BIOL 1105 Test 2 PDF

Lesson 7 7.1: Energy Flow Differentiate between kinetic and potential energy. - Energy: the potential to do work - Kinetic energy: energy of motion - Potential energy: stored energy Contrast oxidation and reduction reactions - Oxidation: loss of electrons (lower energy) - Reductio...

Lesson 7 7.1: Energy Flow Differentiate between kinetic and potential energy. - Energy: the potential to do work - Kinetic energy: energy of motion - Potential energy: stored energy Contrast oxidation and reduction reactions - Oxidation: loss of electrons (lower energy) - Reduction: gain of electrons (higher energy) - The combination of the two is termed redox reactions where one atom gains electrons (is reduced) and the other loses electrons (is oxidized) Explain the first and second laws of thermodynamics. - The First Law of Thermodynamics: energy can not be created nor destroyed - The second Law of Thermodynamics: entropy (disorder) is constantly increasing - Disorder happens spontaneously - Order/organization requires energy 7.2: Calculating Energy Relate free energy changes to the outcome of chemical reactions. - ΔG° = ΔH° - TΔS° - ΔG= free energy (energy available to do work in a system) - ΔH= change in enthalpy (energy in chemical bonds) - T=absolute temperature (K=C+273) - ΔS= change in entropy (disorder) - If ΔG is positive…energy is supplied - Products have more free energy than the reactants - Energy must be input for the reaction to occur (high ΔH) - Do not occur spontaneously (low ΔS) - Endergonic - If ΔG is negative…energy is released - Products have less free energy than the reactants - Reaction releases energy (low ΔH) - Occurs spontaneously (high ΔS) - Exergonic - If ΔG=0 - Reaction is at equilibrium - Not net change is occurring Contrast the course of a reaction with and without an enzyme catalyst. - Without catalyst - Higher activation energy - Reaction is slower - With catalyst - Lower activation energy - Reaction is quicker - Overall free energy change (ΔG) of the reaction remains unchanged 7.3: Enzymes Discuss the role of enzymes as biological catalysts. - Speed up chemical reactions within cells - Are not consumed or changed in the process - Do this by stabilizing the temporary association between substrates, facilitating the reaction by lowering activation energy - Bind to substrates at active site  - This creates an enzyme-substrate complex - This lowers the energy needed to break or form chemical bonds, allowing reactions to occur more efficiently - The specific collection of enzymes in a cell defines its capabilities - Can catalyze reaction repeatedly, increasing efficiency in cellular metabolism List factors that influence enzyme-catalyzed reaction rates. - Substrate concentration: an increase in substrate concentration generally increases the reaction rate, up to a point of saturation where all enzyme molecules are bound to substrates - Enzyme concentration: a higher concentration of enzymes leads to a higher rate of reaction, assuming substrate availability is sufficient - Temperature: enzyme activity increases with temperature up to an optimum level. Beyond this, high temperatures can denature the enzyme, reducing its effectiveness - pH levels: enzymes have an optimal pH range, and deviation from this can disrupt the enzyme’s structure and function, affecting the reaction rate - Regulatory molecules: enzyme activity can be regulated by molecules like inhibitors (reduce activity) or activators (increase activity) - Distinguish competitive and non-competitive inhibitors - Competitive inhibitors - Bind directly to the active site - Compete with the substrate - Block the substrate from binding to the active site of the enzyme - Can be overcome by increasing the substrate concentration - Non-competitive inhibitors - Bind to allosteric site - Induces a change in the enzymes shape, making it unable to bind the substrate - Cannot be reversed by increasing the substrate concentration Describe the significance of biochemical pathways and feedback inhibition - Biochemical pathways: a series of linked enzymatic reactions where the product of one reaction serves as the substrate for the next reaction - Allow for a stepwise and regulated conversion of substrates into products, which ensures efficient use of resources and energy - Many pathways are confined to specific locations within the cell (ex. Inner membrane of mitochondria for ATP synthesis - Feedback inhibition: mechanism by which cells regulate biochemical pathways  - The final product of a pathway binds to an enzyme that catalyzes an earlier step (often the first step), usually at an allosteric site, causing the enzyme to become inactive - Prevents the pathway from producing more product than necessary, thereby conserving energy and resources - When enough product is present, the pathway is shut down 7.4: ATP Describe the role of ATP in short-term energy storage. - Adenosine triphosphate stores energy in the covalent bonds between its three phosphate groups, specifically in the two high-energy bonds between the phosphates  - Bonds broken through hydrolysis - Substantial amount of energy released which can be used to drive endergonic reactions (reactions requiring an input of energy) - Not a good long-term energy storage because of the instability of its high-energy bonds - Repulsion between the negatively charged phosphate groups makes the bond easily breakable - High turnover rate: it is continually synthesized and consumed by cells - Fats and carbohydrates are better for long-term energy storage - Cells rely on ATP’s continuous regeneration through processes like cellular respiration Explain how ATP is related to control of protein activity. - Phosphorylation - Enzyme: kinase - Hydrolyzes ATP and attaches a phosphate group (Pi) to a specific amino acid residue (such as serine, threonine, or tyrosine) on a target protein - This can either activate or inactive the protein, depending on the specific protein - “Molecular switch” - Turns protein on by inducing a conformational change that enables the protein to perform its function - Dephosphorylation - Enzyme: phosphatase  - Removes the phosphate group, inactivating the protein - Ensures that proteins are only active when needed Lesson 8 8.1: Energy From Electrons Distinguish between autotrophs and heterotrophs. - Autotrophs - Capable of converting the sun’s energy into chemical energy, primarily in the form of ATP and chemical bonds within inorganic molecules - Examples: plants, algae, and photosynthetic bacteria - Photosynthesis is main process - Heterotrophs - 95% of known species - Cannot produce their own energy from the sun - Rely on consuming organic molecules produced by autotrophs - Extract energy through cellular respiration, converting chemical energy into ATP - Both - Have the ability to extract energy from organic molecules using cellular respiration Describe the role of electrons and electron carriers in energy metabolism. - Oxidation of organic molecules (removal of electrons) - Electrons are rich in energy, and their movement is harnessed to produce ATP  - Harvested electrons go through a series of redox reactions where they transfer energy from one molecule to another - Each transfer is not 100% efficient - Some energy is lost as heat - Other energy can be used for other cellular processes - Electron carriers facilitate the transfer of electrons - NAD+ (nicotinamide adenine dinucleotide) - Cofactor in enzymatic reactions - Picks up 2 electrons and 1 proton from an oxidized substrate to form NADH - NADH - Can donate electrons to other molecules, reducing them and returning to its oxidized state, NAD+ - This cycle allows for the continuous transport of electrons which is essential for the production of ATP during cellular respiration - Electron carriers allow energy to be harvested in small, manageable steps to prevent the cell from combusting 8.2: The Beginning of Cellular Respiration-Glycolysis Identify the four stages that comprise the aerobic respiration of glucose and where in the cell each occurs. 1. Glycolysis a. Occurs in the cytosol in eukaryotic cells and the cytoplasm in prokaryotic cells b. Glucose is split into two pyruvate molecules 2. Pyruvate oxidation a. Occurs in the mitochondrial matrix in eukaryotic cells and the plasma membrane in prokaryotic cells b. Pyruvate is oxidized to form acetyl-CoA 3. Krebs cycle (Citric Acid Cycle) a. Occurs in the mitochondrial matrix in eukaryotic cells and the cytoplasm in prokaryotic cells b. Acetyl-CoA is further oxidized to produce electron carriers 4. Electron transport chain and chemiosmosis a. Occurs in the inner mitochondrial membrane in eukaryotic cells and the plasma membrane in prokaryotic cells b. Majority of ATP is produced in this step c. Electron move through chain and generate a proton gradient Summarize the key events and products of glycolysis 1. Phase 1: Energy Input—---Endergonic a. 6 carbon glucose molecule is phosphorylated twice by using 2 hydrolyzed ATP b. It is then split into two 3 carbon molecules of glyceraldehyde 3-phosphate (G3P) 2. Phase 2: Energy Production—--Exergonic a. Each G3P molecule is oxidized, transferring 2 electrons and 1 proton to NAD+, forming NADH b. An inorganic phosphate is added to each G3P, and 4 ATP molecules are produced in total c. G3P is converted to pyruvate  - Products - 8.3: Cellular Respiration: Pyruvate Oxidation and Krebs Cycle Summarize the key events and products of pyruvate oxidation and the Krebs cycle. Pyruvate Oxidation - Occurs in the mitochondrial matrix - Enzyme: pyruvate dehydrogenase—oxidized pyruvate - Pyruvate undergoes decarboxylation (releasing of one molecule of CO2) - 2 high energy electrons are transferred to NAD+, reducing it to NADH - The remaining 2 carbon acetyl group is combined with coenzyme A, forming acetyl-CoA which is fed into the Krebs cycle - Products (for each pyruvate molecule) (double to find products for each glucose molecule) - 1 molecule CO2 - 1 molecule NADH - 1 molecule Acetyl-CoA Krebs Cycle - Occurs in the mitochondrial matrix - Acetyl group from acetyl-CoA (2 carbons) combines with the four-carbon oxaloacetate to form a six-carbon molecule, citrate - The CoA can be recycled to pyruvate oxidation to pick up another acetyl group - Citrate undergoes decarboxylation and rearrangement, releasing 2 CO2 molecules - Several redox reactions occur, reducing 3 NAD+ to 3 NADH and 1 FAD to 1 FADH2 - The cycle generates 1 molecule of ATP via substrate-level phosphorylation - The four-carbon molecule succinate undergoes further reactions to regenerate oxaloacetate, allowing the cycle to continue - Products (for each acetyl-CoA molecule) (double to find products of one glucose molecule) - 2 molecule of CO2 - 3 molecules of NADH - 1 molecule of FADH2 - 1 molecule of ATP - 1 molecule of oxaloacetate (reused in the next cycle)  Lesson 9 9.1: Electron Transport Chain and Chemiosmosis Diagram the flow of electrons through the electron transport chain. 1. NADH Dehydrogenase a. Electrons from NADH are delivered to this enzyme complex  b. Energy from these electrons is used to pump protons from the mitochondrial matrix into the intermembrane space c. Electrons are then passed to ubiquinone (Q) 2. Ubiquinone (Q) a. Lipid-soluble electron carrier receives electrons from NADH b. Passes electrons to the bc1 complex 3. Bc1 complex a. Extracts additional energy from the electrons and pumps more protons into the intermembrane space b. Transfers electrons to cytochrome c 4. Cytochrome c a. Carrier protein transfers the electrons to the cytochrome oxidase complex 5. Cytochrome oxidase complex a. Final complex in the ETC b. Harvests energy to pump more protons c. Catalyzes the reduction of molecular oxygen using two hydrogen protons, producing water as a byproduct Describe how chemiosmosis couples electron transport to ATP synthesis during oxidative phosphorylation. 1. Proton gradient a. The movement of electrons through the ETC creates a proton concentration gradient (higher concentration in the intermembrane space than in the mitochondrial matrix) 2. Proton motive force a. This references that the proton gradient represents potential energy 3. ATP synthase a. Protons can only move back into the mitochondrial matrix through a specialized enzyme called ATP synthase b. As protons flow down their gradient through this enzyme, they cause the enzyme to rotate and change its conformation 4. ATP production a. This mechanical energy is used by ATP synthase to catalyze the formation of ATP from ADP and inorganic phosphate (Pi) b. The movement of 4 protons synthesizes 1 molecule of ATP Summarize the energy yield after each stage of aerobic respiration. 1. Glycolysis a. Direct ATP yield: 2 ATP (through substrate-level phosphorylation) b. NADH yield: 2 NADH (which yield 5 ATP through oxidative phosphorylation) c. Total ATP: 7 ATP 2. Pyruvate Oxidation  a. NADH yield: 2 NADH (which yield 5 ATP through oxidative phosphorylation) b. Total ATP: 5 ATP 3. Krebs cycle a. Direct ATP yield: 2 ATP (substrate-level phosphorylation) b. NADH yield: 6 NADH (which yield 15 ATP through oxidative phosphorylation) c. FADH2 yield: 2 FADH2 (which yield 3 ATP through oxidative phosphorylation) d. Total ATP: 20 ATP - Overall Yield for One Glucose Molecule in bacteria: 32 ATP - Overall Yield for One Glucose Molecule in eukaryotes: 30 ATP - This is because it costs 1 ATP for each molecule of NADH produced in glycolysis to be transported from the cytosol to the electron transport chain in the inner mitochondrial membrane 9.2: Alternate Methods of ATP Production Distinguish aerobic respiration, anaerobic respiration, and fermentation. 1. Aerobic respiration a. Electron acceptor: oxygen  b. ATP yield: typically produces a high yield of ATP due to the strong affinity of oxygen for electrons c. Organisms: commonly occurs in many cells and organisms, including eukaryotes and aerobic prokaryotes 2. Anaerobic respiration a. Electron acceptor: uses inorganic molecules other than oxygen as the final acceptor (ie sulfur, carbon dioxide, or inorganic metals) b. ATP yield: produces less ATP compared to aerobic respiration because these alternative electron acceptors have a lower affinity for electrons c. Organisms: methanogens, a type of archaea, use carbon dioxide as an electron acceptor and reduce it to methane 3. Fermentation: regenerate NAD+ so glycolysis can continue (no oxygen present) a. Electron acceptor: specific organic molecules (ie pyruvate) b. ATP yield: produces significantly less ATP than both aerobic and anaerobic respiration c. Types i. Ethanol fermentation: yeast converts pyruvate into ethanol and carbon dioxide ii. Lactic acid fermentation: certain animal cells (especially muscle cells) convert pyruvate into lactic acid Describe how proteins and fats are catabolized to produce energy. 1. Proteins  a. Broken down into individual amino acids b. Amino group is removed from the amino acids through a deamination reaction c. Remaining carbon skeleton of the amino acid is converted into molecules that can enter glycolysis or the Krebs cycle i. Ex. glutamate can be converted into alpha-ketoglutarate, which is an intermediate in the Krebs cycle d. Once the products enter the Krebs cycle, high-energy electrons are extracted to produce ATP 2. Fats a. Broken down into fatty acids and glycerol b. Undergo beta-oxidation, which converts them into two-carbon acetyl groups c. Acetyl groups are combined with coenzyme A (CoA) to form acetyl-CoA, which can then enter the Krebs cycle d. Respiration of fats yields significantly more energy than glucose i. Respiration of 6 carbon fatty acid yield 20% more than a 6 carbon glucose molecule ii. Makes fats an efficient energy storage  Lesson 10 10.1: Photosynthesis-Overview and Light Absorption Describe how photosynthesis and respiration are connected. - Form an energy cycle that is essential for life on Earth - Products of photosynthesis (glucose/pyruvate and oxygen) are used as substrates in cellular respiration - Products of respiration (carbon dioxide and water) are used as substrates in photosynthesis - Connection allows plants to produce glucose to power their own cellular respiration and the respiration of heterotrophs 1. Photosynthesis a. Reduces carbon dioxide and water into glucose and oxygen using the energy from the sun  b. Occurs in chloroplasts and includes both light dependent reactions and the Calvin cycle (light-independent reactions) 2. Respiration a. Oxidized glucose to carbon dioxide using oxygen as the final electron acceptor to produce ATP b. Occurs in mitochondria through glycolysis, the Krebs cycle, and the ETC (oxidative phosphorylation) Differentiate between the light-dependent and light-independent reactions. 1. Light-Dependent Reactions a. Location: thylakoid membranes of chloroplasts b. Capture energy from sunlight using photosystems (protein complexes with pigments like chlorophyll)  c. Energy is used to produce ATP via photophosphorylation, reduce NADP+ to NADPH, and produce oxygen as a byproduct from the splitting of water d. Requires light energy to excite electrons and drive the production of ATP and NADPH 2. Light-Independent Reactions (Calvin Cycle) a. Location: stroma of chloroplasts b. Use ATP and NADPH produced in light-dependent reactions to fix carbon from carbon dioxide into organic molecule like glucose c. Do not require light (however they depend on the products of light-dependent reactions Explain the connection between light energy and photosynthetic pigments. 1. Light Energy a. Light consists of photons (particles of energy) b. Energy of a photon is inversely proportional to its wavelength c. Blue light (short wavelength) contains more energy than red light (longer wavelength) 2. Photosynthetic Pigments: Pigments in the chloroplasts absorb photons, excite electrons, and transfer electrons to carriers (photoelectric effect) which initiates the conversion of light energy into chemical energy (photosynthesis) a. Chlorophyll a i. Primary pigment  ii. Absorbs violet-blue and red light iii. Directly converts light energy into chemical energy by exciting electrons b. Chlorophyll b i. Accessory pigment ii. Extend the range of light absorption by capturing blue and red-orange light c. Carotenoids i. Absorb blue-green light ii. Act as antioxidants, protecting the cell iii. Give plants orange hue in fall after chlorophyll degrades 10.2: The Light Dependent Reactions Describe the structure and compare the functions of the two photosystems in green plants. - Photosystems are made of pigments and proteins that capture light energy - Embedded in the thylakoid membrane of chloroplasts - Antenna Complex: consists of accessory pigments (chlorophyll b and carotenoids) that capture photons of light and pass the energy between pigment molecules - Reaction center: contains chlorophyll a, the primary pigment responsible for transferring excited electrons to an electron acceptor 1. Photosystem II a. First photosystem b. Absorbs light (primarily at wavelength 680 nm) and excites electrons within reaction center c. Photolysis: uses energy from absorbed photons to split water molecules into oxygen (O2), protons (H+), and electrons d. Electrons released from water replace those lost by the excited chlorophyll molecules e. Excited electrons are passed through the ETC to Photosystem I 2. Photosystem I a. Second photosystem b. Absorbs light (primarily at wavelength 700 nm to re-energize the electrons coming from PSII c. High energy electrons are used to reduce NADP+ to NADPH  d. Does not split water, but rather receives electrons from PSII which replenishes its electron supply Explain how the light-dependent reactions generate ATP and NADPH. 1. Generation of ATP - Electrons excited by light is PSII are passed to the b6f complex in the ETC - As electrons move through the b6f complex, their energy is used to pump protons (H+) from the stroma into the thylakoid space (creating a proton gradient) - Buildup of protons in the thylakoid space generates a high concentration of protons inside compared to the stroma which creates a proton gradient (potential energy) - Photophosphorylation: ATP synthase allows protons to flow into the stroma which drives the conversion of ADP to ATP using inorganic phosphate 2. Generation of NADPH - After electrons pass through PSII and the b6f complex, they arrive at PSI - PSI absorbs photon to re-energize these electrons - Re-energized electrons are transferred to ferredoxin and ultimately used to reduce NADP+ to form NADPH via the enzyme NADP+ reductase 10.3: Carbon Fixation and Photorespiration Describe how the Calvin cycle carries out carbon fixation. - Occurs in the stroma of the chloroplasts - Converts inorganic carbon dioxide into organic molecules like glucose - Referred to as C3 photosynthesis because first stable product formed is a 3 carbon molecule call 3-phosphoglycerate (PGA) 1. Carbon Fixation a. Carbon dioxide from atmosphere is fixed by attaching a 5 carbon molecule called ribulose 1,5-bisphosphate (RuBP) b. Catalyzed by enzyme rubisco and results in 6 carbon intermediate that immediately splits into two molecules of PGA 2. Reduction a. ATP and NADPH (from light-dependent reactions) are used to reduce PGA to glyceraldehyde-3-phosphate (G3P) b. 3 molecules of CO2 fixed=6 molecules of G3P produced i. However only one G3P molecule is released from the cycle to potentially form glucose 3. Regeneration a. Remaining 5 G3P molecules are used to regenerate RuBP, allowing the cycle to continue b. It takes 6 turns of the Calvin cycle to produce one molecule of glucose Explain the mechanisms of photorespiration. -Definition: a wasteful process that occurs when Rubisco binds to O2 instead of CO2 due to high oxygen concentrations and low CO2 levels, especially under hot and arid conditions; it reverses the effect of carbon fixation and releases CO2 -Mechanism - Under normal conditions, Rubisco acts as a carboxylase, fixing CO2 to RuBP to form PGA  - However, when O2 levels are high and CO2 levels are low (such as when stomata close to prevent water loss), Rubisco functions as an oxygenase, binding to O2 and producing a two-carbon compound called phosphoglycolate - This compound is then recycled through a series of reactions, but it results in the loss of CO2 and the use of energy without producing any useful organic molecules -Consequences - Photorespiration reduces the efficiency of photosynthesis by releasing fixed carbon and consuming ATP and NADPH -It is favored in hot, dry climates where plants close their stomata to reduce water loss, leading to lower internal CO2 concentrations and higher O2 levels Compare carbon fixation in the C3, C4 and CAM pathways. 1. C3 pathway a. Standard Calvin cycle pathway used by most plants b. CO2 is directly fixed by Rubisco into PGA, a three carbon compound c. Efficient in moderate conditions, but suffer from photorespiration in hot, dry climates 2. C4 Pathway  a. Evolved a way to spatially separate carbon fixation from the Calvin cycle to minimize photorespiration b. PEP carboxylase initially fixes CO2 in mesophyll cells, forming a four carbon molecule (oxaloacetate), which is converted to malate c. Malate is transported to bundle sheath cells, where it is decarboxylated to release CO2, which then enters the Calvin cycle d. Concentrates CO2 in the bundle sheath cells, reducing photorespiration e. It requires 12 additional ATP/glucose molecule produced 3. CAM pathway a. Temporally separate carbon fixation and the Calvin cycle b. Stomata open at night, allowing CO2 to be fixed by PEP carboxylase into a four carbon compound, which is stored in the vacuole c. During the day, stomata close, and the stored CO2 is release from the four carbon compound to be used in the calvin cycle d. Conserves water in arid environments, but results in slower growth due to the limed time for CO2 fixation Lesson 11 11.1: The DNA Model Identify component nucleotides of DNA and describe how they interact using phosphodiester and hydrogen bonds. -Nucleotides are the building blocks of DNA and consist of three main components: 1. Five-carbon sugar (deoxyribose): lacks an oxygen on the 2’ carbon 2. Nitrogenous Base a. Adenine (A): purine b. Guanine (G): purine c. Cytosine C: pyrimidine d. Thymine (T): pyrimidine 3. Phosphate group: attached to the 5’ carbon of the sugar - Phosphodiester bonds - Link nucleotides together to form a DNA strand  - Formed between the phosphate group of one nucleotide (5’ carbon) and the hydroxyl group of the next nucleotide (3’ carbon) - Linking occurs through dehydration synthesis - Hydrogen bonds - Nitrogenous bases on opposite strands pair through hydrogen bonds - Form the double helix structure of DNA - Adenine with Thymine through 2 hydrogen bonds - Guanine with Cytosine through 3 hydrogen bonds Describe the significance of complementarity for DNA structure and function - Stable structure - Specific pairing of nitrogenous bases ensures consistent diameter of the DNA double helix - Accurate replication - Allows each strand to serve as a template for the formation of a new complementary strand - Information storage - Encoding of genetic information in a way that is easily readable and retrievable  - Sequence of bases on one strand can be used to determine the sequence on the other strand Summarize the key features of the Watson and Crick DNA model - Double helix - Antiparallel strands - Two strands run in the opposite directions - One strand has a 5’ to 3’ orientation, while the other runs 3’ to 5’ - Important for DNA replication and transcription - Sugar-phosphate backbone - Backbone of each strand consists of alternating sugar (deoxyribose) and phosphate groups linked by phosphodiester bonds - Complementary base pairing - Nitrogenous bases from opposite strands pair through hydrogen bonds - Major and minor grooves - Twisting of the helix creates two types of grooves (major and minor) that are important for protein binding - Consistent diameter - Specific base pairing of bases maintains a uniform width of the double helix (about 2 nanometers) Determining the structure of DNA - Maurice Wilkins / Rosalind Franklin ❖ Performed X-ray diffraction studies to identify 3-D structure ❖ Discovered that DNA is helical ❖ DNA has a diameter of 2 nm and makes a complete turn of the helix every 3.4 nm 11.2: DNA Polymerase Describe the action of DNA polymerase 1. Adding nucleotides a. “Reads” the parent (template) strand in the 3’ to 5’ direction and “writes” or synthesizes the new strand in the 5’ to 3’ direction b. Adds nucleotides to the 3’ end of the growing daughter strand 2. Base pairing a. Ensures that the nucleotides added are complementary to the bases on the template strand 3. Phosphodiester Bond formation a. Catalyzes the formation of phosphodiester bonds between new nucleotides and the growing chain b. Links the phosphate group of the new nucleotides to the 3’ carbon of the previous nucleotide’s sugar 4. Proofreading a. 3’ to 5’ exonuclease activity i. Allows it to recognize and remove mispaired bases Explain continuous and discontinuous replication -DNA is semi-discontinuous due to the antiparallel structure which results in two different modes of replication 1. Continuous replication (leading strand) a. Synthesized continuously in the same direction as the movement of the replication fork b. DNA polymerase moves along the template strand in the 3’ to 5’ direction, adding nucleotides to the growing strand in the 5’ to 3’ direction without interruption 2. Discontinuous replication (lagging strand) a. Synthesized discontinuously in the opposite direction of the replication fork movement  b. DNA polymerase synthesizes short fragments of DNA (Okazaki fragments) c. Each fragment begins with a short RNA primer, synthesized by the enzyme primase d. Fragments are later joined together by the enzyme DNA ligase to form a continuous strand 11.3: DNA Replication List the components required for DNA replication and identify their function 1. DNA helicase—unwinds the double helix, allowing the two parental strands to separate and serve as templates for replication 2. Single-stranded binding proteins (SSBs)---bind to the separated DNA strands to keep them from reforming hydrogen bonds with each other 3. DNA gyrase(topoisomerase in eukaryotes)---relieves torsional strain caused by the unwinding of the DNA helix to prevent supercoiling 4. Primase—synthesizes short RNA primers that provide a starting point for DNA synthesis 5. DNA polymerase III—main enzyme responsible for synthesizing new DNA strands by adding nucleotides to the 3’ end of the primer/growing DNA strand 6. Clamp loader and sliding clamp—hold DNA polymerase III in place on the DNA 7. DNA polymerase I—replaces RNA primers with DNA nucleotides on the lagging strand after the Okazaki fragments have been synthesized  8. DNA ligase—seals gaps between the Okazaki fragments on the lagging strand by forming phosphodiester bonds to create a continuous DNA strand 11.4: DNA Modification Compare the key features of eukaryotic and prokaryotic replication 1. Genome Size and structure a. Prokaryotes i. have small genomes with a single circular chromosome ii. Replication starts from a single origin of replication (ORI) and proceeds bidirectionally around the chromosome b. Eukaryotes i. Much larger genomes with multiple linear chromosomes ii. Require multiple ORIs (human genome has approximately 30,000 ORIs to ensure replication can be completed efficiently 2. Replication Machinery  a. Prokaryotes i. Main DNA polymerase is DNA polymerase III which synthesizes the leading and lagging strands ii. DNA polymerase I removes RNA primers and fills in the gaps with DNA b. Eukaryotes i. Main replication enzymes are DNA polymerase delta and DNA polymerase epsilon (perform the same function as DNA polymerase III) ii. DNA polymerase alpha (similar to DNA polymerase I removes RNA primers and replaces them with DNA nucleotides 3. Chromosome Ends a. Prokaryotes i. Circular chromosomes, so there are no ends to replicate b. Eukaryotes i. Linear chromosomes, meaning lagging strand cannot be fully replicated due to the removal of the RNA primer at the chromosome end ii. Enzyme telomerase extends the telomeres to ensure the entire chromosome is copied 4. Speed of Replication a. Prokaryotes i. Faster due to simpler genome structure and less regulatory processes b. Eukaryotes i. Slower and more tightly regulated ii. Due to larger genome size, chromatin structure (DNA wrapped around histones), and the need to coordinate replication with other cell cycle events (ie mitosis) Describe the function and importance of telomeres and telomerase in eukaryotic replication -Function of Telomeres - Located at the end of linear eukaryotic chromosomes - Consist of short repeating DNA sequences that protect the chromosome ends from degradation and damage -Function of Telomerase  - Enzyme responsible for maintaining the length of telomeres - Contains RNA subunit that is complementary to the telomere DNA sequence - Extends the lagging strand of the DNA during replication by adding repeated stretches of DNA to the end of telomeres - Allows the replication machinery to finish copying the entire chromosome - Without it, the lagging strand would remain incomplete after each round of replication, leading to the gradual shortening of chromosome over time -Importance of Telomeres and Telomerase - Prevents Chromosome Shortening - Aging: most cells lose the ability to produce telomerase, which leads to telomere shortening, which eventually leads to cells no longer dividing - Cancer: cancer cells reactivate telomerase, which allows them to avoid the shortening of telomeres which allows for unchecked cell division and growth Explain the importance of DNA repair mechanisms and identify examples -Importance of DNA repair mechanisms - Maintains the integrity and stability of the genome - DNA is constantly exposed to damage (replication errors, environmental factors) - W/out mechanisms, these errors could accumulate, leading to mutations, loss of genetic info, and diseases (cancer) - Reduce mutation rates and ensure cells function properly -Examples of DNA repair mechanisms - Specific Repair Mechanism: Photorepair - Fixes DNA damage caused by UV light, specifically thymine dimers (covalent bonds between two adjacent thymine bases - Enzyme called photolyase absorbs visible light and uses the energy to break the bond between the thymine bases, restoring normal DNA structure - Non-Specific Repair Mechanism: Excision Repair - General mechanism that can fix multiple types of DNA damage 1. Recognition of the damage 2. Removal/Excision of damaged DNA section 3. Resynthesis of the excised region using DNA polymerase, which copies the info from the undamaged template strand