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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. 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. The constitutive secretory pathway operates in all cells. The lumen of the gut is acidic. An example of transcytosis is the movement of maternal antibodies across the intestinal epithelial cells of the newborn rat. Cell Structure and Functions plasma membrane at the opposite side. 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. Many soluble proteins are continually secreted from the cell by this pathway.

On exposure to the neutral pH of the extracellular fluid that bathes the basolateral surface of the cells. Examples of proteins released by such constitutive or continuous secretion include collagen by fibroblasts.

The two pathways diverge in the trans Golgi network. The receptor-antibody complexes are internalized via clathrin coated vesicles and are delivered to early endosomes. The regulated secretion of small molecules. This pathway also supplies the plasma membrane with newly synthesized lipids and proteins. 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.

In this secretory pathway. In all eukaryotes studied so far. Table 3. Cell Structure and Functions The regulated secretory pathway is found mainly in cells specialized for secreting products rapidly on demand such as hormones. The sedimentation coefficient has units of second. The human genome contains about copies of rRNA genes per haploid set. It is the ratio of a velocity to the centrifugal acceleration.

Proteins destined for secretion called secretory proteins are packaged into appropriate secretory vesicles in the trans Golgi network. The functional ribosomes consist of two subunits of unequal size.

The signal that directs secretory proteins into such vesicles is not known. Many other species. The secreted product can be either a small molecule such as histamine or a protein such as a hormone or digestive enzyme. There are generally more copies of the 5S genes than of the rRNA genes. Ribosomes consist of rRNA and r-proteins. The ribosome is approximately globular structure. The r-proteins are termed as L or S depending on whether the protein is from the large or small subunit.

The transport of selected proteins from the cytosol into the ER lumen or into mitochondria is an example of transmembrane transport. Within the cell. It is an extensive network of closed and flattened membrane-bound structure.

The transfer of proteins from the endoplasmic reticulum to the Golgi apparatus. ER membranes are physiologically active. Transmembrane transport: In transmembrane transport. Vesicular transport: In vesicular transport. Microsomes lacking attached ribosomes are called smooth microsome. This process is called gated transport because the nuclear pore complexes function as selective gates that can actively transport specific macromolecules.

Gated transport: The protein translocation between the cytosol and nucleus occurs through the nuclear pore complexes.

Proteins synthesized by membrane bound ribosomes are translocated co-translationally. Protein translocation describes the movement of a protein across a membrane. The enclosed compartment is called the ER lumen. When cells are disrupted by homogenization.

Microsomes derived from RER are studded with ribosomes on the outer surface and are called rough microsomes. All proteins synthesized by membrane free ribosomes are translocated post-translationally. Protein translocation may occur co-translationally or post-translationally.

Figure 3. The cisternal space or lumen remains continuous with the perinuclear space. 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 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.

The sugar molecules participate. 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: Glycosylation of proteins N-linked oligosaccharide chains on proteins are altered as the proteins pass through the Golgi cisternae en route from the ER. High-mannose www. As we have seen. The chemical make-up of each face is different and the enzymes contained in the cisternae between the faces are distinctive.

The Golgi apparatus is especially prominent in cells that are specialized for secretion. In such cells.

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Further modifications of N-linked oligosaccharide in the Golgi apparatus gives two broad classes of N-linked oligosaccharides. Proteins and lipids enter the cis Golgi network in vesicular tubular clusters arriving from the ER and exit from the trans Golgi network.

When completed. Secretory vesicles form from the trans Golgi network. The vesicles fuse with the Golgi membranes and release their internally stored molecules into the organelle. Both networks are thought to be important for protein sorting. The modifications to molecules that take place in the Golgi apparatus occur in an orderly fashion.

ER - lysosome. 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. Once inside. Substances from ER enter into the cis face of a Golgi stack for processing and exit from trans face.

Synthesis and release of the signaling molecule by the signaling cell. Extracellular signaling usually involves the following steps: 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. Initiation of signal-transduction pathways. Depending on the eukaryotic organism.

Each cell is programmed to respond to specific extracellular signal molecules. It consists of a long array of short. 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.

Chromosome number All eukaryotic cells have multiple linear chromosomes. Origin of replication The origin of replication also called the replication origin is a particular sequence in a chromosome at which replication is initiated. The majority of eukaryotic cells are diploid. The centromeres serve both as the sites of association of sister chromatids and as the attachment sites for microtubules of the mitotic spindle.

Every cell maintains a characteristic number of chromosomes. Cell Structure and Functions termed as heterochromatin. Telomere Telomeres are specialized structures.

Because of its condensed state. Binding of the signal by a specific receptor leading to its activation. Species Haploid number of chromosome Saccharomyces cerevisiae budding yeast 16 Schizosaccharomyces pombe fission yeast 03 Caenorhabditis elegans 06 Arabidopsis thaliana 05 Drosophila melanogaster 04 Tetrahymena thermophilus Micronucleus 5.

Transport of the signal to the target cell. One chromosome contains multiple origin of replication. Although this constriction is called the centromere. Centromere The constricted region of linear chromosomes is known as the centromere. Certain types of T- lymphocytes respond to antigenic stimulation by synthesizing a growth factor that drives their own proliferation. It is a long-range signaling in which signal molecule is transported by the blood stream.

An example of this is the action of neurotransmitters in carrying signals between nerve cells at a synapse. In juxtacrine signaling. These molecules are divided into two categories — membrane bound and secretory signal molecules. In autocrine signaling. In paracrine signaling. Notch signalling and classical cadherin signalling are examples of juxtacrine signaling. Cell Structure and Functions In animals.

Secreted extracellular signal molecules are further divided into three general categories based on the distance over which signals are transmitted: One important example of such is the response of cells of the vertebrate immune system to foreign antigens. Unlike other modes of cell signaling. In most cases. In endocrine signaling. Membrane bound signal molecules remain bound to the surface of the cells and mediate contact dependent signaling.

Some activated BH3- only proteins may stimulate mitochondrial protein release more directly by binding to and activcting the BH proteins. They invade surrounding normal tissues called invasiveness and spread throughout the body through circulatory or lymphatic systems called metastasis. Bad and Bmf. Tumor or neoplasm any abnormal proliferation of cells may be of two types: Benign tumor and Malignant tumor.

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. Important members of the BH3-only proteins are Bid.

BH3-only proteins are activated and bind to the anti-apoptotic Bcl2 proteins so that they can no longer inhibit the BH proteins. Bcl2 was the first protein shown to cause an inhibition of apoptosis. It is the mammalian homologue of the CED-9 in C. Cell Structure and Functions pro-apoptotic. The main BH proteins are Bax and Bak.

When an apoptotic stimulus triggers the intrinsic pathway. Threaded Mode. Sep 1 , Aug 2 , Oct 3 , Sep 4 , Find Reply patlesarin Junior Member Posts: Apr 5 , Apr 6 , Jul 7 , Jul 8 , Sep 9 , Sep 10 , Nov 11 , Mar 12 , Mar 13 , Jomesh Joseph Illustration and layout: Pradeep Verma Cover design: Pradeep Verma Marketing director: Arun Kumar Production coordinator: Murari Kumar Singh Printer: The exponential increase in the quantity of scientific information and the rate, at which new discoveries are made, require very elaborate, interdisciplinary and up-to-date information and their understanding.

This fourth edition of Life sciences, Fundamentals and practice includes extensive revisions of the previous edition. We have attempted to provide an extraordinarily large amount of information from the enormous and ever-growing field in an easily retrievable form.

It is written in clear and concise language to enhance self-motivation and strategic learning skill of the students and empowering them with a mechanism to measure and analyze their abilities and the confidence of winning. We have given equal importance to text and illustrations. The fourth edition has a number of new figures to enhance understanding.

At the same time, we avoid excess detail, which can obscure the main point of the figure. We have retained the design elements that have evolved through the previous editions to make the book easier to read. Sincere efforts have been made to support textual clarifications and explanations with the help of flow charts, figures and tables to make learning easy and convincing.

Although the chapters of this book can be read independently of one another, they are arranged in a logical sequence. Each page is carefully laid out to place related text, figures and tables near one another, minimizing the need for page turning while reading a topic.

I have given equal importance to text and illustrations as well. We hope you will find this book interesting, relevant and challenging. Acknowledgements Our students were the original inspiration for the first edition of this book, and we remain continually grateful to them, because we learn from them how to think about the life sciences, and how to communicate knowledge in most meaningful way. We thank, Dr.

Diwakar Kumar Singh and Mr. Ajay Kumar, reviewers of this book, whose comment and suggestions were invaluable in improving the text. Any book of this kind requires meticulous and painstaking efforts by all its contributors. Several diligent and hardworking minds have come together to bring out this book in this complete form.

We are much beholden to each of them and especially to Dr. Neeraj Tiwari. This book is a team effort, and producing it would be impossible without the outstanding people of Pathfinder Publication. It was a pleasure to work with many other dedicated and creative people of Pathfinder Publication during the production of this book, especially Pradeep Verma.

The total pages displayed will be limited. Contents Chapter 1 Biomolecules and Catalysis 1. Calvin cycle 2. Bacterial chromosome and plasmid 4. Structure and function 5. Chapter 01 Biomolecules and Catalysis A biomolecule is an organic molecule that is produced by a living organism.

Biomolecules act as building blocks of life and perform important functions in living organisms. More than 25 naturally occurring chemical elements are found in biomolecules. Most of the elements have relatively low atomic numbers.

Biomolecules consist primarily of carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur. Nearly all of the biomolecules in a cell are carbon compounds, which account for more than one-half of the dry weight of the cells. Covalent bonding between carbon and other elements permit formation of a large number of compounds.

Most biomolecules can be regarded as derivatives of hydrocarbons. The hydrogen atoms may be replaced by a variety of functional groups to yield different families of organic compounds.

Typical families of organic compounds are the alcohols, which have one or more hydroxyl groups; amines, which have amino groups; aldehydes and ketones, which have carbonyl groups; and carboxylic acids, which have carboxyl groups. Many biomolecules are polyfunctional, containing two or more different kinds of functional groups. Functional groups determine chemical properties of biomolecules.

Sugars, fatty acids, amino acids and nucleotides constitute the four major families of biomolecules in cells. Many of the biomolecules found within cells are macromolecules and mostly are polymers composed of small, covalently linked monomeric subunits. These macromolecules are proteins, carbohydrates, lipids and nucleic acids. Proteins are polymers of amino acids and constitute the largest fraction besides water of cells.

They store, transmit, and translate genetic information. The polysaccharides, polymers of simple sugars, have two major functions. They serve as energy-yielding fuel stores and as extracellular structural elements.

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The general structure of an amino acid is: In the simplest case, the R group is a hydrogen atom and amino acid is glycine. Amino acids can act as acids and bases When an amino acid is dissolved in water, it exists in solution as the dipolar ion or zwitterion.

A zwitterion can act as either an acid proton donor or a base proton acceptor. Hence, an amino acid is an amphoteric molecule. At high concentrations of hydrogen ions low pH , the carboxyl group accepts a proton and becomes uncharged, so that the overall charge on the molecule is positive. Similarly at low concentrations of hydrogen ion high pH , the amino group loses its proton and becomes uncharged; thus the overall charge on the molecule is negative.

At low pH, the positively charged species predominates. As the pH increases, the electrically neutral zwitterion becomes predominant. At higher pH, the negatively charged species predominates.

Optically active molecules contain chiral carbon. A tetrahedral carbon atom with four different constituents are said to be chiral. All amino acids except glycine have chiral carbon and hence they are optically active.

Biomolecules and Catalysis 1. A mixture of amino acids in hydrolysates can be separated by ion exchange chromatography or by reversed phase HPLC. The identity of the amino acid is revealed by its elution volume and quantified by reaction with ninhydrin.

N-terminal analysis Reagent 1-fluoro-2,4-dinitrobenzene FDNB and Dansyl chloride are used for determination of N-terminal amino acid residue. FDNB reacts in alkaline solution pH 9. It can be released from the peptide by either acid or enzymic hydrolysis of the peptide bond and subsequently identified.

Sanger first used this reaction to determine the primary structure of the polypeptide hormone insulin. Similarly, Dansyl chloride reacts with a free amino group of the N-terminal amino acid residue of a peptide in alkaline solution to form strongly fluorescent derivatives of free amino acids and N-terminal amino acid residue of peptides. Edman degradation Edman degradation method for determining the sequence of peptides and proteins from their N-terminus was developed by Pehr Edman.

This chemical method uses phenylisothiocyanate also termed Edman reagent for sequential removal of amino acid residues from the N-terminus of a polypeptide chain. Biomolecules and Catalysis trypsin, chymotrypsin, elastase, thermolysin and pepsin. Various other chemicals also cleave polypeptide chains at specific locations. The most widely used is cyanogen bromide CNBr , which cleaves peptide bond at C-terminal of Met residues. Similarly hydroxylamine cleaves the polypeptide chain at Asn-Gly sequences.

Table 1. Carboxypeptidase A cleaves the C-terminal peptide bond of all amino acid residues except Pro, Lys and Arg. Carboxypeptidase B is effective only when Arg or Lys are the C-terminal residues. Carboxypeptidase C acts on any C-terminal residue. Aminopeptidases catalyze the cleavage of amino acids from the amino terminus of the protein.

Aminopeptidase M catalyzes the cleavage of all free N-terminal residues. Cleavage of disulfide bonds If protein is made up of two or more polypeptide chains and held together by noncovalent bonds then denaturing agents, such as urea or guanidine hydrochloride, are used to dissociate the chains from one another.

But polypeptide chains linked by disulfide bonds can be separated by two common methods. These methods are used to break disulfide bonds and also to prevent their reformation. Oxidation of disulfide bonds with performic acid produces two cysteic acid residues. Because these cysteic acid side chains are ionized SO3— groups, electrostatic repulsion prevents S-S recombination.

This reaction is followed by further modification of the reactive —SH groups to prevent reformation of the disulfide bond.

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Acetylation by iodoacetate serves this purpose which modifies the —SH group. Protein assays To determine the amount of protein in an unknown sample is termed as protein assays. The simplest and most direct assay method for proteins in solution is to measure the absorbance at nm UV range. Amino acids containing aromatic side chains i. Consequently, proteins absorb UV-light in proportion to their aromatic amino acid content and total concentration.

Several colorimetric, reagent-based protein assay techniques have also been developed. Protein is added to the reagent, producing a color change in proportion to the amount added. Protein concentration is determined by reference to a standard curve consisting of known concentrations of a purified reference protein. Some most commonly used colorimetric, reagent-based methods are: Biuret method: This method is not highly sensitive since the complex does not have a high extinction coefficient.

Folin method: The Folin assay also called Lowry method is dependent on the presence of aromatic amino acids in the protein. Bradford method: Bradford method is based on a blue dye Coomassie Brilliant Blue that binds to free amino groups in the side chains of amino acids, especially Lys.

This assay is as sensitive as the Folin assay. Pages 38 to 41 are not shown in this preview. Nuclein was later shown to be a mixture of a basic protein and a phosphorus- containing organic acid, now called nucleic acid.

There are two types of nucleic acids polynucleotides: Nucleic acids therefore are also called polynucleotides. Nucleotides are phosphate esters of nucleosides and made up of three components: A base that has a nitrogen atom nitrogenous base 2.

A five carbon sugar 3. An ion of phosphoric acid Nitrogenous bases Nitrogenous bases are heterocyclic, planar and relatively water insoluble aromatic molecules. Adenine has an amino group —NH2 on the C6 position of the ring carbon at position 6 of the ring. Guanine has an amino group at the C2 position and a carbonyl group at the C6 position. Pyrimidines The two major pyrimidine bases found in DNA are thymine 5-methyl-2,4-dioxypyrimidine and cytosine 2-oxy aminopyrimidine and in RNA they are uracil 2,4-dioxypyrimidine and cytosine.

Thymine contains a methyl group at the C5 position with carbonyl groups at the C4 and C2 positions. Cytosine contains a hydrogen atom at the C5 position and an amino group at C4.

Uracil is similar to thymine but lacks the methyl group at the C5 position. Uracil is not usually found in DNA. It is a component of RNA. Ribose and deoxyribose sugar. All known sugars in nucleic acids have the D-stereoisomeric configuration. Deoxyribose sugar is found in DNA. This non-planarity is termed puckering. Pentose ring can be puckered in two basic conformations: In the envelope form, the four carbons of the pentose sugar are nearly coplanar and the fifth is away from the plane.

In twisted form three atoms are coplanar and the other two lie away on opposite sides of this plane. Sugar pucker can be endo or exo. Exo-pucker describes a shift in the opposite direction. Nucleoside Sugar and nitrogenous base join to form nucleoside. The bond between the sugar and the base is called the glycosidic bond. Biomolecules and Catalysis Table 1.

The condensation most commonly occurs between the alcohol of a 5'-phosphate of one nucleotide and the 3'-hydroxyl of a second, with the elimination of H2O, forming a phosphodiester bond. All nucleotides in a polynucleotide chain have the same relative orientation. The backbones of these polynucleotide are formed by 3' to 5' phosphodiester linkages. The backbone follows a zigzag path as opposed to a smooth path in B-DNA.

Electrostatic interactions play a crucial role in the Z-DNA formation. Therefore, Z-DNA is stabilized by high salt concentrations or polyvalent cations that shield interphosphate repulsion better than monovalent cations. C2'-endo, G: The triple helix will be written as dT. A third strand makes a hydrogen bond to another surface of the duplex. The third strand pairs in a Hoogsteen base-pairing scheme. The central strand of the triplex must be purine rich.

Thus, triple-stranded DNA requires a homopurine: If the third strand is purine rich, it forms reverse Hoogsteen hydrogen bonds in an antiparallel orientation with the purine strand of the Watson-Crick helix. If the third strand is pyrimidine rich, it forms Hoogsteen bonds in a parallel orientation with the Watson-Crick-paired purine strand. Triple helix can be intermolecular or intramolecular.

In the intermolecular Pu. Py triple helix, the poly-purine third strand is organized antiparallel with respect to the purine strand of the original Watson-Crick duplex.

In the intermolecular Py. Py triplex, the polypyrimidine third strand is organized parallel with respect to the purine strand and the phosphate backbone is positioned.

Py triple 5' helix. The polypurine third strand black colour is organized antiparallel with respect to the purine strand of 5' the original double strand DNA. As in intermolecular triplexes, when the third strand is the pyrimidine strand, it forms Hoogsteen pairs in a parallel fashion with the central purine strand. When the third strand is the purine strand, it forms reverse Hoogsteen pairs in an antiparallel fashion with the central purine strand.

These consist of a square arrangement of guanines a tetrad , stabilized by Hoogsteen hydrogen bonding. The formation and stability of the G-quadruplexes is a monovalent cation-dependent.

A monovalent cation is presents in the center of the tetrads. Depending on the direction of the strands or parts of a strand that form the tetrads, structures may be described as parallel or antiparallel. All parallel quadruplexes have all guanine glycosidic angles in an anti conformation. Anti-parallel quadruplexes have both syn and anti conformations.

How, then, all these data are transmitted to the body of the cell itself where they are put to use? The answer: RNA molecules play essential roles in the transfer of genetic information during protein synthesis and in the control of gene expression.

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. This fundamental interaction between bases leads to the formation of double-helical structures of varying length.

In RNA, double-helical tracts are generally short. Thus, formation of the secondary structure dominates the process of RNA folding. RNA tertiary structure forms through relatively weak interactions between preformed secondary structure elements. At physiological pH, denaturation of a double stranded helical RNA often requires higher temperatures than those required for denaturation of a DNA molecule with a comparable sequence.

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However, the physical basis for these differences in thermal stability is not known. Features of few major forms of RNA present in prokaryotic and eukaryotic cells are given below. Most of the eukaryotic mRNAs represent only a single gene: In these cases, a single mRNA is transcribed from a group of adjacent genes.

Most of the prokaryotic mRNA are polycistronic. All mRNAs contain two types of regions. The coding region consists of a series of codons starting with an AUG and ending with a termination codon. But the mRNA is always longer than the coding region, extra regions are present at both ends. A polycistronic mRNA also contains intercistronic regions. They vary greatly in size. They may be as long as 30 nucleotides. Eukaryotic mRNA molecules often require extensive processing and transport, while prokaryotic molecules do not.

The concept of an adaptor to provide the interface between nucleic acid language and protein language was introduced by Crick in Holley and his co-workers determined the first tRNA sequence in Dictated by their primary sequence, tRNA folds into cloverleaf-like secondary structures with well-defined stems and loops that make up the acceptor arm, D arm and loop, anticodon arm and loop, and the T-arm and loop.

Regardless of the length of the tRNA, the numbering of conserved nucleotides remains constant. Biomolecules and Catalysis maintaining the telomeres. They are always associated with specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins snRNP or sometimes as snurps.

The proteins then catalyze modification of the RNA gene. RNA editing was first reported in the mitochondria of kinetoplastids, in which mRNAs are edited by inserting or deleting stretches of uridylates Us. After the discovery of the first small silencing RNA in year , several small RNA classes have been identified which differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate.

The pre-miRNA molecule is then actively transported out of the nucleus into the cytoplasm by exportin protein. Whereas the other strand which is ultimately destroyed, is the passenger strand. It has currently only been found in bacteria. This attached tag targets the protein for destruction or proteolysis.

RNA with catalytic activity is termed as ribozyme. Because RNA can perform the tasks of both genetic materials and enzymes, RNA is believed to have once been capable of independent life.

Fraenkel-Conrat and B. In the majority of carbohydrates, H and O are present in the same ratio as in water, hence also called as hydrates of carbon.

Carbohydrates are the most abundant biomolecules on Earth. 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.

Oligosaccharides are polymers made up of two to ten monosaccharide units joined together by glycosidic linkages. Oligosaccharides can be classified as di-, tri-, tetra- depending upon the number of monosaccharides present.

Amongst these the most abundant are the disaccharides, with two monosaccharide units. Polysaccharides are polymers with hundreds or thousands of monosaccharide units.

Polysaccharides are not sweet in taste hence they are also called non-sugars. Monosaccharides are the simple sugars, which cannot be hydrolyzed further into simpler forms and they have a general formula CnH2nOn.

Monosaccharides are colourless, crystalline solids that are freely soluble in water but insoluble in nonpolar solvents. The most abundant monosaccharide in nature is the D-glucose. 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. Monosaccharides with four, five, six and seven carbon atoms are called tetroses, pentoses, hexoses and heptoses, respectively.

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. Ketoses are monosaccharides containing a ketone group. The monosaccharide glucose is an aldohexose; that is, it is a six-carbon monosaccharide -hexose containing an aldehyde group aldo-.

Similarly fructose is a ketohexose; that is, it is a six-carbon monosaccharide -hexose and containing a ketone group keto-. Trioses are simplest monosaccharides. There are two trioses— dihydroxyacetone and glyceraldehyde. Dihydroxyacetone is called a ketose because it contains a keto group, whereas glyceraldehyde is called an aldose because it contains an aldehyde group. Glyceraldehyde has a central carbon C—2 which is chiral or asymmetrical.

Chiral molecules such as glyceraldehyde can exist in two forms or configurations that are non-superimposable mirror images of each other. These two forms are called enantiomers. An enantiomer is identified by its absolute configuration. Glyceraldehyde has two absolute configurations. When the hydroxyl group attached to the chiral carbon is on the left in a Fischer projection, the configuration is L; when the hydroxyl group is on the right, the configuration is D.

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.

The configuration of groups around the chiral carbon 2 shown in bold distinguishes D-glyceraldehyde from L-glyceraldehyde. The two molecules are mirror images and cannot be superimposed on one another.

All the monosaccharides except dihydroxyacetone contain one or more chiral carbon atoms and thus occur in optically active isomeric forms. As the number of chiral carbon atoms increases, the number of possible stereoisomers also increases.

For example, D-glucose and D-mannose differ only at carbon 2. Sugars that differ only by the stereochemistry at a single carbon other than anomeric carbon are called epimers.

Similarly D-glucose and D-galactose are epimers. D-mannose and D-galactose are not epimers because their configuration differ at more than one carbon. 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.

A reducing sugar is any sugar that either has an aldehyde group or is capable of forming one in solution through isomerisation. This functional group allows the sugar to act as a reducing agent.

All monosaccharides whether aldoses and ketoses, in their hemiacetal and hemiketal form are reducing sugars. All disaccharides formed from head to tail condensation are also reducing sugar i.

All reducing sugars undergo mutarotation in aqueous solution. Sugars like sucrose, trehalose not capable of reducing ferric or cupric ion are called non-reducing sugar. In sucrose and trehalose, anomeric carbon becomes involved in a glycosidic bond. So they donot contain free anomeric carbon atoms. Sucrose and trehalose are therefore not a reducing sugar, and have no reducing end. So it cannot be oxidized by cupric or ferric ion.

In describing disaccharides or polysaccharides, the end of a chain that has a free anomeric carbon i. They are readily soluble in nonpolar solvents such as ether, chloroform, or benzene. Unlike the proteins, nucleic acids, and polysaccharides, lipids are not polymers. Functions Biological lipids have diverse functions. The four general functions of biological lipids have been identified.

Apart from the general functions biological lipids serve as pigments carotene , hormones vitamin D derivatives, sex hormones , signaling molecules eicosanoids, phosphatidylinositol derivatives , cofactors vitamin K , detergents bile salt and many other specialized functions. Biomolecules and Catalysis The notation In this nomenclature the carboxyl carbon is designated carbon 1.

For example, palmitoleic acid has 16 carbons and has a double bond between carbons 9 and It is designated as There is an alternative convention for naming polyunsaturated fatty acids.

In this convention, number 1 is assigned to the methyl carbon. Essential fatty acids Mammals lack the enzymes to introduce double bonds at carbon atoms beyond C-9 in the fatty acid chain.

Hence, mammals cannot synthesize linoleate and linolenate. Linoleate and linolenate are the two essential fatty acids. The term essential means that they must be obtained from the diet because they are required by an organism and cannot be endogenously synthesized. Fatty acids that can be endogenously synthesized are termed as nonessen- tial.

They are nonessential also in the sense that they do not have to be obligatorily included in the diet. Melting point of fatty acids The melting point of fatty acids depend on chain length and degree of unsaturation. The longer the chain length, the higher the melting point; and the greater the number of double bonds, the lower the melting point.

The presence of double bonds makes unsaturated chain more rigid. As a result, unsaturated chains cannot pack themselves in crystals efficiently and densely as saturated chain, so, they have lower melting point as compared to saturated fatty acids.

Similarly, the unsaturated fatty acids with cis configuration have lower melting points than the unsaturated fatty acids with trans configuration. Problem Why unsaturated fatty acids have low melting points?

Solution The presence of double bonds makes unsaturated chain more rigid. They are composed of three fatty acids and a glycerol molecule. Triacylglycerols are of two types — simple and mixed type. 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 general formula of triacylglycerol is given below: Because triacylglycerols have no charge i. Triacylglycerol molecules contain fatty acids of varying lengths, which may be unsaturated or saturated.

Triacylglycerols can be distinguished as fat and oil on the basis of physical state at room temperature. Fats, which are solid at room temperature, contain a large proportion of saturated fatty acids. 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 number of milligrams of KOH required to saponify one-gram of fat is known as saponification number.

The saponification number measures the average molecular weight of fats. Similarly, the number of grams of iodine that can be added to g sample of fat or oil is called iodine number, which is used to determine the degree of unsaturation i.

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Waxes Natural waxes are typically esters of fatty acids and long chain alcohols. They are formed by esterification of long chain fatty acids saturated and unsaturated and high molecular weight monohydroxy alcohols C14 to C Waxes are biosynthesized by many plants or animals. The best known animal wax is beeswax. 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.

Phosphoglycerides Phospholipids derived from glycerol are called phosphoglycerides or glycerophospholipids. A phosphoglyceride consists of a glycerol molecule, two fatty acids, a phosphate, and an alcohol e. Phosphoglycerides are the most numerous phospholipid molecules found in cell membranes.

In phosphoglycerides, the hydroxyl groups at C-1 and C-2 of glycerol are esterified to the carboxyl groups of the two fatty acid chains. The C-3 hydroxyl group of the glycerol backbone is esterified to phosphoric acid. When no further additions are made, the resulting compound is phosphatidic acid, the simplest phosphoglyceride. Phos- phatidic acids are found in small amount in most natural systems. 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.

The common alcohol moieties of phosphoglycerides are serine, ethanolamine, choline, glycerol, and the inositol. If the alcohol is choline, the phosphoglyceride molecule is called phosphatidylcholine also referred to as lecithin and if serine then it is called phosphotidylserine. They can be classified according to their solubility and their functions in metabolism. The requirement for any given vitamin depends on the organisms.

Not all vitamins are required by all organisms. Vitamins are not synthesized by humans, and therefore must be supplied by the diet. Vitamins may be water soluble or fat soluble. Nine vitamins thiamines, riboflavin, niacin, biotin, pantothenic acid, folic acid, cobalamin, pyridoxine, and ascorbic acid are classified as water soluble, whereas four vitamins vitamins A, D, E and K are termed fat-soluble.

Except for vitamin C, the water soluble vitamins are all precursors of coenzymes. Thiamine is composed of a substituted thiazole ring joined to a substituted pyrimidine by a methylene bridge. The oxidized form of the isoalloxazine structure absorbs light around nm. The colour is lost, when the ring is reduced. Niacin Niacin, or nicotinic acid, is a substituted pyridine derivative. Nicotinamide, is a derivative of nicotinic acid that contains an amide instead of a carboxyl group. Deficiency of niacin causes pellagra, a disease involving the skin and central nervous system.

The symptoms of pellagra progress through the three Ds: Dermatitis, Diarrhoea, Dementia, and, if untreated, death.

Biotin Biotin is a coenzyme in carboxylation reactions, in which it serves as a mobile carboxyl group carrier. It is a remarkable molecular device that determines the pattern of chemical transformations. Virtually all cellular reactions or processes are mediated by enzymes. Enzymes have several properties that make them unique.

With the exception of a small group of catalytic RNA molecules, all enzymes are proteins. Their catalytic activity depends on the integrity of their native protein conformation. If an enzyme is denatured or dissociated into its subunits, catalytic activity is usually lost.

They are highly specialized proteins and have a high degree of specificity for their substrates.