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Mathematically, it can be expressed as: The Second law of thermodynamics states that the total entropy of a system must increase if a process is to occur spontaneously. At const ant t em perat ure and pressure, t he follow ing relat ion can be derived: The chem ical react ion has a charact erist ic st andard free energy change and it is const ant for a giv en react ion.

I t can be calculat ed from t he equilibrium const ant of the r eact ion under st andard conditions i. I n t his st at e, t he rat io of [ B] t o [ A] is const ant , regardless of t he act ual concent rat ions of t he t w o com pounds: The concent rat ion of react ant s and product s at equilibrium define t he equilibrium const ant , Keq. The equilibrium const ant Keq depends on t he nat ure of react ant s and product s, t he t em perat ure and t he pressure.

Bioenergetics and Metabolism 2. It consists of hundreds of enzymatic reactions organized into discrete pathways. These pathways proceed in a stepwise manner, transforming substrates into end products through many specific chemical intermediates.

Each step of metabolic pathways is catalyzed by a specific enzyme. Reaction 1 Reaction 2 Reaction 3 A B C D Enzyme 1 Enzyme 2 Enzyme 3 Starting Product molecule Metabolic pathways can be linear such as glycolysis , cyclic such as the citric acid cycle or spiral such as the biosynthesis of fatty acids.

Metabolism serves two fundamentally different purposes: To achieve these, metabolic pathways fall into two catego- ries: Anabolic pathways are involved in the synthesis of compounds and ender- gonic in nature.

Catabolic pathways are involved in the oxidative breakdown of larger complex molecules and usually exergonic in nature. The basic strategy of catabolic metabolism is to form ATP and reducing power for biosyntheses. Some pathways can be either anabolic or catabolic, depending on the energy conditions in the cell. They are referred to as amphibolic pathways.

Characteristics of metabolic pathways are: They are irreversible. Each one has a first committed step. Those in eukaryotic cells occur in specific cellular locations.

They are regulated. Regulation occurs in following different ways: Availability of substrate; the rate of reaction depends on substrate concentration.

Allosteric regulation of enzymes by a metabolic intermediate or coenzyme. By extracellular signal such as growth factors and hormones that act from outside the cell in multicellular organisms; changes the cellular concentration of an enzyme by altering the rate of its synthesis or degradation.

A number of central metabolic pathways are common to most cells and organisms. These pathways, which serve for synthesis, degradation, interconversion of important metabolites, and energy conservation, are referred to as the intermediary metabolism. Metabolic pathways involve several enzyme-catalyzed reactions.

Most of the reactions in living cells fall into one of five general categories: Feedback inhibition and feedback repression In feedback inhibition or end product inhibition , the end product of a biosynthetic pathway inhibits the activity of the first enzyme that is unique to the pathway, thus controlling production of the end product.

The first enzyme in the pathway is an allosteric enzyme. Its allosteric site will bind to the end product of the pathway which alters its active site so that it cannot mediate the enzymatic reaction.

The feedback inhibition is different from feedback repression. An inhibitory feedback system in which the end product produced in a metabolic pathway acts as a co-repressor and represses the synthesis of an enzyme that is required at an earlier stage of the pathway is called feedback repression.

Energy is required for the maintenance of highly organized structures, synthesis of cellular components, movement, generation of electrical currents and for many other processes. Cells acquire free energy from the oxidation of organic compounds that are rich in potential energy.

Respiration is an oxidative process, in which free energy released from organic compounds is used in the formation of ATP. The compounds that are oxidized during the process of respiration are known as respiratory substrates, which may be carbohydrates, fats, proteins or organic acids. Carbohydrates are most commonly used as respiratory substrates. During oxidation within a cell, all the energy contained in respiratory substrates is not released free in a single step.

Free energy is released in multiple steps in a controlled manner and used to synthesise ATP, which is broken down whenever and wherever energy is needed. Hence, ATP acts as the energy currency of the cell. During cellular respiration, respiratory substrates such as glucose may undergo complete or incomplete oxidation. The complete oxidation of substrates occurs in the presence of oxygen, which releases CO2, water and a large amount of energy present in the substrate. A complete oxidation of respiratory substrates in the presence of oxygen is termed as aerobic respiration.

Although carbohydrates, fats and proteins can all be oxidized as fuel, but here processes have been described by taking glucose as a respiratory substrate. Oxidation of glucose is an exergonic process. An exergonic reaction proceeds with a net release of free energy. When one mole of glucose g is completely oxidized into CO2 and water, approximately kJ or kcal energy is liberated. Part of this energy is used for synthesis of ATP.

For each molecule of glucose degraded to carbon dioxide and water by respiration, the cell makes up to about 30 or 32 ATP molecules, each with 7. As the substrate is never totally oxidized, the energy generated through this type of respiration is lesser than that during aerobic respiration. Glycolysis takes place in the cytosol of cells in all living organisms. The citric acid cycle takes place within the mitochondrial matrix of eukaryotic cells and in the cytosol of prokaryotic cells.

The oxidative phosphorylation takes place in the inner mitochondrial membrane. However, in prokaryotes, oxidative phosphorylation takes place in the plasma membrane. Table 2. Glycolysis occurs in the cytosol of all cells. It is a unique pathway that occurs in both aerobic as well as anaerobic conditions and does not involve molecular oxygen. Phosphorylation Glucose is phosphorylated by ATP to form a glucose 6-phosphate.

The negative charge of the phosphate prevents the passage of the glucose 6-phosphate through the plasma membrane, trapping glucose inside the cell. This irreversible reaction is catalyzed by hexokinase. Hexokinase is present in all cells of all organisms. Hexokinase and glucokinase are isozymes. Glucokinase is present in liver and beta-cells of the pancreas and has a high Km and Vmax as compared to hexokinase.

Step 2: Isomerization A readily reversible rearrangement of the chemical structure isomerization moves the carbonyl oxygen from carbon 1 to carbon 2, forming a ketose from an aldose sugar. Thus, the isomerization of glucose 6-phosphate to fructose 6-phosphate is a conversion of an aldose into a ketose.

Bioenergetics and Metabolism Solution a. Inhibition of NADH dehydrogenase by rotenone decreases the rate of electron flow through the respiratory chain, which in turn decreases the rate of ATP production.

Antimycin A strongly inhibits the oxidation of Q in the respiratory chain, reducing the rate of electron transfer and leading to the consequences described in a. Voltage gradient membrane potential across the inner mitochondrial membrane with the inside negative and outside positive. The electrochemical proton gradient exerts a proton motive force pmf. A mitochondrion actively involved in aerobic respiration typically has a membrane potential of about mV negative inside matrix and a pH gradient of about 1.

In a typical cell, the proton motive force across the inner mitochondrial membrane of a respiring mitochondrion is about mV. Determination of electric potential and pH gradient Because mitochondria are very small, the electric potential and pH gradient across the inner mitochondrial membrane cannot be determined by direct measurement. However, the inside pH can be measured by trapping fluorescent pH-sensitive dyes inside vesicles formed from the inner mitochondrial membrane.

Valinomycin is an ionophore. Bioenergetics and Metabolism Experimental proof of chemiosmotic hypothesis Experimental proof of chemiosmotic hypothesis was provided by Andre Jagendorf and Ernest Uribe in In an elegant experiment, isolated chloroplast thylakoid vesicles containing F0F1 particles were equilibrated in the dark with a buffered solution at pH 4.

When the pH in the thylakoid lumen became 4. A burst of ATP synthesis accompanied the transmembrane movement of protons driven by the electrochemical proton gradient. In similar experiments using inside-out preparations of submitochondrial vesicles, an artificially generated membrane electric potential also resulted in ATP synthesis. The multiprotein ATP synthase or F0F1 complex or complex V catalyzes ATP synthesis as protons flow back through the inner membrane down the electrochemical proton gradient.

The F0 component is embedded in the inner mitochondrial membrane. An aspartic acid residue in the second helix lies on the center of the membrane. Rotational motion is imparted to the rotor by the passage of protons. The free energy released on proton translocation is harnessed to interconvert three states. Calculation of free energy change The standard free energy change for the movement of protons across the membrane along the electrochemical proton gradient can be calculated from the Nernst equation: Thus, electron transport continues unabated, but ATP synthesis stops.

DNP is a weak acid that is soluble in lipid bilayer both in their protonated neutral forms and in their anionic states. DNP in an anionic state picks up protons in the inter-mitochondrial space and diffuse readily across mitochondrial membranes.

After entering the matrix in the protonated form, they can release a proton, thus dissipating the proton gradient and inhibiting ATP synthesis.

Dicoumarol and FCCP act in the same way. Similarly, thermogenin is a physiological uncoupler found in brown adipose tissue that functions to generate body heat, particularly for the new born and during hibernation in animals. Ionophores are lipophilic molecules that bind specific cations and facilitate their transport through the membrane.

Ionophore uncouple electron transfer from oxidative phosphorylation by dissipating the electrochemical gradient across the mitochondrial membrane. Valinomycin, an antibiotic, is an example of ionophore.

It decreases the memberane potential component of pmf without a direct effect on the pH gradient and thus ATP synthesis. Most of the ATP generated by oxidative phosphorylation in mitochondria is exported to the cytoplasm. Because ATP-ADP translocase moves four negative charges out of every three moved in, its activity is favoured by the transmembrane electrochemical proton gradient, which gives the matrix a net negative charge. ATP-ADP exchange is energetically expensive; proton-motive force across the inner mitochondrial membrane powers the exchange.

This transport process is also powered by the transmembrane proton gradient. NADH synthesized during the glycolytic process finally transfers the electrons to electron transport chain. But, NADH cannot cross the inner mitochondrial membrane. So, two different shuttle systems help in the transfer of electrons from NADH to the electron transport chain.

The malate-aspartate shuttle is the principal mechanism for the movement of NADH from the cytoplasm into the mitochondrial matrix. The electrons are carried into the mitochondrial matrix in the form of malate. Malate then enters the mitochondrial matrix, where the reverse reaction is carried out by mitochondria malate dehydrogenase and the regeneration of NADH occurs.

NADH in the cytosol transfers electrons to oxaloacetate, producing malate. Malate is transported across the inner membrane by the help of transporter. H2O2, a toxic product of various oxidative processes, reacts with double bonds in the fatty acid residues of the erythrocyte cell membrane to form organic hydroperoxides.

These, in turn, result in premature cell lysis. Peroxides are eliminated through the action of glutathione peroxidase, yielding glutathione disulfide GSSG. So, G6PD deficiency results in hemolytic anemia caused by the inability to detoxify oxidizing agents. This pathway, first reported by Michael Doudoroff and Nathan Entner, occurs only in prokaryotes, mostly in gram-negative bacteria such as Pseudomonas aeruginosa, Azotobacter, Rhizobium.

In this pathway, glucose phosphate is oxidized to 2-ketodeoxyphosphogluconic acid KDPG which is cleaved by 2-ketodeoxyglucose-phosphate aldolase to pyruvate and glyceraldehydephosphate. The latter is oxidized to pyruvate by glycolytic pathway where in two ATPs are produced by substrate level phosphorylations. The first process is a light dependent one light reactions that requires the direct energy of light to make energy carrier molecules that are used in the second process.

The calvin cycle light independent process occurs when the products of the light reaction are used in the formation of carbohydrate. On the basis of generation of oxygen during photosynthesis, the photosynthetic organisms may be oxygenic or anoxygenic. Oxygenic photosynthetic organisms include both eukaryotes as well as prokaryotes whereas anoxygenic photosynthetic organisms include only prokaryotes.

Oxygenic photosynthetic organisms Eukaryotes — Plants and Photosynthetic protists Prokaryotes — Cyanobacteria Anoxygenic photosynthetic organisms Prokaryotes — Green and purple photosynthetic bacteria In oxygenic photosynthetic organisms, photosynthetic oxygen generation occurs via the light-dependent oxidation of water to molecular oxygen. This can be written as the following simplified chemical reaction: Different types of pigments, described as photosynthetic pigment, participate in this process.

The major photosynthetic pigment is the chlorophyll. Chlorophylls Chlorophyll, a light-absorbing green pigment, contains a polycyclic, planar tetrapyrrole ring structure. Chlorophyll is a lipid soluble pigment. It has the following important features: Chlorophyll has a cyclopentanone ring ring V fused to pyrrole ring III.

The propionyl group on a ring IV of chlorophyll is esterified to a long-chain tetraisoprenoid alcohol. In chlorophyll a and b it is phytol. Chlorophyll is composed of two parts; the first is a porphyrin ring with magnesium at its center, the second is a hydrophobic phytol tail. The tail is a 20 carbon chain that is highly hydrophobic.

In the pure state, chlorophyll a is blue-green. In the pure state, chlorophyll b is olive-green. It is an essential photosynthetic pigment. It is accessory photosynthetic pigment. Pyrrole ring II contains methyl —CH3 group. It absorbs more red wavelengths than violet- 5. It absorbs more violet-blue wavelength than red blue wavelength of light.

Oxygenic photosynthetic organisms contain different types of chlorophyll molecules like Chl a, Chl b, Chl c and Chl d. These chlorophyll molecules differ by having different substituent groups on the tetrapyrrole ring. Anoxygenic photosynthetic organisms contain bacteriochlorophyll molecules. They are related to chlorophyll molecules. Different groups of anoxygenic photosynthetic organisms contain different types of bacteriochlorophyll: Bacteriochlorophyll molecules absorb light at longer wavelengths as compared to chlorophyll molecules.

Accessory pigments Besides the major light-absorbing chlorophyll molecules, there are two groups of accessory pigments which absorb light in the wavelength region, where chlorophylls do not absorb strongly. The two types of accessory pigments are carotenoids and phycobilins. Carotenoids are long-chain, conjugated hydrocarbons containing a string of isoprene residues and distinguished from one another by their end groups.

They are generally C40 terpenoid compounds formed by the condensation of eight isoprene units. Carotenoids are lipid soluble pigments and can be subdivided into two classes, xanthophylls which contain oxygen and carotenes which are purely hydrocarbons, and contain no oxygen. Bioenergetics and Metabolism Glycogen storage diseases Glycogen storage diseases are caused by a genetic deficiency of one or another of the enzymes of glycogen metabolism. Many diseases have been characterized that result from an inherited deficiency of the enzyme.

These defects are listed in the table. In animals, many cell types and organs have the ability to synthesise triacylglycerols, but the liver and intestines are most active. Within all cell types, even those of the brain, triacylglycerols are stored as cytoplasmic lipid droplets also termed fat globules, oil bodies, lipid particles, adiposomes, etc. Two main biosynthetic pathways are known, the sn-glycerol phosphate pathway, which predominates in liver and adipose tissue, and a monoacylglycerol pathway in the intestines.

The most important route to triacylglycerol biosynthesis is the sn-glycerolphosphate or Kennedy pathway. Hence, this synthesis is often called the succinate-glycine pathway. Porphyrin biosynthesis involves three distinct processes: Synthesis of a substituted pyrrole compound, porphobilinogen from ALA.

Condensation of four porphobilinogen molecules to yield a partly reduced precursor called a porphyrinogen. Modification of the side chains, dehydrogenation of the ring system, and the introduction of iron, to give the porphyrin product, heme. In de novo means anew pathways, the nucleotide bases are assembled from simpler compounds.

The framework for a pyrimidine base is assembled first and then attached to ribose. In contrast, the framework for a purine base is synthesized piece by piece directly onto a ribose-based structure. In salvage pathways, preformed bases are recovered and reconnected to a ribose unit.

All deoxyribonucleotides are synthesized from the corresponding ribonucleotides. The deoxyribose sugar is generated by the reduction of ribose within a fully formed nucleotide. Furthermore, the methyl group that distinguishes the thymine of DNA from the uracil of RNA is added at the last step in the pathway. The C-2 and N-3 atoms in the pyrimidine ring come from carbamoyl phosphate, whereas the other atoms of the ring come from aspartate.

Pyrimidine rings are synthesized from carbamoyl phosphate and aspartate. The precursor of carbamoyl phosphate is bicarbonate and ammonia. The synthesis of carbamoyl phosphate from bicarbonate and ammonia occurs in a multistep process, requiring the cleavage of two molecules of ATP. This reaction is catalyzed by cytosolic carbamoyl phosphate synthetase II. Carbamoylaspartate then cyclizes to form dihydroorotate which is then oxidized to form orotate. Chapter 03 Cell Structure and Functions 3.

The basic structural and functional unit of cellular organisms is the cell. It is an aqueous compartment bound by cell membrane, which is capable of independent existence and performing the essential functions of life. All organisms, more complex than viruses, consist of cells.

Viruses are noncellular organisms because they lack cell or cell-like structure. In the year , Robert Hooke first discovered cells in a piece of cork and also coined the word cell.

The word cell is derived from the Latin word cellula, which means small compartment. Hooke published his findings in his famous work, Micrographia. Actually, Hooke only observed cell walls because cork cells are dead and without cytoplasmic contents.

Anton van Leeuwenhoek was the first person who observed living cells under a microscope and named them animalcules, meaning little animals. On the basis of the internal architecture, all cells can be subdivided into two major classes, prokaryotic cells and eukaryotic cells. Cells that have unit membrane bound nuclei are called eukaryotic, whereas cells that lack a membrane bound nucleus are prokaryotic. Eukaryotic cells have a much more complex intracellular organization with internal membranes as compared to prokaryotic cells.

Besides the nucleus, the eukaryotic cells have other membrane bound organelles little organs like the endoplasmic reticulum, Golgi complex, lysosomes, mitochondria, microbodies and vacuoles. The region of the cell lying between the plasma membrane and the nucleus is the cytoplasm, comprising the cytosol or cytoplasmic matrix and the organelles.

The prokaryotic cells lack such unit membrane bound organelles. Cell theory In , Schleiden, a German botanist, and Schwann, a British zoologist, led to the development of the cell theory or cell doctrine. According to this theory all living things are made up of cells and cell is the basic structural and functional unit of life. In , Rudolf Virchow proposed an important extension of cell theory that all living cells arise from pre-existing cells omnis cellula e cellula.

The cell theory holds true for all cellular organisms. Non- cellular organisms such as virus do not obey cell theory. Over the time, the theory has continued to evolve. The modern cell theory includes the following components: Evolution of the cell The earliest cells probably arose about 3. A very significant evolutionary event was the development of photosynthetic ability to fix CO2 into more complex organic compounds.

The original electron hydrogen donor for these photosynthetic organisms was probably H2S, yielding elemental sulfur as the byproduct, but at some point, cells developed the enzymatic capacity to use H2O as the electron donor in photosynthetic reactions, producing O2.

The cyanobacteria are the modern descendants of these early photosynthetic O2 producers. One important landmark along this evolutionary road occurred when there was a transition from small cells with relatively simple internal structures - the so-called prokaryotic cells, which include various types of bacteria - to a flourishing of larger and radically more complex eukaryotic cells such as are found in higher animals and plants.

The fossil record shows that earliest eukaryotic cells evolved about 1. Details of the evolutionary path from prokaryotes to eukaryotes cannot be deduced from the fossil record alone, but morphological and biochemical comparison of modern organisms has suggested a reasonable sequence of events consistent with the fossil evidence.

Three major changes must have occurred as prokaryotes gave rise to eukaryotes. First, as cells acquired more DNA, mechanisms evolved to fold it compactly into discrete complexes with specific proteins and to divide it equally between daughter cells at cell division.

These DNA-protein complexes called chromosomes become especially compact at the time of cell division. Second, as cells became larger and intracellular membrane organelles developed.

Finally, primitive eukaryotic cells, which were incapable of photosynthesis or of aerobic metabolism, pooled their assets with those of aerobic bacteria or photosynthetic bacteria to form symbiotic associations that became permanent. Some aerobic bacteria evolved into the mitochondria of modern eukaryotes, and some photosynthetic cyanobacteria became the chloroplasts of modern plant cells.

It acts as a selectively permeable membrane and regulates the molecular traffic across the boundary. The plasma membrane exhibits selective permeability; that is, it allows some solutes to cross it more easily than others.

Different models were proposed to explain the structure and composition of plasma membranes. In , Jonathan Singer and Garth Nicolson proposed fluid-mosaic model, which is now the most accepted model. In this model, membranes are viewed as quasi-fluid structures in which proteins are inserted into lipid bilayers.

It describes both the mosaic arrangement of proteins embedded throughout the lipid bilayer as well as the fluid movement of lipids and proteins alike. Peripheral protein Phospholipid bilayer Integral protein Peripheral protein Figure 3. The fatty acyl chains in the lipid bilayer form a fluid, hydrophobic region. Integral proteins float in this lipid bilayer.

Both proteins and lipids are free to move laterally in the plane of the bilayer, but movement of either from one face of the bilayer to the other is restricted. The ratio of protein to lipid varies enormously depends on cell types. Carbohydrates bound either to proteins as constituents of glycoproteins or to lipids as constituents of glycolipids. Carbohydrates are especially abundant in the plasma membranes of eukaryotic cells.

Lipid bilayer The basic structure of the plasma membrane is the lipid bilayer. This bilayer is composed of two leaflets of amphipathic lipid molecules, whose polar head groups are in contact with the intra- or extracellular aqueous phase, whereas their non-polar tails face each other, constituting the hydrophobic interior of the membrane.

The primary physical forces for organizing lipid bilayer are hydrophobic interactions. Three classes of lipid molecules present in lipid bilayer - phospholipids, glycolipids and sterol.

The hydrophilic unit, also called the polar head group, is represented by a circle, whereas the hydrocarbon tails are depicted by straight lines. Phospholipids Phospholipids are made up of four components: The fatty acid components are hydrophobic, whereas the remainder of the molecule has hydrophilic.

There are two types of phospholipids: Phospholipids derived from glycerol are called glycerophospholipids. Glycerophospholipids or phosphoglycerides contain glycerol, fatty acids, phosphate and an alcohol e. Phosphoglyceride molecules are classified according to the types of alcohol linked to the phosphate group.

For example, if the alcohol is choline, the molecule is called phosphatidylcholine also referred to as lecithin and if serine, then it is called phosphotidylserine.

Phosphoglycerides are the most numerous phospholipid molecules found in plasma membranes. Sphingophospholipids contain an amino alcohol called sphingosine instead of glycerol, a fatty acid, phosphate and an alcohol attached to the phosphate.

In sphingophospholipid, the amino group of the sphingosine backbone is linked to a fatty acid by an amide bond. Sphingomyelin is the most abundant sphingophospholipid.

The plasma membrane of animal cells contains four major phospholipids, such as phosphatidylcholine the most abundant glycerophospholipids in the plasma membrane , phosphatidylserine, phosphatidylethanolamine and sphingomyelin. At neutral pH, the polar head group may have no net charge phosphatidylcholine and phosphatidyl- ethanolamine or it may have net negative charges phosphatidylinositol and phosphatidylserine.

Rarer phospholipids have a net positive charge. Cell Structure and Functions 3. Electrogenic transport affects and can be affected by the membrane potential. Its electrogenic operation directly contributes to the negative inside membrane potential, which is evidenced by the fact that stopping the pump using an alkaloid inhibitor, ouabain, causes an immediate and slight depolarization of the cell membrane.

All cells have an electrical potential difference, or membrane potential, across their plasma membrane. Electrical potential across cell membranes is a function of the electrolyte concentrations in the intracellular and extracellular solutions and of the selective permeabilities of the ions.

Active transport of ions by ATP-driven ion pumps, generate and maintain ionic gradients. In addition to ion pumps, which transport ions against concentration gradients, plasma membrane contains channel protein that allows ions to move through it at different rates down their concentration gradient. Ion concentration gradients and selective movements of ions create a difference in electric potential or voltage across the plasma membrane. This is called membrane potential.

How membrane potentials arise? The resulting separation of charge across the membrane constitutes an electric potential, or voltage, with the left side of the membrane having excess negative charge with respect to the right. At equilibrium, an electrical potential is established across the membrane due to an accumulation of negative charges on the left side and positive charges on the right.

Cell Structure and Functions Let us now consider the changes in potential during an action potential, and the permeability and ion movements responsible for generating this change in potential. Movement of ions occurs through ion channels. Ion channels may be either leaky channels or gated channels.

Leaky channels, which are open all the time, permit unregulated leakage of specific ion across the membrane.

Gated channels, in contrast, have gates that can be open or closed, permitting ion passage through the channels when open and preventing ion passage through the channels when closed. Action potentials are the direct consequence of the voltage-gated cation channels. The channel undergoes through these various conformations as a result of voltage changes that take place during an action potential.

This process is called repolarization. Instead, they alternate between closed and open states. Hence, an action potential has two main phases: During the depolarizing phase, the negative membrane potential becomes less negative, reaches zero, and then becomes positive. During the repolarizing phase, the membrane potential is restored to the resting state of —70 mV.

Following the repolarizing phase there may be an after-hyperpolarizing phase, during which the membrane potential temporarily becomes more negative about —90 mV than the resting level. Gated Na and K channels closed Time millisecond Figure 3. The top graph depicts an action potential. The period of time after an action potential begins during which an excitable cell cannot generate another action potential in response to a normal threshold stimulus is called the refractory period.

It can be absolute or relative.

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During the absolute refractory period, even a very strong stimulus cannot initiate a second action potential. The relative refractory period is the time period during which a second action potential can be initiated, but only by a larger-than normal stimulus. The refractory period limit the number of action potentials that can be produced by an excitable membrane in a given period of time. Cell Structure and Functions plasma membrane at the opposite side.

An example of transcytosis is the movement of maternal antibodies across the intestinal epithelial cells of the newborn rat. The lumen of the gut is acidic, and, at this low pH, the antibodies in the milk bind to specific receptors on the apical absorptive surface of the gut epithelial cells.

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The receptor-antibody complexes are internalized via clathrin coated vesicles and are delivered to early endosomes. The complexes remain intact and are retrieved in transport vesicles that bud from the early endosome and subsequently fuse with the basolateral domain of the plasma membrane. It may be a constitutive secretory pathway carried out by all cells or regulated secretory pathway carried out by specialized cells.

Examples of proteins released by such constitutive or continuous secretion include collagen by fibroblasts, serum proteins by hepatocytes, and antibodies by activated B-lymphocytes. Vesicle containing soluble proteins for constitutive secretion Constitutive secretory pathway Trans-Golgi network Extracellular space Regulated secretory pathway Secretory Golgi complex vesicle containing secretory proteins Plasma membrane Figure 3.

The two pathways diverge in the trans Golgi network. The constitutive secretory pathway operates in all cells. Many soluble proteins are continually secreted from the cell by this pathway. This pathway also supplies the plasma membrane with newly synthesized lipids and proteins. Specialized secretory cells also have a regulated secretory pathway, by which selected proteins in the trans Golgi network are diverted into secretory vesicles, where the proteins are concentrated and stored until an extracellular signal stimulates their secretion.

The regulated secretion of small molecules, such as histamine and neurotransmitters, occurs by a similar pathway. In this secretory pathway, secretory vesicles form from the trans Golgi network, and they release their contents to the cell exterior by exocytosis in response to specific signals.

The secreted product can be either a small molecule such as histamine or a protein such as a hormone or digestive enzyme. Proteins destined for secretion called secretory proteins are packaged into appropriate secretory vesicles in the trans Golgi network. The signal that directs secretory proteins into such vesicles is not known.

The ribosome is approximately globular structure, its average diameter ranging from 2. The functional ribosomes consist of two subunits of unequal size, known as the large and small subunits.

Ribosomes consist of rRNA and r-proteins. The r-proteins are termed as L or S depending on whether the protein is from the large or small subunit. Table 3. It is the ratio of a velocity to the centrifugal acceleration. The sedimentation coefficient has units of second.

In all eukaryotes studied so far, the organization of the ribosomal RNA genes is recognizably similar to that of prokaryotes, but with major differences; the size of the small subunit RNA has increased from 16S to 18S, and that of the large subunit from 23S and 28S; a new small 5. There are generally more copies of the 5S genes than of the rRNA genes.

The human genome contains about copies of rRNA genes per haploid set. Many other species, including most plants, have several thousand copies. Protein translocation describes the movement of a protein across a membrane. Within the cell, translocation of proteins from cytosol to specific organelle or organelle to cytosol and from one organelle to another occur in three different ways: Gated transport: The protein translocation between the cytosol and nucleus occurs through the nuclear pore complexes.

This process is called gated transport because the nuclear pore complexes function as selective gates that can actively transport specific macromolecules. Transmembrane transport: In transmembrane transport, membrane-bound protein translocators directly transport specific proteins across a membrane from the cytosol into a organelle.

The transport of selected proteins from the cytosol into the ER lumen or into mitochondria is an example of transmembrane transport. Vesicular transport: In vesicular transport, proteins move from one organelle to another through transport vesicles.

The transfer of proteins from the endoplasmic reticulum to the Golgi apparatus, for example, occurs in this way. Protein translocation may occur co-translationally or post-translationally. Proteins synthesized by membrane bound ribosomes are translocated co-translationally. All proteins synthesized by membrane free ribosomes are translocated post-translationally.

It is an extensive network of closed and flattened membrane-bound structure. The enclosed compartment is called the ER lumen.

ER membranes are physiologically active, interact with the cytoskeleton and contain differentiated domains specialized for distinct functions. ER membranes are differentiated into rough and smooth regions RER and SER, respectively , depending on whether ribosomes are associated with their cytoplasmic surfaces.

When cells are disrupted by homogenization, the ER breaks into fragments and reseals into small vesicles called microsomes. Microsomes derived from RER are studded with ribosomes on the outer surface and are called rough microsomes. Microsomes lacking attached ribosomes are called smooth microsome.

The cisternal space or lumen remains continuous with the perinuclear space. Function of ER Proteins synthesized by ribosomes associated with the membrane of RER enter into the lumen and membrane of RER by the process of co-translational translocation.

In the lumen of the RER, five principal modifications of proteins occur before they reach their final destinations: The SER acts as the site of lipid biosynthesis, detoxification and calcium regulation.

N-linked glycosylation of proteins N-linked glycosylation is the attachment of a sugar molecule to a nitrogen atom in an amino acid residue in a protein. In the RER, this process involves the addition of a large preformed oligosaccharide precursor to a protein. This precursor oligosaccharide is linked by a pyrophosphoryl residue to dolichol, a long-chain 75—95 carbon atoms polyisoprenoid lipid that is firmly embedded in the RER membrane and acts as a carrier for the oligosaccharide.

The structure of N-linked oligosaccharide is the same in plants, animals and single-celled eukaryotes - a branched oligosaccharide, containing three glucose Glc , nine mannose Man and two N-acetylglucosamine GlcNAc molecules which is written as Glc3 Man9 GlcNAc2.

Biosynthesis of oligosaccharide begins on the cytosolic face of the ER membrane with the transfer of N-acetyl glucosamine to dolichol phosphate. Two N-acetylglucosamine GlcNAc and five mannose residues are added one at a time to a dolichol phosphate on the cytosolic face of the ER membrane. The first sugar, N-acetyl glucosamine, is linked to dolichol by a pyrophosphate bridge. This high-energy bond activates the oligosaccharide for its transfer from the dolichol to an asparagine side chain of a nascent polypeptide on the luminal side of the rough ER.

Tunicamycin, an antibiotic, blocks the first step in this pathway and thus inhibits the synthesis of oligosaccharide. After the seven-residue dolichol pyrophosphoryl intermediate is flipped to the luminal face. The remaining four mannose and all three glucose residues are added one at a time in the luminal side. Cell Structure and Functions Table 3. ER-resident proteins often are retrieved from the Cis-Golgi As we have mentioned in the previous section that proteins entering into the lumen of the ER are of two types- resident proteins and export proteins.

How, then, are resident proteins retained in the ER lumen to carry out their work? The answer lies in a specific C-terminal sequence present in resident ER proteins.

Several experiments demonstrated that the KDEL sequence which acts as sorting signal, is both necessary and sufficient for retention in the ER. If this ER retention signal is removed from BiP, for example, the protein is secreted from the cell; and if the signal is transferred to a protein that is normally secreted, the protein is now retained in the ER.

The finding that most KDEL receptors are localized to the membranes of small transport vesicles shuttling between the ER and the cis-Golgi also supports this concept. The retention of transmembrane proteins in the ER is carried out by short C-terminal sequences that contain two lysine residues KKXX sequences. How can the affinity of the KDEL receptor change depending on the compartment in which it resides?

The answer may be related to the differences in pH. Clearly, the transport of newly synthesized proteins from the RER to the Golgi cisternae is a highly selective and regulated process. The selective entry of proteins into membrane-bound transport vesicles is an important feature of protein targeting as we will encounter them several times in our study of the subsequent stages in the maturation of secretory and membrane proteins.

The Golgi complex, also termed as Golgi body or Golgi apparatus, is a single membrane bound organelle and part of endomembrane system. It consists of five to eight flattened membrane-bound sacs called the cisternae. Each stack of cisternae is termed as Golgi stack or dictyosome. The cisternae in Golgi stack vary in number, shape and organization in different cell types.

The typical diagrammatic representation of three major cisternae cis, medial and trans as shown in the figure 3. In some unicellular flagellates, however, as many as 60 cisternae may combine to make up the Golgi stack.

The number of Golgi complexes in a cell varies according to its function. A mammalian cell typically contains 40 to stacks. In mammalian cells, multiple Golgi stacks are linked together at their edges.

Each Golgi stack has two distinct faces: Both cis and trans faces are closely associated with special compartments: Proteins and lipids enter the cis Golgi network in vesicular tubular clusters arriving from the ER and exit from the trans Golgi network. Both networks are thought to be important for protein sorting.

Similarly, proteins exiting from the TGN can either move onward and be sorted according to whether they are destined for lysosomes, secretory vesicles, or the cell surface, or be returned to an earlier compartment. The Golgi apparatus is especially prominent in cells that are specialized for secretion, such as the goblet cells of the intestinal epithelium, which secrete large amounts of polysaccharide-rich mucus into the gut.

In such cells, unusually large secretory vesicles are found on the trans side of the Golgi apparatus. Secretory vesicles form from the trans Golgi network, and they release their contents to the cell exterior by exocytosis.

It modifies proteins and lipids that have been built in the endoplasmic reticulum and prepares them for export outside of the cell or for transport to other locations in the cell. Proteins and lipids from the smooth and rough endoplasmic reticulum bud off in tiny bubble-like vesicles that move through the cytoplasm until they reach the Golgi apparatus.

The vesicles fuse with the Golgi membranes and release their internally stored molecules into the organelle. Once inside, the compounds are further processed by the Golgi apparatus. When completed, the product is extruded from the Golgi apparatus in a vesicle and directed to its final destination inside or outside the cell.

The modifications to molecules that take place in the Golgi apparatus occur in an orderly fashion. Substances from ER enter into the cis face of a Golgi stack for processing and exit from trans face. Consequently, the cis face is found near the endoplasmic reticulum and the trans face is positioned near the plasma membrane of the cell.

The chemical make-up of each face is different and the enzymes contained in the cisternae between the faces are distinctive. Glycosylation of proteins N-linked oligosaccharide chains on proteins are altered as the proteins pass through the Golgi cisternae en route from the ER.

Further modifications of N-linked oligosaccharide in the Golgi apparatus gives two broad classes of N-linked oligosaccharides, the complex oligosaccharides and the high-mannose oligosaccharides. Cell Structure and Functions termed as heterochromatin. Because of its condensed state, this heterochromatin is generally believed to be transcriptionally silent.

Centromere The constricted region of linear chromosomes is known as the centromere. The centromeres serve both as the sites of association of sister chromatids and as the attachment sites for microtubules of the mitotic spindle. Telomere Telomeres are specialized structures, which cap the ends of eukaryotic chromosomes.

It consists of a long array of short, tandemly repeated sequences. Origin of replication The origin of replication also called the replication origin is a particular sequence in a chromosome at which replication is initiated.

One chromosome contains multiple origin of replication. Chromosome number All eukaryotic cells have multiple linear chromosomes. Every cell maintains a characteristic number of chromosomes. Depending on the eukaryotic organism, the number of chromosomes varies from 2 to several hundreds. The number of chromosomes in a species has no specific significance nor does it indicate any relationship between two species which may have the same chromosome number.

The majority of eukaryotic cells are diploid; that is, they contain two copies of each chromosome. This is accomplished by a variety of signal molecules that are secreted or expressed on the surface of one cell and bind to receptors expressed by other cells, thereby integrating and coordinating the functions of the many individual cells that make up organisms. Each cell is programmed to respond to specific extracellular signal molecules. Extracellular signaling usually involves the following steps: Synthesis and release of the signaling molecule by the signaling cell; 2.

Transport of the signal to the target cell; 3. Binding of the signal by a specific receptor leading to its activation; 4. Initiation of signal-transduction pathways. In endocrine signaling, the signaling molecules act on target cells distantly located from their site of synthesis. It is a long-range signaling in which signal molecule is transported by the blood stream. In paracrine signaling, the signaling molecules released by a cell affect target cells only in close proximity.

An example of this is the action of neurotransmitters in carrying signals between nerve cells at a synapse. In autocrine signaling, the signaling molecules produce an effect on same cell that produces it. One important example of such is the response of cells of the vertebrate immune system to foreign antigens. Certain types of T- lymphocytes respond to antigenic stimulation by synthesizing a growth factor that drives their own proliferation, thereby increasing the number of responsive T-lymphocytes and amplifying the immune response.

In juxtacrine signaling, signal molecules do not diffuse from the cell producing it and cell bearing signal molecules interact with receptor proteins of adjacent responding cells.

Unlike other modes of cell signaling, juxtacrine signaling requires physical contact between the cells involved. Notch signalling and classical cadherin signalling are examples of juxtacrine signaling. These molecules are divided into two categories — membrane bound and secretory signal molecules. Membrane bound signal molecules remain bound to the surface of the cells and mediate contact dependent signaling. In most cases, signal molecules are secreted by signaling cells.

Secreted extracellular signal molecules are further divided into three general categories based on the distance over which signals are transmitted: Cell Structure and Functions pro-apoptotic. Mammalian Bcl2 family of proteins regulate the intrinsic pathway of apoptosis mainly by controlling the release of cytochrome c and other intermembrane mitochondrial proteins into the cytosol. Bcl2 was the first protein shown to cause an inhibition of apoptosis. It is the mammalian homologue of the CED-9 in C.

The pro-apoptotic Bcl2 proteins consist of two subfamilies - the BH proteins and the BH3-only proteins. When an apoptotic stimulus triggers the intrinsic pathway, the pro-apoptotic BH proteins become activated and induces the release of cytochrome c and other intermembrane proteins by an unknown mechanism.

In the absence of an apoptotic stimulus, anti-apoptotic Bcl2 proteins bind to and inhibit the BH proteins on the mitochondrial outer membrane and in the cytosol. In the presence of an apoptotic stimulus, BH3-only proteins are activated and bind to the anti-apoptotic Bcl2 proteins so that they can no longer inhibit the BH proteins.

Some activated BH3- only proteins may stimulate mitochondrial protein release more directly by binding to and activcting the BH proteins. When normal cells have lost the usual control over their division, differentiation and apoptosis they become tumor cells. So, a tumor is the result of an abnormal proliferation of cells without differentiation and apoptosis. Tumor or neoplasm any abnormal proliferation of cells may be of two types: Benign tumor and Malignant tumor. Benign and malignant tumor In benign tumor, neoplastic cells remain clustered together in a single mass and cannot spread to other sites.

It contains cells that closely resemble normal cells and that may function like normal cells. They invade surrounding normal tissues called invasiveness and spread throughout the body through circulatory or lymphatic systems called metastasis. The term cancer refers specifically to malignant tumors. Most cancers originate from single abnormal cell i.

Most cancers are initiated by genetic changes and majority of them are caused by changes in somatic cells and therefore are not transmitted to the next generation. Conceptually, this process can be divided into three distinct stages: The first step in the process is tumor initiation.

It is a process in which normal cells are changed so that they are able to form tumors. Promotion is generally associated with increased proliferation of initiated cells, which increases the population of initiated cells.

Progression refers to the process of acquiring additional genetic changes that lead to malignancy and metastasis. Additional genetic changes in cancer critical genes are the force that drives tumorigenesis. Each successive genetic change is thought to provide the developing tumor cell with important growth advantages that allow cell clones to outgrow their more normal neighboring cells. Properties of cancer cells Cancer cells typically display several abnormal properties as compared to normal cells that provide a description of malignancy at the cellular level.

Density dependent inhibition Normal cells in culture display density dependent inhibition of cell proliferation and proliferate until they reach a finite cell density, which is determined partly by availability of growth factors in culture medium. But the proliferation of cancer cells is not sensitive to density dependent inhibition.

Contact inhibition Normal cells migrate across the surface of a culture dish until they make contact with a neighboring cell. Further cell migration is then inhibited and normal cells adhere to each other forming an orderly array of cells on the culture dish surface. This inhibition of growth after contact is called contact inhibition. Tumor cells in contrast continue moving after contact with their neighbouring cells migrating over adjacent cells and growing in disordered multilayered patterns.

Immortalization Normal cells have a limited capacity to grow and divide both in vivo and in vitro. Even if provided with optimal growth conditions, in vitro normal cells will cease dividing after about 50 generations and then senesce and die. In contrast, malignant cells are immortal and can grow indefinitely.

Invasiveness and Metastasis One of the most important characteristics of transformed cells is their invasiveness.

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Invasion refers to the direct migration and penetration by cancer cells into neighboring tissues. Metastasis refers to the ability of cancer cells to penetrate into lymphatic and blood vessels, circulate through the bloodstream, and then invade normal tissues elsewhere in the body.

There are two properties of cancer cells that play important roles in invasion and metastasis. First, malignant cells generally secrete proteases that digest extracellular matrix components, allowing the cancer cells to invade adjacent normal tissues.

Second, cancer cells also secrete growth factors that promote the formation of new blood vessels angiogenesis. Angiogenesis is needed to support the growth of a tumor by supplying oxygen and nutrients to the proliferating tumor cells. Loss of anchorage dependence Most normal cells must be attached to a rigid substratum i.

Transformed cells can grow even when they are not attached to the substratum, as for example when they are suspended in a semisolid medium containing agar or methyl cellulose. Chapter 04 Prokaryotes and Viruses 4. The term eubacteria refer specifically to bacteria. The informal name bacteria are occasionally used loosely in the literature to refer to all the prokaryotes, and care should be taken to interpret its meaning in any particular context.

Prokaryotes can be distinguished from eukaryotes in terms of their cell structure and molecular make-up. Prokaryotic cells have a simpler internal structure than eukaryotic cells.

Although many structures are common to both cell types, some are unique to prokaryotes. Most prokaryotes lack extensive, complex, internal membrane systems. The major distinguishing characteristics of prokaryotes and eukaryotes are as follows: In eubacteria, it is made up of peptidoglycan.

Features of eukaryotic organisms True membrane bound nucleus — Present DNA complexed with histone — Present Number of chromosomes — More than one Mitosis and meiosis — Present Genetic recombination — By crossing over during meiosis Sterol in the plasma membrane — Present Ribosome — 80S in cytosol and 70S in organelles Unit membrane bound organelles — Present Cell wall — Made up of cellulose in plant and chitin in fungi.

Absent in animal cells. Prokaryotic cells show similarities with eukaryotic organelles like mitochondria and chloroplast. The endosymbiotic theory Margulis, proposes that the mitochondria and chloroplasts of eukaryotic cells originated as symbiotic prokaryotic cells. The presence of circular, covalently closed DNA and 70S ribosomes in mitochondria and chloroplast support this theory. Prokaryotic taxonomy therefore involved measuring a large number of characteristics, including morphology and biochemical characteristics e.

This contrasts with the classification of eukaryotic organisms, for which phylogenetic evolution-based classification was possible through the availability of fossil evidence. A major revolution occurred with the realization that evolutionary relationships could be deduced on the basis of differences in gene sequence.

The gene is approximately bp in length and possesses signature sequences. These sequences are conserved and found in the organisms of one taxonomic group but not in other groups. Based on ribosomal RNA signature sequences, Carl Woese proposed a radical reorganization of the five kingdoms into three domains. In his classification system, Woese placed all four eukaryotic kingdoms protista, fungi, plantae, animalia into a single domain called Eukarya, also known as the eukaryotes.

He then split the former kingdom of Monera into the Eubacteria and the Archaea domains. Size, shape and arrangement of bacterial cells Bacteria range in size from 0.

However, a few species — for example, Thiomargarita namibiensis and Epulopiscium fishelsoni — are very large and visible to the unaided eye. The rod shaped E. Regardless of the length of the tRNA. In these cases. RNA double helices adopt the A-form structure. Eukaryotic mRNA molecules often require extensive processing and transport. In RNA. The diverse functions of RNA molecules in living organisms also include the enzymatic activity of ribozymes and the storage of genetic information in RNA viruses and viroids.

But the mRNA is always longer than the coding region. At physiological pH. RNA molecules play essential roles in the transfer of genetic information during protein synthesis and in the control of gene expression.

Most of the prokaryotic mRNA are polycistronic. D arm and loop. Holley and his co-workers determined the first tRNA sequence in RNA tertiary structure forms through relatively weak interactions between preformed secondary structure elements.

The concept of an adaptor to provide the interface between nucleic acid language and protein language was introduced by Crick in RNA molecules are found in multiple copies and in multiple forms. They may be as long as 30 nucleotides. RNA may be genetic or non genetic. This fundamental interaction between bases leads to the formation of double-helical structures of varying length. The coding region consists of a series of codons starting with an AUG and ending with a termination codon.

Dictated by their primary sequence. Types of RNA Within a given cell. The answer: This attached tag targets the protein for destruction or proteolysis. Whereas the other strand which is ultimately destroyed. They are always associated with specific proteins. RNA editing was first reported in the mitochondria of kinetoplastids. The pre-miRNA molecule is then actively transported out of the nucleus into the cytoplasm by exportin protein. The proteins then catalyze modification of the RNA gene.

The Dicer enzyme. Out of two strands. In the presence of a hydroxide ion. Biomolecules and Catalysis maintaining the telomeres. It has currently only been found in bacteria. After the discovery of the first small silencing RNA in year Fraenkel-Conrat and B. Because RNA can perform the tasks of both genetic materials and enzymes. RNA is believed to have once been capable of independent life. RNA with catalytic activity is termed as ribozyme.

Ketoses are monosaccharides containing a ketone group. The most abundant monosaccharide in nature is the D-glucose. System for numbering the carbons: The carbons are numbered sequentially with the aldehyde or ketone group being on the carbon with the lowest possible number.

Dihydroxyacetone is called a ketose because it contains a keto group. Carbohydrates are the most abundant biomolecules on Earth. There are two trioses— dihydroxyacetone and glyceraldehyde.

In the majority of carbohydrates. Monosaccharides with four. Oligosaccharides are polymers made up of two to ten monosaccharide units joined together by glycosidic linkages. Monosaccharides are colourless. Polysaccharides are not sweet in taste hence they are also called non-sugars.

Monosaccharides are the simple sugars. Amongst these the most abundant are the disaccharides. Polysaccharides are polymers with hundreds or thousands of monosaccharide units.

Similarly fructose is a ketohexose. Oligosaccharides can be classified as di-. Carbohydrates are classified into following classes depending upon whether these undergo hydrolysis and if so on the number of products form: Monosaccharides are simple carbohydrates that cannot be hydrolyzed further into polyhydroxy aldehyde or ketone unit.

Monosaccharides can be further sub classified on the basis of: The number of the carbon atoms present Monosaccharides can be named by a system that is based on the number of carbons with the suffix-ose added. H and O are present in the same ratio as in water. The monosaccharide glucose is an aldohexose. Trioses are simplest monosaccharides. The configuration of groups around the chiral carbon 2 shown in bold distinguishes D-glyceraldehyde from L-glyceraldehyde.

These two forms are called enantiomers. D-glucose and D-mannose differ only at carbon 2. Glyceraldehyde has two absolute configurations. The absolute configurations of monosaccharide containing more than one chiral centers like hexose are determined by comparing the configuration at the highest-numbered chiral carbon the chiral carbon farthest from the aldehyde group to the configuration at the single chiral carbon of glyceraldehyde.

As the number of chiral carbon atoms increases. Sugars that differ only by the stereochemistry at a single carbon other than anomeric carbon are called epimers. Glyceraldehyde has a central carbon C—2 which is chiral or asymmetrical.

For example. All the monosaccharides except dihydroxyacetone contain one or more chiral carbon atoms and thus occur in optically active isomeric forms. Chiral molecules such as glyceraldehyde can exist in two forms or configurations that are non-superimposable mirror images of each other.

The two molecules are mirror images and cannot be superimposed on one another. When the hydroxyl group attached to the chiral carbon is on the left in a Fischer projection. Similarly D-glucose and D-galactose are epimers. An enantiomer is identified by its absolute configuration. D-mannose and D-galactose are not epimers because their configuration differ at more than one carbon.

The four general functions of biological lipids have been identified. So they donot contain free anomeric carbon atoms. Sucrose and trehalose are therefore not a reducing sugar.

Apart from the general functions biological lipids serve as pigments carotene. Sugars like sucrose. Sugars are attached either to the amide nitrogen atom in the side chain of asparagine termed an N-linkage or to the oxygen atom in the side chain of serine or threonine termed an O-linkage.

All disaccharides formed from head to tail condensation are also reducing sugar i. Functions Biological lipids have diverse functions. Unlike the proteins. In sucrose and trehalose. All reducing sugars undergo mutarotation in aqueous solution.

All monosaccharides whether aldoses and ketoses. A reducing sugar is any sugar that either has an aldehyde group or is capable of forming one in solution through isomerisation. They are readily soluble in nonpolar solvents such as ether. So it cannot be oxidized by cupric or ferric ion. In describing disaccharides or polysaccharides. This functional group allows the sugar to act as a reducing agent. Problem Why unsaturated fatty acids have low melting points? Solution The presence of double bonds makes unsaturated chain more rigid.

As a result. Biomolecules and Catalysis The notation In this convention. The presence of double bonds makes unsaturated chain more rigid. The longer the chain length. The general formula of triacylglycerol is given below: Melting point of fatty acids The melting point of fatty acids depend on chain length and degree of unsaturation. In this nomenclature the carboxyl carbon is designated carbon 1.

Triacylglycerols are of two types — simple and mixed type. Essential fatty acids Mammals lack the enzymes to introduce double bonds at carbon atoms beyond C-9 in the fatty acid chain. Fatty acids that can be endogenously synthesized are termed as nonessen- tial. It is designated as They are composed of three fatty acids and a glycerol molecule. Those containing a single kind of fatty acids are called simple triacylglycerols and with two or more different kinds of fatty acids are called mixed triacylglycerols.

The term essential means that they must be obtained from the diet because they are required by an organism and cannot be endogenously synthesized. Linoleate and linolenate are the two essential fatty acids. They are nonessential also in the sense that they do not have to be obligatorily included in the diet. There is an alternative convention for naming polyunsaturated fatty acids. Waxes Natural waxes are typically esters of fatty acids and long chain alcohols. Phos- phatidic acids are found in small amount in most natural systems.

They are formed by esterification of long chain fatty acids saturated and unsaturated and high molecular weight monohydroxy alcohols C14 to C The major phosphoglycerides are derived from phosphatidic acid by the formation of an ester bond between the phosphate group and the hydroxyl group of one of several alcohols.

Phosphoglycerides are the most numerous phospholipid molecules found in cell membranes. Waxes are biosynthesized by many plants or animals. In phosphoglycerides. Oils are liquid at room temperature because of their relatively high unsaturated fatty acid content.

Saponification yields salts of free fatty acids termed soap and glycerol. The best known animal wax is beeswax. When no further additions are made. Triacylglycerol molecules contain fatty acids of varying lengths. A phosphoglyceride consists of a glycerol molecule. Triacontanoylpalmitate an ester of palmitic acid with the alcohol triacontanol is the major component of beeswax. The platform on which phospholipids are built may be glycerol or sphingosine.

The C-3 hydroxyl group of the glycerol backbone is esterified to phosphoric acid. Phosphoglycerides Phospholipids derived from glycerol are called phosphoglycerides or glycerophospholipids.

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Triacylglycerols can be distinguished as fat and oil on the basis of physical state at room temperature. The saponification number measures the average molecular weight of fats. Biomolecules and Catalysis Triacylglycerols are nonpolar. If the alcohol is choline. The number of milligrams of KOH required to saponify one-gram of fat is known as saponification number. Because triacylglycerols have no charge i. The common alcohol moieties of phosphoglycerides are serine.

Nine vitamins thiamines. Except for vitamin C. They can be classified according to their solubility and their functions in metabolism. Vitamins are not synthesized by humans. The oxidized form of the isoalloxazine structure absorbs light around nm. The requirement for any given vitamin depends on the organisms.

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Thiamine is composed of a substituted thiazole ring joined to a substituted pyrimidine by a methylene bridge. E and K are termed fat-soluble. Not all vitamins are required by all organisms. The colour is lost. Vitamins may be water soluble or fat soluble. The symptoms of pellagra progress through the three Ds: Deficiency of niacin causes pellagra.

Biotin Biotin is a coenzyme in carboxylation reactions. Niacin Niacin. Some cofactors are simple metal ions and other cofactors are complex organic groups. Cofactors which are tightly associated with the protein covalently or non-covalently are called prosthetic group.

It is a remarkable molecular device that determines the pattern of chemical transformations. Enzymes can be divided into two general classes: A cofactor can be linked to the protein portion of the enzyme either covalently or non- covalently. It changes only the rate at which equilibrium is achieved. With the exception of a small group of catalytic RNA molecules.

Enzymes have several properties that make them unique. Xanthine oxidase Se Glutathione peroxidase 89 www. If an enzyme is denatured or dissociated into its subunits. Lysyl oxidase. They are highly specialized proteins and have a high degree of specificity for their substrates. It increases the rate of a reaction by lowering the activation energy. Removal of cofactor from a conjugated enzyme leaves only protein component. Virtually all cellular reactions or processes are mediated by enzymes. The complete.

Alcohol dehydrogenase. Their catalytic activity depends on the integrity of their native protein conformation. Peroxidases Use H2O2 as an electron acceptor. These classes are: EC 1 Oxidoreductase Oxidoreductase catalyzes oxidation-reduction reactions.

According to this rule. Oxygenases Directly incorporate oxygen into the substrate. The first three numbers define major class. Many enzymes are named for their substrates and for the reactions that they catalyze. The Enzyme Commission EC has given each enzyme a number with four parts. The enzyme commission has developed a rule for naming enzymes.

Phosphorylases Transfer inorganic phosphate to a substrate. As for example. EC 3 Hydrolases Hydrolases catalyze reactions in which the cleavage of bonds is accomplished by adding water. Common trivial names for the transferases often include the prefix trans. The last number is a serial number in the sub-subclass. Because of the confusion that arose from these common names. Examples of such groups include amino.

There are six classes to which different enzymes belong. Common names provide little information about the reactions that enzymes catalyze. Kinases Transfer phosphate from ATP to a substrate. EC 2 Transferases Transferases catalyze reactions that involve the transfer of groups from one molecule to another.

Transaminases Transfer amino group from amino acids to keto acids. Dehydrogenases Use molecules other than oxygen e. Thermodynamic principles The First law of thermodynamics states that the energy is neither created nor destroyed. The Second law of thermodynamics states that the total entropy of a system must increase if a process is to occur spontaneously.

Under constant temperature and pressure. Chapter 02 Bioenergetics and Metabolism 2. The change in the free energy. B is also being converted to A. At constant temperature and pressure. The concentration of reactants and products at equilibrium define the equilibrium constant.

If the reaction A B is allowed to go to equilibrium at constant temperature and pressure. The chemical reaction has a characteristic standard free energy change and it is constant for a given reaction.

In this state. R is the gas constant. T is the absolute temperature. It can be calculated from the equilibrium constant of the reaction under standard conditions i.

The free energy change which corresponds to this standard state is known as standard free energy change. The equilibrium constant Keq depends on the nature of reactants and products.. It consists of hundreds of enzymatic reactions organized into discrete pathways. Feedback inhibition and feedback repression In feedback inhibition or end product inhibition. These pathways proceed in a stepwise manner. Each step of metabolic pathways is catalyzed by a specific enzyme.

The first enzyme in the pathway is an allosteric enzyme. Some pathways can be either anabolic or catabolic. Metabolic pathways involve several enzyme-catalyzed reactions.

Each one has a first committed step. Those in eukaryotic cells occur in specific cellular locations. Allosteric regulation of enzymes by a metabolic intermediate or coenzyme. An inhibitory feedback system in which the end product produced in a metabolic pathway acts as a co-repressor and represses the synthesis of an enzyme that is required at an earlier stage of the pathway is called feedback repression.

Catabolic pathways are involved in the oxidative breakdown of larger complex molecules and usually exergonic in nature. A number of central metabolic pathways are common to most cells and organisms. They are regulated. Regulation occurs in following different ways: Characteristics of metabolic pathways are: The basic strategy of catabolic metabolism is to form ATP and reducing power for biosyntheses. They are referred to as amphibolic pathways. Availability of substrate.

Its allosteric site will bind to the end product of the pathway which alters its active site so that it cannot mediate the enzymatic reaction. To achieve these. By extracellular signal such as growth factors and hormones that act from outside the cell in multicellular organisms.

Bioenergetics and Metabolism 2. These pathways. They are irreversible. Metabolism serves two fundamentally different purposes: Anabolic pathways are involved in the synthesis of compounds and ender- gonic in nature.

The feedback inhibition is different from feedback repression. Most of the reactions in living cells fall into one of five general categories: Oxidation of glucose is an exergonic process. For each molecule of glucose degraded to carbon dioxide and water by respiration. During cellular respiration. Carbohydrates are most commonly used as respiratory substrates.

ATP acts as the energy currency of the cell. A complete oxidation of respiratory substrates in the presence of oxygen is termed as aerobic respiration. Free energy is released in multiple steps in a controlled manner and used to synthesise ATP. Cells acquire free energy from the oxidation of organic compounds that are rich in potential energy. Glycolysis — Cytosol Citric acid cycle — Cytosol Oxidative phosphorylation — Plasma membrane www.

Respiration is an oxidative process. When one mole of glucose g is completely oxidized into CO2 and water. An exergonic reaction proceeds with a net release of free energy. Part of this energy is used for synthesis of ATP. The compounds that are oxidized during the process of respiration are known as respiratory substrates. As the substrate is never totally oxidized. The oxidative phosphorylation takes place in the inner mitochondrial membrane.

Energy is required for the maintenance of highly organized structures. Table 2. Glycolysis takes place in the cytosol of cells in all living organisms. Although carbohydrates. During oxidation within a cell. The citric acid cycle takes place within the mitochondrial matrix of eukaryotic cells and in the cytosol of prokaryotic cells. Glycolysis — Cytosol Citric acid cycle — Mitochondrial matrix Oxidative phosphorylation — Inner mitochondrial membrane In prokaryotes. The complete oxidation of substrates occurs in the presence of oxygen.

Phosphorylation Glucose is phosphorylated by ATP to form a glucose 6-phosphate. Glycolysis occurs in the cytosol of all cells. Glucokinase is present in liver and beta-cells of the pancreas and has a high Km and Vmax as compared to hexokinase. Hexokinase and glucokinase are isozymes. Hexokinase is present in all cells of all organisms. This irreversible reaction is catalyzed by hexokinase.

Step 2: Isomerization A readily reversible rearrangement of the chemical structure isomerization moves the carbonyl oxygen from carbon 1 to carbon 2. The negative charge of the phosphate prevents the passage of the glucose 6-phosphate through the plasma membrane.

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It is a unique pathway that occurs in both aerobic as well as anaerobic conditions and does not involve molecular oxygen. A mitochondrion actively involved in aerobic respiration typically has a membrane potential of about mV negative inside matrix and a pH gradient of about 1. In a typical cell. Valinomycin is an ionophore. The electrochemical proton gradient exerts a proton motive force pmf. Determination of electric potential and pH gradient Because mitochondria are very small. Because antimycin A blocks all electron flow to oxygen.

Voltage gradient membrane potential across the inner mitochondrial membrane with the inside negative and outside positive. In the presence of valinomycin. Inhibition of NADH dehydrogenase by rotenone decreases the rate of electron flow through the respiratory chain. Antimycin A strongly inhibits the oxidation of Q in the respiratory chain.

Bioenergetics and Metabolism Solution a. When the pH in the thylakoid lumen became 4. A burst of ATP synthesis accompanied the transmembrane movement of protons driven by the electrochemical proton gradient. Bioenergetics and Metabolism Experimental proof of chemiosmotic hypothesis Experimental proof of chemiosmotic hypothesis was provided by Andre Jagendorf and Ernest Uribe in In an elegant experiment. In similar experiments using inside-out preparations of submitochondrial vesicles.

Rotational motion is imparted to the rotor by the passage of protons. An aspartic acid residue in the second helix lies on the center of the membrane. The multiprotein ATP synthase or F0F1 complex or complex V catalyzes ATP synthesis as protons flow back through the inner membrane down the electrochemical proton gradient.

The F0 component is embedded in the inner mitochondrial membrane. Most common uncoupling agents are 2. Ionophores are lipophilic molecules that bind specific cations and facilitate their transport through the membrane.

It decreases the memberane potential component of pmf without a direct effect on the pH gradient and thus ATP synthesis. DNP is a weak acid that is soluble in lipid bilayer both in their protonated neutral forms and in their anionic states. Dicoumarol and FCCP act in the same way. Ionophore uncouple electron transfer from oxidative phosphorylation by dissipating the electrochemical gradient across the mitochondrial membrane.

Most of the ATP generated by oxidative phosphorylation in mitochondria is exported to the cytoplasm. A specific transport protein. ADP and Pi: An O state open state that binds ATP. The free energy released on proton translocation is harnessed to interconvert three states. Calculation of free energy change The standard free energy change for the movement of protons across the membrane along the electrochemical proton gradient can be calculated from the Nernst equation: ADP and Pi very weakly.

After entering the matrix in the protonated form. DNP in an anionic state picks up protons in the inter-mitochondrial space and diffuse readily across mitochondrial membranes. NADH cannot cross the inner mitochondrial membrane. Bioenergetics and Metabolism and vice versa. NADH in the cytosol transfers electrons to oxaloacetate. NADH synthesized during the glycolytic process finally transfers the electrons to electron transport chain.

In the matrix. The malate-aspartate shuttle is the principal mechanism for the movement of NADH from the cytoplasm into the mitochondrial matrix. The electrons are carried into the mitochondrial matrix in the form of malate. Malate then enters the mitochondrial matrix. This transport process is also powered by the transmembrane proton gradient.

A second membrane transport system is the phosphate translocase. Malate is transported across the inner membrane by the help of transporter. H2O2, a toxic product of various oxidative processes, reacts with double bonds in the fatty acid residues of the erythrocyte cell membrane to form organic hydroperoxides. These, in turn, result in premature cell lysis.

Peroxides are eliminated through the action of glutathione peroxidase, yielding glutathione disulfide GSSG. So, G6PD deficiency results in hemolytic anemia caused by the inability to detoxify oxidizing agents. This pathway, first reported by Michael Doudoroff and Nathan Entner, occurs only in prokaryotes, mostly in gram-negative bacteria such as Pseudomonas aeruginosa, Azotobacter, Rhizobium. In this pathway, glucose phosphate is oxidized to 2-ketodeoxyphosphogluconic acid KDPG which is cleaved by 2-ketodeoxyglucose-phosphate aldolase to pyruvate and glyceraldehydephosphate.

The latter is oxidized to pyruvate by glycolytic pathway where in two ATPs are produced by substrate level phosphorylations. Figure 2. The first process is a light dependent one light reactions that requires the direct energy of light to make energy carrier molecules that are used in the second process. The calvin cycle light independent process occurs when the products of the light reaction are used in the formation of carbohydrate.

On the basis of generation of oxygen during photosynthesis, the photosynthetic organisms may be oxygenic or anoxygenic. Oxygenic photosynthetic organisms include both eukaryotes as well as prokaryotes whereas anoxygenic photosynthetic organisms include only prokaryotes. Oxygenic photosynthetic organisms Eukaryotes — Plants and Photosynthetic protists Prokaryotes — Cyanobacteria. Anoxygenic photosynthetic organisms Prokaryotes — Green and purple photosynthetic bacteria.

In oxygenic photosynthetic organisms, photosynthetic oxygen generation occurs via the light-dependent oxidation of water to molecular oxygen. This can be written as the following simplified chemical reaction:. Different types of pigments, described as photosynthetic pigment, participate in this process. The major photosynthetic pigment is the chlorophyll. Chlorophyll, a light-absorbing green pigment, contains a polycyclic, planar tetrapyrrole ring structure.

Chlorophyll is a lipid soluble pigment. It has the following important features: Chlorophyll has a cyclopentanone ring ring V fused to pyrrole ring III. The propionyl group on a ring IV of chlorophyll is esterified to a long-chain tetraisoprenoid alcohol.

In chlorophyll a and b it is phytol. Oxygenic photosynthetic organisms contain different types of chlorophyll molecules like Chl a. Pyrrole ring II contains methyl —CH3 group. BChl c. It is accessory photosynthetic pigment. Anoxygenic photosynthetic organisms contain bacteriochlorophyll molecules. Bacteriochlorophyll molecules absorb light at longer wavelengths as compared to chlorophyll molecules.

The tail is a 20 carbon chain that is highly hydrophobic. BChl d and BChl e. Chlorophyll is composed of two parts. Carotenoids are lipid soluble pigments and can be subdivided into two classes. BChl b. It is an essential photosynthetic pigment. The two types of accessory pigments are carotenoids and phycobilins.

Carotenoids are long-chain. They are generally C40 terpenoid compounds formed by the condensation of eight isoprene units. Different groups of anoxygenic photosynthetic organisms contain different types of bacteriochlorophyll: BChl a.

Chl b. In the pure state. Chl c and Chl d. It absorbs more red wavelengths than violet. The characteristic www. These chlorophyll molecules differ by having different substituent groups on the tetrapyrrole ring. They are related to chlorophyll molecules. Accessory pigments Besides the major light-absorbing chlorophyll molecules.

It absorbs more violet-blue wavelength than red blue wavelength of light. Bioenergetics and Metabolism Glycogen storage diseases Glycogen storage diseases are caused by a genetic deficiency of one or another of the enzymes of glycogen metabolism. Within all cell types. Many diseases have been characterized that result from an inherited deficiency of the enzyme. These defects are listed in the table. In animals. Two main biosynthetic pathways are known.

The most important route to triacylglycerol biosynthesis is the sn-glycerolphosphate or Kennedy pathway. The deoxyribose sugar is generated by the reduction of ribose within a fully formed nucleotide. In contrast.

All deoxyribonucleotides are synthesized from the corresponding ribonucleotides. Porphyrin biosynthesis involves three distinct processes: Modification of the side chains. In de novo means anew pathways. The framework for a pyrimidine base is assembled first and then attached to ribose.. Condensation of four porphobilinogen molecules to yield a partly reduced precursor called a porphyrinogen. Synthesis of a substituted pyrrole compound. In salvage pathways. The C-2 and N-3 atoms in the pyrimidine ring come from carbamoyl phosphate.

This reaction is catalyzed by cytosolic carbamoyl phosphate synthetase II. The synthesis of carbamoyl phosphate from bicarbonate and ammonia occurs in a multistep process. The precursor of carbamoyl phosphate is bicarbonate and ammonia. Carbamoylaspartate then cyclizes to form dihydroorotate which is then oxidized to form orotate. Pyrimidine rings are synthesized from carbamoyl phosphate and aspartate. Orotate couples to ribose.

The word cell is derived from the Latin word cellula. The cell theory holds true for all cellular organisms. The region of the cell lying between the plasma membrane and the nucleus is the cytoplasm. The modern cell theory includes the following components: Robert Hooke first discovered cells in a piece of cork and also coined the word cell. It is an aqueous compartment bound by cell membrane. Golgi complex. Besides the nucleus.

Eukaryotic cells have a much more complex intracellular organization with internal membranes as compared to prokaryotic cells. Viruses are noncellular organisms because they lack cell or cell-like structure. On the basis of the internal architecture. Over the time. Anton van Leeuwenhoek was the first person who observed living cells under a microscope and named them animalcules.

According to this theory all living things are made up of cells and cell is the basic structural and functional unit of life. In the year Hooke only observed cell walls because cork cells are dead and without cytoplasmic contents.

Evolution of the cell The earliest cells probably arose about 3. Primitive heterotrophs gradually acquired www.

The basic structural and functional unit of cellular organisms is the cell. All organisms. Chapter 03 Cell Structure and Functions 3. Hooke published his findings in his famous work. Rudolf Virchow proposed an important extension of cell theory that all living cells arise from pre-existing cells omnis cellula e cellula. The prokaryotic cells lack such unit membrane bound organelles. Non- cellular organisms such as virus do not obey cell theory.

In Cells that have unit membrane bound nuclei are called eukaryotic. Cell theory In It describes both the mosaic arrangement of proteins embedded throughout the lipid bilayer as well as the fluid movement of lipids and proteins alike. Integral proteins float in this lipid bilayer.

These DNA-protein complexes called chromosomes become especially compact at the time of cell division. Cell Structure and Functions the capability to derive energy from certain compounds in their environment and to use that energy to synthesize more and more of their own precursor molecules.

The plasma membrane exhibits selective permeability. Both proteins and lipids are free to move laterally in the plane of the bilayer. Different models were proposed to explain the structure and composition of plasma membranes. The fossil record shows that earliest eukaryotic cells evolved about 1. Jonathan Singer and Garth Nicolson proposed fluid-mosaic model. Peripheral protein Phospholipid bilayer Integral protein Peripheral protein Figure 3.

The fatty acyl chains in the lipid bilayer form a fluid. The DNA is. One important landmark along this evolutionary road occurred when there was a transition from small cells with relatively simple internal structures. The original electron hydrogen donor for these photosynthetic organisms was probably H2S. In this model. A very significant evolutionary event was the development of photosynthetic ability to fix CO2 into more complex organic compounds.

It acts as a selectively permeable membrane and regulates the molecular traffic across the boundary. Three major changes must have occurred as prokaryotes gave rise to eukaryotes. The cyanobacteria are the modern descendants of these early photosynthetic O2 producers. Details of the evolutionary path from prokaryotes to eukaryotes cannot be deduced from the fossil record alone.

Some aerobic bacteria evolved into the mitochondria of modern eukaryotes. Phosphoglycerides are the most numerous phospholipid molecules found in plasma membranes. The fatty acid components are hydrophobic. At neutral pH. Phosphoglyceride molecules are classified according to the types of alcohol linked to the phosphate group. The primary physical forces for organizing lipid bilayer are hydrophobic interactions.

There are two types of phospholipids: The ratio of protein to lipid varies enormously depends on cell types.

Carbohydrates are especially abundant in the plasma membranes of eukaryotic cells. Cell Structure and Functions Chemical constituents of plasma membrane All plasma membranes. Carbohydrates bound either to proteins as constituents of glycoproteins or to lipids as constituents of glycolipids. Lipid bilayer The basic structure of the plasma membrane is the lipid bilayer. This bilayer is composed of two leaflets of amphipathic lipid molecules.

In sphingophospholipid. Rarer phospholipids have a net positive charge. Glycerophospholipids or phosphoglycerides contain glycerol. Sphingomyelin is the most abundant sphingophospholipid. Phospholipids derived from glycerol are called glycerophospholipids. Phospholipids Phospholipids are made up of four components: Three classes of lipid molecules present in lipid bilayer.

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The plasma membrane of animal cells contains four major phospholipids. The hydrophilic unit. Sphingophospholipids contain an amino alcohol called sphingosine instead of glycerol. At equilibrium. Ion concentration gradients and selective movements of ions create a difference in electric potential or voltage across the plasma membrane.

Active transport of ions by ATP-driven ion pumps. In addition to ion pumps. The resulting separation of charge across the membrane constitutes an electric potential. Its electrogenic operation directly contributes to the negative inside membrane potential. Electrical potential across cell membranes is a function of the electrolyte concentrations in the intracellular and extracellular solutions and of the selective permeabilities of the ions.

All cells have an electrical potential difference. Cell Structure and Functions 3. Electrogenic transport affects and can be affected by the membrane potential. How membrane potentials arise? To help explain how an electric potential across the plasma membrane can arise. This is called membrane potential. Cell Structure and Functions Let us now consider the changes in potential during an action potential. During the repolarizing phase. At resting potential about —70 mV. The influx of positive charge depolarizes the membrane further.

Movement of ions occurs through ion channels. During an action potential. This process is called repolarization. Leaky channels. Following the repolarizing phase there may be an after-hyperpolarizing phase. Action potentials are the direct consequence of the voltage-gated cation channels.

Gated channels. Ion channels may be either leaky channels or gated channels. The channel undergoes through these various conformations as a result of voltage changes that take place during an action potential.

During the depolarizing phase. The refractory period limit the number of action potentials that can be produced by an excitable membrane in a given period of time.

It can be absolute or relative. The top graph depicts an action potential. The x-axis for time is the same in both graphs. The relative refractory period is the time period during which a second action potential can be initiated.

Gated Na and K channels closed Time millisecond Figure 3. The period of time after an action potential begins during which an excitable cell cannot generate another action potential in response to a normal threshold stimulus is called the refractory period.

During the absolute refractory period. Specialized secretory cells also have a regulated secretory pathway.