Module 1: Cell and Molecular Biology

Cell Structure

Objectives:

• Describe and interpret drawings and electron micrographs of the structure of membrane systems and organelles of typical plant and animal cells

• Make drawings of typical plant and animal cells as seen under the light microscope (differences between electron and light microscopes as well as differences between resolution and magnification to be included.)

• Outline the functions of membrane systems and organelles• Compare the structures of typical plant and animal cells• Describe the structure of a prokaryotic cell• Compare the structure of prokaryotic cells with that of eukaryotic cells• Explain the concepts of tissue and organs using as an example the

dicotyledonous root.• Make plan drawings to show the distribution of tissues within an organ

such as the dicot root.

Electron Microscopy

What are Electron Microscopes?

Electron Microscopes are scientific instruments that use a beam of

highly energetic electrons to examine objects on a very fine scale. This

examination can yield the following information:

• Topography: the surface features of an object or "how it looks", its

texture

• Morphology: the shape and size of the particles making up the object

• Composition: the elements and compounds that the object is

composed of and the relative amounts of them

• Crystallographic Information: how the atoms are arranged in the object

Where did Electron Microscopes come From?

Electron Microscopes were developed due to the limitations of Light

Microscopes which are limited by the physics of light to 500x or 1000x

magnification and a resolution of 0.2 micrometers. In the early 1930's

there was a scientific desire to see the fine details of the interior

structures of organic cells (nucleus, mitochondria...etc.) and this

required 10,000x plus magnification which was just not possible using

light microscopes.

The Transmission Electron Microscope (TEM) was the first type of

Electron Microscope to be developed and is patterned exactly on the

Light Transmission Microscope except that a focused beam of

electrons is used instead of light to "see through" the specimen.

How do Electron Microscopes Work?

Electron Microscopes (EMs) function exactly as their optical counterparts

(light microscopes) except that they use a focused beam of electrons

instead of light to "image" the specimen and gain information as to its

structure and composition.

Light Microscopy

The light microscope, so called because it employs visible light to detect small objects, is probably the most well-known and well-used research tool in biology.

Fig 1: Light microscope.

Magnification and Resolution

Magnification is how much bigger a sample appears to be under the

microscope than it is in real life.

Overall magnification = Objective lens x

Eyepiece lens

Resolution is the ability to distinguish between two points on an image i.e.

the amount of detail

Resolution consists of the capacity to show minute details of an object

distinctly, and is determined by the aperture of the beam of light that enters

the objective (the eyepiece in general has little effect on the resolution of the

microscope).

Cell Structure

M- Mitochondrion

V-vacuole

ER-Endoplasmic reticulum

C- Chloroplast

Go-Golgi body

CW-Cell wall

N- Nucleus

Fig 2: electron micrograph of a plant cell

A B C

Fig 3: A- Mitochondrion, note the highly folded inner membrane into cristae.

External to the mitochondrion are the rough endoplasmic reticulum studded

with ribosomes, the sites of protein synthesis; B-chloroplast, G indicates the

presence of granules, which are the sites of starch storage. Non-

membranous regions indicate the sites of the dark reactions of

photosynthesis. Stacks of photosynthetic membranes are the sites of the

light reactions of photosynthesis and also where chlorophyll resides; C- Golgi

body, site of packaging and modification of synthesized proteins from the

ribosomes.

Fig 4: Electron micrograph of animal cell

Membrane Systems

The membrane system of a cell performs many important functions. This

system controls the entrance and exit of substances into and out of the cell,

and also provides for the manufacture and packaging of substances within

the cell. The membrane system of the cell consists of the plasma membrane,

which encloses the cell contents; the endoplasmic reticulum, which

manufactures lipids and proteins; the Golgi body, which packages

substances manufactured within the cell; and various vesicles, which

perform different functions.

The Plasma Membrane

The plasma membrane of the cell is often described as "selectively permeable;" that is, the plasma membrane is designed so that only certain substances are allowed to pass through. The plasma membrane is composed

of two layers of molecules called phospholipids. Each phospholipid molecule consists of a phosphate "head" and two fatty acid chains tails.

The orientation of these two sections of the phospholipid molecule is crucial to the functioning of the plasma membrane. The phosphate region is hydrophilic (literally, "water-loving") and attracts water. The fatty acid region is hydrophobic (literally, "water-hating") and repels water. In the phospholipid bilayer of the plasma membrane, the phospholipid layers are arranged so that the two phosphate hydrophilic regions face outward, towards the watery extracellular environment, and inward, towards the cellular cytoplasm, which also contains water. The two hydrophobic fatty acid portions of the chains face each other, forming a water-tight shield. The plasma membrane, then, is both water-proof and water-attracting. It functions both as a boundary between the cell's contents and the external cellular environment, yet also allows the transport of water-containing and other substances across its boundaries.

Endoplasmic Reticulum

The endoplasmic reticulum (meaning "within the cytoplasm" and "net") consists of flattened sheets, sacs, and tubes of membrane that cover the entire expanse of a eukaryotic cell's cytoplasm. This internal system of membrane is continuous with the double membrane that surrounds the cell's nucleus. Therefore, the encoded instructions that the nucleus sends out for the synthesis of proteins flow directly into the endoplasmic reticulum. Within the cell, the endoplasmic reticulum synthesizes lipids and proteins. The proteins that the endoplasmic reticulum synthesizes, such as enzymes, are exported from the cell to perform various functions in the body. Proteins that are made in the cell for use by the cell-for instance, as channels in the plasma membrane-are made by the free ribosomes that are situated within the cytoplasm.

Two types of endoplasmic reticulum are found in the eukaryotic cell. Rough endoplasmic reticulum is studded with ribosomes on its outer face. These ribosomes are the sites of protein synthesis. Once a protein is synthesized on a ribosome, it is enclosed within a vesicle, a small, membrane-bound "bubble." The vesicle travels to another organelle, the Golgi body. Within the Golgi body, the proteins within the vesicle are further modified before they are exported from the cell. Cells that specialize in protein secretion contain large amounts of rough endoplasmic reticulum. For instance, beta cells of the pancreas that produce the protein insulin, have abundant rough endoplasmic reticulum.

The other type of endoplasmic reticulum is smooth endoplasmic reticulum. Smooth endoplasmic reticulum does not have ribosomes and is the site of lipid metabolism. Here, macromolecules containing lipids are broken down

into their constituent parts. In addition, smooth endoplasmic reticulum functions in the synthesis of lipid-containing macromolecules. Smooth endoplasmic reticulum is not as common in cells as rough endoplasmic reticulum. Large amounts of smooth endoplasmic reticulum are found in cells that specialize in lipid metabolism. For instance, liver cells remove alcohol and drugs from the bloodstream. Liver cells have an impressive network of smooth endoplasmic reticulum. Similarly, cells of the ovaries and testes, which produce the lipid-containing hormones estrogen and testosterone, contain large amounts of smooth endoplasmic reticulum.

The Golgi Body

The Golgi body is one of the most unusually shaped organelles. The Golgi body consists of stacked, membrane-bounded, flattened sacs. Surrounding the Golgi body are numerous, small, membrane-bounded vesicles. The Golgi body and its vesicles function in the sorting, modifying, and packaging of macro-molecules,such as lipids or proteins, that are secreted by the cell or used within the cell for various functions.

The Golgi body can be compared to the shipping and receiving department of a large company. Each Golgi body within a cell has a cis face, which is analogous to the receiving division of the department. Here, the Golgi body receives macromolecules synthesized in the endoplasmic reticulum encased within vesicles. The trans face of the Golgi body is analogous to the shipping division of the department, and is the site from which modified and packaged macromolecules are transported to their destinations.

Within the Golgi body, various chemical groups are added to the macromolecules so ensure that they reach their proper destination. In this way, the Golgi body attaches an "address" to each macromolecule it receives. For example, cells called goblet cells in the lining of the intestine secrete mucous. The protein component of mucous, called mucin, is modified in the Golgi body by the addition of carbohydrate groups. From the Golgi body, the modified mucin is packaged within a vesicle. The vesicle containing its mucous cargo fuses with the plasma membrane of the goblet cell, and is released into the extracellular environment.

Vesicles

Vesicles are small, membrane-bounded spheres that contain various macromolecules. Some vesicles are used to transport macromolecules from the endoplasmic reticulum to the Golgi body and from the Golgi body to various destinations. Special kinds of vesicles perform other functions as well.

Lysosomes are vesicles that contain enzymes involved in cellular digestion. Some protists, for instance, engulf other cells for food. In a process called phagocytosis, the protist surrounds a food particle and engulfs it within a vesicle. This food containing vesicle is transported within the protist's cytoplasm until it comes into contact with a lysosome. The food vesicle and lysosome merge, and the enzymes within the lysosome are released into the food vesicle. The enzymes break the food down into smaller parts for use by the protist.

Lysosomes, however, are found in all kinds of cells. In all cells, lysosomes digest old, worn-out organelles. They also play a role in cell death, known as apoptosis. Cell death is a component of normal developmental processes. For instance, a human fetus has web-like hands and feet. As the fetus develops, the cells that compose these webs slowly self-destruct, freeing the fingers.

Peroxisomes contain hydrogen peroxide. Peroxisomes function in the oxidation of many materials, including fats. In oxidation, oxygen is added to a molecule. When oxygen is added to fats, hydrogen peroxide is formed. The oxidation of fats takes place within the membranes of peroxisomes so that the harmful chemical does not leak out into the cell's cytoplasm.

The Nucleus

The nucleus is the control center of the cell. Under a microscope, the nucleus looks like a dark blob, with a darker region, called the nucleolus, centered within it. The nucleolus is the site where the subunits of ribosomes(70s and 80s subunits) are manufactured. Surrounding the nucleus is a double membrane called the nuclear envelope. The nuclear envelope is studded all over with tiny openings called nuclear pores.

The nucleus directs all cellular activities by controlling the synthesis of proteins. The nucleus contains encoded instructions for the synthesis of proteins in a helical molecule called deoxyribonucleic acid (DNA). The cell's DNA is packaged within the nucleus in a structural form called chromatin. Chromatin consists of DNA wound tightly around spherical proteins called histones. When the cell prepares to divide, the DNA unwinds from the histones and assumes the shape of chromosomes, the X-shaped structures visible within the nucleus prior to cell division. Chromatin packaging of DNA allows the cell’s entire complement of DNA to fit into the combined space of the nucleus. If DNA was not packaged into chromatin, it would spill out over a space about 100 times as large as the cell itself.

Chloroplasts

Plant chloroplasts are large organelles (5 to 10 μm long) that, like mitochondria, are bounded by a double membrane called the chloroplast envelope. In addition to the inner and outer membranes of the envelope, chloroplasts have a third internal membrane system, called the thylakoid membrane. The thylakoid membrane forms a network of flattened discs called thylakoids, which are frequently arranged in stacks called grana. Because of this three-membrane structure, the internal organization of chloroplasts is more complex than that of mitochondria. In particular, their three membranes divide chloroplasts into three distinct internal compartments: (1) The intermembrane space between the two membranes of the chloroplast envelope; (2) The stroma, which lies inside the envelope but outside the thylakoid membrane; and (3) The thylakoid lumen.The major difference between chloroplasts and mitochondria, in terms of both structure and function, is the thylakoid membrane. This membrane is of central importance in chloroplasts.The inner membrane of the chloroplast envelope (which is not folded into cristae) does not function in photosynthesis.

Comparing plant and animal cells

Similarities

Plant cells Animals cells

1. Nucleus present Nucleus present2. Cell membrane present Cell membrane present3. Mitochondria present Mitochondria present4. Cytoplasm Cytoplasm5.6.

Differences

Plant cells Animal cells1. Chloroplasts present No chloroplasts present2. Cell wall present No cell wall present3. Large cell vacuoles Smaller vacuoles4.5.6.

Prokaryotes

The Basic Structure of a Prokaryote

Prokaryotes are the single-celled organisms, such as bacteria, and are roughly one micrometer in diameter. Unlike Eukaryotes, prokaryotes do not have a nucleus that houses its genetic material. Rather, the genetic material of a prokaryote cell consists of a large DNA molecule compacted in an area of cytoplasm called the nucleoid region. The nucleoid region is protected and encased by the cell wall, or cell membrane, the outer layering of the cell (similar to human's skin). Finally, a flagellum (flagetta - plural), a rudder-like device, affords the prokaryote the luxury of mobility.

Fig 5: Prokaryotic Structure

Pili: are hollow, hairlike structures made of protein allow bacteria to attach to other cells. A specialized pilus, the sex pilus, allows the transfer from one bacterial cell to another. Pili (sing., pilus) are also called fimbriae (sing., fimbria.

Flagella: The purpose of flagella (sing., flagellum) is motility. Flagella are long appendages which rotate by means of a "motor" located just under the cytoplasmic membrane. Bacteria may have one, a few, or many flagella in different positions on the cell.

Cell Wall: Composed of peptidoglycan (polysaccharides + protein), the cell wall maintains the overall shape of a bacterial cell. The three primary shapes in bacteria are coccus (spherical), bacillus (rod-shaped) and spirillum (spiral).

Mycoplasma are bacteria that have no cell wall and therefore have no definite shape.

Capsule: This layer of polysaccharide (sometimes proteins) protects the bacterial cell and is often associated with pathogenic bacteria because it serves as a barrier against phagocytosis by white blood cells.

Inclusions: Nutrient reserves for the bacterial cell, present to afford additional, specialised functions. These may take many diverse forms such as carbohydrates, proteins as well as other forms.

The major similarities between the two types of cells (prokaryote and eukaryote) are:

1. They both have DNA as their genetic material. 2. They are both membrane bound. 3. They both have ribosomes . 4. They have similar basic metabolism . 5. They both exist in diverse forms.

The major and extremely significant difference between prokaryotes and eukaryotes is that eukaryotes have a nucleus and membrane-bound organelles , while prokaryotes do not. The DNA of prokaryotes floats freely around the cell; the DNA of eukaryotes is held within its nucleus. The organelles of eukaryotes allow them to exhibit much higher levels of intracellular division of labour than is possible in prokaryotic cells. Additional obvious differences between prokaryotes and eukaryotes include:

Size Eukaryotic cells are, on average, ten times the size of prokaryotic cells.

Genomic composition and length The DNA of eukaryotes is much more complex and therefore much more extnsive than the DNA of prokaryotes.

Cell Wall Prokaryotes have a cell wall composed of peptidoglycan, a single large polymer of amino acids and sugar. Many types of eukaryotic cells, such as plant cells, also have cell walls, made of cellulose instead of peptidoglycan.

The Endosymbiotic Development of Eukaryotic cells, the Endosymbiotic theory

The Endosymbiotic Theory concerns the origins of mitochondria and chloroplasts, which are organelles of eukaryotic cells. According to this

theory, these organelles originated as prokaryotic endosymbionts, which came to live inside eukaryotic cells. The theory postulates that the mitochondria evolved from aerobic bacteria, that is, prokaryotes which use oxygen, and that the chloroplast evolved from endosymbiotic cyanobacteria (autotrophic prokaryotes). The evidence for this theory is compelling as a whole, and it is now generally accepted. Evidence of this is provided through observations that:

• Both mitochondria and chloroplasts can arise only from pre-existing mitochondria and chloroplasts. They cannot be formed in a cell that lacks them because nuclear genes encode only some of the proteins of which they are made.

• Both mitochondria and chloroplasts have their own genome and it resembles that of bacteria not that of the nuclear genome.

o Both genomes consist of a single circular molecule of DNA. o There are no histones associated with the DNA.

• Both mitochondria and chloroplasts have their own protein-synthesizing machinery, and it more closely resembles that of bacteria than that found in the cytoplasm of eukaryotes.

Tissues and Organ Systems

Cells group together to form tissues. Tissues are essentially collections of cells having specialised functions.

Organs are the next level of organisation. An organ is a structure consisting of at least two types of tissues functioning together for a common purpose.

Plants are made up of two organ systems: the shoot system and the root

system. For terrestrial plants the shoot system is above ground and consists

of a number of organs. These include stems, leaves, and flowers. On the

other hand, the root system is most often underground and consists of

organs such as roots, underground stems (tubers), and rhizomes.

Each of these organs performs a different function. Stems are support

structures and mediate the growth of the plant. Shoot tips contain actively

dividing regions called meristems, which produce auxin, a hormone that

regulates the growth and shape of the plant. Leaves are the primary sites of

photosynthesis, so they are the food production centers of the plant. Flowers

are reproductive structures, where eggs and sperm (pollen) are produced

and where pollination and fertilization occur. Roots, tubers, and rhizomes are

the main system for nutrient and water acquisition and storage. All of these

organs are made up of cells that can be categorized into three major tissue

types: dermal, ground, and vascular tissue.

Dermal Tissue

Dermal tissue makes up the outer layers of the plant and contains epidermal

cells that secrete and are coated with a waxy layer. This waxy coating, the

cuticle, prevents excessive water loss from the plant. While the dermal tissue

primarily serves a protective role, it also has a variety of other specialized

functions depending on the particular organ where it is located.

In leaves, dermal tissue contains specialized cells called guard cells that

make up structures called stomata . Stomata facilitate the exchange of

gases in the leaf. Carbon dioxide (CO 2 ) diffuses into the leaf through the

stomata for use in photosynthesis, and oxygen (O 2 ), the waste product of

photosynthesis, diffuses out of the leaf through stomata. Stomata are also

crucial for water transport through the xylem . Stomatal opening results in

the evaporation of water from the air spaces of the leaf. This creates

negative water pressure that pulls on the column of water in the xylem. The

evaporation of water from the stomata is the main driving force for water

transport through the water. In roots, epidermal cells have a specialized

structure that facilitates water and nutrient absorption, the main function of

the root. Some of the root epidermal cells have long membranous extensions

called root hairs that increase the absorptive surface area of the root. Root

epidermis also interacts with symbiotic fungi that form mycorrhizae , which

increase nutrient absorption.

Ground Tissue

Many different functions are performed by ground tissue including

photosynthesis, storage, and support. Ground tissue makes up the majority

of the plant structure and is composed of three cell types: parenchyma,

collenchyma, and sclerenchyma cells.

Parenchyma cells are the least specialized cells in a plant. These cells are

responsible for the production and storage of nutrients. Photosynthesis

occurs in the chloroplasts of parenchyma cells in leaves. Parenchyma cells in

stems, roots, and fruits have structures that store starch. Most developing

plant cells are structurally similar to parenchyma cells. During their

differentiation, they become specialized in form and function and lose the

potential to divide. Mature parenchyma cells do not usually divide, but they

retain the ability to divide and differentiate into different cell and tissue

types in the event of an injury to the plant.

Collenchyma and sclerenchyma cells provide structural support for the plant.

Collenchyma cells have thick, yet pliable, cell walls. These cells give

structural support to newly formed portions of a plant without restricting

growth. Collenchyma cells are stacked end on end and are oriented in

strands just beneath the epidermis of the young structure. The relatively soft

cell wall allows the collenchyma cells to elongate as the structure grows.

Sclerenchyma cells provide support to mature plant structures. Like

collenchyma cells, they have very thick cell walls. However, the cell walls of

sclerenchyma cells contain lignin , a molecule that makes the cell wall hard.

This provides strength to the cell wall, but restricts the ability of the cells to

elongate and grow. Since a sclerenchyma cell functions solely to provide

structural support, many sclerenchyma cells are actually dead at functional

maturity. The cell membrane, protoplasm (cytoplasm) and organelles are

gone, leaving only the rigid cell wall that serves as a scaffolding system for

that structure.

Vascular Tissue

Vascular tissues make up the organs that transport water, minerals , and

food throughout the plant. Vascular tissue can be divided into two functional

units. Xylem transports water and minerals from root to shoot. phloem

transports nutrients (such as sugar and amino acids ) from leaves and other

production sites to roots, flowers, stems, and other tissues that need them.

The cells that make up vascular tissue are unique in their structure. Their

specialized characteristics allow them to transport material through the plant

efficiently while providing structural support to the plant.

Xylem tissue contains two types of cells: tracheids and vessel elements. Like

sclerenchyma, both of these cell types are dead at functional maturity and

therefore lack protoplasm. Tracheids are long, thin cells that have tapered

ends. They overlap on another, and water passes from tracheid to tracheid

via small pores. Vessel elements are shorter and are stacked end to end,

forming more of a tube structure. Water flows in the tube by passing through

perforated end walls between cells.

Phloem tissue is made up of two different types of cells: sieve tube members

and companion cells. Sieve tube members are the main conducting cells,

and are named for the sievelike areas along their cell walls through which

the phloem sap moves from cell to cell. Unlike cells of the xylem, sieve tube

members are alive at functional maturity, but do not have nuclei. For this

reason, companion cells are closely associated with sieve tube members.

These cells do have nuclei and serve to support the sieve tube members.

The cytoplasm of sieve tube members and companion cells is connected

through numerous pores called plasmodesmata. These pores allow the

companion cells to regulate the content and activity of the sieve tube

member's cytoplasm. Moreover, the companion cells help to load the sieve

tube members with sugar and the other metabolic products that they

transport throughout the plant.

Fig 6:Cross Section through dicotyledonous root

Fig 7: TS through dicot root.