These transporters are temporarily phosphorylated during transport.

Select one:

a. P-type ATPases

b. more than one of these answers is correct

c. ABC transporters

d. F-type ATPases

e. V-type ATPases

Protein:

(1) What are proteins, from a biochemical perspective? Discuss in detail, and in terms of what is presented in this course’s lessons and materials.

(2) What functional groups and structural characteristics are involved, and what chemical and physical properties does this lead them to possess?

(3) What are the major functions of proteins in the body?

Chapter 5: Ground Rules of Metabolism

* Section 5.1 – Life Runs on Energy

o Describe what energy is (definition). Explain how this definition applies to life. Use a cell as an example. Use an entire organism as an example.

o What are the first and second law’s of thermodynamics? What does each one mean for life, from the perspective of a cell?

o Compare kinetic versus potential energy. How does life obtain potential energy?

* Section 5.2 – Energy in the Molecules of Life

o Interpret a chemical formula (just identify which are products, which are reactants)

o Explain activation energy. After defining it, explain what life does to deal with activation energy (hint: think enzymes)

* Section 5.3 – How Enzymes Work

o What is an enzyme? First, which macromolecule is it? Then, what does an enzyme do?

o How does an enzyme accomplish its job? (Read about induced fit model)

o What is a substrate?

* Section 5.4 – Metabolic Pathways

o Describe allosteric regulation

o Describe feedback inhibition

o What is an electron transfer chain?

* Section 5.5 – Cofactors and Coenzymes

o Define cofactor and coenzyme. What is the difference in the two?

o What does ATP stand for? Explain what about ATP gives it lots of energy.

o Explain what ADP is and how it is related to ATP

* Section 5.6 – Diffusion and Membranes

o Describe what diffusion is. Give an example

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o Explain the factors that can affect the speed (rate) of diffusion. Most importantly, HOW do each of these factors cause a change in the rate of diffusion?

o Describe what osmosis is. How does this compare to diffusion?

* Hint – in osmosis, water will move across a membrane to dilute the concentrated side, since the solute cannot always move on its own by diffusion

o Define the terms hypotonic and hypertonic. If I were to give you the salt concentration, for example, inside a cell versus outside a cell, be able to state whether the solution outside the cell is hypotonic or hypertonic to the cell. Also, what is isotonic?

o Explain turgor, and how this term applies to wilting (think of how a cut flower will wilt out of water)

o Critical thinking regarding turgor and osmosis – think of a leftover salad. You have salad dressing on the salad, which is typically salty and concentrated so that it is flavorful. Can you link osmosis and turgor to the fact that salads do not stay fresh very long after they are dressed?

* Section 5.7 – Membrane Transport Mechanisms

o Compare passive transport versus active transport in a simple definition of the two.

* What is the cellular form of energy that active transport requires?

* How are membrane proteins important for active and passive transport?

* Section 5.8 – Membrane Trafficking

o Define phagocytosis. What sorts of molecules might a cell ingest, and why would the want to ingest such things?

Describe the major structural differences between the Arachnida, Crustacea, Myriapoda and Insecta. Use diagrams if this assists you to answer the question.

In stressful conditions, a cell wants to limit expression of Protein X. List all the ways that this can occur.

You are employed as research scientists (biologists) in an agricultural company that is looking for a solution to the problem of brown apple. First, define the problem and then write down what direction of research you would offer the company owner to test to make non-browned apples.

(refer to Polyphenol oxidase)

Please answer ALL parts of the question fully with detailed explanations.

#Q5

a)Looking at the rat’s heart, how does the mammalian heart differs from those of reptiles? And from those of fishes? How similar is it to a bird’s heart?

b)What advantage has the mammalian heart over the reptilian heart? Use diagrams if necessary.

c) Compare & contrast both the skeletal systems and digestive systems individually in pigs, cats, and sheep.

d) pig vs cat :

1. What is the length of the small intestine relative to the body? Why?
2. What is the length of the large intestine relative to the body? Why?
3. Is the spinal column bent or straight? Why?
4. Are the legs straight or highly bent? And what is the length of the leg bones in each animal? Why? How do you think this relates to locomotion in each animal, or what type of locomotion is possible?
5. Is the body elongate or tall?

Chapter 6 – Where it Starts - Photosynthesis
* Section 6.1 – Overview of Photosynthesis
o Apply the terms autotrophs and heterotrophs to the previously learned terms of producer and consumer. Going forward, autotrophs and heterotrophs are the terms you should use.
o How does the textbook define photosynthesis? From this textbook definition, what is the purpose (useful product) of photosynthesis?
o What are the names of each of the two sets of reactions in which photosynthesis occurs?
o Memorize the summary equation of photosynthesis. What goes in (reactants)? What comes out (products)?
o Be able to label the main parts of a chloroplast (figure 6.3 of your textbook)
o Where does the first set of photosynthetic reactions occur in a chloroplast? Where in the chloroplast does the last set of reactions occur?
* Section 6.2 – Sunlight as an Energy Source
o Explain the experiment by Theodor Engelmann. How did it work (Describe the set up)? What did he discover?
o What is a pigment? How is it involved in photosynthesis?
o Which pigment is most common in plants?
o What is an accessory pigment? How can this describe why many leaves change color in autumn?
* Section 6.3 – Light-Dependent Reactions
o What is a photosystem?
o In the non-cyclic pathway of light-dependent reactions, how many times is light required?   
o Look at figure 6.8 in your textbook (light-dependent non cyclic pathway). Understand that all of these motions and steps are working to build up Hydrogen ions inside the thylakoid compartment in large amounts, so that they naturally want to diffuse out of this space (like a inflated balloon wanting to burst). When the hydrogens flow out, they flow through the ATP synthase enzyme, and the flow of the ions powers the ATP synthase enzyme to do work. What work is it actually doing?
o Calvin-Benson Cycle (aka – light independent reactions). What goes in at the beginning? What comes out? Where do the carbon atoms in the sugar that is produced in photosynthesis come from (where do the plants get the carbon atoms)?
o What are stomata and why are they important for plants?
o Where do you find C4 plants? How about CAM plants? How do each of these types of plants perform photosynthesis differently so that they can survive in their environments?

1. Why do ions have a difficult time getting through plasma membranes despite their small size? How are ions transported through biological membranes?
   
2. Where does the cell get energy for active transport processes?
   
3. Describe the position of the transition state on a vertical energy scale, from low to high, relative to the position of the reactants and products, for both endergonic and exergonic reactions. How do enzymes affect the energy of the reactants, product, and transition state.
   
4. Do you think that the E_A for ATP hydrolysis is relatively low or high? Explain your reasoning.

5. Explain in your own words the difference between a spontaneous reaction and one that occurs instantaneously, and what causes this difference.

6. Nearly all organisms on Earth carry out some form of glycolysis. How does this fact support or not support the assertion that glycolysis is one of the oldest metabolic pathways?

7. What is the primary goal of glycolysis and the citric acid cycle (think about what is being produced and what it is used for)?
   
8. Why is it important to have regulatory control over metabolic pathways like glycolysis?

T.J. is a 46-year-old science professor brought to urgent care this afternoon by his wife. T.J. has been at home for 3 days with severe diarrhea and vomiting. His youngest daughter was hospitalized earlier in the week with similar symptoms. T.J. has no significant medical history and takes no medications. Examination reveals an ill-appearing, pale, diaphoretic man who is having difficulty concentrating and answering questions. He has diffuse abdominal pain. Vital signs are as follows: Lying—HR 100, BP 100/80, resp 26, temp 100. Sitting—HR 136, BP 90/60. He has not urinated since yesterday morning.

1. What other laboratory or clinical data would be helpful in assessing T.J.’s fluid-electrolyte and acid-base status? (select all that apply)

a Further assessment could include inspection of mucous membranes for dryness, skin turgor, status of neck veins, and presence of dizziness with position change.

b A chemistry panel would be helpful in assessing for imbalances of serum sodium, potassium, and bicarbonate.

c Blood test to assess the level of glucose.

D Assessment of body temperature.

2. Which assessment data should be monitored during fluid replacement therapy to determine when adequate volume has been restored? (select all that apply)

A. Mental status should be assessed and expected to improve with adequate fluid replacement.

B. Vital signs should be monitored for resolution of tachycardia and postural symptoms, as well as intake and output.

C. Electrolytes should be monitored for resolution of any electrolyte imbalance.

D. Skin turgor and mucous membranes should be monitored for improvement of dehydration.

3. How might persistent vomiting and diarrhea alter acid-base balance? (select all that apply)

A. Metabolic acidosis may occur as a result of persistent diarrhea.

B. Vomiting may contribute to metabolic alkalosis.

C. Metabolic alkalosis may occur as a result of persistent diarrhea.

D. Vomiting may contribute to metabolic acidosis.

In the turkey population studied by Krakauer (2005), would you expect to see the formation of coalitions composed of two male first cousins for whom r was 0.125?

1.) Ibu, a 39-year-old busy dad of three kids, finally gets the time to relax one lazy Sunday afternoon. Ibu is feeling tired but figures he is run-down from the busy week. Within just a few hours, Ibu finds himself laying in bed with chills and the onset of a fever. Ibu works at a hospital and wonders if he has contracted the virus which causes COVID-19.

1a.) What type of second line of defense non-specific immune cell is going to communicate with the third line of defense to help fight Ibu’s viral infection? (1p)

1b.) List the major third line of defense specific lymphocytes and their functions in fighting off Ibu’s viral infection. (3pts)

1c.) Fill in the blanks. A cytotoxic T cell will bind to the SARS-CoV-2 epitope presented on MHC I found on ___________ host cells. (1p)

1d. ) Which type of third line of defense specific lymphocyte is required to help “activate” the cytotoxic T cell (Th1 or Th2)? (1p)

1e.) Fill in the blanks. B cells will phagocytize and present the epitope on _______ (MHC I or MHC II) and become active through costimulation from _______ (Th1 or Th2) (T cell dependent activation). (1pt)

1f.) Which three major antibodies are produced by plasma B cells in response to Ibu’s viral infection? State where they are found in the body. (3pts)

1g.) Compare and contrast what Ibu’s immune response to the virus would look like with and without a vaccine. (4pts)

Describe the principles behind and the applications of the following:

a) Reverse transcriptase-PCR b) Cloning DNA into a plasmid vector

c) SDS-PAGE

d) Restriction mapping

e) Sanger Sequencing of DNA

Note

Detail explanation is required for each .