CHAPTER-I INTRODUCTION TO BIOCHEMISTRY CELL AND ITS

30000_7Introduction_To_Biochemistry.pdf

CHAPTER-I

INTRODUCTION TO BIOCHEMISTRY

CELL AND IT'S ORGANIZATION

The cell is the basic structural and functional unit of all known living organisms. It is the

smallest unit of life that is classified as a living thing, and is often called the building block of

life. Organisms can be classified as unicellular (consisting of a single cell; including most bacteria) or multicellular (including plants and animals). Humans contain about 10 trillion (1013 ) cells. Most plant and animal cells are between 1 and 100 µm and therefore are visible only under the microscope. The cell was discovered by Robert Hooke in 1665. The cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that all cells come from preexisting cells, that vital functions of an organism occur within cells, and that all cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells.

TYPES OF CELLS

There are two types of cells: eukaryotic and prokaryotic The prokaryote cell is simpler, and therefore smaller, than a eukaryote cell, lacking a nucleus and most of the other organelles of eukaryotes.

SUBCELLULAR COMPONENTS

All cells, whether prokaryotic or eukaryotic, have a membrane that envelops the cell, separates its interior from its environment, regulates what moves in and out (selectively permeable), and maintains the electric potential of the cell. Inside the membrane, a salty cytoplasm takes up most of the cell volume. All cells possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build various proteins such as enzymes, the cell's primary machinery. There are also other kinds of biomolecules in cells. This article lists these primary components of the cell, then briefly describe their function.

MEMBRANE

The cytoplasm of a cell is surrounded by a cell membrane or plasma membrane. The plasma membrane in plants and prokaryotes is usually covered by a cell wall. This membrane serves to separate and protect a cell from its surrounding environment and is made mostly from a double layer of lipids (hydrophobic fat-like molecules) and hydrophilic phosphorus molecules. Hence, the layer is called a phospholipid bilayer. It may also be called a fluid mosaic membrane. Embedded within this membrane is a variety of protein molecules that act as channels and pumps that move different molecules into and out of the cell. The membrane is said to be 'semi- permeable', in that it can either let a substance ( molecule or ion) pass through freely, pass through to a limited extent or not pass through at all. Cell surface membranes also contain receptor proteins that allow cells to detect external signaling molecules such as hormones

CYTOSKKELETON

The cyt

o helps du separatio and mob filaments controllin cytoskele cytokines

GENETI

Two diff

(RNA). M retroviru organis m (e.g., mR genetic c translatio

Prokaryo

chromoso different, genetic m

A human

mitochon of linear molecul e compared productio

Foreign g

by a proc genome, ORGA N

The hum

organ pe that are a and prok and may oskeleton ac uring endocy on of daughte bility. The s and micro ng a cell's eton is less sis.

IC MATERI

ferent kinds

Most organis

ses ) have R m is encoded

RNA) and en

code itself. T on. otic genetic ome) in the n , linear mole material in so n cell has ge ndria (the mi

DNA mole

e distinct fr d to nuclear on and speci genetic mate cess called t or stable, if

NELLES

man body con rforming a d adapted and/ karyotic cells be membran cts to organi ytosis, the er cells after eukaryotic otubules. Th structure by well-studied IAL of genetic m sms use DNA

RNA as their

d in its DNA nzymatic fun

Transfer RNA

material is nucleoid reg ecules called ome organel enetic materi itochondrial ecules called rom the nuc r chromosom ific tRNAs. erial (most c transfection. fit is. Certain ntains many different fun /or specializ s have organ ne bound. ize and mai uptake of e r cell divisio cytoskeleto n here is a gre y directing, d but is invo material exist

A for their lo

r genetic m

A or RNA se

nctions (e.g.,

A (tRNA) m

organized gion of the cy d chromosom les like mito ial contained genome). In d chromosom clear DNA. mes, it code commonly D This can be n viruses als different o r nction. Cells ed for carry nelles but or intain the ce external ma n; and move n is com eat number bundling, a olved in the ell's shape; aterials by a es parts of th mposed of m of proteins and aligning maintenanc anchors org a cell, and he cell in pro microfilamen associated g filaments. ce of cell sh ganelles in p cytokinesis ocesses of gr nts, interme with them,

The proka

r ape, polarity place; s, the rowth ediate each ryotic y and t: deoxyribo ong-term inf material. The equence. RN , ribosomal R molecules are nucleic acid formation sto biological

NA is also us

RNA) in org

e used to ad d (DNA) and orage, but so information sed for infor ganisms that d amino aci d d ribonucleic ome viruses n contained rmation tran use DNA fo ds during pr c acid (e.g., in an nsport or the rotein in a simpl e ytoplasm. Eu mes inside a ochondria an e circular D ukaryotic ge discrete nuc nd .

DNA molecu

enetic materi cleus, usuall ule (the bac ial is divided ly with addit cterial d into tional d in the cell n humans the mes. The m Although es for 13 pro nucleus (the e nuclear gen mitochondrial the mitocho oteins involv e nuclear gen nome is divi l genome is ondrial DNA ved in mito nome) and i ided into 23 a circular D

A is very s

chondrial en in the pairs DNA small nergy

DNA) can al

e transient, i o insert their lso be artific if the DNA r genetic ma cially introdu is not insert aterial into th uced into the ted into the he genome e cell cell's rgans, such a s also have a ing out one rganelles in as the heart, a set of "littl or more vita eukaryotes lung, and k le organs," c al functions. are generall kidney, with called organ . Both eukar ly more com each nelles, ryotic mplex

There are

are typic numerou surround e several typ cally solitary us (hundreds ds the organe pes of organ y, while othe s to thousan elles. nelles in a c ers (such as nds). The cy ell. Some (s s mitochondr ytosol is the such as the n ria, peroxiso e gelatinous nucleus and omes and ly fluid that f golgi appar ysosomes) ca fills the cell ratus) an be l and Diagra mm of a cell nnucleus C co th nu nu m D R in w th

Cell nucleus

onspicuous o he place whe ucleus is sph uclear envel molecules tha

During proce

RNA (mRNA

nto a specific where ribosom he cytoplasm - eukaryote organelle fou ere almost al herical and lope. The nu at could acc essing, DNA

A). This mRN

c protein mo me subunits m. es only - A c und in a euk ll DNA repli separated fr uclear envelo cidentally da

A is transcrib

RNA is then

olecule. The s are assemb cell's inform karyotic cell. ication and R rom the cyto ope isolates amage its st bed, or copie transported e nucleolus i bled. In prok mation center . It houses th

RNA synthe

oplasm by a and protec t tructure or i ed into a spe out of the n s a specializ karyotes, DN r, the cell nu he cell's chro esis (transcrip double mem ts a cell's DN interfere wit ecial RNA, c nucleus, whe zed region w

NA processin

ucleus is the omosomes, a ption) occur mbrane calle

NA from va

th its proces called messe ere it is trans within the nu ng takes pla most and is r. The ed the arious ssing. enger slated ucleus ace in M ar cy th u g i n

Mitochondri

re self-repli ytoplasm of he eukaryoti sing oxyge n lucose) to g n the cell mit ia and Chlo cating orga n fall eukaryot c cell. Mitoc n to release enerate ATP tochondria. roplasts - e nelles that o tic cells. Mit chondria gen e energy st

P. Mitochon

eukaryotes on occur in var tochondria p nerate the ce tored in cel ndria multipl nly - the pow rious numbe play a critica ell's energy b llular nutrie y by splittin wer generato ers, shapes, al role in gen by oxidative ents (typical ng in two. R ors: Mitocho and sizes in nerating ener phosphoryla lly pertainin

Respiration o

ondria n the rgy in ation, ng to ccurs

Diagra

mm of an endoomembrane system E tr d f o cy se

Endoplasmic

ransport net estinations, orms: the ro ytoplasm, an equestration c reticulum twork for as compare d ough ER, wh nd the smoo and release m - eukaryo molecules d to molecul hich has ribo oth ER, whi . otes only: T targeted fo les that float osomes on i ich lacks the

The endopla

or certain freely in th e its surface a em. Smooth asmic reticul modification e cytoplasm. and secretes h ER plays a lum (ER) i ns and spe . The ER ha proteins in t a role in cal s the ecific s two to the lcium G pr by

Golgi appara

rocess and p y the cell. atus - euka package the aryotes only macromole c : The prima cules such a ary function s proteins a n of the Golg nd lipids tha gi apparatus at are synthe is to esized R co to b m

Ribosomes: T

onsist of two o synthesise ound to a m membrane in

The ribosom

o subunits, a proteins fro membrane ( prokaryotes me is a large and act as an m amino aci (the rough e s). complex o f n assembly li ids. Ribosom endoplasmat f RNA and p ine where R mes can be f tic reticulum protein mole

RNA from th

found either m in eukary ecules. They he nucleus is floating fre e yotes, or the each used ely or e cell L (a v c e b

Lysosomes a

acid hydrola iruses or ba ell could not ound system and Peroxis ases). They d acteria. Perox t house these m. omes - eu k digest excess xisomes hav e destructive karyotes only s or worn-ou ve enzymes e enzymes if y: Lysosome ut organelles that rid the f they were n es contain di , food partic cell of toxi not contained igestive enz cles, and eng ic peroxides d in a memb ymes gulfed . The brane- C a t h ce pr

Centrosome

cell - a ke y he Golgi app ell division resent in the - the cytosk y component paratus. Cent and help in e animal cell keleton orga t of the cyto trosomes are n the format s. They are a aniser: The c oskeleton. It e composed tion of the m also found in centrosome p directs the t of two centr mitotic spin n some fung produces the transport thr rioles, which ndle. A sing gi and algae c e microtubul rough the ER h separate d gle centrosom cells. les of

R and

during me is V o m th p

Vacuoles: Va

ften describ most notably here is too m lants than an acuoles stor bed as liquid

Amoeba

, ha much water. nimals. re food and d filled spac ave contracti

The vacuol

waste. Som ce and are s ile vacuoles, les of eukary me vacuoles urrounded b , which can yotic cells a store extra by a membr pump water are usually l water. They rane. Some r out of the c larger in tho y are cells, cell if ose of

THE BI

OOLOGICALL MEMBRRANE

Cross se

cction view of the structuures that can be formed bby phospholiipids in aqueeous solutionns

A biolo

g selective may co n confused membran gical membr barrier, with nstitute close d with isola nes. rane or biom hin or aroun e to 50% o ating tissues membrane i nd a cell. It co of membran s formed by is an enclosi onsists of a l ne content. T y layers of ng or separ a lipid bilayer

The cellular

fcells, such ating membr r with embed r membrane h as mucou rane that acts dded protein es should no us and base s as a s that ot be ement

Functio

nn

Membra

n maintain membra n separates and are c nes in cells a chemical ne around pe s a cell from called "memb s typically d or biochem eroxisomes s m its surroun brane-bound define enclo mical environ shields the re nding medium d" organelles osed spaces nment that di est of the cel m. Most org s. or compa r iffers from t ll from perox ganelles are rtments in w the outside. xides, and th defined by s which cells

For exampl

e he cell memb such membr may e, the brane ranes,

Probabl

y structure molecul e permeabi

Biologica

y the most i . This mean es attemptin ility is essen al membrane important fe ns that the g to cross i ntial for eff es also have eature of a size, charg e it will deter fective separ certain mec biomembran e, and other rmine wheth ration of a chanical or e ne is that it r chemical p her they suc cell or orga lastic proper t is a select properties o cceed in doi anelle from rties. tively perm of the atoms ing so. Sele its surround meable s and ective dings.

Particles

enter thr o that are requ ough a mem uired for cel mbrane transp llular functio port protein o on but are un or are taken nable to diffu in by means use freely ac s of endocyto cross a memb osis. brane

TRANSPORT ACROSS THE BIOLOGICAL MEMBRANE

Passive diffusion-movement of solute along the concentration gradient Facilitated diffusion-movement of solute along the conc gradient with the help of carrier proteins Active transport-movement of solute against the conc gradient with the utilization of energy in the form of ATP

TRANSPORT MODES

Uniport Symport Cotransport Antiport

TRANSPORT OF MACROMOECULES

Endocytosis Exocytosis

HIGH ENERGY COMPOUNDS

High-energy phosphate can mean one of two things: The phosphate-phosphate bonds formed when compounds such as adenosine diphosphate and adenosine triphosphate are created. The compounds that contain these bonds, which include the nucleoside diphosphates and nucleoside triphosphates, and the high-energy storage compounds of the muscle, the phosphagens. When people speak of a high-energy phosphate pool, they speak of the total concentration of these compounds with these high-energy bonds. High-energy phosphate bonds are pyrophosphate bonds, acid anhydride linkages, formed by taking phosphoric acid derivatives and dehydrating them. As a consequence, the hydrolysis of these bonds is exergonic under physiological conditions, releasing energy. Energy released by high energy phosphate reactions

Reaction ǻG [kJ/mol]

ATP + H

2

O ĺ ADP + P

i -36.8

ADP + H

2

O ĺ AMP + P

i -36.0

ATP + H

2

O ĺ AMP + PP

i -40.6 PP i + H 2 O

AMP + H

Except

f human c completi pr co dr

The one

to effect i PP i being two step

ATP by

t glycolysi

Often, hi

ATP bec

proposed special n

ATP is

o high-ener bonds in above. L having a

Lipman

n respect t directly t breaking free ene r products

Adenosi

n for PP i ĺ 2 cell but are on. Thus, hi rovide energ ouple proces rive the reac exception is ively supply g allowed to s, with the the usual me is. igh-energy p comes A-P~P d ATP as th ature of thes often called a rgy bonds. T the sense th

Lipmann's te

high phosph n's squiggle o these bon to the break of any bond rgy change c relative to th ne triphosp

O ĺ 2 P

i H 2

O ĺ A + P

2 P i , these re e instead co gh-energy p gy to cellular sses to a part ction to the r s of value be y the energy go to com p equilibrium eans, oxidati phosphate bo

P~P. The squ

he main ene se bonds. a high energ

There is not

hat free ener erm "high-en hate group t did much to nds can be m king of the d, is an ende comes instea he reactants hate eactions are oupled to o hosphate rea r processes, ticular nucle right, by taki ecause it allo of hydrolys pletion in a s reaction AT ive phosphor onds are den uiggle notat ergy transfer gy compoun thing special rgy is releas nergy bond" transfer pote o stimulate i misleading, b bonds them ergonic step ad from the i . P i -31.8 -12.6 e, in general other proces actions can: l, not allowe sses needing ed to go un g energy to ncontrolled i o drive them n the m to allowing th e eoside, allow em to run ing a reversi wing for regu ows a single sis of two hi separate reac

TP + AMP

rylation or o noted by the ion was inv e r molecule nd and its ph l about the b sed when th " and his sy ential are viv interest in bi because the mselves. The (i.e., it abso ncreased res ble process ulatory contr hydrolysis, igh-energy b ction. The A

ļ 2ADP,

other energy character ' ~ ented by Fri of the cell, hosphoanhyd bonds thems ey are hydro ymbol ~P (s vid, concise, ioenergetics negative fre e breaking orbs energy, sonance stab and making rol of the pro it irreversib ocess le.

ATP + 2H

2 O bonds, with

AMP is regen

followed by -producing p

O ĺ AMP +

the hydrolys nerated to AT y regeneratio pathways su + PP i , sis of

TP in

on of uch as ~'. In this "sq itz Albert Li in 1941. I t quiggle" nota pmann , who t emphasize ation, o first es the dride bonds a selves. They olyzed, for t squiggle P) and useful s.The term 'h ee energy ch of these bo not releases bilization and are referred y are high-en the reasons g for a comp notations. In high energy' hange is no nds, as wit h it). The neg d solvation o to as nergy given pound n fact with t due h the gative of the Adenosine-5'-triphosphate (ATP) is a multifunctional nucleoside triphosphate used in cells as a coenzyme . It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism. It is one of the end products of photophosphorylation and cellular respiration and used by enzymes and structural proteins in many cellular processes, including biosynthetic reactions, motility, and cell division. One molecule of ATP contains three phosphate groups, and it is produced by ATP synthase from inorganic phosphate and adenosine diphosphate (ADP) or adenosine monophosphate (AMP). The three main ways of ATP synthesis are substrate level phosphorylation, oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis. Cyclic adenosine monophosphate (cAMP, cyclicAMP or 3'-5'-cyclic adenosine monophosphate) is a second messenger important in many biological processes. cAMP is derived from adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway

K.ANITA PRIYADHARSHINI

LECTURER

DEPT.OF PHARMACEUTICAL CHEMISTRY

SRM COLLEGE OF PHARMACY