Cellular Biochemistry

UNIT- 2

B.Sc Biochemistry II

Ultra structure of cell Ultrastructure (or ultra-structure) is the

nanostructure of a biological specimen, such as a cell,tissue, or organ, at scales smaller than can be viewedwith light microscopy. It is viewed with ultramicroscopy or electron microscopy.

Such cellular structures as organelles, which allow thecell to function properly within its specifiedenvironment, can be examined at the ultrastructurallevel.

CELL: The cell is the living functional unit of all organisms.

An organism may be composed of one cell only (Unicellular) e.g. Bacteria and Algae or of several cells (Multicellular) e.g. Man. The cell exists in two forms:

1.Eukaryotic cell, which has a nucleus that is enclosed in a nuclear envelope and several membrane- limited compartments e.g. the human cell.

2.Prokaryotic cell which has no nucleus and is devoid of membrane-limited compartments e.g. the bacterial cell.

NUCLEUS This is the largest organelle of the cell often located in

the central part of the cytoplasm and enclosed in a double-layered nuclear membrane. Its shape usually corresponds to the shape of the cell in which it is found.

It contains a nucleolus/nucleoli (which produces ribosomal subunits) and chromatin (DNA).

The latter is the genetic material implicated in cell division and in the synthesis of several molecules particularly proteins.

The contents of thenucleus are present as aviscous, amorphousmass of materialenclosed by a complexnuclear envelope thatforms a boundarybetween the nucleusand cytoplasm.

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Included within the nucleus of a typical interphase (i.e.,nonmitotic)cell are:(1) the chromosomes, which are present as highly

extended nucleoprotein fibers, termed chromatin;

(2) one or more nucleoli, which are irregularly shaped electron-dense structures that function in the synthesis of ribosomal RNA and the assembly of ribosomes

(3) the nucleoplasm, the fluid substance in which the solutes of the nucleus are dissolved; and

(4) the nuclear matrix, which is a protein-containing fibrillar network.

Nuclear Envelope

Double membrane surrounding nucleus

Also called nuclear membrane

Contains nuclear pores for materials to enter & leave nucleus

Connected to the rough ER

Nuclear pores

The Nuclear Envelope The separation of a cell’s genetic material from the

surrounding cytoplasm may be the single most important feature that distinguishes eukaryotes from prokaryotes, which makes the appearance of the nuclear envelope a landmark in biological evolution.

The nuclear envelope consists of two cellular membranes arranged parallel to one another and separated by 10 to 50 nm

The membranes of the nuclear envelope serve as a barrier that keeps ions, solutes, and macromolecules from passing freely between the nucleus and cytoplasm.

The two membranes are fused at sites forming circular pores that contain complex assemblies of proteins. The average mammalian cell contains several thousand nuclear pores.

The Structure of the Nuclear Pore Complex and Its Role inNucleocytoplasmic Exchange

The nuclear envelope is the barrierbetween the nucleus and cytoplasm,and nuclear pores are the gatewaysacross that barrier. Unlike the plasmamembrane, which prevents passage ofmacromolecules between thecytoplasm and the extracellular space,the nuclear envelope is a hub of activityfor the movement of RNAs and proteinsin both directions between the nucleusand cytoplasm.

The replication and transcription ofgenetic material within the nucleusrequire the participation of largenumbers of proteins that aresynthesized in the cytoplasm andtransported across the nuclearenvelope.

Inside the Nucleus -The genetic material (DNA) is found

DNA is spread out And appears as CHROMATINin non-dividing cells

DNA is condensed & wrapped around proteins forming as CHROMOSOMES in dividing cells

What Does DNA do?DNA is the hereditary

material of the cell

Genes that make up the DNA molecule code for different proteins

Mitochondria

Mitochondria are membrane-bound enzyme storage organelles. Mitochondrial enzymes are involved in aerobic respiration, production of ATP and heat energy for maintenance of body temperature.

The mitochondrion is enclosed in two sheets of membrane. An outer sieve-like unfolded membrane and an inner membrane which is thrown into long finger-like folds called cristae.

The number of cristae corresponds to the cell’s energy needs. The space between the two membranes is the intermembranous space while the space deep to the inner membrane is referred to as the matrix.

The Matrix also contains chromosomes DNA, ribosomes, messenger RNA and Transfer RNA which are utilized in the synthesis of small amount of proteins for use within the matrix.

However the bulk of the proteins required in the mitochondrion is synthesised in the cytosol. The mitochondrial matrix also contains granules which store calcium ions.

The mitochondrion produces about 100 molecules of ATP per second.

Mitochondrion(plural = mitochondria)

“Powerhouse” of the cell

Generate cellular energy (ATP)

More active cells like muscle cells have MORE mitochondria

Both plants & animal cells have mitochondria

Site of CELLULAR RESPIRATION (burning glucose) 2

MITOCHONDRIASurrounded by a DOUBLE

membrane

Folded inner membrane called CRISTAE(increases surface areafor more chemical Reactions)

Has its own DNA

Interior called MATRIX

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Interesting Fact --- Mitochondria Come

from cytoplasm in the EGG cell during fertilization

Therefore …

You inherit your mitochondria from your mother!

Muscle tissues are most commonly affected by mitochondrial deficiency diseases because of their high-energy metabolism.

Most mitochondrial diseases often result from chromosomal defect in the nucleus or in the mitochondrion.

Hereditary mitochondrial diseases are usually maternal in origin because only very few paternal mitochondria are left in the zygote following fertilization.

Rod shape

Cell Powerhouse

Mitochondrion( mitochondria )

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THE ENDOPLASMIC RETICULUM (ER)

This organelle is made up of anastomosing network of intercommunicating channels/cisternae/sacs enclosed in a continuous membrane.

ER occurs in two forms, namely Rough and Smooth which are also interconnected. While the cisternae of smooth ER are tubular in shape, those of Rough ER are flattened. The roughness on the surface of rough ER is due to the adsorption of polyribosome on their outer surface.

Polyribosome also impacts the basophilic staining characteristic on RER. Furthermore, its membrane is continuous with that of the nuclear envelope.

Distribution and Functions of RER

RER is prominent in protein synthesising cells such as; Pancreatic acinarcells, cells of the endocrine glands, plasma cells, fibroblast etc.

Proteins synthesised in RER are stored in Lysosomes or granules; stored temporarily before exocytosis or used as integral membrane proteins.

Smooth Endoplasmic Reticulum (SER)

This is ER not bund to polyribosomes but continuous with RER and are less abundant is cell containing RER.

Distribution and Functions of SER

SER is found in all cells where they are involved in: ‘The synthesis phospholipids and cholesterol used in all cellular membranes including membranes of organelles.

They occur in abundance in other cells where they are involved in: Sequestration and release of Calcium ions a vital process in muscular contraction Biosynthesis of Lipids required for synthesis of steroid hormones

Detoxification of potentially harmful compounds such as alcohol and barbiturates

RIBOSOMES Ribosomes are small,

electron-dense particles not enclosed in membrane and are located in the cytosol.

Measuring about 20-30 nanometer they are basophilic and stained by all basic dyes.

Ribosome is composed of rRNA and about 80 different proteins. It usually occur in two subunits, large and small subunits.

The rRNA of the ribosome is synthesised in the nucleus while its protein is synthesised in the cytosol.

Ribosomes are involved in protein synthesis. While cytosolic proteins (free proteins) are synthesised by polyribosomes, secretory and endoplasmic reticulum proteins are synthesised on the membrane of rough endoplasmic reticulum.

THE CYTOPLASM

The fluid component of the cytoplasm is the Cytosol(pH 7.2) while the metabolically active contents of the cytoplasm are the Organelles.

Apart from being metabolically active, organelles are permanent residents of the cell which would survive cell division i.e. they reappear in the daughter cells following cell division.

Organelles occur in two forms, freely within the cytosol or enclosed in membrane. The cytoplasm also contains substances which are not metabolically active.

• Jelly-like substance enclosed by cell membrane

• Provides a medium for chemical reactionsto take place

Cytoplasm of a Cell

cytoplasm

• Contains organelles to carry out specific jobs

• Found in ALL cells

More on Cytoplasm

cytoplasm

Chloroplasts Chloroplasts are large green organelles that are found

only in the cells of plants and algae, not in the cells of animals or fungi.

These organelles have an even more complex structure than mitochondria: in addition to their two surrounding membranes, chloroplasts possess internal stacks of membranes containing the green pigment chlorophyll

When a plant is kept in the dark, its greenness fades; when put back in the light, its greenness returns. This suggests that the chlorophyll—and the chloroplasts that contain it

Animals and plants all need energy to live, grow, and reproduce.

Animals can use only the chemical energy they obtain by feeding on the products of other living things. But plants can get their energy directly from sunlight, and chloroplasts are the organelles that enable them to do so. From the standpoint of life on Earth, chloroplasts carry out an even more essential task than mitochondria: they perform photosynthesis—that is, they trap the energy of sunlight in chlorophyll molecules and use this energy to drive the manufacture of energy-rich sugar molecules.

In the process they release oxygen as a molecular by-product.

Plant cells can then extract this stored chemical energy when they need it, by oxidizing these sugars in their mitochondria, just as animal cells can. Chloroplasts thus generate both the food molecules and the oxygen that all mitochondria use.

Chloroplasts Found only in producers

(organisms containing chlorophyll)

Use energy from sunlight to make own food (glucose)

Energy from sun stored in the Chemical Bonds of Sugars

Chloroplasts Surrounded by DOUBLE

membrane

Outer membrane smooth

Inner membrane modified into sacs called Thylakoids

Thylakoids in stacks called Grana & interconnected

Stroma – gel like material surrounding thylakoids

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Like mitochondria, they are surrounded by two membranes, an outer membrane that is permeable to small molecules and ions, and an inner membrane that encloses the internal compartment.

This compartment contains many flattened, membrane-surrounded vesicles or sacs, the thylakoids, usually arranged in stacks called grana.

Embedded in the thylakoid membranes (commonly called lamellae) are the photosynthetic pigments and the enzyme complexes that carry out the light reactions and ATP synthesis.

The stroma (the aqueous phase enclosed by the inner membrane) contains most of the enzymes required for the carbon assimilation reactions.

Chloroplasts

Contains its own DNA

Contains enzymes & pigments for Photosynthesis

Never in animal or bacterial cells

Photosynthesis – food making process

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Cytoskeleton Helps cell maintain cell

shape

Also help move organellesaround

Made of proteins

Microfilaments are threadlike & made of ACTIN

Microtubules are tubelike& made of TUBULIN

Centrioles

Found only in animal cells

Paired structures near nucleus

Made of bundle of microtubules

Appear during cell division forming mitotic spindle

Help to pull chromosome pairs apart to opposite ends of the cell

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Golgi Bodies

Look like a stack of pancakes

Modify, sort, & package

molecules from ER

for storage OR transport out of cell

Golgi Animation

Materials are transported from Rough ER to Golgi to the cell membrane by VESICLES

Lysosomes• Contain digestive

enzymes

• Break down food, bacteria, and worn out cell parts for cells

• Programmed for cell death (AUTOLYSIS)

• Lyse (break open) & release enzymes to break down & recycle cell parts)

Lysosome Digestion

• Cells take in food by phagocytosis

• Lysosomes digest the food & get rid of wastes

Cilia & Flagella:

Made of protein tubes called microtubules

Microtubules arranged (9 + 2 arrangement)

Function in moving cells, in moving fluids, or in small particles across the cell surface

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Cilia & Flagella

Cilia are shorter and more numerous on cells

Flagella are longer and fewer (usually 1-3) on cells

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Vacuoles

Fluid filled sacks for

storage

Small or absent in

animal cells

Plant cells have a

large Central

Vacuole

No vacuoles in

bacterial cells

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Vacuoles

In plants, they store Cell Sap

Includes storage of sugars,proteins, minerals, lipids,wastes, salts, water, andenzymes

Contractile Vacuole

Found in unicellular protists like paramecia

Regulate water intake by pumping out excess (homeostasis)

Keeps the cell from lysing (bursting)

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Contractile vacuole animation

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Chloroplasts Found only in producers

(organisms containing chlorophyll)

Use energy from sunlight to make own food (glucose)

Energy from sun stored in the Chemical Bonds of Sugars

Chloroplasts Surrounded by DOUBLE

membrane

Outer membrane smooth

Inner membrane modified into sacs called Thylakoids

Thylakoids in stacks called Grana & interconnected

Stroma – gel like material surrounding thylakoids

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Like mitochondria, they are surrounded by two membranes, an outer membrane that is permeable to small molecules and ions, and an inner membrane that encloses the internal compartment.

This compartment contains many flattened, membrane-surrounded vesicles or sacs, the thylakoids, usually arranged in stacks called grana.

Embedded in the thylakoid membranes (commonly called lamellae) are the photosynthetic pigments and the enzyme complexes that carry out the light reactions and ATP synthesis.

The stroma (the aqueous phase enclosed by the inner membrane) contains most of the enzymes required for the carbon assimilation reactions.

Chloroplasts:

Contains its own DNA

Contains enzymes & pigments for Photosynthesis

Never in animal or bacterial cells

Photosynthesis – food making process

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Vacuoles: Fluid filled sacks

for storage Small or absent in animal cells

Plant cells have a large Central Vacuole

No vacuoles in bacterial cells

Vacuoles

In plants, they store Cell Sap

Includes storage of sugars, proteins, minerals, lipids, wastes, salts, water, and enzymes

Contractile Vacuole

Found in unicellular protists like paramecia

Regulate water intake by pumping out excess (homeostasis)

Keeps the cell from lysing (bursting)

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Contractile vacuole animation

Microtubules: Microtubules are a component of the cytoskeleton,

found throughout the cytoplasm.

These tubular polymers of tubulin can grow as long as 50 micrometres, with an average length of 25 µm, and are highly dynamic.

The outer diameter of a microtubule is about 24 nm while the inner diameter is about 12 nm. They are found in eukaryotic cells and are formed by the polymerization of a dimer of two globular proteins, alpha and beta tubulin.

Microtubules are very important in a number of cellular processes. They are involved in maintaining the structure of the cell and, together with microfilaments and intermediate filaments, they form the cytoskeleton. They also make up the internal structure of cilia and flagella.

They provide platforms for intracellular transport and are involved in a variety of cellular processes, including the movement of secretory vesicles, organelles, and intracellular substances (see entries for dynein and kinesin).

They are also involved in cell division (mitosis and meiosis), including the formation of mitotic spindles, which are used to pull apart eukaryotic chromosomes.

Microtubules are nucleated and organized in microtubule organizing centres (MTOCs), such as the centrosome or the basal bodies found in cilia and flagella. These MTOCs may or may not possess centrioles.

There are many proteins that bind to microtubules, including motor proteins such as kinesin and dynein, severing proteins like katanin, and other proteins important for regulating microtubule dynamics

Microfilaments: Microfilaments or actin filaments are the thinnest

filaments of the cytoskeleton, a structure found in the cytoplasm of eukaryotic cells.

These linear polymers of actin subunits are flexible and relatively strong, resisting buckling by multi-piconewtoncompressive forces and filament fracture by nanonewtontensile forces.

Microfilaments are highly versatile, functioning in cytokinesis, amoeboid movement, and changes in cell shape. In inducing this cell motility, one end of the actin filament elongates while the other end contracts, presumably by myosin II molecular motors.

Additionally, they function as part of actomyosin-driven contractile molecular motors, wherein the thin filaments serve as tensile platforms for myosin's ATP-dependent pulling action in muscle contraction and pseudopod advancement.

Microfilaments have a tough, flexible framework which helps the cell in movement.

Peroxisomes and glyoxysomes: Peroxisomes, also known as microbodies, are single

membrane cellular organelles. They are spherical or oval in shape and contain the enzyme catalase.

Catalase protects the cell from the toxic effects of H2O2, by converting it to H2O and O2.

Peroxisomes are also involved in the oxidation of long chain fatty acids (> C18), and synthesis of plasmalogens and glycolipids.

Plants contain glyoxysomes, a specialized type of peroxisomes, which are involved in the glyoxylate pathway

Peroxisome biogenesis disorders (PBDs), are a group of rare diseases involving the enzyme activities of peroxisomes. The biochemical abnormalities associated with PBDs include increased levels of very long chain fatty acids and decreased concentrations of plasmalogens.

The most severe form of PBDs is Zellweger syndrome, a condition characterized by the absence of functional peroxisomes.

The Victims of this disease may die within one year after birth

References Images references:

1. http://www.uic.edu/classes/bios/bios100/summer2002/nucleus.jpg

2. http://pixgood.com/electron-micrograph-mitochondria.html

3. https://www.pinterest.com/tserex/mitochondrial-disease/

4. http://www.slideshare.net/tas11244/cell-structure-lecture

5. http://en.wikipedia.org/wiki/Chloroplast

6. http://creationrevolution.com/chloroplasts-%E2%80%93-simple-cell-part-15/

7. http://www.bioanim.com/CellTissueHumanBody6/O3mitosisMeiosisChrom/celCentriol1lgws.html

8. http://biology4isc.weebly.com/cell-organelles.html

9. http://engineering.curiouscatblog.net/2006/12/12/micro-robots-to-swim-through-veins/

10. http://torresbioclan.pbworks.com/w/page/22377199/Prokaryotes%20and%20Eukaryotes

11. http://www.sparknotes.com/biology/microorganisms/protista/section2.rhtml

12. http://en.wikipedia.org/wiki/Chloroplast

Reading references:

Cell and Molecular Biology, 6th Ed By Karp

Molecular Cell Biology by Lodish 5th Edition