Biology Exam 2 Study Guide-1 PDF

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Unit 1 exam study guide...

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Useful site: http://www.sciencemusicvideos.com/high-school-biology/Has materials (quizzes & videos) on: Photosynthesis (#13), Respiration (#12), DNA Replication, Transcription, & Translation (#14) and Mitosis (#16) For videos: http://www.sciencemusicvideos.com/music-videos/ DNA Structure & Replication (#5 & #6)Respiration (#11, #20, #9)Photosynthesis (#27, #28) Translation (#29) Mitosis (#23) Chapter 5: Photosynthesis (11-13 questions) General information Can you explain the difference between an autotroph and a heterotroph? ● An autotroph produces their own organic compounds from inorganic starting materials such as CO2 and water ○ Plants are autotrophs ● Heterotrophs rely on organic molecules produced by other organisms ○ Animals are heterotrophs Can you provide examples of autotrophs? Can you provide examples of heterotrophs? ● Heterotrophs—Animals, FUNGI ● Autotrophs—Plants, Algae, some Bacteria How do you know they belong in these specific categories? Are these organisms prokaryotes, eukaryotes? What are some differences between prokaryotes and eukaryotes? ● These organisms are eukaryotes—you can look at the links in the Domain ancestor chainàDomain Archaea, Domain Bacteria, Domain Eukarya ● Eukaryotes—Plants/Animals ○ Have a nucleus ● Prokaryotes--Bacteria ○ Have no nucleus, no membrane bounded organelles What does the molecule ATP look like (How would you recognize it?)?

· It looks like Adenine and Guanine (RNA/DNA) What type of monomer is ATP? ● It is a nucleotide—3 phosphate groups, 1 ribose, 1 adenine Why is hydrolysis (breaking) of ATP considered an exergonic reaction? ● Exergonic reaction—energy released

● Hydrolysis—It is a reaction in which a large molecule is split into two smaller molecules upon the addition of water (H2O). ● ADP is combined with a phosphate to form ATP in the reaction. ADP+Pi+Free energy ATP+H2O ○ The energy released from the hydrolysis of ATP into ADP is used to perform cellular work, usually by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions ○ ATP (with three phosphate groups) is split into ADP (two phosphate groups) and Pi. What is “broken” in ATP hydrolysis? What are the products of ATP hydrolysis?

How could you represent this exergonic reaction on a graph? / How could you represent an endergonic reaction on a graph?

Why is ATP hydrolysis “coupled” with endergonic reactions? Because endergonic reactions need to perform cellular work. Why is photosynthesis, overall, considered an endergonic reaction? ● Photosynthesis is endergonic because it requires energy; and glucose- the product- has more energy than its reactants.

● Could you write the chemical reaction for photosynthesis? What are the reactants (inputs)? What are the products (outputs)?

Is photosynthesis an anabolic or catabolic reaction? Why? ● Anabolic—Energy REQUIRED ● Catabolic—Energy RELEASED ● It is anabolic because it builds big molecule, glucose, from small molecules, CO2 and H2O. Why do we think that eukaryotes such as plants have chloroplasts? Where did these organelles come from? What evidence supports this theory? ● Chloroplasts are organelles found in plant cells and eukaryotic algae that conduct photosynthesis. Chloroplasts absorb sunlight and use it in conjunction with water and carbon dioxide gas to produce food for the plant. ● Photosynthesis occurs through chloroplasts ● Eukaryotic cells containing mitochondria engulfed photosynthetic bacteria, which evolved to become specialized chloroplast organelles ● The endosymbiotic theory explains the origin ○ Endosymbiotic meaning it has its own DNA from the nucleus ○ Mitochondria and Chloroplasts have striking similarities to bacteria cells Could you roughly sketch a chloroplast, labeling the various components? What does each component do? How does each component relate to photosynthesis?

● Thought to have evolved from endosymbolic relationship ● The stroma is a fluid-filled compartment—contains ribosomes, DNA, and enzymes ● Suspended in the stroma are between 10 and 100 grana (granum) each composed of a stack of 10 to 20 pancake-shaped thylakoids ● The thylakoid consists of a membrane fluid-filled compartment studded with photosynthetic pigments ● Thylakoids stack together to form Granum Where do the light reactions of photosynthesis take place in a chloroplast? ● Photosynthesis occurs in the thylakoid membranes Where does the Calvin cycle of photosynthesis take place in a chloroplast? ● The Calvin cycle (aka carbon reactions) take place in the chloroplast stroma Light reactions In what form do plants absorb light energy? What molecules in the chloroplast are responsible for directly absorbing this form of light? Where are these molecules located in the chloroplast? How is the absorbing of light and transfer of that energy to electrons related to the first law of thermodynamics? -Plants absorb light as photons -Chlorophyll b Absorbs the photons -They are within the Thylakoid Membrane It is related to the first law of thermodynamics because energy cannot be created or destroyed but only transformed into different forms. Photons are being transferred into energy that power ION Pumps and etc. · We know that the movement of electrons between molecules is very important in photosynthesis. Why? If a molecule loses an electron, it has become oxidized. If a molecule has gained an electron, it has become reduced. What do we call when these two processes happen together?: a redox reaction. Why do these processes need to occur together? These processes occur · Why are the light reactions considered to be a series of redox reactions? Could you walk me through which molecules are being oxidized or reduced?

Light reactions are considered redox reactions because a combination of things are being oxidized and reduced in this process. H2O is oxidized and the electrons from the water molecule go into the reaction center of Photosystem 2. NADP+ is reduced during the light reaction gaining an electron and turning into NADPH. · Can you draw the series of molecules needed to perform the light reactions? The placement is important, do you know the order of these components? Be sure to label: photosystem I, photosystem II, H2O, ADP, P, ATP, NADP+, NADPH, thylakoid membrane, H+, Electron transport chain (ETC), stroma, ATP synthase, NADP+ reductase, O2, e- (electrons), chlorophyll, reaction centers REFER TO THE DRAWINGS WE DID TOGETHER · Why is it important to “boost” e- during the light reactions? What component(s) is/are responsible for boosting the electrons from a ground state to a high-energy state? How are these components able to boost the electrons? -It is important to boost e- during light reactions because you need them to power or Hydrogen Ion pumps that help Hydrogen Ions go against the concentration gradient that help power the ATP Synthase that synthesize ADP+P into ATP · What is the source of electrons to keep the light reactions going? The “stripping” or oxidizing of this molecule leads to the formation of what by-products? Why would one of these by-products be a useful input in cellular respiration? What component is responsible for stripping this molecule of its electrons to keep the light reactions going? What does this component do with the electrons? Hint: Why are there two photosystems in the light reactions? Where do these photosystems get their electrons? What do these photosystems do with their electrons? Once they have accomplished their task, whom do the photosystems give these electrons to in the light reactions? Why are these electrons analogous to “hot potatoes”? H20 is being stripped of its electrons and the byproducts are a hydrogen ion and oxygen. Oxygen is very important in cellular respiration because certain processes like the Krebs cycle are aerobic reactions. -Photosystem 2 is what is responsible for stripping its electrons. -It brings the electrons to the reaction center to be brought from a ground state to a high state. -The electrons are given to NADP+ and turned into NADPH · Why is a concentration gradient of H+ (protons) important in the light reactions? Which components in the light reactions are directly responsible for maintaining the proton gradient? How do they do this? Hint: Why could we nick name these components proton pumps? Why is this considered a form of active transport? How do these components “pay” to perform this active transport?

· Which molecule relies on facilitated diffusion of protons to perform its reactions? What reaction does this component catalyze? Where are the products of this reaction used in the process of photosynthesis? Why can’t plants just use the products of this system to “run” their cells instead of having to proceed to the Calvin cycle? · What does NADP+ reductase do in the light reactions? What is its product? Why is the product necessary for the Calvin cycle? What does this enzyme need to interact with in order to produce this product? · What products from the light reactions are required in the Calvin cycle? ● ATP AND NADPH Calvin cycle · What is the “goal” of the Calvin cycle aka what product is the chloroplast trying to synthesize? What molecule is the source of the carbons to produce this product? ● Goal : produce Glucose · Can you list the three stages of the Calvin cycle? Which stage(s) require products(outputs) from the light reactions to proceed? Can you keep track of the “carbons” during the Calvin cycle, being able to tell me how many we have at each step? ● Carbon Fixation, PGAL synthesis, regeneration of RUBP ● PGAL synthesis · Why is the first stage referred to as “Carbon fixation”? What molecule is the source of carbon? How does the plant acquire these molecules? How many of these molecules are needed to build one glucose (C6H12O6)? The first step in carbon fixation requires what molecules? What enzyme catalyzes this reaction? What is the product of carbon fixation? It is called carbon fixation because we are trying to convert carbon dioxide and water into organic compounds that can be used by the organism Carbon dioxide is the source of carbon used Plants acquire these molecules by · If the enzyme in stage one interacts with oxygen instead of its target molecule, we refer to this as PHOTORESPIRATION instead of photosynthesis. Why is it bad for a plant to perform CALVIN CYCLE NEED CO2 ? · This happens more frequently in warmer weather, explain how have plants evolved to address this issue. What type of photosynthesis do these plants perform? ● C4 use mesophyll cells to produce 4 carbon sugars ● CAM opens stoma at night to store CO2 · During the acquiring of these molecules needed in the first stage as the carbon source, plants can lose water through their __________________. Why

water loss a problem for plants? Why can water loss negatively affect the light reactions? Explain how plants that have evolved in dry conditions where water loss is an issue (deserts) address this issue. What type of photosynthesis do these plants perform?

· Why is the second stage referred to as “Energizing and reducing the sugar”? What molecules are needed to accomplish this stage? What is the product of this stage? What are by-products of this stage? Why would this stage fail if a plant were unable to perform the light reactions? Why do some of the products from this stage leave the Calvin cycle while others must continue in the cycle? Redox reactions take place during this stage. Could you walk me through which molecules are being oxidized or reduced? It is referred to as energizing and reducing the sugar because you are energizing ATP and reducing the negative electrons into sugar. Product of this stage is 12 PGAL (36 carbons)

· Why is the third stage referred to as “Regenerating the sugar”? What type of molecules enter the third stage? What molecules from the light reactions are necessary to complete the third stage? What is the product of the third stage? Why is this product important for the cycle? · Could you draw the Calvin cycle, labeling all of the inputs/outputs? Chapter 6: Respiration (11-13 questions) · Explain how catabolism and anabolism are linked. How is ATP involved in these processes? How do endergonic and exergonic reactions relate to catabolism & anabolism? -Catabolism is the breaking of bonds and Anabolism are the synthesizing of bonds and it requires energy. They are linked because some of the energy from the Catabolism reaction is used during Anabolism reactions to synthesize those bonds again to break once more for energy. ATP is the main energy currency. Catabolism reactions break the bond of one of the 3 phosphates groups in ATP and Anabolism is the synthesis of ADP+P back into ATP which requires energy from Catabolism energy. · How is synthesis of ATP and hydrolysis (breaking) of ATP related to the 1st and 2nd laws of thermodynamics? 1st law of thermodynamics- Energy cannot be created or destroyed and 2nd law of thermodynamics entropy will increase overtime. Breaking of ATP increases entropy(2nd LAW) and creates energy and then the synthesis of ATP transforms energy from the hydrolysis reaction and uses it to synthesize ATP.(1st LAW) · How could you represent respiration on a graph? Where do you position the reactants relative to the products? What is the formula for respiration (inputs and outputs)? C6H12O6+6O2=6CO2+6H2O+36 ATP · How are oxidation & reduction reactions related to the process of cellular respiration? · Why does cellular respiration only have a 37% energy efficiency? 37% of the energy stored in the bonds of glucose are stored in ATP The 63 % are mostly lost as heat. · We discussed four stages of respiration: what are the four stages? What is the proper order of the four stages? Where does each stage take place within a cell? Which stage(s) require O2? Which stage is oxygen-independent? 1.Glycolysis - cytosol 2. Pyruvate Oxidation - mitochondria 3. Krebs Cycle - mitochondria matrix 4. ETC - inner membrane of mitochondria ETC requires O2 The rest is oxygen-independent · Walk me through glycolysis. Where does it take place in the cell? What are the inputs? What are the outputs? Where do these outputs go relative to the rest

of the stages of cellular respiration (what is their role?)? What is the difference between total number of molecules synthesized and net gain? Takes place in the cytoplasm Inputs: 2 NADP+, glucose, 2 ATP Outputs: 2 NADH, 2 pyruvate acids, 4 ATP (2 ATP net gain) 2 NADH and 4 ATP go through the ETC and 2 pyruvate acids are used in the pyruvate oxidation (transition step) · Walk me through pyruvate oxidation. Where does it take place in the cell? What are the inputs? What are the outputs? Where do these outputs go relative to the rest of the stages of cellular respiration? Why can one of these outputs potentially be used in the Calvin cycle of photosynthesis (what stage of photosynthesis?)? Why must the cell perform pyruvate oxidation twice every time one glucose is processed in glycolysis? Pyruvate Oxidation takes place in the mitochondria. Inputs:2 pyruvate molecules, 2NAD+ Outputs: acetyl CoA , NADH Acetyl CoA is needed during the Krebs cycle and the NADH carries electrons for energy. -Pyruvate oxidation must be done twice because for every glucose molecule it yields 2 Pyruvate molecules so it must be done twice, one for each pyruvate. · Walk me through the Citric Acid Cycle (aka CAC or Krebs cycle). Where does it take place in the cell? What are the inputs? What are the outputs? Where do these outputs go relative to the rest of the stages of cellular respiration? Why can one type of these outputs potentially be used in the Calvin cycle of photosynthesis (what stage of photosynthesis?)? Why must the cell perform the citric acid cycle twice every time one glucose is processed in glycolysis? It takes place in the mitochondria matrix Inputs: 6 NAD+, 2 FAD, 2 CoA, 2 ADP + P Outputs: 6 NADH, 2 FADH2, 2 CO2, 2 ATP · Walk me through the electron transport chain (ETC). Where does it take place in the cell. What are the inputs? What are the outputs? Can you draw the series of molecules needed in the ETC? The placement is important; do you know the order of these components? Be sure to label: Enzyme complexes I, II, III, IV H2O, ADP, P, ATP, NAD+, NADH, FAD, FADH2, H+, mobile protein I, mobile protein II, ATP synthase, O2, e- (electrons). What is the source of electrons to keep the ETC going? The “stripping” or oxidizing of these molecules leads to the formation of what? What component is responsible for stripping this molecule of its electrons to keep the ETC going? What does this component do with the electrons? Why does this component need these high-energy electrons? Once they have accomplished their task, whom do these components give these electrons to in the ETC? Why are these electrons analogous to “hot potatoes”?

ETC takes place in the inner membrane of the mitochondria · Why is a concentration gradient of H+ (protons) important in the ETC? Which components in the ETC are directly responsible for maintaining the proton gradient? How do they do this? Hint: Why could we nick name these components proton pumps? Why is this considered a form of active transport? How do these components “pay” to perform this active transport? Which molecule relies on facilitated diffusion of protons to perform its reactions? What reaction does this component catalyze? Why are the products of this reaction so important to the cell (how is it related to anabolism?)? · What happens to the ETC if oxygen is not available? How would this affect the rest of cellular respiration? Why is fermentation linked to the absence of oxygen? What is the output of fermentation that allows a cell the ability to keep doing glycolysis? What is an output of fermentation that can build up in human? What is an output of fermentation for yeast that we use a commercial product? · How are Photosynthesis and Respiration related? Compare their inputs and outputs. How could you follow carbon atoms through both processes? Chapter 7: DNA Structure & Function (11-13 questions) · Explain to me how Watson & Crick were able to use Chargoff’s data and Franklin’s data to determine the structure of DNA. -Watson and Crick used found out that there were a equal number of each base pair on both sides of the helix and Franklin used x-ray diffraction to see the 3d dimensions of DNA· Do you know the nucleotides that make up DNA? Name them. Which are purines and which are pyrimidines? How do you know which are which? -Adenine and Guanine are PURINES AND Cytosine and Thymine are PYRIMIDINES Uracil is also pyrimidine! · What is a gene? A chromosome? A homologous pair of chromosomes? How many chromosomes do most humans have? How many pairs of chromosomes? What is the difference between autosomes & sex chromosomes? -Gene- A sequence of DNA nucleotides that encodes a specific protein or RNA molecule -Chromosome- Discrete Package of DNA coiled around Proteins Homologous Chromosomes- A pair of chromosomes that are similar in length, gene position, and centromere -Humans have 46 chromosomes and if put into pairs you would get 23 pairs The difference between autosomes and sex chromosomes is that autosomes are truly homologous and sex chromosomes differ in shape and length. There is also 22 pairs that are autosomes and one pair that are sex chromosomes. · What does complementary mean with regard to base pairing?

-Complementary base pairing means that with every G there is a C and with every A there is a T or U for RNA or one strand determines the sequence of the other strand. · Explain how DNA base pairing works. What type and part of the molecules are involved? What type of bonds form? What can you tell me about this type of bond? -Dna base pairing is when 2 nucleobases are bound together and form a hydrogen bond. Nucleotides are involved in base pairing and Deoxyribose Nucleic Acid(DNA) Nitrogenous bases are point inward on the ladder and forms pairs with bases on the other side. · How is a DNA double helix organized? Where are different parts of the nucleotides located in the double helix? -Dna is organized by 2 strands that wind around each other like a twisted ladder and both strands are antiparallel. One strand is 5 prime to 3 prime and the other is 3 prime to 5 pri...