Assignment Code: BBCCT-111 / TMA / 2021-2022

Course Code: BBCCT-111

Assignment Name: Membrane Biology and Bioenergetics

Year: 2021-2022

Verification Status: Verified by Professor

Note: Attempt all questions. The marks for each question are indicated against it.

For any question worth 2 marks, the word limit is 50 words, for 5 marks question it is 100 words; and for 10 marks it is 250-300 words.

PART-(A)

Maximum marks:  50

1. (a) Describe the general composition of a biomembrane. [5]

Ans) Proteins, lipids, and carbohydrates, in various quantities, are the primary components of biological membranes. Carbohydrates make up less than 10% of the mass of most membranes, and they are usually coupled to lipid or protein components. Myelin is almost entirely made up of lipids and has only a few functions. The weight ratio of lipid to protein in plasma membranes is close to one; in many specialised membranes (such as mitochondrion and bacterial cells), the ratio is closer to two or three. As a result, it appears that the number of actions conducted by and the amount of protein in a membrane are related.

Phospholipids, cholesterol, and glycolipids are the three primary membrane lipids. Glycolipids appear to be cell antigens, and they, along with glycoproteins, may determine a cell's surface properties that differentiate it from others. The majority of the protein material in plasma membranes is made up of 10 polypeptide chains of various molecular weights.

Q1. (b) Name the components of glycocalyx [2]

Ans) Carbohydrates or oligosaccharides bonded covalently to proteins or lipids to produce glycoproteins or glycolipids. Some carbohydrates are proteoglycans, which are polysaccharide chains connected to the core of an integral membrane protein. The glycocalyx is a carbohydrate-rich coating on the membrane's surface.

The glycocalyx is the plasma membrane's thick outer layer. It is made up of sugar and protein strands that are bonded together. The end result is a thick, sticky covering that helps cells stay put in high-stress settings.

Q1. (c) Name any three-method used for studying proteins. [3]

Ans) Proteins are investigated using various technologies such as X-ray crystallography and nuclear magnetic resonance (NMR) in order to understand the activities of a membrane.

2. Define the following terms: [10]

Q2. (a) Krafft temperature

Ans) The Critical Micelle Concentration (CMC) is the concentration at which 50% of the fatty acid salts or detergents are in micelle form. Micelles form only above a certain concentration, known as the critical micelle concentration, and also above a certain temperature, known as the Krafft temperature (TK).

Q2. (b) v-SNARE and t-SNARE

Ans) Each type of transport vesicle has a unique v-SNARE that binds to the target membrane's corresponding t-SNARE. The C-terminal region of most SNAREs is anchored to transmembrane proteins, while the N-terminal domain faces the cytoplasm. They have a 60-70 amino acid heptad (group or set of seven) repeat motif that helps to create coiled coils. The SNARE complex generated by the coupling of v-SNARE and t-SNARE is a four-helix bundle with one helix contributed by v-SNARE and three alpha-helices contributed by t-SNARE.

Q2. (c) Lipid raft

Ans) Lipid rafts are specialised subdomains of cellular membranes high in cholesterol and sphingolipids with saturated acyl chains. The concept of lipid "rafts" within the membrane is a means to control membrane function geographically and temporally. Because their proteins are typically engaged in the reception and transmission of extracellular signals, lipid rafts can be thought of as signalling platforms. The creation of rafts is thermodynamically advantageous in theory. The average diameter of a lipid raft is 50nm, however it can range from 10-100nm.

Q2. (d) Flip-flop

Ans) The movement of a molecule from one membrane surface to the other, or from one face of the membrane to the other, is known as transverse diffusion or flip-flop. It takes a long time for lipids to flip from one side of a membrane to the other. A phospholipid molecule flipflops after several hours.

Q3. Differentiate between [5+5]

Q3. (a) Simple and facilitated diffusion.

Ans) Small noncharged molecules or lipid soluble molecules flow between the phospholipids to enter or leave the cell, migrating from places of high concentration to areas of low concentration in simple diffusion (they move down their concentration gradient). Simple diffusion transports oxygen and carbon dioxide, as well as most lipids, into and out of cells.

Substances migrate into or out of cells down their concentration gradient through protein channels in the cell membrane in assisted diffusion. Simple diffusion and assisted diffusion are both types of diffusion that include moving down a concentration gradient. The distinction lies in the manner in which the material passes through the cell membrane. The substance travels between the phospholipids in simple diffusion; in assisted diffusion, there are specialised membrane channels. Facilitated diffusion is how charged or polar molecules that can't fit between the phospholipids get into and out of cells.

Q3. (b) Phagocytosis and pinocytosis

Ans) The main distinction between phagocytosis and pinocytosis is that phagocytosis is a type of endocytosis that transports solids through the plasma membrane to the cell, whereas pinocytosis transports fluids, such as solutes and tiny molecules, through the plasma membrane to the cell.

Endocytosis is the process by which a cell takes in material by invaginating its membrane and generating a vacuole. Phagocytosis and pinocytosis are two types of endocytosis. Cell eating is referred to as phagocytosis, while cell drinking is referred to as pinocytosis. The primary distinction between phagocytosis and pinocytosis is that phagocytosis involves the ingestion of relatively large solid particles such as bacteria and amoeboid protozoans, whereas pinocytosis involves the ingestion of liquid into the cell via the budding of a small vesicle from the cell membrane.

4. (a) Discuss the working of sodium–potassium pump. [5+5]

Ans) The sodium-potassium pump is an active transport process that transports Na+ and K+ from low-concentration to high-concentration regions. The sodium-potassium pump functions by causing trans-membrane protein conformational changes.

The main steps of the process are as follows:

1. Three sodium ions bind to the cytoplasmic side of the pump leading to change in its conformation.

2. In this new conformation, the protein binds a molecule of ATP and cleaves it into adenosine diphosphate and phosphate (ADP + Pi). ADP is released; but the phosphate group remains bound to the protein. The protein is now in the phosphorylated state.

3. The phosphorylation of the protein induces a second conformational change in the protein. This change translocates three Na+ across the membrane, so they now face the exterior. In this new conformation, the protein has a low affinity for Na+, and the bound Na+ dissociate from the protein and diffuse into the extracellular fluid.

4. However, the new conformation has a high affinity for K+, two of which bind to the extracellular side of the protein as soon as the Na+ is released.

5. The binding of the K+ causes another conformational change in the protein, and the bound phosphate group is released.

6. De-phosphorylated protein reverts back to its original conformation, exposing the two K+ to the cytoplasm and releasing them into the interior of the cell. The original conformation has a high affinity for Na+; when these ions bind, they initiate another cycle.

Three Na+ ions leave the cell and two K+ ions enter inside every cycle. The changes in protein conformation that occur during the cycle are rapid, enabling each carrier to operate about 100 cycles and transporting as many as 300 Na+ per second.

Q4. (b) Explain the working of a mechano-gated channel.

Ans) Stretch-gated ion channels are another name for mechano-gated channels. They can help with touch-mediated responses, hearing, and balance. Mechanical forces keep them in check.

Mechanically gated channels are involved in generating graded potentials and open and close in response to mechanical vibration or pressure, such as sound waves or the pressure of touch (found in sense receptors in the skin, ear, and other places). A protein must respond to a mechanical deformation of the membrane to be termed mechanosensitive. Changes in the tension, thickness, or curvature of the membrane are examples of mechanical deformations. Mechanosensitive channels change their conformation between an open and a closed state in response to membrane tension. [50] [51] In response to stresses applied on proteins, one form of mechanically sensitive ion channel activates specific sensory cells, such as cochlear hair cells and some touch sensory neurons.

Mechanically gated channels, which are directly influenced by mechanical deformations of the membrane, and mechanically sensitive channels, which are opened by second messengers released by the true mechanically gated channel, are the two types of stretch-activated channels to identify.

5. Write short notes on the following: [5+5]

Q5. (a) Group Translocation

Ans) Another type of active transport found in prokaryotes is group translocation. Group translocation is a process that uses chemical energy in the form of phosphoenol pyruvate to shift solutes from low to high concentrations (PEP). The solute molecule is changed (phosphorylated by PEP) as it passes across the membrane, which necessitates a variety of cytoplasmic and membrane proteins.

The phosphoenol pyruvate: carbohydrate phosphotransferase system (PEP: PTS) is an enzyme/transport system in prokaryotes that phosphorylates its extracellular carbohydrate substrate as it is carried in the cell, resulting in the accumulation of sugar phosphate esters intracellularly. Sugar uptake, particularly glucose uptake, is aided by a number of phosphoryl transfer proteins. The entering sugar serves as the ultimate phosphoryl acceptor, whereas PEP serves as the phosphoryl donor.

Q5. (b) Transport Vesicle

Ans) Transport vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus's cis face, where they fuse with the Golgi membrane and release their contents into the Golgi lumen.

Protein transport vesicles are made in a highly coordinated process. At least three conditions must be met for a functioning vesicle to form. Because distinct coat protein complexes are involved in vesicle budding at different membrane compartments in the cell, a given donor membrane must assemble the relevant species of cytosolic coat proteins. Second, the budding process must include the proper complement of proteins required for vesicle trafficking and fusion at the acceptor membrane compartment. Third, the proper cargo proteins must be recruited to the budding location of the vesicle. Additional proteins may be needed in rare circumstances to scission the budding vesicle from the donor compartment.

PART-(B)

Maximum marks: 50

Q1. Define the following terms: [10]

Q1. (a) System

Ans) In thermodynamics, a ‘system' is defined as the portion of the universe that is being studied. A single cell or a whole organism can be considered a system, which can be large or small, simple or complicated. A thermodynamic system must also have a clearly defined border that separates it from the environment.

Q1. (b) Surrounding

Ans) In thermodynamics, a ‘system' is defined as the part of the universe that is being studied, while the ‘surrounding' is defined as the rest of the universe (not including the system). The universe is made up of the system and its surroundings.

Q1. (c) Universe

Ans) The universe is made up of the system and its surroundings. For practical purposes, however, the surrounds can be thought of as the part of the cosmos with which the system can interact.

Q1. (d) Closed system

Ans) A closed system is one in which the system's boundary prevents the passage of matter between the system and its surroundings but enables the movement of energy. It would become a closed system if the glass test tube containing hot water was properly covered, preventing matter exchange.

Q1. (e) Isolated system

Ans) An isolated system is defined as one with a border that prevents the transmission of heat or matter to or from the environment. It becomes an isolated system if the properly capped glass test tube containing hot water is wrapped in a thick thermally insulating material.

Q2. (a) What is biochemical standard state? [5+5]

Ans) The biochemical standard state is required for applying thermodynamics to biological systems. The biochemical standard state is rarely mentioned in texts, and when it is, it is usually dismissed in three sentences: ‘The pH zero equilibrium constant is K. Because this is inconvenient for biological systems, the biochemical reference state is set to pH 7. After then, K becomes K. Everything works when K ′ is substituted for K in all equations.' This is really unsatisfactory: it's unclear why K is associated with pH 0 and substituting K with K ′ appears to be a clerical error. This chapter clarifies why K is related to pH 0, why this is significant, how K ′ is related to the biologically more relevant pH 7, how the biochemical standard is created and utilised, and how equations based on conventional standards can be changed to the biochemical standard.

Q2. (b) Explain the ADP-ATP cycle.

Ans) The chemical ATP (adenosine triphosphate) is found in all living things. Think of it as the cell's "energy currency." When a cell requires energy to complete a task, the ATP molecule divides one of its three phosphates, resulting in ADP (Adenosine diphosphate) + phosphate. The energy that was holding that phosphate molecule is now free to work for the cell. When a cell has additional energy (from breaking down eaten food or, in the case of plants, from photosynthesis), it stores it by reattaching a free phosphate molecule to ADP and converting it back to ATP. The ATP molecule works in a similar way as a rechargeable battery. It's ATP when it's completely charged. It's ADP when it's depleted. When the battery is depleted, however, it is not discarded; instead, it is recharged.

All biological systems, from microorganisms to people, employ ATP as their fundamental energy currency. Most biological responses can be mediated by the energy it carries. Photosynthesis produces ATP in phototrophic cells, while catabolism of other molecules produces ATP in heterotrophic cells. The conversion of ATP to ADP and Pi provides energy for biosynthetic pathways as well as other activities like muscle contraction. The energy is stored in the form of high-energy phosphoric anhydride bonds in the ATP molecule.

ATP is located between extremely high-energy phosphates and lower-energy acceptor molecules on an energy scale. ADP is an excellent acceptor of energy and phosphates because of its unique location, whereas ATP can give both phosphates and energy to low-energy acceptor molecules. As a result, the ATP/ADP couple is a good donor/acceptor system, making it a versatile energy shuttle capable of interacting with a wide range of molecules to give or receive energy.

Q3. Give the details of respiratory complexes. [10]

Ans) The cytochrome c oxidase complex is also known as respiratory Complex IV. It catalyses the one-electron oxidation of four consecutive reduced cytochrome c molecules, as well as the four-electron reduction of one molecule of O2 at the same time. This is the penultimate stage of electron transport in mitochondria.

The overall reaction is:

4Cyt c [Fe (II)] + 4H+ + O2 􀁯 4Cyt c [Fe (III)] + 2H2O

Cytochrome oxidase, like the other respiratory complexes, is a component of the inner mitochondrial membrane and contains cytochromes a and a3, as well as two Cu ions (CuA and CuB) that help with electron transport. Cytochrome c oxidase reduces O2 to 2 H2O on the cytochrome a3-CuB binuclear complex, which includes four one-electron transfers from CuA and cytochrome a sites in a row. As a result of this process, proton pumping across the inner mitochondrial membrane occurs. Figure 1 depicts the overall flow of electrons across the four complexes of the mitochondrial electron transport chain: Flow of reducing equivalents through mitochondria's respiratory complexes (electron transport chain).

The vectorial proton pumping across the inner mitochondrial membrane causes a proton gradient, which is related with the mitochondrial electron transport chain. The energy stored in the form of a proton gradient is lost in a controlled manner, causing ADP to be phosphorylated and ATP to be produced. Oxidative phosphorylation is the term for this process.

Q4. (a) What is thermogenesis? What is its significance? [5]

Ans) Thermogenesis, or the creation of heat, is an important physiological variable and a natural by-product of metabolic activities. Increased thermogenesis is a frequent aspect of the acute-phase response, and it can be seen after injury, inflammation, infection, physical or emotional stress, as well as in some chronic conditions like cancer. In homeotherms, thermogenesis is also a primary effector of thermoregulation and a key modulator of fever.

Significance of Thermogenesis

This tissue is high in mitochondria and lipid droplets, and it is a key source of non-shivering thermogenesis, which most mammals employ to keep warm in cold environments. A protein called UCP1 is responsible for this function (uncoupling protein 1 or thermogenin). UCP1 is found in the inner membrane of mitochondria and decreases the H+ gradient by transferring protons from the intermembrane gap to the matrix. The proton motive force that drives ATP generation is reduced as a result, while electron transport in uncoupled mitochondria continues, releasing energy solely as heat. In skeletal muscle, another uncoupling protein called UCP3 is found and has a similar role in thermogenesis. Free fatty acids liberated from triacylglycerols in response to hormones like thyroid hormone, epinephrine, and nor epinephrine stimulate this dissipative proton route.

Q4. (b) Differentiate between cyclic and non-cyclic photophosphorylation. [5]

Ans) Photophosphorylation is defined as the addition of phosphate group during the light reaction of photosynthesis in the presence of light. Here the phosphorylation occurs in the presence of light and therefore termed as photophosphorylation.

Photophosphorylation is divided into two types, viz, cyclic photophosphorylation and non-cyclic photophosphorylation.

Some important differences between cyclic and non-cyclic photophosphorylation:

5. Write short notes on the following: [5+5]

Q5. (a) Z- scheme

Ans) The “Z‐scheme” describes the oxidation/reduction changes during the light reactions of photosynthesis. The vertical axis in the figure represents the reduction potential of a particular species—the higher the position of a molecular species, the more negative its reduction potential, and the more easily it donates electrons.

In the Z‐scheme, electrons are removed from water (to the left) and then donated to the lower (non‐excited) oxidized form of P680. Absorption of a photon excites P680 to P680*, which “jumps” to a more actively reducing species. P680* donates its electron to the quinone‐cytochrome bf chain, with proton pumping. The electron from cytochrome bf is donated to PSI, converting P700 to P700*. This electron, along with others, is transferred to NADP, forming NADPH. Alternatively, this electron can go back to cytochrome bf in cyclic electron flow.

Q5. (b) Light harvesting systems in microbes.

Ans) Photosynthetic bacteria contain a well-organized and developed system for harvesting sunlight and converting it into biochemical energy. In this process, photons of sunlight are absorbed by specialized pigment-protein complexes, known as light harvesting complexes (LHC) which are similar to those of plants. The energy of photons is used to excite the reaction canter which initiates the electron flow through a series of redox carriers eventually culminating into phosphorylation of ADP to produce ATP.

A light-harvesting complex is made up of chromophores, which are complex component proteins that are sometimes part of a bigger super complex of a photosystem, which is the functional unit of photosynthesis. Plants and photosynthetic microorganisms use it to collect more of the incoming light than the photosynthetic reaction centre alone could. The light that the chromophores catch has the ability to excite molecules from their ground state to a higher energy level called the excited state. This enthusiastic state is known to be short-lived and does not last long. The diverse photosynthetic species have a vast range of light-harvesting complexes. The complexes, which are made up of proteins and photosynthetic pigments, enclose a photosynthetic reaction centre and use Förster resonance energy transfer to direct energy obtained from photons absorbed by the pigment toward the reaction centre