptor of 02-> Creating H20 as a bi-product (as well as the desired ATP) + ATP synthase generates ATP -> 17: ETC structure and function + ETC= integral proteins within the inner mitochondrial matrix and inter complex shuttles + The complexes of the ETC are made up of many proteins doing the work of taking the higher energy e- from the carriers NADH and FADH2 + Each complex has progressively lower free energy and higher affinity for e-'s - O2 has the highest affinity for e-'s (electronegativity) and is placed at the end of the ETC + The energy released from transporting e-s is used to pump H+ -> 18: ETC structure and function + High energy e-s enter the ETC being carried by NADH and FADH2 - NAD+ is oxidized and returns to earlier steps + E-s lose energy as they are passed from one complex to the next - Chemical potential energy is transformed into the potential energy of the H+ gradient. + The e-s then bind to O2 forming water - without oxygen the ETC is null -> 19: Cengage Chapter 7 Slides: -> 41: 7.4 Oxidative Phosphorylation: The ETS and Chemiosmosis + High-energy electrons removed from fuel molecules and picked up by carrier molecules (NAD+ or FAD) are released into the electron transfer system of mitochondria + Mitochondrial electron transfer system (ETS) - Series of electron carriers that alternately pick up and release electrons and ultimately transfer them to their final acceptor - oxygen -> 42: Energy Flow in the ETS + In the ETS, electrons release free energy used to build the H+ gradient across the inner mitochondrial membrane. - High H + concentration in the intermembrane compartment - Low H+ concentration in the matrix + The H + gradient supplies energy that drives ATP synthesis by mitochondrial ATP synthase -> 43: Protein Complexes in the Inner Mitochondrial Membrane + Three major protein complexes (numbered I, III, and IV) in the inner mitochondrial membrane serve as electron carriers + A smaller complex (complex II) is bound to the inner mitochondrial membrane on the matrix side + Electrons from NADH enter the ETS at complex I - electrons from FADH enter the ETS at complex II -> 44: Transfers Between Proteins + Two small, mobile electron carriers, cytochrome c and ubiquinone (coenzyme Q), shuttle electrons between the major complexes + Cytochromes - Proteins with a heme prosthetic group that contains an iron atom that accepts and donates electrons -> 45: Electron Flow + Individual electron carriers of the ETS are organized specifically from high to low free energy - NADH and FADH2 contain abundant free energy and are easily oxidized - The terminal electron acceptor (O2) is easily reduced + Electron movement through the system is spontaneous, releasing free energy -> 46: Figure 7.11 -> Fig 7.11

Learning Objective 38: Explain what proton motive force is: where does it come from, what is it used for

Class 12 PPT Slides: -> 21: Proton motive force + Concentration gradient established by pumping H+ across the inner mitochondrial membrane + Proteins of the ETC are H+ pumps + The energy for the pumps come from the electrons movement from high to low energy. - Coupling Cengage Chapter 7 Slides: -> 47: Forming the H+ Gradient + Ubiquinone and complexes I, III, and IV actively transport protons (H+) from matrix to intermembrane compartment + Concentration of H+ in the intermembrane compartment generates an electrical and chemical gradient across the inner mitochondrial membrane + Proton-motive force - Stored energy produced by proton and voltage gradient - Energy is used for ATP synthesis and cotransport of substances to and from mitochondria -> 48: ATP Synthase and Chemiosmosis + In the mitochondrion, ATP is synthesized by ATP synthase, an enzyme embedded in the inner mitochondrial membrane + The H+ gradient powers ATP synthesis by ATP synthase by chemiosmosis (the chemiosmotic hypothesis) + ATP synthase uses proton-motive force to add phosphate to ADP to generate ATP (phosphorylation -> 49: ATP Synthase Structure and Function + A basal unit in the inner membrane is connected by a stalk to a headpiece located in the matrix - a peripheral stator bridges the basal unit and headpiece + Proton-motive force moves protons in the intermembrane space through the enzyme's basal unit into the matrix + H+ flow powers ATP synthesis by rotation of the ATP synthase headpiece (chemiosmosis) -> Fig 7.11

Learning Objective 39: Explain how chemiosmosis fuels oxidative phosphorylation and ATP synthase.

Class 12 PPT Slides: -> 23: How does the ETC lead to ATP production + ATP synthase - Uses the gradient set up by the H+ proton force - Couples the movement of H+ back down their concentration gradient and the phosphorylation of ADP. -> 24: How do we know ATP synthase does this? + Question: Does the gradient power ATP synthase? supporting Mitchell's chemiosmotic theory + Experiment: Racker and Stoeckenius made vesicles containing a proton pump and ATP synthase in order to determine whether proton- motive forces drove the production of ATP -> 25: What would happen if the vesicles were originally placed in the light then moved to the dark? Cengage Chapter 7 Slides: -> 50: Summary: ATP Production + 32 ATP are produced from each molecule of glucose oxidized (about 2.5 ATP per NADH, and 1.5 per FADH2) - Glycolysis: 2ATP + 2 NADH (5 ATP) - Pyruvate oxidation: 2 NADH (5 ATP) - Citric acid cycle: 2 ATP + 6 NADH (15 ATP) + 2 FADH2 (3 ATP) -> 51: Figure 7.14 -> 52: Conservation of Chemical Energy + Hydrolysis of ATP to ADP yields about 7.0 kcal/mol - total energy conserved in 32 ATP is about 224 kcal/mol + Glucose burned in air releases 686 KCal/Mol + Efficiency of cellular glucose oxidation 33% - The rest of the chemical energy is released as body heat. -> 53: Experimental Research + E. Racker of Cornell and W. Stoeckenius of UCSF showed that the H+ gradient powers ATP synthesis by ATP synthase + Experiment: Racker and Stoeckenius made membrane vesicles that had a proton pump and ATP synthase to determine whether proton-motive force drives ATP synthesis -> 54: Figure 7.13 -> Fig. 7.13 + The experiments of Racker and Stoeckenius -> https://www.youtube.com/watch?v=b_cp8MsnZFA

Learning Objective 40: Explain how the bacterial transformation experiments supported the hypothesis that DNA is the genetic material of cells.

Class 13 PPT Slides: -> 12: Bacterial transformation experiment + How was DNA established as the hereditary molecule? + Experiment 1: - One strain of Virulent bacteria (S) - One strain of non-infection bacteria (R) = Group of mice with dead (S)- survived = Group of mice with alive (S) - died = Group of mice with alive (R) - survived = Group of mice with alive (R) and Dead (S)= Died - Conclusion something must have been passed from the dead infectious virulent strand to the living non-infectious strand. This something is most likely not protein because they would have denatured due to the heat killing process.-> therefore: DNA -> 14: Bacterial transformation experiment (part 2) + Tested whether DNA makes sense + In order to examine the virulent S bacteria more closely three different enzymes were added to different groups: - An enzyme that breaks down proteins- the bacteria was still virulent - An enzyme that breaks down RNA- the bacteria was still virulent - And an enzyme that breaks down DNA- the bacteria lost its pneumonia causing abilities. + Conclusion: it is DNA that causes bacteria to have its infectious abilities - eg. DNA is the hereditary molecule. - But this conclusion was controversial and people still believed there was a fluke in the experiment. -> 15: Why do you think it was hard for people to process that DNA is the hereditary molecule, not protein? Why was that tough to believe? + Proteins are much more varied, there are 20 different amino acids so it is much easier to postulate the fact that that variation could cause different traits rather than some long stringy thing with only 4 nitrogenous bases to choose from. - DNA is made up of: Nitrogenous base, a phosphate group, and five carbon sugar - Proteins are made up of: long chains of amino acids. Class 14 PPT Slides: -> 7: Review - section 14.1 + Example: Experiment 1 - transformation of bacteria - Why was the experiment done - to understand what makes some bacteria infectious and some not, to understand how traits are passed from one organism to the next - What was actually done - a scientist took two kinds of bacteria, Type S that caused disease, and Type T that didn't. They heat-killed S and mixed it with R and injected the blend into mice. - What was observed - the blend still caused disease. The R bacteria gained the ability to cause disease by being mixed with the S bacteria. - What did that mean - something was coming out of the dead S and going into the live R and making the R change (transform) into a disease-causing bacteria. -> 9: The experiment with enzyme-targeted destruction of macromolecules in S bacteria + Why was the experiment done: To determine what came OUT of S bacteria and made R bacteria become virulent + What was actually done: Treated S bacteria with an enzyme that did 1 of the following: either destroyed protein, destroyed RNA, or destroyed DNA. Then mixed the extract of enzyme-treated S bacteria with R bacteria. Observed whether this mixture caused disease. + What was observed: The mixture of R and S could still cause disease when proteins or RNA were destroyed. The R bacteria were not transformed by the S extract if the extract had been treated with DNA-destroying enzyme. + What did that mean: DNA must be necessary for bacterial transformation. DNA affects the function of an organism. -> 10. The experiment with T2 Phages + Why was the experiment done: -To distinguish whether genetic material is DNA or protein + What was actually done - Grew a batch of bacteria in the presence of radioactive sulfur, infected them with T2, isolated the T2 now labeled with radioactive sulfur. Gave those sulfur-labeled T2 to fresh, new bacteria. Isolated what was inside the bacteria post-infection. Grew a second batch of bacteria in the presence of radioactive phosphorus, infected them with T2, isolated the T2 now labeled with radioactive phosphorus. Gave those phosphorus-labeled T2 to fresh, new bacteria. Isolated what was inside the bacteria post-infection. + What was observed - phosphorous, not sulfur. So the infecting material that the virus uses to code for its own replication inside the bacteria must contain phosphorus + What did that mean - because DNA and NOT protein contains phosphorus, DNA must be genetic material. Life is encoded by 4 nucleotides in various sequences, not 20 amino acids. -> 11. The experiment with heavy vs light nitrogen assessing dna replication (14.3) + To figure out how DNA is copied (replicated) + Bacteria were grown in the presence of a heavy isotope of nitrogen à then isolated a sample. Remaining bacteria in the heavy nitrogen mixture were transferred to an environment containing a lighter isotope of nitrogen and allowed to divide. After 1 division à isolated a sample. After 2 divisions à isolated a sample. They compared the weight of DNA isolated from those three samples. + Observed: -1st sample: heavy -2nd sample: somewhat lighter -3rd sample: somewhat lighter, and then some really light DNA + DNA replicates in a way where the parent DNA molecule is split, each strand acts as a template, and the new molecule contains some 1 old and 1 new polynucleotide strand. This is called semiconservative replication. - 13. Steps of dna replication - learning objective 42/43 + The two strands of the DNA molecule unwind for replication to occur. - helicase + DNA polymerase adds nucleotides (dNTPs - deoxyribonucleoside triphosphate-phosphate) to an existing chain using the parental template strand to determine which nucleotide to use. - The overall direction of new synthesis is in the 5'-3' direction, which is a direction antiparallel to that of the template strand. - Nucleotides enter onto a newly synthesized chain according to the A-T and G-C complementary base-pairing rules. -> Fig 14.2

Learning Objective 41: Explain how the T2 phage experiments provided evidence that DNA, not proteins, is the genetic material of cells.

Class 13 PPT Slides: -> 17: T2 phage experiment + A virus is composed of either DNA or RNA encased in a protein shell. - The virus used in this experiment is the T2 phage, which is DNA based and infects bacteria. + Question: is DNA or RNA the hereditary molecule? - Experiment: Hershey and Chase used a T2 phage and radioactive isotope labeling to determine whether DNA was hereditary. DNA contains only phosphorus while proteins contain only sulfur and not phosphorus. The two radioactive labels used were 32P and 35S. The T2 phages were used to infect other bacterial cells and the progeny phages were analyzed. Because DNA is the hereditary molecule the progeny phages each were found to contain the 32P while in the 35S trial the progeny phages did not contain even trace amounts of the radioactive material. - this proved and concluded the argument that DNA is the hereditary molecule, not proteins. Cengage Chapter 14 Slides: -> 6: 14.1 Establishing DNA as the Hereditary Molecule + Many scientists once believed that proteins were the most likely hereditary molecules + Several experiments showed that DNA, not protein, is the genetic material -> Fig. 14.3

Learning Objective 42: Understand what the semi-conservative model of DNA replication implies about the composition of how DNA is assembled.

Class 13 PPT Slides: -> 24: DNA replication - semiconservative model + in each new DNA double helix, one strand is from the original molecule, and one strand is new -> 25: DNA replication- conservative model + The original double helix splits into double stranded segments onto which new double stranded segments form. The newly forced segments split into two helices, creating 4 new strands of DNA interspersed with parent strand segments. -> 26: Dna replication overview + Two strands of DNA unwind (helicase) in order for replication to occur + DNA polymerase adds nucleotides to the parent strand using the complementary base pairing rules (A:T C:G) + Synthesis of the new strand occurs antiparallel to the parental strand -> 27: Great review - why do we think dna replicates semi-conservatively? + The meselson and Stahl experiment + Step 1: Bacteria was grown in a 15N medium creating heavy DNA molecules + Step 2: Some Bacteria was transferred to a 14N medium creating all new "light" DNA strands + Step 3: The DNA was extracted and separated according to different densities. -> 28: Results of Meselson and Stahl + The heavy DNA (cultured in 15N) sank lowest in the solution + The hybrid DNA (cultured in the 14N for only one generation) Floated in the middle of the solution + The light DNA (cultured in the 14N for two generations) floated to the top of the solution. Cengage Chapter 14 Slides: -> 21: Semiconservative Replication + Watson and Crick's model for DNA replication + Product molecules are half old and half new Figure: 14.7 -> 22: Other Proposed Models + Conservative replication model - The two strands of the original molecule serve as templates for the two strands of a new DNA molecule, then rewind into an all "old" molecule + Dispersive replication model - Neither parental strand is conserved and both chains of each replicated molecule contain old and new segments -> 23: Figure 14.8 -> 24: DNA Polymerases + DNA polymerases assemble complementary polynucleotide chains from individual deoxyribonucleotides + Four different deoxyribonucleoside triphosphates (one for each DNA base) are used: dATP, dGTP, dCTP, and dTTP + DNA polymerase adds a nucleotide only to the 3′ end (the exposed hydroxyl group) of an existing nucleotide chain -> Fig. 14.8 -> https://youtu.be/4gdWOWjioBE

Learning Objective 43: Describe the functions of the enzymes of DNA replication

Class 13 PPT Slides: -> 30: Enzymes in dna replication + Helicase- Unwinds the two parental strands + Primase- Adds DNA primers to DNA strands signaling where to start replication. + DNA polymerase- Adds complementary nucleotides to the parental strands + Another DNA polymerase- Removes and replaces RNA primers + DNA ligase- Connects the primer replacements with the nucleotide strand. Class 14 PPT Slides: -> 12: Semi-conservative DNA Replication + Resulting DNA strands have one parental strand and one new strand. -> 14: Learning objectives + Be able to describe the functions of the enzymes of DNA replication. + Be able to describe how the replisome is assembled at the origin of replication in E. coli and how leading and lagging strand replication proceeds. -> 17: Breaking down dna replication- what do you notice? + 3' end - this part of the 5-C sugar is the end of the DNA template strand + Phosphodiester bonds formed through dehydration synthesis -> 18: DNA polymerase + DNA polymerase can add a nucleotide only to an exposed 3' end of an existing nucleotide chain. - As a new DNA strand is assembled, a 3' group is always exposed at its "newest" end. The "oldest" end of the new chain has an exposed 5' triphosphate. - DNA polymerase READS the parent/template strand 3'-5' - DNA polymerase WRITES the new strand 5'-3' Cengage Chapter 14 Slides: -> 25: Antiparallel Strands + A 3′-OH group is exposed at the "newest" end of a new DNA strand; the "oldest" end has an exposed 5′ triphosphate -> DNA polymerases only assemble nucleotide chains in the 5′→3′ direction -> Because DNA strands run antiparallel to each other, the template strand is "read" in the 3′→5′ direction -> 26: Figure 14.10 -> 27: DNA Polymerase Structure + Consists of several polypeptide subunits arranged in different "hand shaped" domains. + The template DNA is pulled through the palm held by the "fingers" and "thumb" + The template strand and the 3' OH of the new strand meet at active site for the polymerization reaction of DNA synthesis, located in the palm domain. -> 28: Figure 14.11 -> 29: Sliding DNA Clamp + DNA polymerase extends the new strand one nucleotide at a time as it slides through the palm + Sliding DNA Clamp: - Protein that encircles DNA and attaches to the rear of DNA polymerase (relative to forward movement) + Tethers DNA polymerase to the template strand and increases rate of DNA synthesis -> 30: Figure 14.11 -> 31: Molecular Insights: Sliding Clamp + Research Question: How is the sliding clamp loaded and unloaded onto replicating DNA in humans? - Conclusion: The efficient unloading of sliding clamps by clamp loaders once DNA polymerase has dissociated from DNA is probably important for the overall efficiency of DNA replication -> 32: Summary: DNA Replication + The two strands of the DNA molecule unwind + DNA polymerase adds nucleotides to an existing chain + Direction of new synthesis is in the 5′→3′ direction, which is antiparallel to the template strand + Nucleotides enter a newly synthesized chain according to the A-T and G-C complementary base-pairing rules -> 33: Unwinding and Stabilizing DNA + In the bacterial chromosome unwinding of DNA for replication occurs at a small, specific region (origin of replication: Ori) + DNA helicase unwinds the DNA strands, producing a Y-shaped replication fork + Single-stranded binding proteins (SSBs) coat the exposed single-stranded DNA segments, keeping them from pairing + Topoisomerase cuts and rejoins DNA to prevent twisting in circular bacterial chromosomes -> 34: Figure 14.12 -> 35: RNA Primers and Primase + DNA polymerases add nucleotides only to an existing strand + A new strand begins with a short chain of RNA (primer), synthesized by the enzyme primase - Primase leaves the template, and DNA polymerase takes over, extending the RNA primer with DNA nucleotides as it synthesizes the new DNA chain - RNA primers are replaced with DNA later in replication -> Table 14.1.

Learning Objective 44: Describe how DNA is polymerized on the leading and lagging strand.

Class 14 PPT Slides: -> 20: Model of DNA replication in prokaryotes + Replication fork: Formed when Helicase separate the parental strands at the origin of replication. + Topoisomerase: Prevents the overwinding of the DNA double helix ahead of the DNA replication fork as the DNA is opening up. + SSBPs (Single stranded binding proteins): bind to the single-stranded DNA to prevent the helix from re-forming. + Primase: Synthesizes an RNA primer. DNA polymerase III uses this primer to synthesize the daughter DNA strand. + DNA Polymerase I: Replaces the RNA primer with DNA + DNA Ligase: Seals the gaps between okazaki fragments creating one cohesive molecule. -> 21: Be able to describe how DNA is polymerized on the leading and lagging strand. + Monomers are linked using phosphodiester bonds - Endergonic reaction (anabolic) - This is catalyzed by a complex of enzymes called DNA polymerase = energy is supplied by the hydrolysis of the nucleotide triphosphate = This energy is used to form a phosphor-diester bond between the Nucleotides 5' phosphate and the 3' OH of the last nucleotide on a strand (this is a condensation reaction) -> 23: Be able to describe how DNA is polymerized on the leading and lagging strand. (Cont.) + DNA can only synthesize from the 3'-5' end of the template strands + DNA synthesis occurs on the daughter strand 5'-3' -> 26: Synthesis on the leading and lagging strand + leading: continuous + lagging: discontinuous (okazaki fragments) Class 15 PPT Slides: -> 7: Replication bubbles + DNA replication is bidirectional from an origin of replication in prokaryotic and eukaryotic organisms + 1 ori in a circular plasmid - Many points of origin in replicating a linear DNA mol Cengage Chapter 14 Slides: -> 37: Continuous and Discontinuous DNA Synthesis + Because the two strands of a DNA molecule are antiparallel, only one template strand runs in a direction that allows DNA polymerase to make a continuous 5′→3′ copy + DNA polymerase copies the other strand in short lengths (Okazaki fragments) synthesized in the direction opposite to that of DNA unwinding (discontinuous replication) -> 38: Leading and Lagging Strands + Leading strand - In DNA replication, the new DNA strand is synthesized in the direction of DNA unwinding - Synthesized on the leading strand template + Lagging strand - New DNA strand synthesized discontinuously, in the direction opposite DNA unwinding - Synthesized on the lagging strand template -> 39: Figure 14.14 -> 40: Enzymes in DNA Replication + Many enzymes coordinate to replicate DNA + DNA helicase unwinds DNA + Primase initiates all new strands + DNA polymerase III is the main polymerase + DNA polymerase I forms the lagging strand + DNA ligase binds Okazaki fragments together -> 41: Figure 14.15 -> 44: Table 14.1 -> 47: Replication Bubbles and Multiple Origins + Unwinding at an origin creates to replication forks which once sealee together form a replication bubble. + eukaryotic chromosomes have multiple origins- replication initiates and a replication bubble forms at each origin + Forks eventually meet along the chromosomes to produce fully replicated DNA molecules. -> 48: Figure 14.17 -> 49: Figure 14.19 -> 50: Telomeres + The RNA primer in DNA replication causes a problem for replicating linear chromosomes of eukaryotes - When the primer is removed, it leaves a gap at the 5′ end of the new DNA strand that DNA polymerase can't fill - causing the chromosome to shorten with each replication - The ends of most eukaryotic chromosomes are protected by a buffer of noncoding DNA (the telomere) consisting of short, repeating sequences (the telomere repeat) -> 51: Telomerase + With each replication, some telomere repeats are lost, but the genes are unaffected - Buffering fails when the entire telomere is lost + Telomerase stops the shortening of telomeres by adding telomere repeats to chromosome ends - An RNA section binds to DNA and is the template for addition of telomere repeats - Active only in rapidly dividing embryonic cells, in germ cells - and in cancerous somatic cells -> 52: Figure 14.20 -> 53: Study Break 14.3 + 1.What is the importance of complementary base pairing to DNA replication? + 2.Why is a primer needed for DNA replication? How is the primer made? + 3.DNA polymerase III and DNA polymerase I are used in DNA replication in E. coli. What are their roles? Why are telomeres important? -> 54: 14.4 Repair of Errors in DNA + Errors made during replication (base-pair mismatches) are corrected in a proofreading mechanism by DNA polymerases + After replication is complete, remaining base-pair mismatches are corrected by a DNA repair mechanism -> Fig. 14.14 -> 14.15 -> 14.17 -> 14.19 -> image found on slide 7 of Class 15

Learning Objective 45: Explain the overall process (transcription, translation) of how DNA encodes protein, including the relationship between a sequence of nucleotides and a sequence of amino acids.

Class 15 PPT Slides: -> 14: Genetic Code + Codon is a sequence of three nucleosides that coincides to a specific amino acid. -> 15: Coding for amino acids + The genetic code is a three-letter code. What are the "letters"? + There are no spaces or punctuation between codons - The genetic code is commaless. +The genetic code is universal. With a few exceptions, the same codons specify the same amino acids in all living organisms, and also in viruses +The genetic code is redundant. Multiple Codons encode the same amino acid but only 1 amino acid is encoded by a single codon. - wobble - There are 64 possible codons that code for the 20 amino acids and 3 stop codons meaning that multiple codons can specify one amino acid. -The genetic code has start and stop signals. Start = initiator codon. Stop = termination, nonsense codons. The rest of the codons are "sense codons" and they code for amino acids. -> 16: Transcription + Transcription will begin when a gene product (protein) is needed. - The promoter of a gene includes information that will cause gene expression: = In correct cell types = Under specific circumstances + Transcription Factors (proteins that interact with DNA) are able to bind to specific DNA sequences. + Ex: - Pax6: binds to genes required for the lens of the eye and causes them to be expressed - Prox1: binds to genes required for just the posterior cells of the lens of the eye and turns these on and turns the other genes targeted by Pax6 off -> 17: Transcription is a point of gene expression regulation + Transcription will begin when a gene product (protein) is needed. + Signals from internal and external cell receptors will reach the nucleus as Transcription Factors + If: - 1.enough positive transcriptional regulators are present - 2.negative regulators are removed, + Then these factors will recruit the enzymes necessary for transcription. Cengage Chapter 15 Slides: -> 4: 15.1 The Connection Between DNA, RNA, and Protein + Two key pieces of research proved that genes code for the sequence of amino acids in proteins - Garrod's work concluded that alkaptonuria is an inherited trait - In the 1940s George Beadle and Edward Tatum's experiments with the bread mold Neurospora showed a direct relationship between genes and enzymes -> 5: Beadle and Tatum's Experiments + Beadle and Tatum grew nutritional mutants (auxotrophs) of Neurospora on a minimal medium supplemented with a single amino acid such as arginine (arg) + Hypothesized that each auxotrophic strain had a defect in a gene that codes for an enzyme needed to synthesize a particular amino acid (one gene-one enzyme hypothesis) - Their hypothesis was later updated to the one gene-one polypeptide hypothesis -> 6: Pathway from Gene to Polypeptide + In 1956 Francis Crick gave the name central dogma to the flow of information from DNA → RNA → protein - Transcription is the mechanism by which information encoded in the DNA template strand is copied into a complementary RNA strand - Translation uses the information encoded in the RNA copy to assemble amino acids into a polypeptide -> 7: Transcription and Translation + In transcription, RNA polymerase copies the DNA sequence of a gene into an RNA sequence - a protein-coding gene is transcribed into messenger RNA (mRNA) + In translation, an mRNA associates with a ribosome, on which amino acids specified by the mRNA are joined one by one to form the polypeptide encoded by the gene + Some genes do not encode a polypeptide - they encode various molecules that function in transcription, translation, and other processes in the cell -> 8: Prokaryotes and Eukaryotes + In eukaryotes, transcription in the nucleus produces a precursor-mRNA that must be altered to generate the functional mRNA + Pre-mRNA ends are modified and extra segments are removed by RNA processing - functional mRNA exits the nucleus and is translated in the cytoplasm + In prokaryotes, transcription in the cytoplasm produces a functional mRNA directly, with no modifications -> 9: Figure 15.2 -> 10: DNA and RNA Nucleotides + The DNA "alphabet" consists of four letters representing the four bases of DNA nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C) + The RNA "alphabet" consists of A, U, G, and C - the base uracil (U) acts in place of thymine (T) + The sequence of RNA nucleotides in mRNA is translated into a polypeptide containing 20 different types of amino acids -> 11: The Genetic Code + The nucleotide information that specifies the amino acid sequence of a polypeptide is called the genetic code + To code for 20 different amino acids, the four bases in an mRNA (A, U, G, and C) are used in combinations of three + Each three-letter word (triplet) of the code is called a codon + Three-letter codons in DNA are transcribed into complementary three-letter RNA codons -> Fig 15.5

Learning Objective 46: Describe the steps of transcription

Class 15 PPT Slides: -> 19: Transcription has 3 stages + 1. Initiation: - Transcription machinery (transcription factors, and RNA polymerase) assemble at the promoter and begin creating the complementary RNA chain (to that of the unwound template strand) + 2. Elongation - RNA polymerase II moves along the gene extending the RNA chain with the DNA continuing to unwind in front of the enzyme. + 3. Termination - Transcription ends and the RNA strand and RNA polymerase II are released from the strand. -> 20: Initiation + Transcription factors recognize the promoter. + RNA polymerase II then binds and forms the transcription initiation complex. -> 21: Elongation + During elongation, the prokaryotic RNA polymerase tracks along the DNA template. + Then it synthesizes mRNA in the 5' to 3' direction, and unwinds and rewinds the DNA as it is read. + Elongation occurs at a rate of 40 nucleotides per second. -> 22: termination + RNA pol separates from the gene at a termination signal Cengage Chapter 15 Slides: -> 17: 15.2 Transcription: DNA-Directed RNA Synthesis + The gene consists of two main parts: + Promoter (control sequence for transcription) + Transcription unit (section of the gene that is copied into an RNA molecule) + Transcription takes place in three stages: - Initiation - Elongation - Termination -> 18: Transcription Initiation + Initiation - Molecular machinery assembles at the promoter and begins synthesizing an RNA copy of the gene - The molecular machinery includes: + Transcription factors (TFs) that bind to the promoter in the area of a special sequence known as the TATA box + RNA polymerase, an enzyme that catalyzes the assembly of RNA nucleotides into an RNA strand -> 19: Transcription Initiation (cont'd.) + DNA is unwound to expose the template strand - RNA polymerase II begins RNA synthesis + RNA is made in the 5′→3′ direction using the 3′→5′ DNA strand as template + When adenine appears in the DNA template strand, a uracil is paired with it in the RNA transcript -> 20: Transcription Elongation and Termination + Elongation - RNA polymerase II moves along the gene extending the RNA chain - DNA continues to unwind ahead of the enzyme + Termination - The RNA transcript and RNA polymerase II are released from the DNA template -> 21: Figure 15.5 -> 22: Figure 15.5 (part 2) -> 23: Differences Between DNA Replication and Transcription + Only one of the two DNA nucleotide strands acts as a template for synthesis of a complementary copy + Only the sequence encoding a single gene is copied + RNA polymerases catalyze the assembly of RNA nucleotides into an RNA strand + RNA molecules are single polynucleotide chains + Uracil (U) pairs with adenine (A) -> 24: Differences in Transcription in Eukaryotes and Bacteria + Specific sequences in the promoter where the transcription apparatus assembles differ + In eukaryotes, RNA polymerase II cannot bind directly to DNA, transcription factors must first bind to the promoter - in bacteria, RNA polymerase binds directly to DNA + In bacteria, specific DNA sequences (Terminators) end transcription of the gene - eukaryotic DNA has no equivalent sequences -> Fig 15.3

Learning Objective 47: Understand the significance of a reading frame and the consequences of a frame shift.

Class 15 PPT Slides: -> 24: Coding for amino acids + Nucleotides in an mRNA sequence code for amino acids in 3 nucleotide portions known as codons. + The "reading frame" refers to which nucleotide starts the first codon; for each segment of DNA, there are 6 possible reading frames. https://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/readingframe.html Cengage Chapter 15 Slides: -> 71: Missense Mutation + Missense mutation + A sense codon is changed to a different sense codon that specifies a different amino acid + Whether the function of a polypeptide is altered significantly depends on the amino acid change that occurs + Genetic diseases caused by missense mutations include sickle-cell disease, albinism, hemophilia, and achondroplasia -> 79: Frameshift Mutation + Frameshift mutation + A single base pair deletion or insertion in the coding region of a gene alters the reading frame of the resulting mRNA - After the point of mutation, the ribosome reads codons that are not the same as for the normal mRNA, producing a different amino acid sequence in the polypeptide + The resulting polypeptide typically is nonfunctional because of the significantly altered amino acid sequence -> 80: Figure 15.19 -> FIg. 15.4, https://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/readingframe.html

Learning Objective 48: Describe how mRNA is processed prior to translation in eukaryotes.

Class 16 PPT Slides: -> 10: Translation requires a transcript + The product of transcription is an mRNA molecule (messenger RNA, sometimes called transcript or message) + That raw unprocessed mRNA will be directly and immediately translated in prokaryotes (transcription and translation occur in cytosol bc there is no nucleus) - In eukaryotes, the mRNA transcript is edited. -> 11: mRNA editing in eukaryotes + The primary, fresh-from-the-DNA transcript = pre-mRNA + pre-mRNA will be capped (5' cap) - this is a sign a ribosome will recognize during translation + The cap is a "reversed" nucleotide, inserted backwards + pre-mRNA will be given a polyadenylated tail (on 3' side) - 50-250 A's in a row, protects the transcript from RNA-degrading enzymes that exist in the cytoplasm + pre-mRNA may be spliced - cut out regions of RNA that do not code for proteins (introns) and link together the RNA that will be expressed (exons) Carried out by enzymes of the spliceosome - a splicing complex -> 12: Transcription to translation + In eukaryotes, the mRNA is transported from the nucleus to the cytoplasm for translation. - mRNA transcript = Sent to - Ribosomes (rRNA + Protein "ribonucleoprotein" 3 functional sites: A = aminoacyl P = peptidyl E = exit) = tRNA - Amino acids in a chain, arranged N terminus to C terminus Cengage Chapter 15 Slides: -> 28: 15.3 Production of mRNAs in Eukaryotes + mRNAs contain regions that code for proteins, along with noncoding regions that are important in protein synthesis + The coding region is flanked by untranslated ends: - 5′ untranslated region (5′ UTR) - 3′ untranslated region (3′ UTR) + A eukaryotic protein-coding gene is transcribed into a precursor-mRNA (pre-mRNA) that must be processed in the nucleus to produce the translatable mRNA -> 29: Modifying Pre-mRNA Ends + At the 5′ end of the pre-mRNA is the 5′ cap, consisting of a guanine-containing nucleotide that is reversed so that its 3′-OH group faces the beginning of the molecule + A capping enzyme adds the 5′ cap to the pre-mRNA after RNA polymerase II begins transcription + The 5′ cap (connected by three phosphate groups) is the site where ribosomes attach to mRNAs at the start of translation -> 30: Modifying Pre-mRNA Ends (cont'd.) + Proteins bind to a polyadenylation signal transcribed near the 3′ end of the pre-mRNA, and cleave the pre-mRNA downstream of that sequence + Poly(A) polymerase adds a chain of 50 to 250 adenine nucleotides (the poly(A) tail) to the 3′ end of the pre-mRNA - The poly (A) trail protects the pre-mRNA from attack by RNA-digesting enzymes in the cytoplasm -> 31: Introns and Exons + Pre-mRNA for a eukaryotic protein-coding gene contains one or more non-protein-coding sequences called introns that are removed during processing in the nucleus + The amino acid-coding sequences that are retained in finished mRNAs are called exons + The exons in the finished mRNAs are read continuously, without interruptions -> 32: Figure 15.6 -> 33: Figure 15.6 (cont.) -> 34: mRNA Splicing + mRNA splicing, which occurs in the nucleus, removes introns from pre-mRNAs and joins exons together + mRNA splicing takes place in a spliceosome formed between pre-mRNA and several small ribonucleoprotein particles (snRNPs) - each consisting of a short small nuclear RNA (snRNA) bound to a number of proteins + The spliceosome cleaves the pre-mRNA precisely to release the intron, and joins the flanking exons -> 35: Figure 15.7 -> 36: Figure 15.7 (Cont.) -> 37: Alternative Splicing + Many pre-mRNAs are processed by reactions that join exons in different combinations (alternative splicing) to produce different mRNAs from a single gene + Alternative splicing greatly increases the number and variety of proteins encoded in the cell nucleus without increasing the size of the genome - Example: The α-tropomyosin gene is alternatively spliced in smooth muscle, skeletal muscle, fibroblast, liver, and brain

Learning Objective 49: Describe the structure of an aminoacyl-tRNA and of a ribosome.

Class 16 PPT Slides: -> 14: tRNA + Transfer RNA + 75-90 ribonucleotides arranged in a cloverleaf shape = 4 double helices - 1 leaf - Anti-codon, a 3 nucleotide sequence complementary base-pairing to the codon + 1 leaf = connection to an amino acid -> 15: tRNA + But...only the 1st 2 really matter in terms of determining which amino acid will be added - this is called "wobble" and it means that multiple codon/anti-codon sets will be associated with the addition of the same amino acid (redundancy!) -> 16: How do we get amino acids attached to tRNA? + Aminoacylation - chemical reaction attaching an amino acid to a tRNA + Catalyzed by an enzyme specific for the amino acid that is going to be attached - so there are 20 of these enzymes -> 17: Ribosome + Present in the cytosol of prokaryotic and eukaryotic cells + Has a large subunit and a small subunit + Made of rRNA and protein = ribonucleoproteins + 3 sites - APE Cengage Chapter 15 Slides: -> 44: tRNAs + tRNAs wind into four double-helical segments, forming a cloverleaf pattern + At one end is the anticodon, the three-nucleotide segment that base pairs with a codon in mRNAs + The other end links to the amino acid corresponding to the anticodon - Example: Anticodon 3′-UCA-5′ base pairs with 5′-AGU-3′, serine (Ser) -> 45: Francis Crick's Wobble Hypothesis + Pairing of the anticodon with the first two nucleotides of the codon is always precise, but the anticodon has more flexibility in pairing with the third nucleotide of the codon + In many cases the same tRNA anticodon can read codons that have either U or C in the third position - The special purine inosine allows even more extensive wobble by allowing the tRNA to pair with codons that have either U, C, or A in the third position -> 46: Figure 15.10 -> 47: Aminoacylation + Addition of the correct amino acid to a tRNA (aminoacylation or charging) produces an aminoacyl-tRNA + Twenty different enzymes (aminoacyl-tRNA synthetases) -one for each of the 20 amino acids - catalyze aminoacylation + The process adds free energy as the aminoacyl-tRNAs are formed -> 48: Figure 15.11 -> 49: Ribosomes + Ribosomes are ribonucleoprotein particles that translate mRNA into chains of amino acids + In eukaryotes, ribosomes are either suspended freely in the cytoplasm or attached to the endoplasmic reticulum + A finished ribosome is made up of one large ribosomal subunit and one small ribosomal subunit, each composed of ribosomal RNA (rRNA) and ribosomal proteins + mRNA passes through a groove in the ribosome -> 50: Ribosomes (cont'd.) + tRNAs interact with mRNA at three binding sites on the ribosome: + Aminoacyl-tRNA carrying the next amino acid to be added to the polypeptide binds at the A site (aminoacyl site) + tRNA carrying the growing polypeptide chain is bound at the P site (peptidyl site) + tRNA without an amino acid binds to the E site (exit site) before exiting the ribosome -> 51: Figure 15.12

Learning Objective 50: Describe translation in terms of the 3 sites within a ribosome, how the mRNA is read, and how a polypeptide is formed based on that reading.

Class 16 PPT Slides: -> 19: 3 stages of translation (just like transcription) + 1.Initiation - machinery to translate assembles and starts working at the START CODON (?) + 2.Elongation - involves joining amino acids to form a polypeptide + 3.Termination - disassembly of the ribosome complex - occurs when a STOP codon has entered the ribosome Cengage Chapter 15 Slides: -> 52: Three Stages of Translation + Initiation: - Components assemble on the start codon of the mRNA + Elongation: - Assembled complex reads the string of codons in the mRNA one at a time while joining specified amino acids into the polypeptide + Termination: - Complex disassembles after the last amino acid specified by the mRNA has been added to the polypeptide -> 53: Translation Initiation + In eukaryotes, each step is aided by initiation factors (IFs) + In bacteria, the small ribosomal subunit, the initiator Met-tRNA, GTP, and IFs bind directly to the mRNA, directed by a ribosome binding site + The initiator tRNA-AUG pairing establishes the correct reading frame -> 54: Figure 15.13 -> 55: Translation Elongation + Aminoacyl-tRNA binds to the codon in the A site of the ribosome - facilitated by a protein elongation factor (EF) + A peptide bond forms between the C-terminal end of the growing polypeptide on the P site tRNA and the amino acid on the A site tRNA, catalyzed by peptidyl transferase + The ribosome translocates to the next codon + The empty tRNA is released from the E site and the ribosome is ready to begin the next round of the elongation cycle -> 56: Figure 15.15 -> 57: Translation Termination + Termination takes place when the A site arrives at one of the stop codons on the mRNA (UAG, UAA, or UGA) + The stop codon is read by a protein release factor (RF or termination factor) + Termination is similar in prokaryotes and eukaryotes -> 58: Figure 15.15 -> 59: Polysomes + Once the first ribosome has begun translation, another one can assemble as soon as there is room on the mRNA + Ribosomes continue to attach as translation continues and become spaced along the mRNA like beads on a string, forming a polysome + In prokaryotes, transcription and translation typically are coupled - the polysome forms while mRNA is being made -> 60: Figure 15.16 -> 61: Figure 15.17 -> 62: Processing Polypeptides + Processing includes removal of certain amino acids from the polypeptide chain and addition of carbohydrate or lipid groups + Many proteins require helper proteins (chaperones or chaperonins) to fold into their final, functional 3-D shapes + Some proteins are processed into an initial, inactive form (e.g., pepsinogen) that is later activated by removal of a segment of the amino acid chain -> 63: Finished Proteins Are Sorted + Finished proteins are sorted within the cell to three types of compartments: - The cytosol - The endomembrane system, including endoplasmic reticulum (ER), Golgi complex, lysosomes, secretory vesicles, nuclear envelope, and the plasma membrane - Membrane-bound organelles other than the endomembrane system, including mitochondria, chloroplasts, microbodies, and within the nucleus -> 64: Protein Sorting to the Cytosol + Proteins that function in the cytosol are synthesized on free ribosomes in the cytosol + These polypeptides are simply released from ribosomes once translation is completed - Examples: microtubule proteins, enzymes that carry out glycolysis -> 65: Protein Sorting to the Endomembrane System + Polypeptides sorted to the endomembrane system begin synthesis on free ribosomes in the cytosol: + Amino acid signal sequence near N-terminal ends + Polypeptide enters the lumen of the rough ER while attached to ribosome (cotranslational import) + Proteins fold into final form and are "tagged" for their destination (ER or Golgi complex) + Proteins transported to the Golgi complex are further modified, packed in vesicles, and delivered to lysosomes, plasma membrane, or secreted from the cell -> 66: Figure 15.18