1-Basics of Cell Bio

8/13/2019 1-Basics of Cell Bio

1/16

Chapter One

Cell Biology Basics

1.1 INTRODUCTION

Cell biology (also called cellular biology or formerly cytology) is an discipline that studies cell's

physiological properties, structure, the organelles they contain, their interactions with their

environment, their life cycle, division and death.

1.2 CELL

The cell is the basic unit of organisation or structure of all living matter. The organism with only

one cell in their body are called unicellular organisms. The organism with many cells in their body

are called multicellular organisms. Any cellular organism may contain only any one type of cell

from the following type of cells :

ro!aryotic cells (pro" primitive or before # karyon" nucleus)

$u!aryotic cells (eu" well# karyon" nucleus)

COMPARISION BETWEEN PROKARYOTIC AND EUKARYOTIC CELLS

Characteristic Proar!otes E"ar!otes

Si#e o$ ce%% Typically %.&&.% m m in

diameter

Typically %%% m m in

diameter

"c%e"s do not have a welldefined

nucleus

True nucleus, consisting of

nuclear membrane * nucleoli

Me&'ra(e)e(c%ose*

or+a(e%%es

Absent resent# e+amples include

lysosomes, olgi comple+,

endoplasmic reticulum,

mitochondria * chloroplasts,%a+e%%a Consist of two protein building

bloc!s

Comple+# consist of multiple

microtubules

-%!coca%! resent as a capsule or slime

layer

resent in some cells that lac! a

cell wall

Ce%% /a%% -sually present# chemically

comple+

hen present, chemically

simple

P%as&a &e&'ra(e o carbohydrates and generally

lac!s sterols

/terols and carbohydrates that

serve as receptors present

C!to0%as& o cytos!eteton or cytoplasmic Cytos!eleton# cytoplasmic


2/16

streaming streaming

Ri'oso&es /ingle circular chromosome#

lac!s histones

0ultiple linear chromosomes

with histones

Chro&oso&e DNA

arra(+e&e(t

/ingle circular chromosome#

lac!s histones

0ultiple linear chromosomes

with histonesCe%% *i3isio( 1inary fission 0itosis

Se"a% re0ro*"ctio( o meiosis# transfer of 2A

fragments only (con3ugation)

4nvolves meiosis

1.4 OR-ANELLES AT A -LANCE

/tructure and function of the components of this basic organi5er in living organisms.

Na&e o$ Or+a(e%%e Ma5or ,"(ctio( Other i($or&atio( Et!&o%o+!

N"c%e"s Controls all cell

activities

6central part of a

thing7

N"c%eo%"s /ynthesi5es r8A and

assembles ribosomes

6little nut7

Chro&oso&es Controls heredity Composed of DNA a(*

0rotei(s

Chromatin a collection of

chromosomes

!hroma 9color9

soma 9body.9 /o

called because the

structures contain a

substance that

stains readily with

basic dyes.N"c%ear E(3e%o0e a(*

N"c%ear Pore Co&0%e

$ncloses the

nucleoplasm and

separates nucleus from

rest of the cell

2ouble membrane

0ade of lipids and proteins

Contains pores

Mitocho(*ria roduces energy

(AT) for the cell by

cellular

respiration

2ouble membrane structure

4nner folded membranes

are called cristae

Area surrounded by cristae

is called the &atri

mitos 9thread9

!hondrion 9little

granule.9

figure:1.3(diagram showing structure of prokaryotic and

eukaryotic cell


3/16

Ri'oso&es rotein synthesis Composed of r8A

;ree ribosomes those

suspended in cytosol

1ound ribosomes those

attached to $8

ribo(nucleic acid)

some 9body.9

E(*o0%as&ic

Retic"%e&

/mooth $8

. important in the

synthesis of lipids,

&. metabolism of

carbohydrates,


4/16

or! best at p= > some7body7

Ce%% Me&'ra(e Also !nown as a

plasma membrane, this

outer layer of a cell

assists in the

movement of

molecules in and out

the cell plays both a

structural and

protective role

Composed of &

phospholipid layers

and proteins

cella 9small room,

hut,9

membrane9parch

ment,9

Ce%% Wa%% A structure that

characteristically isfound in plants and

pro!aryotes and not

animals that plays a

structural and

protective role

Composed of cellulose and

lignin in eu!aryotic cells

cell9small

room,9wall7interior partition,7

Ce(trio%es 4mportant in cell

division

?ocated in pairs Composed

of microtubules.;ound only

in animal cells

from 6center7

Ci%ia a(* ,%a+e%%a . Cell movement

&. 0oves fluids over

surface of tissues

Composed of microtubules

C!tose%eto( /tructural support and

cell movement

Composed of microtubules,

intermediate filaments, and

microfilaments

1.7 BIOLO-ICAL ENER-Y

AT stands for Adenosine Trihosphate, and is the energy used by an organism in its daily

operations.

4t consists of an adenosine molecule and three inorganic phosphates. After a simple reaction

brea!ing down AT to A2, the energy released from the brea!ing of a molecular bond is

the energy we use to !eep ourselves alive.

8espiration is the usual manner in which cells convert food (glucose) into a AT.

figure 1.1:diagram showin plant or

animal


5/16

The form of respiration usually employed by cells is aerobic respiration. Aerobic respiration

re@uires o+ygen. There are three steps to aerobic respiration#

. lycolysis (where glucose is converted into a molecule !nown as pyruvate). This

produces a small amount of energy which is converted into AT.

&. The rebs cycle converts pyruvate into citrate, producing more AT.


6/16

Muntiacus reevesi (the Chinese munt3ac, a deer) &"e(ce. romoter se@uence instructs 8A polymerase from where to initiate synthesis of m8A

and in which direction it should continue.

8A polymerase then unwinds the 2A double heli+ at that point and begins synthesis of

8A strand complementary to one of the strand of 2A.

This strand is called antisense or template strand where as the other strand is called sense or

coding strand.

/ynthesis can then proceed in unidirectional manner.

rocessed eu!aryotic meassages contain 0o%!A a**itio( si+(a%(AA-AAA) at their


11/16

The cellular machinery that is responsible for synthesis of proteins is ri'oso&e.

8ibosome consist of >%/ smaller subunit and F%/ larger subunt.

The process of tra(s%ati(+m8A to protein begins when smaller subunit encounters the

larger subunit.

There are two sites in larger subunit for amino acid binding and thus be close enough to

each other to form a bond.

The 9A site9 accepts a new tra(s$er RNA, or tRNA &o%ec"%e or a*a0tor &o%ec"%e that

acts as a translator between m8A and protein bearing an aminoacid.

The 9P site9 binds the t8A that becomes attached to the growing chain.

$ach t8A has a specific acce0tor sitethat binds a particular triplet of nucleotides, called a

co*o(, and an a(ti)co*o( sitethat binds a se@uence of three unpaired nucleotides.

$ach t8A also has a specific char+er 0rotei(, called an a&i(oac!% tRNA s!(thetase.This protein can only bind to that particular t8A and attach the correct amino acid to the

acceptor site

The start si+(a%for translation is the codon AT, which codes for methionine.

A t8A charged with methionine binds to the translation start signal. The large subunit

binds to the m8A and the small subunit, and so begins e%o(+atio(, the formation of the

polypeptide chain.

After the first charged t8A appears in the A site, the ribosome shifts so that the t8A is

now in the site. ew charged t8As, corresponding the codons of the m8A, enter the A

site, and a bond is formed between the two amino acids.

The first t8A is now released, and the ribosome shifts again so that a t8A carrying two

amino acids is now in the site. A new charged t8A then binds to the A site.

This process of elongation continues until the ribosome reaches what is called a sto0 co*o(,

a triplet of nucleotides that signals the termination of translation.

A protein will often undergo further modification, called 0ost)tra(s%atio(a% &o*i$icatio(.

;or e+ample, it might be cleaved by a proteincutting en5yme, called a protease, at a specific

place or have a few of its amino acids altered.

------------------------------------------------------------------------------------

INPUTS FROM DR MATIN

1. RULES OF METABOLISM

There are several rules for metabolism.


12/16

0etabolism occurs in small steps to release energy in small, usable pac!ets. ;or e+ample,

consider sugar being converted to CB&. This releases a lot of energy, about >% times more

than is needed for any single anabolic conversion in the cell. /o if it happened in one step,

most of the energy released would be lost as heat. 4nstead, it happens in over D% steps, and

energy is released in about a do5en of them.

1ecause each metabolic conversion is determined by a gene, the pathways present in an

organism are genetically determined. ;or e+ample, bacteria have genes that code for

en5ymes that can ta!e the carbon, hydrogen, and o+ygen atoms in simple sugar and

rearrange them to ma!e ascorbic acid, vitamin C. e cant do this because we lac! the

en5ymes. Bther bacteria have the ability to ta!e cellulose from wood or paper and convert it

to sugar so they can use that for energy. Again, we lac! the gene (and en5yme) to do this. Bf

course, there are many things we can do that bacteria cant. The point is, &eta'o%is& &ea(s

0he(ot!0e? a(* this is *eter&i(e* '! +e(es.

2. W9Y IN BIOC9EMISTRY WE SAY T9AT REACTIONS ARE OCURRIN- IN

CYTOSOL@ a(* NOT CYTOPLASM

1ecause JCytoplasm consists of JBrganelles and the intracellular fluid (4C;)

or cytoplasmic matri+ called JCytosol. e !now that certain biochemical reaction occur

e+clusively in Brganelles li!e 0itochondria ( rebs cycle) ' and few occur in JCytosol(lycolysis ) , while few occur in both ( -rea cycle ) ./uppose we say that certain reaction

is occurring in JCytoplasm then we might get confused as to that Jparticular reaction is

occurring in JCytosol Jor 0itochondria A/ CITB?A/0 K CITB/B? B8A$??$/


13/16

4. RE6ERSE TRANSCRIPTION %he process of &everse %ranscription is a comple' one

(hich is very (ell illustrated in site at (((#med#sc#edu)*+,flash,hiv-ltr-fn#htmlas

animation )

The process by which 2A is synthesi5ed from an 8A template by means of the en5yme

reverse transcriptase.

8everse transcription begins when the viral particle enters the cytoplasm of a target cell. The

viral 8A genome enters the cytoplasm as part of a nucleoprotein comple+ that has not been

well characteri5ed. The process of reverse transcription generates, in the cytoplasm, a linear

2A duple+ via an intricate series of steps. This 2A is colinear with its 8A template, but

it contains terminal duplications !nown as the long terminal repeats (?T8s) that are not

present in viral 8A $+tant models for reverse transcription propose that two speciali5ed

template switches !nown as strandtransfer reactions or 63umps7 are re@uired to generate the?T8s.

8etroviral 2A synthesis is absolutely dependent on the two distinct en5ymatic activities of

8T: a 2A polymerase that can use either 8A or 2A as a template, and a nuclease,

termed ribonuclease = (8ase =), that is specific for the 8A strand of 8A:2A

duple+es. Although a role for other proteins cannot be ruled out, and it is li!ely that certain

viral proteins (e.g., nucleocapsid, C) increase the efficiency of reverse transcription, all of

the en5ymatic functions re@uired to complete the series of steps involved in the generationof a retroviral 2A can be attributed to either the 2A polymerase or the 8ase = of 8T

8everse Transcription can be bro!en down into the following steps :

A t8A primer binds to the primer binding site on the =4N 8A.

8everse Transcriptase (8T) starts at this binding site and copies 8A into a single strand of

complementary 2A. At this point it only copies from the primer binding site bac! into

the ?ong Term 8epeat (?T8) , so all that has been copied so far is the ?T8 plus a little

e+tra.

8ase = degrades the section of the 8A which has been copied.

This allows the t8A O 8T O ss2A to come dissociate from the =4N 8A , and then

reattach at the otherend of the stretch of 8A the fresh 2Acopy of one ?T8 associates

with the other ?T8.

8T then pic!s up where it left off, copying =4N's 8A genome into 2A. 8ase = again

3oins in, degrading the 8Aonce it's copied. 4t leaves one section of 8Aintact, a tiny

stretch called the polypurine tract. The polypurine tract lies about twothirds of the way

through the =4N enome .

8T starts to create the second strand of 2A it starts at the polypurine tract and ma!es asecond strand of 2A to complement the code in the first strand.
http://www.med.sc.edu:85/flash/hiv-ltr-fn.htmlhttp://www.mcld.co.uk/hiv/?q=DNAhttp://www.mcld.co.uk/hiv/?q=DNAhttp://www.mcld.co.uk/hiv/?q=RNAhttp://www.mcld.co.uk/hiv/?q=RNAhttp://www.med.sc.edu:85/flash/hiv-ltr-fn.htmlhttp://www.mcld.co.uk/hiv/?q=DNAhttp://www.mcld.co.uk/hiv/?q=RNAhttp://www.mcld.co.uk/hiv/?q=RNA


14/16

8ase = now removes all the remaining 8A the polypurine tract and the t8A primer

(which was until now still attached to one end of the fresh 2A).

The 2A circularises the two ends of the 2A are complementary and easily stic!

together to ma!e the 2A a loop.

8T finishes off its 3ob, completing the second strand of the 2A and also completing the?ong Term 8epeats at each end. 4n the process of this the 2A loop brea!s again, leaving

a doublestranded 2A fragment with a ?ong Term 8epeats at each end.

,i+ Ste0s o$ Re3erse Tra(scri0tio(

8. 9I6 -ENOME What is the *i$$ere(ce 'et/ee( 9I6)1 2 -e(o&e /ise

F

The full =4N genome is encoded on one long strand of 8A. (4n a free virus particle, there are

actually two separate strands of 8A , but they're e+actly the sameP)

This is the form it has when it is a free virus particle. hen the virus is integrated into the host's

2A genome (as pro virus ) then its information too is encoded in 2A.

The following image shows roughly how the genes are laid out in =4N (remember that =4N and

=4N & are @uite different).


15/16

%his diagram is based on a fantastic map of the H./-01 H./-21 and S./ genomes1 available at

hiv-(eb#lanl#gov,content,immunology,pdf,2333,intro,GenomeMaps#pdf

The genes in =4N's genome are as follows:

gag (coding for the viral capsid proteins)

pol (notably, coding for reverse transcriptase)

(1.gagandpoltogether can be e+pressed in one long strand called 9gagpol9)

env (coding for =4N's envelopeassociated proteins)

And the regulatory genes:

tat

rev

nef

vif

vpr

30" N.B. (ot 0rese(t i( 9I6)2 ))Di$$ere(ce 'et/ee( 9I6)1 2

30 N.B. (ot 0rese(t i( 9I6)1

The =4N genome also has a 9 ?ong Term 8epeat ( 9?T8) at each end of its genome not @uite a

gene, but a se@uence of8AO2A which is the same at either end and which serves some

structural and regulatory purposes.

LTR : The ?ong Terminal 8epeat is something which is often found in strands of 8A or 2A is

the ?ong Terminal 8epeat. At each end of the string is the same se@uence of code at each end of the

string. Almost li!e the repeat at the start and finish of these sentences, almost li!eP

There are two important functions for the ?T8:

;irstly they are 9stic!y ends9 (that's a biochemistry term) which the integraseprotein uses to

insert the =4N enome into host 2A .
http://hiv-web.lanl.gov/content/immunology/pdf/2000/intro/GenomeMaps.pdfhttp://www.mcld.co.uk/hiv/?q=gaghttp://www.mcld.co.uk/hiv/?q=gaghttp://www.mcld.co.uk/hiv/?q=polhttp://www.mcld.co.uk/hiv/?q=integrasehttp://www.mcld.co.uk/hiv/?q=integrasehttp://hiv-web.lanl.gov/content/immunology/pdf/2000/intro/GenomeMaps.pdfhttp://www.mcld.co.uk/hiv/?q=gaghttp://www.mcld.co.uk/hiv/?q=polhttp://www.mcld.co.uk/hiv/?q=integrase


16/16

/econdly, they act as promoterOenhancers when integrated into the host genome, they

influence the cell machinery which transcribes 2A,to alter the amount of transcription

which occurs. rotein binding sites in the ?T8 are involved with 8A initiation.

:. PLUS NE-ATI6E RNA 6IRUSES

lus(sense) 8A "the virus genome is the virus m8A

0inus (sense) 8A "the virus m8A is transcribed from the parental genome
http://www.mcld.co.uk/hiv/?q=DNAhttp://www.mcld.co.uk/hiv/?q=DNAhttp://www.mcld.co.uk/hiv/?q=DNA

Documents

1-Basics of Cell Bio