DC3 Cell Biology UII HT

8/3/2019 DC3 Cell Biology UII HT

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Introduction to DyeIntroduction to Dye

AA dye is a colored substance that has an affinity to theis a colored substance that has an affinity to the

substrate to which it is being applied. The dye issubstrate to which it is being applied. The dye is

generally applied in an aqueous solution, and maygenerally applied in an aqueous solution, and may

require a mordant to improve the fastness of the dyerequire a mordant to improve the fastness of the dyeon the fiber.on the fiber.

Chemical affinity is defined as electronic propertiesChemical affinity is defined as electronic properties

by which dissimilar chemical species are capable ofby which dissimilar chemical species are capable of

forming chemical compounds. It can also refer to theforming chemical compounds. It can also refer to thetendency of an atom or compound to combine bytendency of an atom or compound to combine by

chemical reaction with atoms or compounds of unlikechemical reaction with atoms or compounds of unlike

compositioncomposition


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Both dyes and pigments appear to be coloredBoth dyes and pigments appear to be colored

because they absorb some wavelengths of lightbecause they absorb some wavelengths of light

preferentially. In contrast with a dye, a pigmentpreferentially. In contrast with a dye, a pigment

generally is insoluble, and has no affinity forgenerally is insoluble, and has no affinity for

the substrate.the substrate.


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Classification of dyesClassification of dyes

Dyes are characterized by their ability to absorbDyes are characterized by their ability to absorb

visible light (400visible light (400--700 nm).700 nm).

Solids, liquids or gases can absorb light completely,Solids, liquids or gases can absorb light completely,

partially or not at all.partially or not at all. The part that is not absorbed can be reflected at theThe part that is not absorbed can be reflected at the

surface of solids, liquids or transmitted through gases.surface of solids, liquids or transmitted through gases.

The reflected light reaches the retina in human eyeThe reflected light reaches the retina in human eye

and goes through a series of photochemical reaction.and goes through a series of photochemical reaction.


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Dyes containDyes contain chromophoreschromophores andand auxochromesauxochromes

Chromophores

Chromophores refer to functional groupsrefer to functional groupswhich are unsaturated and they cause awhich are unsaturated and they cause a

compound to become coloured. Examples ofcompound to become coloured. Examples of

chromophoreschromophores areare N=NN=N--,,--C=CC=C--,,--C=NC=N--andand --

C=OC=O

AuxochromesAuxochromes are saturated functional groupsare saturated functional groups

and the presence of these groups in aand the presence of these groups in a

compound greatly increases the colorcompound greatly increases the color--yieldingyieldingpower of the compound.power of the compound.

Such asSuch as --NH3,NH3, --COOH,COOH, --OH andOH and NHR.NHR.


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The huge number of commercial dyes isThe huge number of commercial dyes is

classified in terms of structure, colour andclassified in terms of structure, colour andapplication according to Colour Index (C. I).application according to Colour Index (C. I).

Society ofD

yers andC

olourists and theSociety ofD

yers andC

olourists and theAmerican Association of Textile Chemists andAmerican Association of Textile Chemists and

Colourists are societies which are responsibleColourists are societies which are responsible

to revise Colour Index every three months.to revise Colour Index every three months.


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Acid dyes are anionic compounds that areare anionic compounds that are

used for dyeing nitrogenused for dyeing nitrogen--containing fiberscontaining fiberssuch as silk (contains about 250 mmol/kg ofsuch as silk (contains about 250 mmol/kg ofammonium groups), wool (contains about 850ammonium groups), wool (contains about 850mmol/kg of ammonium groups) and syntheticmmol/kg of ammonium groups) and synthetic

polyamides (contains about 30polyamides (contains about 30--50 mmol/kg of50 mmol/kg ofamino groups).amino groups).

The name ofThe name ofacid dyes refers to the dyeingrefers to the dyeingprocess, which means these dyes are applied toprocess, which means these dyes are applied towool, silk and polyamides using from neutralwool, silk and polyamides using from neutralto acidic solutions (pH 2to acidic solutions (pH 2--6). Most synthetic6). Most syntheticfood colours falls in this category.food colours falls in this category.


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Direct dyesDirect dyes are compounds that have a high affinityare compounds that have a high affinityfor cellulose fibers.for cellulose fibers.

Direct or substantive dyeing is normally carried out inis normally carried out ina neutral or slightly alkaline dyebath, at or neara neutral or slightly alkaline dyebath, at or near

boiling point, with the addition of either sodiumboiling point, with the addition of either sodium

chloride (NaC

l) or sodium sulfate (Na2SO

4).D

irectchloride (NaC

l) or sodium sulfate (Na2SO

4).D

irectdyes are used on cotton, paper, leather, wool, silk anddyes are used on cotton, paper, leather, wool, silk andnylon. They are also used as pH indicators and asnylon. They are also used as pH indicators and as

biological stains.biological stains.

During the dyeing process,During the dyeing process, van der Waals forces areareinvolvedinvolved -- cause the sorption of dyes to cellulosecause the sorption of dyes to cellulosefibers.fibers.


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Reactive dyesReactive dyes refer to the colouredrefer to the coloured

compounds with reactive group that form acompounds with reactive group that form acovalent bonds with OHcovalent bonds with OH--, NH, NH-- or SHor SH--groupsgroups

in fibers.in fibers.

The reactive group is usually with two labileThe reactive group is usually with two labilechloride or fluoride.chloride or fluoride.


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Metal complex dyesMetal complex dyes are dye compounds withare dye compounds with

metal atom. Usually metal atom that involvedmetal atom. Usually metal atom that involvedis chromium, copper or cobalt.is chromium, copper or cobalt.

They are normally 1:1 complexes (1 metalThey are normally 1:1 complexes (1 metalatom with 1 dye molecule) or 1:2 complexes (1atom with 1 dye molecule) or 1:2 complexes (1

metal atom with 2 dye molecules).metal atom with 2 dye molecules).

The addition of metal atom improves theThe addition of metal atom improves the

fastness properties of the dye compounds.fastness properties of the dye compounds.


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Basic dyeBasic dye is a class of dyes that contain basicis a class of dyes that contain basic

groups in their chemical structure. They aregroups in their chemical structure. They areused for dyeing acidused for dyeing acid--containing fibers.containing fibers.

Basic dyes are mainly used in paper industry,Basic dyes are mainly used in paper industry,printing industry, cosmetics industry and foodprinting industry, cosmetics industry and food

industry.industry.

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Cell organelles (1)

The nucleus is the largest organelle in the eukaryotic cell:

1020 m in diameter. It:

is surrounded by a double membrane, the nuclear

membrane, with many tiny pores

contains the chromosomes, visible only when the nucleusdivides, which are otherwise dispersed as chromatin

has a role in cell management.


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Mitochondria, rod-shaped organelles, are 0.51.5 m wide

and 310 m long. They:

have a double membrane, the inner one of which is infoldedto form cristae

have an interior, the matrix, containing a solution of

metabolites and enzymes

are the site of the aerobic stages of respiration

occur in very large numbers in metabolically active cells.


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Chloroplasts are biconvex in shape and about 23 m wide

and 410 m long. They:

are the site of photosynthesis, and most occur in themesophyll cells of leaves

have a double membrane

contain branching membranes called thylakoids, arranged

in flattened circular piles, the grana (with photosynthetic

pigments), and between, the stroma (loose membranes inan aqueous matrix).


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Cilia and flagella project from the surface of certain cells.

Cilia occur in large numbers; flagella mostly singly.

Structurally they consist ofmicrotubules enclosed in anextension of the plasma membrane.

Their microtubules are straight, unbranched, hollow cylinders

of protein, only 25 nm wide.

They can move, causing cell movement, e.g. of a sperm, or

movement of fluid across the cell surface, e.g. mucus along

the bronchial lining.


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the nucleus

the nucleus controls the cells activities and contains acytoplasm like substance called nucleoplasm

DNA is bound to proteins and is called

chromatin this condenses to form the

chromosomes during cell division

within the nucleus are 1 or 2

bodies each called a

nucleolus these make rRNA

and assemble ribosomes

the nuclear membrane is a double membrane

structure containing pores that allow the

transport of mRNA and nucleotides


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mitochondria

mitochondria are formed from 2

membranes separated by a narrow

inter-membrane space

the inner membrane is folded toincrease its surface area into

extensions called cristae

the biochemical reactions ofaerobic

respiration take place in themitochondria and they release

chemical energy in the form ofATP


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golgi body

the golgi body (or apparatus) was named after its discovererCamillo Golgi it is similar in structure to smooth ER but has a

more compact form

it is a collection of flattened membrane sacs that are

constantly forming on one side and budding off as vesicles onthe otherits functions are:

to package proteins for secretion

to secrete carbohydrates

to produce glycoproteins

to transport and store lipids

to form lysosomes


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lysosomes

lysosomes contain and isolate digestive enzymes

they are needed to prevent the rest of the cell being

digested by these enzymes

several lysosomes may empty their contents into

one membrane lined vacuole containing a worn out

organelle


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centrioles

centrioles arise from a region ofthe cytoplasm called the

centrosome and consist of 2

hollow cylinders

at cell division they migrate toopposite poles of the cell and

produce the microtubules of the

spindles that pull chromosomes

apart


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endoplasmic reticulum

the endoplasmic reticulum (ER) is an elaborate system ofmembrane bound sacs (cisternae) these are often

continuous with the nuclear envelope and the golgi body

rough endoplasmicreticulum (rER) has

ribosomes lining it

and is involved with

protein synthesis as

a transport system

smooth

endoplasmicreticulum (sER)

lacks

ribosomes it

is involved with

the synthesisand transport of

lipids


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ribosomes

ribosomes are involved in protein synthesis they move along molecules of mRNA and

read the nucleotide code to produce proteins

mRNA

U U U C G A U G C A U C G C A ACU C G C

aa1 aa2 aa3 aa4

C G U

aa5

U G A

aa6

ribosomes are made of rRNA

(produced by the nucleolus) andprotein they consist of one

large and one small sub-unit

large sub-unit

small sub-unit


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cytoplasm

the cytoplasm is the matrix that contains all of the differentorganelles

it is an aqueous mixture of chemicals either in solution or as

colloids including:

simple ions such as sodium (Na+) and chloride (Cl-)

organic molecules such as amino-acids, ATP and sugars

storage materials such as fat droplets

it can be seen to be moving this is called cytoplasmicstreaming


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proteins also totally penetrate

and appear on the inner and

outer surfaces of the

membrane

cell membrane

the main function of a cell membrane is to function as aboundary between the cell and its environment it

controls entry and exit into and from the cell

a phospholipidbilayerforms

the majority of

the membrane

this fluid-mosaic

model was proposed

in 1972 by J Singer

and G Nicholson


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plasmodesmata

there are gaps in the cell wall that allow

neighbouring cells to link together

there is a continuation ofcytoplasm from cell

to cell and the endoplasmic reticulum can

also be linked

cell 1

cell 2


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Cell seen by Light Microscope Cell seen by Electron

Microscope


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Microscopy

Three types:

Transmission Electron electrons transmitted through specimen

@ can see internal organelles

Scanning Electron electrons bounce off from surface of

specimen@ can see external features

Light Microscope Uses photons of white light

ElectronElectron

MicroscopeMicroscope

LightMicroscopeLightMicroscope

AdvantagesAdvantages High Resolution;High Resolution;

PP of electron smallof electron small

See Colour &See Colour &

Living CellsLiving Cells

DisadvantagesDisadvantages Dead Specimens &Dead Specimens &

B & W onlyB & W only

Low Resolution;Low Resolution;

PP of photons tooof photons too

largelarge


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Structure & Function Organelles found in Cells

(Eukaryotic)

Endoplasmic Reticulum (ER)

An internal transport system made of cavities about 4nm

All cavities interconnect, and interconnect with the NuclearMembrane

There are two types:

Rough ER Smooth ER

Flattened cavities * Tubular cavities

Encrusted with Ribosomes on the * Not

encrusted with cytoplasm side.

Ribosomes

Function:

Isolates & Transports Proteins Synthesis & Transport of

Lipids & Steroids


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Golgi Body

Series of flattened cavities, lying parallel to one another,having vesicles pinching of the ends of the cavities.

Function:Synthesis ofGlycoproteins

Packages Glycoproteins in membrane-bound

vesicles

Note: Cells actively involved in Glycoprotein Production

(enzymes), or actively involved in secretory function have large

prominent Golgi body


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Mitochondrion

In Animal Cells Rod Shaped, in Plant Cells,Round Shaped.

Bound by double membrane

1m in , 2.5m in length.

Inner Membrane highly folded to form a number of projections

called CRISTAE.

Function: Sites of Energy (ATP) Production; Site of Respiration.

Cells actively involved in functions requiring large amounts of

energy will have many mitochondria.


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Ribosomes

20nm in

Made in the Nucleolus, migrate to cytoplasm via nuclear

pores

Made up of 2 subunits of RNA

May be attached to ER or lie freely in cutoplasm.

May be in small clusters (called Polysomes)

Function: Sites of Protein Synthesis


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Nucleus

Usually Largest Organelle

Contains the Genetic Material, DNA which is attached to

Proteins called Histones

Surrounded by double membrane, called Nuclear Membrane.

When the cell is not dividing, genetic material appears as tiny

granules called Chromatin.

Function: Contains the Genetic Material@responsible for

protein synthesis, cell division etc.


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Lysosomes

Spherical Organelles 1 - 2.5m in

Contain enzymes (Hydrolases)

Function: Involved in Extracellular or Intracellular digestion,

can also cause Autolysis.


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Cilia / Flagella

Involved in movement

About 0.1 m in

Cilia, up to 1 m in length, flagella up to 10 m

Many cilia present, whereas, usually only 1 flagella

Eukaryotic cells have 9+2 microtuble structureProkaryotes have 9+0


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Cell / Plasma Membrane

Under the light microscope seen as two dark lines separated by a

lighter layer.

Middle lighter layer made up of a Phospholipid-Bilayer

Each Phospholipid has hydrophilic head and hydrophobic tails.

Heads point outwards (may have carbohydrates attached, Glycolipid),

tails interact with each other in the middle

Tails are long chains of hydrocarbons, and may have single or double

bonds, between carbon atoms.

Double bonds (Unsaturated), means tails kink, causing more gaps

between phospholipids, @ membrane is fluid

Proteins found throughout bilayer. Three types:Carrier Proteins span right through bi-layer, involved in transport

Extrinsic Proteins on outer surface, may have carbohydrates

attached (Glycoproteins)

Intrinsic Proteins on cytoplasm side


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Proteins can move in between the phospholipids.

Cholesterol also found in between the bi-layer, causes rigidity.

7.5nm width


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Ultrastructure of a Eukaryotic cell


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Smooth and RoughSmooth and Rough

Endoplasmic ReticulumEndoplasmic Reticulum


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Smooth Endoplasmic ReticulumSmooth Endoplasmic Reticulum

Smooth endoplasmic reticulum is a network of short,

continuous tubes througout the cytoplasm in which there

are no ribosomes on the membrane surfaces.


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Smooth Endoplasmic ReticulumSmooth Endoplasmic Reticulum

It functions to:

package material for transport to the Golgi apparatus

synthesize lipids (fats) and derivatives

detoxify drugs or foreign proteins, particularly in the liver

compartmentalise cellular components


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Rough Endoplasmic RecticulumRough Endoplasmic Recticulum

Rough endoplasmic reticulum is a type of endoplasmic

reticulum in which the membrane-lined cavities are covered

with ribosomes.

The ribosomes are attached to the outer surface of the rER

by specialized protein receptors.


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Rough Endoplasmic RecticulumRough Endoplasmic Recticulum

The rER functions to: produce and compartmentalise proteins, lipids and othercellular constituents.

Polypeptide chains are manufactured at the ribosome and

then are either:set free for passage into the cytoplasm

incorporated into the membrane of the rER for furtherpackaging into plasma membrane or membrane or organellesthroughout the body

extruded into the cisternal space of the rER for laterpackaging into organelles e.g. lysosome, or extracellularsecretionThere are a number of non-ribosomal proteins in the membraneof the rER which are involved in further processing molecules


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Mitosis

Cell

Nucleus

Mitosis is the formation

of two new IDENTICAL

daughter cells from an

original cell.It is how organisms

growand is also the

basis of simpleAsexual

reproduction.

The interesting stuffhappens In the nucleus.


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Nucleus

The nucleus of all

ordinary somatic (body)

cells contains

chromosomes.

In diploid organisms (like us)

there are two copies of

each chromosome.

In human body cells there are

23 pairs of chromosomesmaking a total of 46

chromosomes.


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However - The

DNA is replicated

during this phase

Most of the cells life

is NOT mitosis.

All these othersections are

generally

referred to as

INTERPHASE

DC3 Cell Biology UII HT

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