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Cellular Biology Test Nots, Lecture notes of Medicine

Bowdoin CollegeMedicine

Chapter Learning Goals: Glycolysis Krebs Amino Acids

Typology: Lecture notes

2018/2019

Uploaded on 02/17/2019

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Learning Goals
1. Draw a diagram of the citric acid cycle (see figure 10.10) and be able to identify the steps
where it is regulated.
1.1. Acetyl CoA enters matrix and water is added—Regulated by ATP--
allosteric
1.2. Citrate
1.3. Isocitrate
1.4. NADH and CO2 are produced—Regulation—competitive
1.5. Ketoglutarate
1.6. NADH and CO2 are produced—Regulation—competitive
1.7. Succinyl CoA
1.8. ATP is produced
1.9. Succinate
1.10. FADH2 is produced
1.11. Fumarate
1.12. Malate
1.13. NADH is produced
1.14. Oxaloacetate
1.15. Spin again
2. List the molecules that regulate the citric acid cycle and where they act in the cycle.
1.16. NADH—competitive
2.1. Between Isocitrate and ketoglutarate
2.2. Between ketoglutarate and Succinyl CoA
1.17. ATP—allosteric
2.3. Acetyl CoA entering CA
2.4. Between Succinyl CoA and Succinate
3. Describe the ETC and predict the effect of adding dinitrophenyl to mitochondria
1.18. NADH transfers electrons to Complex I which then sends them to Q
(ubiquinone)
1.19. FADH2 transfers electrons to Complex II which then sends them to Q
1.20. Q is reduced and has moves across the intermembrane taking protons as it
moves
1.21. Q transfers its electrons to Complex III and then releases its protons in the
intermembrane space
1.22. Complex III then reduces cyt c which then travels to Complex IV
1.23. Complex IV oxidizes cyt c which also pushes protons into the
intermembrane space
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Learning Goals

  1. Draw a diagram of the citric acid cycle (see figure 10.10) and be able to identify the steps where it is regulated. 1.1. Acetyl CoA enters matrix and water is added—Regulated by ATP-- allosteric 1.2. Citrate 1.3. Isocitrate 1.4. NADH and CO2 are produced—Regulation—competitive 1.5. Ketoglutarate 1.6. NADH and CO2 are produced—Regulation—competitive 1.7. Succinyl CoA 1.8. ATP is produced 1.9. Succinate 1.10. FADH2 is produced 1.11. (^) Fumarate 1.12. Malate 1.13. NADH is produced 1.14. Oxaloacetate 1.15. Spin again
  2. List the molecules that regulate the citric acid cycle and where they act in the cycle. 1.16. NADH—competitive 2.1. Between Isocitrate and ketoglutarate 2.2. Between ketoglutarate and Succinyl CoA 1.17. ATP—allosteric 2.3. (^) Acetyl CoA entering CA 2.4. Between Succinyl CoA and Succinate
  3. Describe the ETC and predict the effect of adding dinitrophenyl to mitochondria 1.18. NADH transfers electrons to Complex I which then sends them to Q (ubiquinone) 1.19. FADH2 transfers electrons to Complex II which then sends them to Q 1.20. Q is reduced and has moves across the intermembrane taking protons as it moves 1.21. Q transfers its electrons to Complex III and then releases its protons in the intermembrane space 1.22. (^) Complex III then reduces cyt c which then travels to Complex IV 1.23. Complex IV oxidizes cyt c which also pushes protons into the intermembrane space

1.24. Complex IV also hands the electron off to oxygen which combines with hydrogens to create water 1.25. Adding dinitrophenyl would decrease ATP production by stopping the pathway into the matrix

Application/ Analysis

  1. Reproduce the pathway depicted in figures 10.12-13 and clearly describe how the energy in glucose is harnessed 1.1. In each process of respiration, electrons are taken by NADH or FADH2. The electrons are brought to the ETC which will power a gradient that powers ATP synthase
  2. Describe the function of ATP synthase and the production of H2O during cellular respiration 1.2. The H+ drive ATP synthase 1.3. O is the final electron acceptor and attaches with H+ to crease water
  3. (^) Describe and differentiate fermentation that produces lactic acid from fermentation that produced ethanol (see figure 10.21). 1.4. Lactic Acid 3.1. Glucose to 2 Pyruvate to Lactate 3.2. Net 2 ATP 3.3. 2 NADH are created but are used in a redox reaction to create Lactate 1.5. Alcohol 3.4. Glucose to 2 Pyruvate to 2 Acetaldehyde to 2 Ethanol 3.5. Net 2 ATP and 2 CO2 (why bread rises) 3.6. (^) 2 NADH are created but are used in a redox reaction to create Ethanol Learning Goals
  4. Describe the relationship diagrammed in Figure 10. 1.1. Sunlight and water together start the light reactions which produced O2 as a product and ATP and NADPH as intermediates 1.2. CO2 and the intermediates together power the Calvin Cycle which creates sugar
  5. Describe the structure of a chloroplast 1.3. In a chloroplast is the…. 2.1. (^) Stroma—empty space 2.2. Thylakoid (membrane)—site of light reactions 2.3. Lumen—space inside thylakoid 2.4. Granum—stack of thylakoids

5.1. Simple version where only PSI is involved so only ATP is produced and nothing else. Ferredoxin gives electron to cytochrome complex which creates the H+ gradient needed for ATP synthase. Then to PC then all over again

  1. (^) Describe the three stages of carbon fixation (see fig. 10.19) 1.7. Fixation 5.2. CO2 reacts with RuBP—produces 2 molecules of 3PGA 1.8. Reduction 5.3. PGA is phosphorylated by ATP and reduced by NADPH—creates G3P 6.1. Some G3P leaves cycle to be used to create sugar, the rest goes to regeneration 1.9. Regeneration 5.4. The rest of the ATP is used to regenerate the RuBP
  2. (^) Diagram where in the Calvin cycle ATP and NADPH are used 1.10. ATP and NADHP goes in during reduction 1.11. ATP goes in during regeneration

Factual Knowledge/ Comprehension

  1. Describe the structure of the plant cell wall. 1.1. Primary Cell Wall- consists of long strands of cellulose that keep the shape of the cell wall 1.2. Secondary Cell Wall- between the primary and the plasma membrane- occurs when the cell matures and stops growing- can vary from plant to plant
  2. (^) Describe the structure the ECM in animals; what role do carbohydrates play? 1.3. Network of macromolecules outside (are attached to integrin) the cell that help stabilize the cell- main compound is collagen
  3. Define the function of tight junctions, desmosomes, hemi-desmosomes, adhesion junctions, gap junctions, and plasmodesmata. 1.4. TJ- parts of the plasma membranes between cells are sealed together by proteins- limit movement of substances between cells 1.5. Desmosomes- two cells are joined by proteins that act anchors to each other (like bars that connect two pieces of metal)- help resist structural wear and tear 1.6. (^) H-desmosomes- binds a cell to the basal layer- only one cell not two 1.7. AJ- anchors cytoskeleton of one cell with one of the neighboring cell 1.8. GJ- bridge between two cells- allows molecules to go from one cell to another- commonly used to allow the spread of electrical pulses such as in cardiac muscle- animal cells

1.9. Plasmodesmata- open channels between the cell wall of plants

  1. Draw how a steroid signal vs. how lipid-insoluble signals 1.10. Steroid Signaling 4.1. A steroid goes through the cell membrane 4.2. (^) A receptor protein picks up the steroid 4.3. The receptor protein goes into the nucleus and attaches to the DNA for gene expression 1.11. Lipid Insoluble Signaling 4.4. Lipid binds to a membrane receptor protein 4.5. Message is amplified (transduced) 4.6. A message goes into the nucleus, binds to DNA, and gene expression begins
  2. Describe how steroid signals are amplified. 1.12. The message bind to a membrane receptor 1.13. (^) The receptor changes shape and sends a signal to their G protein 1.14. The G proteins becomes active by a GTP and the alpha subunit leaves and attaches to a nearby enzyme 1.15. The enzyme releases an amplified secondary messenger 1.16. The GTP is used up and become GDP 1.17. The alpha subunit goes back to the receptor

Application/ Analysis

  1. Compare and contrast the structure and function of plant cell walls and the animal cell ECM.
  2. Predict the role of cell junctions in tissue formation and multicellularity. Study figure 
    2.1. Keeps the structure strong
  3. Compare and contrast the role in communication played by plasmodesmata and gap junctions. Are there size restrictions? 2.2. Gap junction are larger 2.3. Gap junctions are continuous but split up into different section
  4. List and commit to memory the order in which a signal transduction (steroid or lipid- insoluble) event occurs

Factual Knowledge/ Comprehension

  1. Describe, in detail, GPCR signaling and name a prominent second messenger in the GPCR system. 1.1. A common second messenger is a kinase because they can activate other proteins by phosphorylating them

2.6. GTP is used up and subunit returns to G protein 2.4. RTK 2.7. Message binds to RTK which changes form and phosphorylates itself 2.8. (^) Proteins bind Ras to RTK 2.9. Ras activates a kinase 2.10. A kinase activation chain reaction occurs and second messengers are created

  1. Describe the concept and purpose of a second messenger 2.5. Are able to go through out the cytosol and nucleus unlike the primary messenger

Factual Knowledge/ Comprehension

  1. Place the events of bacterial translation in order (see figs 18.15-18.17) and learn the details of each step. 1.1. Initiation 1.1. mRNA binds to small subunit (has complimentary RNA to the rRNA) 1.2. Initiator aminoacyl tRNA binds to start codon 1.3. Large subunit binds and translation begins 1.2. Elongation 1.4. tRNA with corresponding amino acids enters A-site 1.5. The new amino acid binds to the chain of amino acids and moves to the P-site 1.6. (^) Used tRNA moves to the E-site 1.7. Starts again 1.3. Termination 1.8. Stop codon is read in the A-site 1.9. Polypeptide is released 1.10. Ribosome separates
  2. What type of structure is the ribosome? How does this structure contribute to its function? How do humans manipulate this function with antibiotics? 1.4.
  3. Define transcription and compare it to DNA replication. How is it similar? Different? 1.5. (^) Transcription is changing DNA to mRNA 1.6. Process (eukaryotes)

1.11. Basal transcription factors bind to the promoter region of eukaryotic DNA 3.1. Promoter region has a TATA box about 30 base pairs upstream of the +1 site 1.12. (^) RNA polymerase opens the DNA at the +1 sites and begins transcribing the coding template into mRNA 1.13. A poly(A) signal is read the mRNA is cut with a poly(A) tail of an arbitrary number of bases 1.14. A 5’ cap of guanine and phosphates are added 1.15. Spliceosomes cut out introns

  1. Describe bacterial fission and using the slides from lecture, describe the processes inhibited by antibiotics. 1.7. Bacterial DNA is replicated 1.8. DNA strands move to opposite sides of cell 1.9. (^) Proteins pinch down around the membrane and the bacteria splits in two
  2. Explain the roles of each of the four stages of the cell cycle 1.10. G1- the cell grows and matures- gains needed nutrients to complete cell cycle 1.11. S-Phase- DNA is replicated 1.12. G2- growth and regulation 1.13. M-Phrase- the actual splitting of the cell
  3. Compare and contrast the stages of M phase (prophase, prometaphase, metaphase, anaphase, telophase). Be able to list the dominant characteristics of each stage. 1.14. Prophase- chromosomes condense and spindle begins to form 1.15. (^) Prometaphase- nuclear envelope breaks down and the spindle is formed with kinetochore 1.16. Metaphase- the sister chromatids line up on the spindle 1.17. Anaphase- sister chromatids separate- kinetochore microtubule breaks down on the + end 1.18. Telophase- chromatids move to opposite end and decondense- the spindle disappears and nuclear envelope reappears. 1.19. Cytokinesis- actin and myosin create a ring in the middle of the cell and pinch in

Application/ Analysis

  1. (^) Clearly describe the structure and regulation of the Lac operon 1.1. Negative feedback 1.1. If a protein is abundant it will bind to the repressor and stop transcription (blocks polymerase)