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UNIT -I

LESSON-1 CELL

Contents

1.0 Aims and Objectives1.1 Introduction1.2 Structure of Prokaryotic and Eukaryotic Cell1.3 Let Us Sum Up1.4 Points for Discussion1.5 Check your Progress1.6 Lesson End Activities1.7 References

1.0 Aims and Objectives

To know about the cell and its types, etc.

1.1. Introduction

A cell is a microscopic, structural and functional unit of living organisms capable ofindependent existence (e.g. Amoeba). All living things are composed of cells. Somefunctioning cells come together to form a tissue and tissues collectively form organs. Inmore complex living organisms, organs work together for the purpose of survival assystem. However, in all living organisms, the cell is a functional unit and all of biologyrevolves around the activity of the cell.

The study of cell is impossible without the microscope. The first simple microscope wasprepared by Anton Van Leewenhoek (1632-1723)who studied the structure of bacteria,protozoa, spermatozoa, red blood cells etc. The word cell was first coined by RobertHooke in 1665 to designate the empty honey-comb like structures viewed in a thinsection of bottle cork which he examined. He was impressed by the microscopiccompartments in the cork as they reminded him of rooms in a monastery which areknown as cells. He therefore referred to the units as cells. In 1838, the German botanistMatthios Schleidenproposed that all the plants are made up of plant cells. Then in 1839,his colleague, the anatomist Theodore Schwannstudied and concluded that all animalsare also composed of animal cells. Schwann and Schleiden studied a wide variety of plantand animal tissues and proposed the "cell theory" in 1839. It stated that "all organismsare

composed of cells." But still the real nature of a cell was in doubt. Cell theory was againrewritten by Rudolf Virchow in 1858 and said that all living things are made up of cellsand that all cells arise from pre-existing cells. It was German biologist Schulze whofound in 1861 that the cells are not empty as were seen by Hooke but contain a stuff oflife called protoplasm. During the 1950s scientists developed the concept that allorganisms may be classified as prokaryotes or eukaryotes. For example, in prokaryoticcells, there is no nucleus; eukaryotic cells have a nucleus. Another important differencebetween prokaryotes and eukaryotes is that the prokaryotic cell does not have any

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intracellular components. Bacteria and blue- green algae come under the prokaryoticgroup, and

1.2 Structure of Prokaryotic and Eukaryotic Cell

Cells in our world come in two basic types, prokaryotic and eukaryotic. "Karyose" comesfrom a Greek word which means "kernel," as in a kernel of grain. In biology, we use thisword root to refer to the nucleus of a cell. "Pro" means "before," and "eu" means "true,"or "good." So "Prokaryotic" means "before a nucleus," and "eukaryotic" means"possessing a true nucleus." This is a big hint about one of the differences between thesetwo cell types. Prokaryotic cells have no nuclei, while eukaryotic cells do have true

Fig. 1. Prokaryotic and Eukaryotic Cell

Nuclei:Despite their apparent differences, these two cell types have a lot in common.They perform most of the same kinds of functions, and in the same ways. Both areenclosed by plasma membranes, filled with cytoplasm, and loaded with small structures

called ribosome. Both have DNA which carries the archived instructions for operating thecell. And the similarities go far beyond the visibility; for example, the DNA in the twocell types is precisely the same kind ofDNA, and the genetic code for a prokaryotic cellis exactly the same genetic code used in eukaryotic cells. The difference is that theprokaryotic cell has a cell wall which is absent in animal cells. However, many kinds ofeukaryotic cells do have cell walls. The size and complexity do exist. Eukaryotic cells aremuch larger and much more complex than prokaryotic cells. These two observations arenot unrelated to each other.

If we take a closer look at the comparison of these cells, we see the following differences:

1.

Eukaryotic cells have a true nucleus, bound by a double membrane. Prokaryotic cellshave no nucleus. The purpose of the nucleus is to sequester the DNA-related functionsof the big eukaryotic cell into a smaller chamber, for the purpose of increasedefficiency. This function is unnecessary for the prokaryotic cell, because its muchsmaller size means that all materials within the cell are relatively close together. Ofcourse, prokaryotic cells do have DNA and DNA functions. Biologists describe thecentral region of the cell as its "nucleoid" (-oid=similar or imitating), because it's



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pretty much where the DNA is located. But note that the nucleoid is essentially animaginary "structure." There is no physical boundary enclosing the nucleoid.

2. Eukaryotic DNA is linear complexed with proteins called "histones," and isorganized into chromosomes; prokaryotic DNA is "naked," meaning that it has nohistones associated with it, and it is not formed into chromosomes. Though many aresloppy about it, the term "chromosome" does not technically apply to anything in aprokaryotic cell. A eukaryotic cell contains a number of chromosomes; a prokaryoticcell contains only one circular DNA molecule (has no ends) and a varied assortment ofmuch smaller circlets of DNA called "plasmids." The smaller, simpler prokaryotic cellrequires far fewer genes to operate than the eukaryotic cell.

3. Both cell types have many ribosomes, but the ribosomes of the eukaryotic cells arelarger and more complex than those of the prokaryotic cell. Ribosomes are made outof a special class of RNA molecules (ribosomal RNA, or rRNA) and a specificcollection of different proteins. A eukaryotic ribosome is composed of five kinds ofrRNA and about eighty kinds of proteins. Prokaryotic ribosomes are composed of onlythree kinds of rRNA and about fifty kinds of protein.

4.

The cytoplasm of eukaryotic cells is filled with a large, complex collection oforganelles, many of them enclosed in their own membranes; the prokaryotic cellcontains no membrane-bound organelles which are independent of the plasmamembrane. This is a very significant difference, and the source of the vast majority ofthe greater complexity of the eukaryotic cell.

5. There is much more space within a eukaryotic cell than within a prokaryotic cell,and many of these structures, like the nucleus, increase the efficiency of functions byconfining them within smaller spaces within the huge cell, or with communication andmovement within the cell.

6.

One aspect of that evolutionary connection is particularly interesting withineukaryotic cells by the presence of fascinating organelle called mitochondria. And inplant cells, an additional family of organelles called plastids, the most famous ofwhich is the renowned chloroplast. Mitochondria (the plural of mitochondrion) andchloroplasts almost certainly have a similar evolutionary origin. Both are pretty clearlythe descendants of independent prokaryotic cells, which have taken up permanentresidence within other cells through a well-known and very common phenomenoncalled endosymbiosis.

7.

One structure not shown in our prokaryotic cell is called a mesosome, which is anelaboration of the plasma membrane-a sort of rosette of ruffled membrane intrudinginto the cell and not all prokaryotic cells have these.



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Fig. 2. Prokaryotic cell and Mitochondrion

Fig. 2 shows a trimmed down prokaryotic cell, including only the plasma membrane andacouple of mesosomes. A mitochondrion is included for comparison. The similarities inappearance between these structures are pretty clear. The mitochondrion is a double-membrane organelle, with a smooth outer membrane and an inner membrane which

protrudesinto the interior of the mitochondrion in folds called cristae. This membrane isvery similar in appearance to the prokaryotic plasma membrane with its mesosomes,however not more significant than appearance. Both the mesosomes and the cristae are

used for the same function: the aerobic part of aerobic cellular respiration. Cellularrespiration is the process by which a cell converts the raw, potential energy of food intobiologically useful energy, and there are two general types, anaerobic (not using oxygen)and aerobic (requiring oxygen). In practical terms, the big difference between the two isthat aerobic cellular respiration has a much higher energy yield than anaerobicrespiration. Aerobic respiration is clearly the evolutionary offspring of anaerobicrespiration. (In anaerobic respiration with additional chemical sequences added on to theend of the process to allow utilization of oxygen).

Fig. 3. Prokaryotic and Eukaryotic cells

Protozoa, fungi, animals, and plants come under the eukaryotic group



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1.3 Let Us Sum Up

All living things are composed of cells. The word cell was first coined by Robert Hookein 1665. Cell is basically of two types prokaryotic and eukaryotic.

1.4 Points for Discussion

Cell in the basic unit of life Comment.

1.5 Check your Progress

Write down the main features of a eukaryotic cell

Note: a) Please dont proceed till you attempt the above question.

b) The space given below is for your answer

1.6 Lesson-end activities

1)

Define cell.2)

Write down the main differences between prokaryotic and eukaryotic cells

1.7 References

1. Lehinger, A.L. 1984, Principles of Biochemistry, CBS Publishers and distributors,New Delhi, India.

2. Horton, Moran, Ochs, Rawn, Scrimgeour Principles of Biochemistry, Prentice HallPublishers.

3. Shanmughavel, P. 2005, Principles of Bioinformatics, Pointer Publishers, Jaipur, India.

4. David, E. Sadava Cell Biology: Organelle structure and Fucntion Jones & BartlettPublishers.



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LESSON2: Cell Organellesand Their Functions

Contents


2.1 Mitochondria

2.2 Chloroplasts

2.3 Endoplasmic reticulum

2.4 Golgi apparatus

2.5 Ribosome

2.6 Lysosome

2.7 Nucleus

2.8 Nucleolus2.9 Peroxisome

2.10 Let Us Sum Up



2.13 Check your Progress

2.14 References


In this lesson weve learn about the cell organelles and their functions.

A living cell is a complex, multi-functional unit. Even the simplest of cellsperforms a large array of different tasks and functions by the arrangement of the cellorganelles such as cell wall and plasma membrane and cytosolic substances such asnucleus, Golgi bodies, endoplasmic reticulum, mitochondria etc.



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2.1 Mitochondria

Fig. 4. Mitochondrial Components

Mitochondria are the cells' power sources. They are distinct organelles with twomembranes. Usually they are rod-shaped, however they can be round. The outermembrane limits the organelle. The inner membrane is thrown into folds or shelves thatproject inward are called "cristae mitochondriales". They contain two membranes,separated by a space. Both arethe typical "unit membrane" (railroad track) in structure.Inside the space enclosed by the inner membrane is the matrix. Which contains densestrands of DNA, ribosomes, or small granules and can code for part of their proteins withthese molecular tools.

The food we eat is oxidized to produce high-energy electrons that are converted to storedenergy. This energy is stored in high energy phosphate bonds in a molecule called

adenosine triphosphate, or (ATP). Which is converted from adenosine diphosphate byadding the phosphate group with the high-energy bond. Various reactions in the cell caneither use energy (whereby the ATP is converted back to ADP, releasing the high energybond) or produce it (whereby the ATP is produced from ADP). Let us break down eachof the steps so you can see how food turns into ATP energy packets and water. The foodwe eat must first be converted to basic chemicals that the cell can use. Some of the bestenergy supplying foods contains sugars or carbohydrates. Using bread as an example, thesugars are broken down by enzymes that split them into the simplest form of sugar whichis called glucose. Then, glucose enters the cell by special molecules in the membranecalled glucose transporters.

Once inside the cell, glucose is broken down to make ATP in two pathways. The firstpathway requires no oxygen and is called anaerobic metabolism. This pathway is calledglycolysis and it occurs in the cytoplasm outside the mitochondria. During glycolysis,glucose is broken down into pyruvate. Other foods like fats can also be broken down foruse as fuel (see following cartoon). Each reaction is designed to produce some hydrogenions (electrons) that can be used to make energy packets (ATP). However, only 4 ATPmolecules can be made by one molecule of glucose run through this pathway. That iswhy mitochondria and oxygen are so important. We need to continue the breakdown



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process with the Krebs cycle inside the mitochondria in order to get enough ATP to runall the cell functions.

Fig. 5. ATP Synthase

Pyruvate is carried into the mitochondria and there it is converted into Acetyl Co-Awhich enters the Kreb's cycle. This first reaction produces carbon dioxide because itinvolves the removal of one carbon from the pyruvate

Mitochondrial membrane morphology

The outer membrane of the mitochondria contains the protein "porin". This forms anaqueous channel through which proteins up to 10,000 daltons can pass and go into theintermembrane space. Indeed, the small molecules actually equilibrate between the outermembrane and the cytosol. However, most proteins cannot get into the matrix unless theypass through the inner membrane. This membrane contains cardiolipin which renders it

virtually impermeable and requires transport mechanisms across the membrane that aremore organized and regulated.

Fig. 6. Protein import by Mitochondria



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Transport across the mitochondrial membranes requires the concerted action of a numberof translocation machineries. The machinery in the outer membrane is called the Tomcomplex (Translocator outer membrane) and that for the inner membrane is called the

Tim complex (Translocator Inner Membrane). Proteins that have to go all the way to thematrix have an NH2 cleavable signal sequence and become uncoiled or stretched out togo through the translocators. This involves ATP binding and is monitored and stabilizedby a chaperone protein, including hsp70. Thus, before the protein can go through Tomcomplex, it must become "translocation competent", and processed as follows:

1. First, as with many mitochondrial proteins, Tom40 requires cytosolic chaperonesto prepare it for entry. In the case of this protein, becoming "translocationcompetent" requires ATP and a partially folded state (the latter is mediated by thecytosolic chaperone (hsp70).

2. Second, when it is "competent", it interacts with the surface receptor, Tom20.

There is no cleavable signal peptide however, the experiments showing therequirement for partial folding suggests targeting information is found indiscontinuous sites brought together in the folded domain.

3.

Final insertion is into preexisting Tom complexes and requires an intact Nterminus.

4. Dimerization occurs after entry into the membrane.5.

Tim54 carries a amino terminal, noncleaved translocation sequence that ispositively charged. However, it prefers to use Tom70 as its receptor instead ofTom20. After moving through the GIP, it uses its positively charged aminoterminal sequence to enter the matrix. It required chaperones and ATP to get tothe matrix.

6. Tim22 is a hydrophobic protein that uses Tom20 for targeting to the OM. Then itfollows the Tim route for carrier proteins, like Tim23. and does not require hsp70or ATP for entry.

7. Small Tims are normally found in the intermembrane space and are not membraneproteins. They used Tom20 for their receptor and transfer to theGIP complex.However, when Tom20 was destroyed by trypsin, leaving only Tom5, the smallTims were able to enter.

2.2 Chloroplast

Chloroplastsare organelles found in plant cells and eukaryotic algae that conduct

photosynthesis. Chloroplasts absorb sunlight and use it in conjunction with water andcarbon dioxide to produce sugars, the raw material for energy and biomass production inall green plants and the animals that depend on them, directly or indirectly, for food.Chloroplasts capture light energyfrom the sunto conserve free energy in the form ofATP and reduce NADPt o NADPH through a complex set of processes called

photosynthesis. It is derived from the Greek words chloroswhich means green andplastwhich means form or entity. Chloroplasts are members of a class of organelles known asplastids. They have their own genome, and may contain 60-100 genes.

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Structure

Chloroplasts are observable morphologically as flat discs usually 2 to 10 micrometers indiameter and 1 micrometer thick. The chloroplast is contained by an envelope thatconsists of an inner and an outer phospholipid membrane. Between these two layers is the

intermembrane space. The material within the chloroplast is called the stroma,corresponding to the cytosol of the original bacterium, and contains one or moremolecules of small circular DNA. It also contains ribosomes, although most of itsproteins are encoded by genes contained in the host cell nucleus, with the proteinproducts transported to the chloroplast.

Within the stroma are stacks of thylakoids, the sub-organelles which are the site ofphotosynthesis. The thylakoids are arranged in stacks called grana(singular: granum). Athylakoid has a flattened disk shape. Inside it is an empty area called the thylakoid spaceor lumen. Photosynthesis takes place on the thylakoid membrane; as in mitochondrialoxidative phosphorylation, it involves the coupling of cross-membrane fluxeswith

biosynthesisvia the dissipation of a proton electrochemical gradient. Embedded in thethylakoid membrane is the antenna complex, which consists of proteins, and light-absorbing pigments, including chlorophylland carotenoids. This complex both increasesthe surface area for light capture, and allows capture of photons with a wider range ofwavelengths. The energy of the incident photons is absorbed by the pigments andfunneled to the reaction centre of this complex through resonance energy transfer. Twochlorophyll molecules are then ionised, producing an excited electron which then passesonto the photochemical reaction centre.

Chloroplast membrane: Chloroplasts contain several important membranes, vital fortheir function. Like mitochondria, chloroplasts have a double-membrane envelope, called

the chloroplast envelope. Each membrane is a phospholipid bilayer, between 6 and 8 nmthick, and the two are separated by a gap of 10-20nm, called the intermembrane space.The outer membrane is permeable to most ionsa n d metabolites, but the innermembrane is highly specialised with transport proteins within the inner membrane, in theregion called the stroma, there is a system of interconnecting flattened membranecompartments, called the lamellae, or thylakoids. These are the sites of light absorptionand ATPsynthesis, and contain many proteins, including those involved in the electrontransport chain. Photosynthetic pigments such as chlorophyll and B, and some otherse.g. xanthophylls and carotenoids are also located within this space. The membranes ofthe chloroplasts contain photosystems I and II which harvest solar energy in order toexcite electrons which travel down the electron transport chain. and along the way isused to pump H+ ions from the stroma into the thylakoid space. A concentrationgradient is formed, which allows chemiosmosis to occur, where the protein ATPsynthaseharvests the potential energy of the Hydrogenions and uses it to combine ADPand a phosphate group to form ATP.

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Functions

Photosynthesis:

The heart of photosynthesis as it occurs in most autotrophs consists of two keyprocesses:

the removal of hydrogen (H) atoms from water molecules the reduction of carbon dioxide (CO2) by these hydrogen atoms to form organic

molecules.

The second process involves a cyclic series of reactions named the CalvinCycle (after itsdiscoverer). It is discussed in Photosynthesis: Pathway of Carbon Fixation. The detail ofthe first process is our topic here.

The electrons (e- ) and protons (H+) that make up hydrogen atoms are stripped awayseparately from water molecules.

2H2O -> 4e- + 4H++ O2

The electrons serve two functions:

They reduce NADP+to NADPH for use in the Calvin Cycle. They set up an electrochemical charge that provides the energy for pumping

protons from the stroma of the chloroplast into the interior of the thylakoid.

The protons also serve two functions:

They participate in the reduction of NADP+to NADPH. As they flow back out from the interior of the thylakoid (by facilitateddiffusion),

passing down their concentration gradient), the energy they give up is harnessedto the conversion of ADP to ATP.

Becauseit is drive by light, this process is called photophosphorylation.

ADP + Pi-> ATP

The ATP provides the second essential ingredient for running the Calvin Cycle.

The removal of electrons from water molecules and their transfer to NADP+requiresenergy. The electrons are moving from a redox potentialof about +0.82 volt in water to- 0.32 volt in NADPH. Thus enough energy must be available to move them against atotal potential of 1.14 volts. Where does the needed energy come from? The answer:Light.

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Fig. 7. Calvin Cycle

The Thylakoid Membrane

Chloroplasts contain a system of thylakoid membranes surrounded by a fluid stroma.Six different complexes of integral membrane proteins are embedded in the thylakoidmembrane. The exact structure of these complexes differs from group to group (e.g.,plant vs. alga) and even within a group (e.g., illuminated in air or underwater). But, in

general, one finds:

1. Photosystem I

The structure of photosystem I in a cyanobacterium ("blue-green alga") has beencompletely worked out. It probably closely resembles that of plants as well.

It is a homotrimer with each subunit in the trimer containing:

12 different protein molecules bound to 96 molecules of chlorophyll a

o 2 molecules of the reaction center chlorophyll P700

o 4 accessory molecules closely associated with themo 90 molecules that serve as antenna pigments

22 carotenoid molecules 4 lipid molecules 3 clusters of Fe4S4 2 phylloquinones

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2. PhotosystemII

Photosystem II is also a complex of

> 20 different protein molecules bound to 50 or more chlorophyll a molecules

o 2 molecules of the reaction center chlorophyll P680

o 2 accessory molecules close to themo 2 molecules of pheophytin (chlorophyll without the Mg++)o the remaining molecules of chlorophyll a serve as antenna pigments.

some half dozen carotenoid molecules. These also serve as antenna pigments. 2 molecules of plastoquinone

2.3 Endoplasmic Reticulum

The endoplasmic reticulum or ER is an organelle found in all eukaryotic cellsthat is aninterconnected network of tubules, vesicles and cisternaethat is responsible for several

specialized functions: Protein translation, folding, and transport of proteins to be used inthe cell membrane (e. g. , transmembrane receptors and other integral membrane

proteins), or to be secreted ( exocytosed) from the cell (e.g., digestive enzymes);sequestration of calcium; and production and storage of glycogen, steroids, and othermacromolecules. The endoplasmic reticulum is part of the endomembrane system. The

basic structure and composition of the ER membrane is similar to the plasma membrane.

Structure:The general structure of the endoplasmic reticulum is an extensive membranenetwork of cisternae(sac-like structures) held together by the cytoskeleton. The

phospholipid membrane encloses a space, the cisternal space (or lumen), from thecytosol. The functions of the endoplasmic reticulum vary greatly depending on the exact

type of endoplasmic reticulum and the type of cell in which it resides. The three varietiesare called rough endoplasmic reticulum, smooth endoplasmic reticulum, andsarcoplasmic reticulum.

Rough endoplasmic reticulum: The surface of the rough endoplasmic reticulum isstudded with protein-manufacturing ribosomesgiving it a "rough" appearance (hence itsname). But it should be noted that these ribosomes are not resident of the endoplasmicreticulum incessantly. The ribosomes only bind to the ER once it begins to synthesize aprotein destined for sorting. The membrane of the rough endoplasmic reticulum iscontinuous with the outer layer of the nuclear envelope. Although there isno continuousmembrane between the rough ER and the Golgi apparatus, membrane bound vesicles

shuttle proteins between these two compartments. The rough endoplasmic reticulumworks in concert with the Golgi complex to target new proteins to their properdestinations.

Smooth endoplasmic reticulum: Smooth endoplasmic reticulum is found in a variety ofcell types (both animal and plant) and it serves different functions in each. The SmoothER also contains the enzyme Glucose-6-phosphatase which converts Glucose-6-

phosphateto Glucose, a step in gluconeogenesis. The Smooth ER consists of tubules and

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vesicles that branch forming a network. In some cells there are dilated areas like the sacsof rough endoplasmic reticulum. The network of smooth endoplasmic reticulum allowsincreased surface area for the action or storage of key enzymes and the products of theseenzymes. The smooth endoplasmic reticulum is known for its storage of calcium ions inmuscle cells. The smooth endoplasmic reticulum has functions in several metabolic

processes, including synthesis of lipids, metabolism of carbohydrates and calciumconcentration, drug detoxification, and attachment of receptors on cell membraneproteins. It is connected to the nuclear envelope.

Fig. 8. Endoplasmic Reticulum

Sarcoplasmic reticulum: The sarcoplasmic reticulum is a special type of smooth ER

found in smoothand striated muscle. The only structural difference between thisorganelle and the smooth endoplasmic reticulum is the medley of protein they have, both

bound to their membranes and drifting within the confines of their lumens. Thisfundamental difference is indicative of their functions: the smooth ER is built tosynthesize molecules and the sarcoplasmic reticulum is built to store and pump calciumions. The sarcoplasmic reticulum contains large stores of calcium, which it sequesters andthen releases when the cell is depolarised. This has the effect of triggering musclecontraction.

Functions

The endoplasmic reticulum serves many general functions, including the facilitation ofprotein folding and the transport of synthesized proteins in sacs called cisternae. Correctfolding of newly-made proteins is made possible by several endoplasmic reticulumchaperone proteins, including protein disulfide isomerase (PDI), ERp29, the Hsp70family member Grp78, calnexin, calreticulin, and the peptidylpropyl isomerase family.Only properly-folded proteins are transported from the rough ER to the Golgi complex.

http://www.clicktoconvert.com/http://en.wikipedia.org/wiki/Golgi_complexhttp://en.wikipedia.org/wiki/Golgi_complexhttp://en.wikipedia.org/wiki/Calreticulinhttp://en.wikipedia.org/wiki/Calnexinhttp://en.wikipedia.org/wiki/Hsp70http://en.wikipedia.org/wiki/Protein_disulfide_isomerasehttp://en.wikipedia.org/wiki/Cisternaehttp://en.wikipedia.org/wiki/Striated_musclehttp://en.wikipedia.org/wiki/Sarcoplasmic_reticulum


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Transport of proteins

Secretory proteins, mostly glycoproteins, are moved across the endoplasmic reticulummembrane. Proteins that are transported by the endoplasmic reticulum and from therethroughout the cell are marked with an address tag called a signal sequence. The N-

terminus (one end) of a polypeptidechain (i.e., a protein) contains a few amino acidsthat work as an address tag, which are removed when the polypeptide reaches itsdestination. Proteins that are destined for places outside the endoplasmic reticulum are

packed into transport vesicles and moved along the cytoskeleton toward theirdestination.

The endoplasmic reticulum is also part of a protein sorting pathway. It is, in essence, thetransportation system of the eukaryotic cell. The majority of endoplasmic reticulumresident proteins are retained in the endoplasmic reticulum through a retention motif.This motif is composed of four amino acids at the end of the protein sequence. The mostcommon retention sequence is KDEL( lys-asp-glu-leu). However, variation on KDEL

does occur and other sequences can also give rise to endoplasmic reticulum retention. Itis not known if such variation can lead to sub-endoplasmic reticulum localizations. Thereare three KDEL receptors in mammalian cells, and they have a very high degree ofsequence identity. The functional differences between these receptors remain to beestablished.

Other functions

Insertion of proteins into the endoplasmic reticulum membrane: Integral proteinsmust be inserted into the endoplasmic reticulum membrane after they aresynthesized. Insertion into the endoplasmic reticulum membrane requires the

correct topogenic sequences. Glycosylation: Glycosylation involves the attachment of oligosaccharides. Disulfide bond formation and rearrangement: Disulfide bonds stabilize the tertiary

and quaternary structure of many proteins. Drug Detoxification: The smooth ER is the site at which some drugs are

detoxified.

2.4 Golgi Apparatus

The Golgi apparatus (also called the Golgi body, Golgi complex, or dictyosome) is anorganelle found in typical eukaryotic cells. It was identified in 1898 by the Italian

physician Camillo Golgiand was named after him. The primary function of the Golgiapparatus is to process and package macromoleculessynthesised by the cell, primarilyproteinsand lipids. The Golgi apparatus forms a part of the endomembrane systempresent in eukaryotic cells.

Structure: The Golgi is composed of membrane-bound sacs known as cisternae.Between five and eight are usually present, however as many as sixty have beenobserved. Surrounding the main cisternae are a number of spherical vesicleswhich have

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budded off from the cisternae. The cisternae stack has five functional regions: the cis-Golgi network, cis-Golgi, medial-Golgi, trans-Golgi, and trans-Golgi network. Vesiclesfrom the endoplasmic reticulum (via the vesicular-tubular cluster) fuse with the cis-Golginetwork and subsequently progress through the stack to the trans-Golgi network, wherethey are packaged and sent to the required destination. Each region contains different

enzymes which selectively modify the contents depending on where they are destined toreside.

Fig. 9. The Golgi Apparatus

Function

1.Cells synthesise a large number of different macromolecules required for life. The Golgi

apparatus is integral in modifying, sorting, and packaging these substances for cellsecretion ( exocytosis) or for use within the cell. It primarily modifies proteins deliveredfrom the rough endoplasmic reticulum, but is also involved in the transport of lipidsaround the cell, and the creation of lysosomes. In this respect it can be thought of assimilar to a post office; it packages and labels "items" and then sends them to differentparts of the cell.2. Enzymes within the cisternae are able to modify substances by the addition ofcarbohydrates ( glycosylation) and phosphate (phosphorylation) to them. In order to doso the Golgi transports substances such as nucleotide sugars into the organelle from thecytosol. Proteins are also labelled with a signal sequenceof molecules which determinetheir final destination. For example, the Golgi apparatus adds a mannose-6-phosphatelabel to proteins destined for lysosomes. The Golgi also plays an important role in thesynthesis of proteoglycans, molecules present in the extracellular matrixof animals, andit is a major site of carbohydrate synthesis.3.

This includes the productions of glycosaminoglycansor GAGs, long unbranchedpolysaccharides which the Golgi then attaches to a protein synthesized in theendoplasmic reticulum to form theproteoglycan.http://en.wikipedia.org/wiki/Golgi_apparatus - _note-0Enzymes in the Golgi will

polymerizeseveral of these GAGs via a xyloselink onto the core protein. Another task

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of the Golgi involves the sulfationof certain molecules passing through its lumen viasulphotranferases that gain their sulphur molecule from a donor called PAPs. Thisprocess occurs on the GAGs of proteoglycans as well as on the core protein. The level ofsulfation is very important to the proteoglycans signalling abilities as well as giving theproteoglycan its overall negative charge.

4. The Golgi is also capable of phosphorylatingmolecules. To do so it transports ATPinto the lumen. The Golgi itself contains resident kinases, such as casein kinases. Onemolecule that is phosphorylated in the Golgi is Apolipoprotein, which forms a moleculeknown as VLDL that is a constitute of blood serum. It is thought that thephosphorylation of these molecules is important to help aid in their sorting of secretioninto the blood serum.

5. The Golgi also has a putative role in apoptosis, with several Bcl-2 family memberslocalised there, as well as to the mitochondria. In addition a newly characterised anti-apoptotic protein, GAAP (Golgi anti-apoptotic protein), which almost exclusively resides

in the Golgi, protects cells from apoptosis by an as-yet undefined mechanism (Gubser etal., 2007).

Vesicular transport

Vesicles which leave the rough endoplasmic reticulum are transported to the cis face ofthe Golgi apparatus, where they fuse with the Golgi membrane and empty their contentsinto the lumen. Once inside they are modified, sorted, and shipped towards their finaldestination. As such, the Golgi apparatus tends to be more prominent and numerous incells synthesising and secreting many substances: plasma B cells, the antibody-secretingcells of the immune system, have prominent Golgi complexes.

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Fig. 10. Inner view of Golgi Apparatus

Thoseproteins destined for areas of the cell other than either the endoplasmic reticulumor Golgi apparatus are moved towards the trans face, to a complex network ofmembranes and associated vesicles known as the trans-Golgi network(TGN). This areaof the Golgi is the point at which proteins are sorted and shipped to their intendeddestinations by their placement into one of at least three different types of vesicles,depending upon the molecular marker they carry.

Transport mechanism

The transport mechanismwhich proteins use to progress through the Golgi apparatus isnot yet clear; however a number of hypotheses currently exist. Until recently, thevesicular transport mechanism was favoured but now more evidence is coming to light tosupport cisternal maturation. The two proposed models may actually work in conjunctionwith each other, rather than being mutually exclusive. This is sometimes referred to as thecombinedmodel.

Cisternal maturation model: The cisternae of the Golgi apparatus move bybeing built at the cis face and destroyed at the trans face. Vesicles from theendoplasmic reticulum fuse with each other to form a cisterna at the cisface,

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consequently this cisterna would appear to move through the Golgi stack when anew cisterna is formed at the cisface. This model is supported by the fact thatstructures larger than the transport vesicles, such as collagenrods, were observedmicroscopically to progress through the Golgi apparatus. This was initially apopular hypothesis, but lost favour in the 1980s. Recently it has made a

comeback, as laboratories at the University of Chicago and the University ofTokyo have been able to use new technology to directly observe Golgicompartments maturing. Additional evidence comes from the fact that COP1vesicles move in the retrograde direction,. transporting ER proteins back to wherethey belong by recognizing a signal peptide.

Vesicular transport model: Vesicular transport views the Golgi as a very stableorganelle, divided into compartments is the cis to trans direction. Membrane

bound carriers transported material between the ER and Golgi and the differentcompartments of the Golgi. Experimental evidence inlcudes the abundance ofsmall vesicles (known technically as shuttle vesicles) in proximity to the Golgi

apparatus. Directionality is achieved by packaging proteins into either forward-moving or backward-moving (retrograde) transport vesicles, or alternatively thisdirectionality may not be necessary as the constant input of proteins from theendoplasmic reticulum on the cis face of the Golgi would ensure flow.Irrespectively, it is likely that the transport vesicles are connected to a membranevia actin filaments to ensure that they fuse with the correct compartment.

2.5 Ribosome

Ribosomes were first observed in the mid-1950s by Romanian cell biologist GeorgePalade in the electron microscopea s dense particles or granules for which he was

awarded the Nobel Prize. The term ribosome was proposed by scientist Richard B.Roberts in 1958. A ribosome is a small, dense, functional structure found in all knowncells that assembles proteins. They are about 20nm in diameter and are composed of65% ribosomal RNA and 35% ribosomal proteins (known as a RibonucleoproteinorRNP). It translates messenger RNA (mRNA) to build a polypeptide chain (e.g., aprotein) using amino acids delivered by Transfer RNA (tRNA). It can be thought of as agiant enzyme but, although it contains proteins, its active site is made of RNA, soribosomes are now classified as " ribozymes".

Ribosomes build proteins from the genetic instructions held within a messenger RNA.Free ribosomes are suspended in the cytosol(the semi-fluid portion of the cytoplasm) or

bound to the rough endoplasmic reticulum, or to the nuclear envelope. Since ribosomesare ribozymes, it is thought that they might be remnants of the RNA world. Whilecatalysis of the peptide bond involves the C2' hydroxyl of tRNA's P-site adenosine in asort of proton shuttle mechanism, the full function (ie, translocation) of the ribosome isreliant on changes in protein conformations.

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Fig. 11. Structure of Ribosome

Ribosomes consist of two subunits that fit together and work as one to translate themRNAinto a polypeptide chain during protein synthesis. Prokaryoticsubunits consist ofone or two and eukaryotic of one or three very large RNA molecules (known asribosomal RNA or rRNA) and multiple smaller protein molecules. Prokaryotes have 70 Sribosomes, each consisting of a small ( 30S) and a large ( 50S) subunit. Their largesubunit is composed of a 5S RNAsubunit (consisting of 120 nucleotides), a 23S RNAsubunit (2900 nucleotides) and 34 proteins. The 30S subunit has a 1540 nucleotide RNAsubunit bound to 21 proteins. Eukaryotes have 80S ribosomes, each consisting of a small( 40S) and large ( 60S) subunit. Their large subunit is composed of a 5S RNA (120nucleotides), a 28S RNA (4700 nucleotides), a 5.8S subunit (160 nucleotides) and~49proteins. The 40S subunit has a 1900 nucleotide (18S) RNA and ~33 proteins.Crystallographic work has shown that there are no ribosomal proteins close to the

reaction site for polypeptide synthesis. This suggests that the protein components ofribosomes act as a scaffold that may enhance the ability of rRNA to synthesize proteinrather than directly participating in catalysis.Free ribosomes: Free ribosomes are "free" tomove about anywhere in the cytoplasm (within the cell membrane). Proteins made byfree ribosomes are used within the cell. Proteins containing disulfide bonds usingcysteine amino acids cannot be produced outside of the lumen of the endoplasmicreticulum.

Membrane-bound ribosomes: When certain proteins are synthesized by a ribosomethey can become "membrane-bound". The newly produced polypeptide chains areinserted directly into the endoplasmic reticulum by the ribosome and are then transported

to their destinations. Bound ribosomes usually produce proteins that are used within thecell membrane or are expelled from the cell via exocytosis.

Functionof Ribosomes

1. Ribosomes are the workhorses of protein biosynthesis, the process of translatingmessenger RNA(mRNA) into protein. The mRNA comprises a series of codonsthat dictate to the ribosome the sequence of the amino acidsneeded to make the

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protein. Using the mRNA as a template, the ribosome traverses each codon of themRNA, pairing it with the appropriate amino acid. This is done using moleculesof transfer RNA(tRNA) containing a complementary anticodonon one end andthe appropriate amino acid on the other.

2. Protein synthesis begins at a start codonnear the 5' end of the mRNA. The small

ribosomal subunit, typically bound to a tRNA containing the amino acidmethionine, binds to an AUG codon on the mRNA and recruits the largeribosomal subunit. The large ribosomal subunit contains three tRNA binding sites,designated A, P, and E. The A site binds an aminoacyl- tRNA (a tRNA bound toan amino acid); the P site binds a peptidyl-tRNA (a tRNA bound to the peptidebeing synthesized); and the E site binds a free tRNA before it exits the ribosome.

Both ribosomal subunits (small and large) assemble at the start codon (towards the 5'end of the mRNA). The ribosome uses tRNA which matches the current codon(triplet) on the mRNA to append an amino acid to the polypeptide chain. This is donefor each triplet on the mRNA, while the ribosome moves towards the 3' end of the

mRNA. Usually in bacterial cells, several ribosomes are working parallel on a singlemRNA, forming what we call apolyribosomeor polysome

2.6 Lysosome

Lysosomesare organellesthat contain digestive enzymes (acid hydrolases). They digestexcess or worn out organelles, food particles, and engulfed virusesor bacteria. Themembrane surrounding a lysosome prevents the digestive enzymes inside fromdestroying the cell. Lysosomes fuse with vacuolesand dispense their enzymes into thevacuoles, digesting their contents. They are built in the Golgi apparatus. The namelysosomederives from the Greek words lysis, which means dissolution or destruction, and

soma, which means body. They are frequently nicknamed "suicide-bags" or "suicide-sacs" by cell biologists due to their role in autolysis. Lysosomes were discovered by theBelgian cytologist Christian de Duve in 1949.

Acidic environment

At pH4.8, the interior of the lysosomes is more acidic than the cytosol (pH 7.2). Thelysosome single membranestabilizes the low pH by pumping in protons(H+) from thecytosol via proton pumps and chloride ion channels. The membrane also protects thecytosol, and therefore the rest of the cell, from the degradative enzymes within thelysosome. For this reason, should a lysosome's acid hydrolases leak into the cytosol, their

potential to damage the cell will be reduced, because they will not be at their optimumpH. The hydrolytic enzymes in lysosomes are produced in the endoplasmic reticulumand transported and processed through the Golgi apparatus. The Golgi apparatus

produces lysosomes by budding. Each acid hydrolase is then targetedto a lysosome byphosphorylation. The lysosome itself is likely to be safe from enzymatic action due tohaving proteins in the inner membrane which has a three-dimensional molecular structurethat protects vulnerable bonds from enzymatic attack.

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Fig. 13. Lysosome

Some important enzymes in lysosomes are:

Lipase, which digests lipids, Carbohydrases, which digest carbohydrates (e.g., sugars), Proteases, which digest proteins, Nucleases, which digest nucleic acids. Phosphatases, which digest phosphoric acid monoesters

Lysosomal enzymes are synthesized in the cytosol and the endoplasmic reticulum, wherethey receive a mannose-6-phosphate tag that targets them for the lysosome. Aberrantlysosomal targeting causes inclusion-cell disease, whereby enzymes do not properlyreach the lysosome, resulting in accumulation of waste within these organelles.

Functions

The lysosomes are used for the digestion of macromoleculesf rom phagocytosis(ingestion of other dying cells or larger extracellular material), endocytosis (wherereceptor proteins are recycled from the cell surface), and autophagy (where old or

unneeded organelles or proteins, or microbes which have invaded the cytoplasm aredelivered to the lysosome). Autophagy mayalso lead to autophagic cell death, a form ofprogrammed self-destruction, or autolysis, of the cell, which means that the cell isdigesting itself.

Other functions include digesting foreign bacteria (or other forms of waste) that invade acell and helping repair damage to the plasma membrane by serving as a membrane patch,sealing the wound. Lysosomes also do much of the cellular digestion required to digest

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tails of tadpoles and to remove the web from the fingers of a 3-6 month old fetus. Thisprocess of programmed cell death is called apoptosis.

2.7 Nucleus

In cell biology, the nucleus(pl. nuclei; from Latin nucleusor nuculeus, kernel) is amembrane-enclosed organelle found in most eukaryotic cells. It contains most of thecell's genetic material, organized as multiple long linear DNA molecules in complexwith a large variety of proteins, such as histones, to form chromosomes. The geneswithin these chromosomes make up the cell's nuclear genome. The function of thenucleus is to maintain the integrity of these genes and to control the activities of the cellby regulating gene expression.

Fig. 13. Nuclear

The main structural elements of the nucleus are the nuclear envelope, a doublemembrane that encloses the entire organelle and keeps its contents separated from thecellular cytoplasm, and the nuclear lamina, a meshwork within the nucleus that addsmechanical support much like the cytoskeleton supports the cell as a whole. Because thenuclear membrane is impermeable to most molecules, nuclear poresare required to allowmovement of molecules across the envelope. These pores cross both membranes of theenvelope, providing a channel that allows free movement of small molecules and ions.The movement of larger molecules such as proteins is carefully controlled, and requires

active transport facilitated by carrier proteins. Nuclear transport is of paramountimportance to cell function, as movement through the pores is required for both geneexpression and chromosomal maintenance.

Although the interior of the nucleus does not contain any membrane-delineated bodies,its contents are not uniform, and a number ofsubnuclear bodiesexist, made up of uniqueproteins, RNAmolecules, and DNA conglomerates. The best known of these is the

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nucleolus, which is mainly involved in assembly of ribosomes. After being produced inthe nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA.

2.8 Nucleolus

The nucleolus is a discrete densely-stained structure found in the nucleus. It is notsurrounded by a membrane, and is sometimes called asuborganelle. It forms aroundtandemrepeats of rDNA, DNA coding for ribosomal RNA(rRNA). These regions arecalled nucleolar organizer regions (NOR). The main roles of the nucleolus are tosynthesize rRNA and assemble ribosomes. The structural cohesion of the nucleolusdepends on its activity, as ribosomal assembly in the nucleolus results in the transientassociation of nucleolar components, facilitating further ribosomal assembly, and hencefurther association. This model is supported by observations that inactivation of rDNAresults in intermingling of nucleolar structures.

Fig. 14. Nucleolus

The first step in ribosomal assembly is transcription of the rDNA, by a protein calledRNA polymerase I, forming a large pre-rRNA precursor. This is cleaved into thesubunits 5.8S, 18S, and 28S rRNA. The transcription, post-transcriptional processing, andassembly of rRNA occurs in the nucleolus, aided by small nucleolar RNA(snoRNA)molecules, some of which are derived from spliced intronsfrom messenger RNAsencoding genes related to ribosomal function. The assembled ribosomal subunits are thelargest structures passed through the nuclear pores.

When observed under the electron microscope, the nucleolus can be seen to consist ofthree distinguishable regions: the innermostfibrillar centers (FCs), surrounded by thedense fibrillar component(DFC), which in turn is bordered by thegranular component(GC). Transcription of the rDNA occurs either in the FC or at the FC-DFC boundary, andtherefore when rDNA transcription in the cell is increased more FCs are detected. Mostof the cleavage and modification of rRNAs occurs in the DFC, while the latter stepsinvolving protein assembly onto the ribosomal subunits occurs in the GC.

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2.9 Peroxisome

Peroxisomes are ubiquitous organellesin eukaryotesthat participate in the metabolismof fatty acids and other metabolites. Peroxisomes have enzymes that rid the cellof toxic

peroxides. They have a single lipid bilayer membrane that separates their contents from

the cytosol(the internal fluid of the cell) and contain membrane proteins critical forvarious functions, such as importing proteins into the organelles and aiding in

proliferation. Like lysosomes, peroxisomes are part of the secretory pathway of a cell,but they are much more dynamic and can replicate by enlarging and then dividing.Peroxisomes were identified as cellular organelles by the Belgian cytologist Christian deDuvein 1965after they had been first described in a Swedish Ph.D. thesis a decadeearlier.

Fig. 15. Anatomy of the Peroxisome

Functionof Peroxisomes

Peroxisomes contain oxidative enzymes, such as catalase, D-amino acid oxidaseanduric acid oxidase. Certain enzymes within the peroxisome, by using molecular oxygen,remove hydrogen atoms from specific organic substrates (labeled as R), in an oxidativereaction, producing hydrogen peroxide(H2O2, itself toxic):

. . . . . (1)

Catalase, another enzyme in the peroxisome, in turn uses this H2O2 to oxidizeother substrates, including phenols, formic acid, formaldehydeand alcohol, by meansof the peroxidation reaction:

, . . . (2)thus eliminating the poisonous hydrogen peroxide in the process.

This reaction is important in liver and kidney cells where the peroxisomesdetoxifiy various toxic substances that enter the blood. About 25% of the ethanol we

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drink is oxidized to acetaldehyde in this way. In addition, when excess H2O2accumulatesin the cell, catalase converts it to H2O through this reaction:

. . . (3)

A major function of the peroxisome is the breakdown of fatty acid molecules, in aprocess called beta-oxidation. In this process, the fatty acids are broken down twocarbons at a time, converted to Acetyl-CoA, which is then transported back to thecytosol for further use. In animal cells, beta-oxidation can also occur in themitochondria. In yeast and plant cells this process is exclusive for the peroxisome.Thefirst reactions in the formation of plasmalogen in animal cells also occurs inperoxisomes. Plasmalogen is the most abundant phospholipid in myelin. Deficiency ofplasmalogens causes profound abnormalities in the myelination of nerve cells, which isone of the reasons that many peroxisomal disorders lead to neurologicaldisease.Peroxisomes also play a role in the production of bile acids.

Protein import

Proteins are selectively imported into peroxisomes. Since the organelles contain no DNAor ribosomes and thus have no means of producing proteins, all of their proteins must beimported across the membrane. It is believed that proteins do not transit through theendoplasmic reticulum to get to the peroxisome.

A specific protein signal (PTS or peroxisomal targeting signal) of three amino acids atthe C-terminusof many peroxisomal proteins signals the membrane of the peroxisome toimport them into the organelle. Other peroxisomal proteins contain a signal at the N-terminus. There are at least 32 known peroxisomal proteins, called peroxins, which

participate in the process of importing proteins by means of ATP hydrolysis. Proteins donot have to unfold to be imported into the peroxisome. The protein receptors, theperoxins Pex5and Pex7, accompany their cargoes (containing a PTS1 or a PTS2,respectively) all the way into the peroxisome where they release the cargo and then returnto the cytosol -a step named "recycling". Overall, the import cycle is referred to as the"extended shuttle mechanism". Evidence now indicates that ATP hydrolysis is requiredfor the recycling of receptors to the cytosol. Also, ubiquitinationappears to be crucial forthe export of PEX5 from the peroxisome, to the cytosol. Little is known about the importof PEX7, although it has helper proteins that have been shown to be ubiquitinated.

Deficiencies: Peroxisomal disordersare a class of conditions which lead to disorders of

lipid metabolism. One well known example is Zellweger syndrome.One of these is calleda tight junction or "occluding junction" (zonula occludens). This is shown as the topjunction in the above drawing. At this site, membrane glycoproteins and associated"glue" bind the cells together like double-sided "strapping tape".

http://www.clicktoconvert.com/http://en.wikipedia.org/wiki/Peroxisomal_disordershttp://en.wikipedia.org/wiki/Ubiquitinationhttp://en.wikipedia.org/w/index.php?title=Pex7&action=edithttp://en.wikipedia.org/wiki/ATP_hydrolysishttp://en.wikipedia.org/w/index.php?title=Peroxins&action=edithttp://en.wikipedia.org/wiki/N-terminushttp://en.wikipedia.org/wiki/N-terminushttp://en.wikipedia.org/wiki/Peroxisomal_targeting_signalhttp://en.wikipedia.org/wiki/Endoplasmic_reticulumhttp://en.wikipedia.org/wiki/Bilehttp://en.wikipedia.org/wiki/Neuronhttp://en.wikipedia.org/wiki/Myelinhttp://en.wikipedia.org/wiki/Plasmalogenhttp://en.wikipedia.org/wiki/Coenzyme_Ahttp://en.wikipedia.org/wiki/Coenzyme_Ahttp://en.wikipedia.org/wiki/Coenzyme_Ahttp://en.wikipedia.org/wiki/Beta-oxidationhttp://en.wikipedia.org/wiki/Beta-oxidationhttp://en.wikipedia.org/wiki/Fatty_acidhttp://en.wikipedia.org/wiki/Acetaldehyde


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2.10 Let Us Sum Up

1. Mitochondria are the cells' power house of the cells2. the high energy compound ATP is produced in the mitochondria3. Glucose is breakdown by two pathways in mitochondria. Anaerobic

metabolism and aerobic metabolism.4.

Kreb cycle and oxidative phosphorylation takes place in mitochondria5. The chloroplastconsists of an inner and an outer phospholipid membrane6. Main function is photosynthesis.7. Endoplasmic reticulum is responsible for several specialized functions like

Protein translation, folding.8. There are three varieties of endoplasmic reticulum they are rough endoplasmic

reticulum, smooth endoplasmic reticulum, and sarcoplasmic reticulum.9. The surface of the rough endoplasmic reticulum is studded with protein-

manufacturing ribosomes giving it a "rough" appearance10.Prokaryotes have 70Sribosomes, each consisting of a small (30S) and a large

(50S) subunit.11.

Lysosomes are organellesthat contain digestive enzymes(acid hydrolases)todigest excess or worn out organelles, food particles, and engulfed virusesor

bacteria.12.The nucleolus consists of three distinguishable regions: the innermost

fibrillar centers, surrounded by the dense fibrillar component, which in turnis bordered by the granular component.

13.Peroxisomes are ubiquitous organellesin eukaryotesthat participate in themetabolism of fatty acidsand other metabolites.

14.Peroxisomes contain oxidative enzymes, such as catalase, D-amino acidoxidaseand uric acid oxidase.


Exploring cell organelles is as important as knowing the cell itselfSubstantiate.

2.12 Self-Check Exercise

Discuss the structure of mitochondria and its importance as a power house

Note: a) Please dont proceed till you attempt the above question.

b) The space given below is for your answer.

http://www.clicktoconvert.com/http://en.wikipedia.org/wiki/Uric_acid_oxidasehttp://en.wikipedia.org/wiki/D-amino_acid_oxidasehttp://en.wikipedia.org/wiki/D-amino_acid_oxidasehttp://en.wikipedia.org/wiki/D-amino_acid_oxidasehttp://en.wikipedia.org/wiki/Catalasehttp://en.wikipedia.org/wiki/Enzyme


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1) What are the different types of endoplasmic reticulum?2) Write about the main functions of endoplasmic reticulum3) Define the terms Exocytotic vesicles, Secretory vesicles, Lysosomal vesicles4) How the molecules are transported across the golgi complex?5)

What is zone of exclusion?6) What are the subunits of ribosome?7) Explain the role of ribosomes in protein synthesis.8) What are the different enzymes present in Lysosomes?9) Give short notes on the functions of Lysosome?10)

What is nucleolus?11)

Give short notes on the structure of nucleolus.

2.14References







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LESSON-3 Cell membrane structure and transport proteins

Contents3.0 Aims and Objectives3.1. Membrane Structure3.2 Let us sum up3.3 Points for Discussion3.4 Self check exercise3.5 Lesson-end activities3.6 References


To know about cell membrane structure and transport proteins.

3.1. Membrane Structure

The cell is highly organized with many functional units or organelles. Most of these unitsare limited by one or more membranes. To perform the function of the organelle, themembrane is specialized in that it contains specific proteins and lipid components thatenable it to perform its unique roles for that cell or organelle. In essence membranes areessential for the integrity and function of the cell. Membrane components may:

a) be protectiveb) regulate transport in and out of cell or subcellular domainc)

allow selective receptivity and signal transduction by providing transmembranereceptors that bind signaling molecules

d)

allow cell recognitione) Provide anchoring sites for cytoskeletal filaments or components of the

extracellular matrix. This allows the cell to maintain its shape and perhaps moveto distant sites.

f) help compartmentalize subcellular domains or microdomains

g) Provide a stable site for the binding and catalysis of enzymes.h) regulate the fusion of the membrane with other membranes in the cell via

specialized junctions )i)

Provide a passageway across the membrane for certain molecules, such as in gapjunctions.

j) allow directed cell or organelle motility

Membrane theories:In the early 1930's-40's, Danielli and Davson studied triglyceridelipid bilayers over a water surface. They found them to arrange themselves with the polarheads facing outward. However, they always formed droplets (oil in water) and thesurface tension was much higher than that of cells. However, if proteins were added thesurface tension was reduced and the membranes flattened out.



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Fig. 16 Cell Membrane

In the 1950's Robertson noted the structure of membranes seen in the above electronmicrographs. He saw no spaces for pores in the electron micrographs. He hypothesizedthat the railroad track appearance came from the binding of osmium tetroxide to proteinsand polar groups of lipids.

Fig. 17. Inner View of Cell Membrane

Fluid-mosaic model:

Biological membranes are sheet- like structures composed mainly of lipids and proteins.All biological membranes have a similar general structure. Membrane lipids areorganized in a bilayer (two sheets of lipids making up a single membrane) that isapproximately 60 to 100 thick. The proteins, on the other hand, are scatteredthroughout the bilayer and perform most membrane functions. Membranes are two-dimensional fluids: both lipids and proteins are constantly in motion. The fluid-mosaicmodel encompasses our current understanding of membrane structure. It describes boththe "mosaic" arrangement of proteins embedded throughout the lipid bilayer as well asthe "fluid" movement of lipids and proteins alike.



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Fig. 19. Reaction of Cell Membranes

Membrane Phospholipids:One of the principal types of lipid in the membrane includethe phospholipids . These have a polar head group and two hydrocarbon tails. An

example of a phospholipid is shown in this figure (right). The top region beginning withthe NH3 is the polar group. It is connected by glycerol to two fatty acid tails. One of thetails is a straight chain fatty acid (saturated). The other has a link in the tail because of a

cis double bond (unsaturated).The lipid bilayer gives the membranes its fluidcharacteristics. The following figure shows the effect of temperature on the packing ofthe hydrocarbons. Note that a low temperatures, the bilayer is in a gel state and tightlypacked. At higher (body) temperatures, the bilayer actually "melts' and the interior is

fluid allowing the lipid molecules to move around, rotate, exchange places.

Fig. 20. Reaction of Cell Membranes

Membrane Cholesterol: Another type of lipid in the membrane is cholesterol. Theamount of cholesterol may vary with the type of membrane. Plasma membranes havenearly one cholesterol per phospholipid molecule. Other membranes (like those aroundbacteria) have no cholesterol. The cholesterol molecule inserts itself in the membranewith the same orientation as the phospholipid molecules. The figures show phospholipidmolecules with a cholesterol molecule inbetween. Note that the polar head of the



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cholesterol is aligned with the polar head of the phospholipids. Cholesterol moleculeshave several functions in the membrane: a) They immobilize the first few hydrocarbongroups of the phospholipid molecules. This makes the lipid bilayer less deformable anddecreases its permeability to small water-soluble molecules. Without cholesterol (such asin a bacterium) a cell would need a cell wall b) Cholesterol prevents crystallization of

hydrocarbons and phase shifts in the membrane.

Membrane Glycolipids: Glycolipids are also a constituent of membranes whichprojecting into the extracellular space and hereby serving as protective, insulators, andsites of receptor binding. Among the molecules bound by glycososphingolipids includecell poisons such as cholera and tetanus toxins.Formation of "Microdomains":Sphingolipids and cholesterol work together to help cluster proteins in a region called a"microdomain". They function as "rafts" or platforms for the attachment of proteins asmembranes are moved around the cell and also during signal transduction.

Membrane Proteins: Transmembrane proteins are amphipathic, in that they have

hydrophobic and hydrophilic regions that are oriented in the same regions in the lipidbilayer. Another name for them is "integral proteins". Other types of proteins may belinked only at the cytoplasmic surface (by attachment to a fatty acid chain), or at theexternal cell surface, attached by a oligosaccharide. Or, these non-transmembraneproteins may be bound to other membrane proteins. Collectively these are called"peripheral membrane proteins". We will be studying specific membrane proteins in laterlectures (ion channels, proteins in endoplasmic reticulum, etc). Therefore, thispresentation will not spend much time on them. Proteins inserted once through themembrane are called "single-pass transmembrane proteins." Those that pass throughseveral times are called "multipass transmembrane proteins" and form loops outside themembrane

Fig. 20. Inner View of Cell Membrane



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3.2 Let Us Sum Up

1. Membrane is specialized in that it contains specific proteins and lipid components

to perform the function of the organelle2.

various membrane theories have been proposed3.

Danielli and Davson, Robertson model, and Fluid mosaic model have beenproposed

4. Membrane transport like facilitated diffusion, active transport, channels andpores, active transporters have been discussed.

5. Phagocytosis, pinocytosis, endocytosis are also discussed.


Do an analysis of the structure of the cell membrane and highlight the interesting teachersof it.

3.4 Check your ProgressExplain the models proposed for membrane strcuture?

Note: a) Please dont proceed till you attempt the above question.b) The space given below is for youranswer


1) Which component(s) of membranes give it its fluid characteristics?2) What feature in a membrane helps to prevent freezing? Be specific.3) Which part of a membrane helps it keep its shape (prevents deformation)?4) How are proteins arranged in a membrane? What is the difference between a

transmembrane protein and a peripheral membrane protein?5) What is a microdomain, and how is it formed?6) If one type of membrane contains 76% proteins and another type contains only 18%

proteins, what might you conclude about functional differences? For example, see

Membrane Architecture7) What experiments might you conduct to prove that proteins moved in the plane of the

membrane?8) How do membranes support the polarity of a cell?9) How would you detect receptors in the plasma membrane of a cell?10)

In a freeze-fracture/freeze etch specimen, what are the bumps seen in the plane of themembrane?



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11)How would you distinguish tight, or occluding junction between two cells, bothstructurally and functionally.

12)What experiments would you use to prove cells were communicating via gapjunctions? Do you know how gap junctions are formed?

13)What does the presence of microvilli signify?

14)

What experimental approach could you use to show that a protein is inserted in themembrane?

3.6References







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LESSON4:Mechanisms of transport

Contents4.0 Aims and Objectives4.1 Facilitated diffusion

4.2 Active transport4.3 Let us sum up4.4 Points for Discussion4.5 Check your Progress4.6 Lesson-end activities4.7 References


To know about mechanisms of transports and its branches of transports.

4.1Facilitated diffusion

A facilitated diffusionprotein speeds the movement of a chemical through a membranein the absence of energyinput; therefore, the transported chemical can only move down aconcentration gradient. This can be accomplished by the formation of a high-specificity

pore or channelthat spans the membrane.

4.2Active transport:

Transport proteins are also used in active transport, which by definition does require anenergy input. Chemiosmotic transport utilizes electrochemical gradients to drive

transport. As the creation and maintenance of chemiosmotic gradients require energyinput from the cell, this is a form of active transport. Prokaryotes typically use hydrogenions as the driving force for chemiosmotic transport, while eukaryotes typically usesodium ions. A symporter/ coportertransports a chemical in the same direction as theelectrochemical gradient, while an antiportermoves the target chemical in a directionopposite to the gradient.The uniporter is also often included as a category ofchemiosmotic transporter, although a uniporter can also be considered as a facilitateddiffusion protein on the basis of function.

Binding dependent active transport:Binding dependent active transport also moves thetargeted chemical against a concentration gradient, but uses stored chemical energy,

typically in the form of adenosine triphosphate, to power the transport. Generallyspeaking, a binding dependent transport system consists of a membrane spanningcomponent with a high degree of specifity. The membrane spanning component changesconfiguration with the aid of chemical energy input, thus translocating the chemical fromone side of the membrane to the other.

http://www.clicktoconvert.com/http://en.wikipedia.org/wiki/Adenosine_triphosphatehttp://en.wikipedia.org/wiki/Concentration_gradienthttp://en.wikipedia.org/wiki/Concentration_gradienthttp://en.wikipedia.org/wiki/Facilitated_diffusionhttp://en.wikipedia.org/wiki/Uniporterhttp://en.wikipedia.org/wiki/Antiporterhttp://en.wikipedia.org/wiki/Coporterhttp://en.wikipedia.org/wiki/Symporterhttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Hydrogen_ionhttp://en.wikipedia.org/wiki/Prokaryotehttp://en.wikipedia.org/w/index.php?title=Chemiosmotic&action=edithttp://en.wikipedia.org/wiki/Active_transporthttp://en.wikipedia.org/wiki/Concentration_gradienthttp://en.wikipedia.org/wiki/Energyhttp://en.wikipedia.org/wiki/Facilitated_diffusion


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Channels/Pores

o Voltage-gated ion channel like, including potassium channelsKcsA and KvAP, andinward-rectifier potassium ion channelKirbac

o Large-conductance mechanosensitive channel, MscLo

Small-conductance mechanosensitive ion channel (MscS)o CorA metal ion transporterso Ligand-gated ion channelof neurotransmitter receptors ( acetylcholine receptor)o Aquaporinso Chloride channelso Outer membrane auxiliary proteins (polysaccharide transporter)

ElectrochemicalPotential-driven transporters

o Mitochondrial carrier proteinso Major Facilitator Superfamily (Glycerol-3-hosphate transporter, Lactose permease,

and Multidrug transporter EmrD)o Resistance-nodulation-cell division (multidrug efflux transporter AcrB)o Dicarboxylate/amino acid:cation symporter (proton glutamate symporter)o Monovalent cation/proton antiporter (Sodium/proton antiporter 1 NhaA)o Neurotransmitter sodium symportero Ammonia transporterso Drug/Metabolite Transporter (small multidrug resistance transporter EmrE)

PrimaryActive Transporters

Light absorption-driven transporters:o

Bacteriorhodopsin- like proteins including rhodo

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