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7:31 AM
Charophyceae
Charophyceae
It is almost impossible not to see Spirogyra floating on the surface of a pond on a hot summer day, but most people dismiss it as pond scum. Few realize that what they are looking at is a member of the Charophyceae, a class in the phylum Chlorophyta, or green algae, and a cousin of the ancestor of the Embryophyta, or bryophytes and vascular plants.

Most Charophyceae, like Spirogyra, live in freshwater habitats, but some also occur in moist soil in terrestrial habitats. Charophyceae can live as single cells, colonies, or branched and unbranched filaments and come in a variety of shapes.

The characteristics that unite members of the class—and which link them with the embryophytes—include flagellated cells (similar to sperm cells in vascular plants), a nuclear envelope that breaks down during mitosis, mitotic spindles that persist as phragmoplasts (a type of cytoskeletal scaffolding) through cell division either by furrowing or by forming a cell plate, the presence of chlorophylls a and b and phytochrome, and the storage of starch inside plastids.


Charophytes possess decay-resistant cell walls made of phenolic compounds as well as lignins or ligninlike compounds. Cell walls made of similar compounds are found in bryophytes and vascular plants as well.

Likewise, all three groups of plants also contain sporopollenin, the substance in the walls of spores and pollen grains that makes them virtually indestructible.

Communication channels between cells are similar, too. Plasmodesmata similar to that seen in embryophyte cells allow between-cell communications in charophytes and embryophytes.

Life Cycle

Life Cycle
Charophytes have a two-stage life cycle involving a dominant haploid stage, upon which develops the sex organs; antheridia, which produce sperm cells; and oogonia, which produce egg cells. Typically, individual charophytes produce both antheridia and oogonia, but in some species an individual will produce only one or the other.

Fertilization—which in one group, the Zygnematales, takes place via conjugation—produces a diploid zygote, which quickly undergoes meiosis. If the environment is unfavorable, the zygote will go dormant and remain so for a long period of time. Dormancy ends when the environment improves.

Classification

Genetic analysis supports the recognition of six orders within the Charophyceae: the Mesostigmatales, Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales, and Charales.

Of these, the most abundant group is the Zygnematales, a large order which consists of more than three thousand species, including Spirogyra and the desmids, a group of mostly single-celled organisms with a constriction across the middle which nearly divides the cells in two.

Zygnematales live primarily in freshwater habitats as phytoplankton, as benthic dwellers, or attached to other aquatic plants. Some species live on snow and ice.

The Charales, commonly called stoneworts or brittleworts, are a large group of filamentous charophytes that feature complex branching patterns. Some can reach lengths of more than a meter. The branching pattern—branches reach out from nodes along the filament—is similar to that of higher plants.

Charales reside primarily in freshwater habitats, but some can be found in brackish water as well as on land. The stems of stoneworts and brittleworts can be encrusted with calcium and magnesium carbonates.

As a result, their hard bodies are well known from the fossil record. The lineage extends back to more than 400 million years ago. Two current genera, Chara and Nitella, date back about 200 million years.

The Coleochaetales are a small group of complex, microscopic filamentous algae that can be found only in freshwater habitats. Klebsormidiales are a small group of unbranched, filamentous charophytes that occur in both freshwater and terrestrial environments.

Mesostigmatales and Chlorokybales are two groups of rare algae. The Coleochaetales and Charales are more closely related to bryophytes and vascular plants than the other groups.

Evolutionary Significance

For decades, structural similarities led plant biologists to suspect that the Embryophyta evolved from charophytes. Recently, cladistic analyses of chemical, structural, and genetic characteristics have opened up research on the topic.

In cladistics, characteristics among a number of organisms are analyzed statistically in the hopes of developing a classification system for the group which will reveal evolutionary relationships. Cladistic analyses support the notion that embryophytes are monophyletic; in other words, bryophytes and vascular plants descend from a common ancestor.


Furthermore, several recent analyses support the notion that a member of the Charophyceae gave rise to embryophytes. Cladistic analyses were somewhat unclear, however, about the relationships of the charophyte orders with one another and with other green algae (Chlorophyta), bryophytes, and land plants.

One of the latest analyses of mitochondrial, chloroplast, and nuclear genes helps resolve some of the confusion. The research indicates that the Mesostigmatales were probably the most ancient group of charophytes, followed by the Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales, and Charales.

The work also supports earlier suggestions that the Charales are the closest living relatives to extant embryophytes and that the charophytes descended from other green algae.
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6:33 AM
Chemotaxis
Chemotaxis
Chemotaxis is the ability of a cell to detect certain chemicals and to respond by movement, such as microbial movement toward nutrients in the environment.

Many microorganisms possess the ability to move toward a chemical environment favorable for growth. They will move toward a region that is rich in nutrients and other growth factors and away from chemical irritants that might damage them. Among the organisms that display this chemotactic behavior, none is simpler than bacteria.

Bacteria are single-celled prokaryotic microorganisms, which means that their deoxyribonucleic acid (DNA) is not contained within a well-defined nucleus surrounded by a nuclear membrane, as in eukaryotic (plant and animal) cells.


Prokaryotes lack many of the cellular structures associated with more complex eukaryotic cells; nevertheless, many species of bacteria are capable of sensing chemicals in their environment and responding by movement.

Bacterial Flagella

Bacteria capable of movement are called motile bacteria. Not all bacteria are motile, but most species possess some form of motility. Although there are three different ways in which bacteria can move, the most common means is by long, whiplike structures called flagella.

Bacterial flagella are attached to cell surfaces and rotate like propellers to push the cells forward. A bacterial cell must overcome much resistance from the water through which it swims. In spite of this, some bacteria can move at a velocity of almost 90 micrometers per second, equivalent to more than one hundred bacterial cell lengths per second.


A flagellum is composed of three major structural components: the filament, the hook, and the basal body. The filament is a hollow cylinder composed of a protein called flagellin.

A single filament contains several thousand spherically shaped flagellin molecules bound in a spiral pattern, forming a long, thin cylinder. A typical filament is between 15 and 20 micrometers long but only 0.02 micrometer thick.

The filament is attached to the cell by means of the hook and basal body. The hook is an L-shaped structure composed of protein and slightly wider than the filament. One end of the hook is connected to the filament, and the other end is attached to the basal body.

The basal body, also known as the rotor, consists of a set of protein rings embedded in the cell wall and plasma membrane. Inside these rings is a central rod attached to the hook. The central rod of the basal body rotates inside the rings, much like the shaft of a motor. As it rotates, it causes the hook and the filament to turn.

Bacteria in Motion

While they are moving, bacteria change direction by reversing the rotation of their flagella. As a bacterium swims forward in a straight line, its flagella spin in a counter clockwise direction.

Because of their structure, the flagella twist together when they rotate counter clockwise and act cooperatively to push the cell forward. The forward movement is referred to as a run.

Every few seconds, a chemical change in the basal body of each flagellum causes it to reverse its spin from counter clockwise to clockwise. When the flagella spin clockwise, they fly apart and can no longer work together to move the cell forward.

The cell stops and tumbles randomly until the flagella reverse again, returning to counterclockwise spin and a forward run. This type of movement, in which the cell swims forward for a short distance and then randomly changes its direction, is called run and tumble movement.

Certain eukaryotic microorganisms, such as Euglena and some other protozoa, are also motile by means of flagella. The structure and activity of eukaryotic flagella are, however, completely different from those of bacteria.

Eukaryotic flagella are composed of protein fibers called microtubules, which move back and forth in a wave like fashion to achieve movement. The rotation of bacterial flagella and the run and tumble movement they produce are unique to bacteria.

Attractants and Repellants

Bacteria respond by chemotaxis to two broad classes of substances, attractants and repellants. They move toward high concentrations of attractants (positive chemotaxis) and away from high concentrations of repellants (negative chemotaxis).

Attractants and Repellants
Attractants and Repellants

Attractants are most often nutrients and growth factors, such as monosaccharides (simple sugars), amino acids (the building blocks of protein), and certain vitamins required for bacterial metabolism. Repellants include waste products given off by the bacteria as well as other toxic substances found in the environment.

Bacteria respond to attractants and repellants by altering the time between tumbles in their run and tumble movement. When a bacterial cell detects an attractant, the time between tumbles and the time of the runs increase.

As long as the cell is moving toward a higher concentration of attractant, its runs will be longer. The opposite effect occurs when a cell encounters a repellant.

A repellant causes the time between tumbles to decrease, resulting in shorter runs as the cell changes direction more frequently while trying to avoid the repellant. The net result is that the cell tends to move toward a lower concentration of the repellant.

Chemotactic Receptors

Bacteria recognize attractants and repellants through specialized proteins called chemotactic receptors, also called methyl-accepting chemotactic proteins (MCPs), which are embedded in their plasma membranes just inside the cell wall.

Biologists have identified roughly twenty different receptors for attractants and some ten for repellants. Each receptor protein is believed to respond to only a single type of attractant or repellant.

When an attractant molecule binds to its chemotactic receptor, two separate events occur. First, there is a rapid activation of the receptor. The attractant molecule binds to a special site on the receptor protein to form an activated receptor.

This binding is not permanent, however, so a cell must remain in an area with attractant molecules for its receptors to remain activated. The activated receptor sends a chemical signal to the basal bodies of flagella, which causes them to spin in a counter clockwise direction, producing continuous swimming in one direction.

At the same time, there is adaptation of the activated receptors to the attractant. Adaptation is important because it keeps the cell from swimming too long in one direction.

It is accomplished by methylation of the receptors, a process in which methyl groups are attached to the protein by an enzyme in the cell. (A methyl group consists of an atom of carbon attached to three atoms of hydrogen.) Methylated receptors do not stimulate the basal bodies for counter clockwise rotation as effectively as nonmethylated receptors.

After a cell has been in the presence of an attractant for a short while, its receptors adapt to the attractant, and it returns to the original pattern of run and tumble movement. Adaptation is reversed by demethylation, the removal of methyl groups from the receptor by a separate enzyme.

Together, the balance between methylation and demethylation makes the receptors very sensitive to small changes in attractant concentration, so that cells remain in the region with the greatest concentration of attractant.

The action of repellants appears to be similar to that of attractants. Repellant molecules bind to sites on their chemotactic receptors, activating the receptors.

The activated receptors signal the flagella to spin clockwise instead of counterclockwise, causing the cell to tumble and to change direction. Repellant receptors also adapt through methylation and demethylation, much like attractant receptors.

It is not entirely understood how an activated chemotactic receptor can signal flagella to rotate. Four different proteins inside the bacterial cell have been identified as a possible link between the chemotactic receptors and the basal bodies of flagella.

These proteins are believed to regulate flagellar rotation using a process called phosphorylation. Phosphorylation, the attachment of phosphate molecules to a protein, is used in all types of cells as a kind of “on and off” switch to regulate protein activity.
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9:02 PM
Chlorophyceae
Chlorophyceae
Chlorophyceae (from the Greek word chloros, meaning “green”) make up an extremely large and important class of green algae. Members may be unicellular, colonial, or filamentous. Cells of unicellular and colonial chlorophyceans may have two or more flagella.

There are about 2,650 living species of chlorophyceans. The main features of the class (and most plants) are the use of starch as the principal food reserve and the green chloroplasts with chlorophylls a and b. In spite of plant characteristics, this algal group is not directly related to early land plants.

Chlorophyceans are almost entirely restricted to freshwater and terrestrial habitats. Some members of this class have adapted to life on snow as snow algae. Snow algae cause snow to appear red-burgundy or orange in color because of high levels of unusual carotenoid pigments within the algal cells.


There are a variety of asexual and sexual reproduction modes among members of this class. Sexual reproduction is characterized by the formation of a zygote produced by gametic fusion.

Chlorophyceans show differences during cell division compared to other green algal groups. For example, they produce a set of microtubules, the phycoplast, that is parallel to the plane of cell division.

Diversity

Diversity
Diversity
The Chlorophyceae include some familiar green algae. Perhaps the most famous chlorophyceans are Chlamydomonas (from the Greek word chlamys, meaning “cloth”) and Volvox (from the Latin volvo, meaning “to roll”).

Both are important research models in laboratories. Chlorophyceans fall into several orders, including Volvocales, Chlorococcales, Chaetophorales, and Oedogoniales.

Volvocales

Members of the order Volvocales include both unicellular organisms, such as those in the genus Chlamydomonas with their two equal flagella, and colonial forms. The Chlamydomonas are a large genus of chlorophyceans.

More than six hundred species have been described worldwide. The Chlamydomonas probably represent the most primitive structure among chlorophyceans. Nevertheless, their basic cell features may be found among other representatives of this order.

A cell wall made of glycoproteins, rather than cellulose, surrounds each Chlamydomonas cell. Inside the cell, there is a single large chloroplast and a pyrenoid, which forms starch.

Other cytoplasmic structures include the contractile vacuole rather than a central vacuole. The contractile vacuole is responsible for the removal of water from the cell. Cells of Chlamydomonas are capable of phototaxis: They swim toward moderate light but away from high-intensity light.

Rhodopsin-like pigment is their primary lightsensing photoreceptor. Under dry conditions, Chlamydomonas form a palmelloid stage, in which nonflagellate cells are held together by common mucilage.

Chlamydomonas reproduce asexually via cell division. Also, cells of this alga can become gametes. In most species of Chlamydomonas, the male and female gametes appear the same; they are designated (+) and (–).

Colonial flagellates of the order Volvocales range from simple colonies of Gonium to visible-without-magnification spheres of Volvox with up to several thousands of cells and some sort of cellular specialization.

Volvox are one of the most structurally advanced colonial forms of green algae.Only specialized cells participate in reproduction. During asexual reproduction, some cells of Volvox divide and bulge inward, forming new daughter colonies, which are held for some time within the parent colony. Volvox are also capable of sexual reproduction. They produce gametes that differentiate into sperm and eggs.

Chlorococcales

Members of the order Chlorococcales include nonmotile unicellular and colonial algae. Typical representatives of the unicellular nonmotile form are found in Chlorococcum. They occur as spherical single cells or cell aggregates and produce flagellated zoospores.

Examples of colonial representatives of Chlorococcales are Hydrodictyon, commonly known as the “water net”; Pediastrum, famous for their distinctive, starlike shape; and Scenedesmus, wide-spread inhabitants of the freshwater phytoplankton.

The order Chlorococcales has now been divided on the basis of small subunit ribosomal ribonucleic acid (RNA) sequence data into several groups, including the Sphaeropleales, Tetracystis clade, and Dunaliella clade.

Chaetophorales and Oedogoniales

Chaetophorales and Oedogoniales
Chaetophorales and Oedogoniales
The most complex of the class Chlorophyceae are the filamentous members in orders Chaetophorales and Oedogoniales, some of which exhibit features that are observed primarily in plants. The chaetophoralean green algae have plantlike bodies with a system of primary and secondary branches.

The Draparnaldia (named for Jacques Phillipe Raymond Draparnaud, a French naturalist) from order Chaetophorales have a main filamentous axis with relatively large cells, primary branches with smaller cells, and secondary branches with even smaller cells.

One representative of Oedogoniales, the green alga Oedogonium (from the Greek oidos, meaning “swelling”), has been a subject of intense study for its unusual cell division technique.

The entire contents of an Oedogonium cell may be used in the for mation of one large zoospore with multiple flagella. Members of Bulbochaete (from the Greek bolbos, meaning “bulb”) resemble Oedogonium in cell division but differ in being branched and having a distinctive hair cell at the end of each branch.

Technological Uses

A few chlorophycean green algae have commercial value. These algae are good candidates for the industrial production of hydrogen gas because they are able to release the gas from water using solar energy. Hydrogen gas is an environmentally desirable fuel because the burning of hydrogen produces water, and it can be converted effectively to electricity.

Another “commercial” organismis Dunaliella salina, a saltwater alga that accumulates massive amounts of beta-carotene, a vital antioxidant also used in food coloring and in pharmaceuticals.

Selenastrumcapricornutum are the most widely used algal biomonitors in the detection of water pollution. Chlorophyceans are used in freshwater aquaculture systems as food for fish.One alga with possible potential for salmon feeds is Haematococcus.

Algae contain large amounts of the pigment astaxanthin, which is responsible for the red coloration typical of salmon flesh. Chlorella (formerly classified in the order Chlorococcales) are famous both as the experimental systems in the discovery of the photosynthetic Calvin cycle and as health food in Asia.
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3:15 AM
Chloroplast DNA
Chloroplast DNA
Plants are unique among higher organisms in that they meet their energy needs through photosynthesis. The specific location for photosynthesis in plant cells is the chloroplast, which also contains a single, circular chromosome composed of DNA. Chloroplast DNA contains many of the genes necessary for proper chloroplast functioning.

A better understanding of the genes in chloroplast deoxyribonucleic acid (cpDNA) has improved the understanding of photosynthesis, and analysis of the deoxyribonucleic acid (DNA) sequence of these genes has been useful in studying the evolutionary history of plants.

Discovery of Chloroplast Genes

The work of nineteenth century Austrian botanist Gregor Mendel showed that the inheritance of genetic traits follows a predictable pattern and that the traits of offspring are determined by the traits of the parents.

For example, if the pollen from a tall pea plant is used to pollinate the flowers of a short pea plant, all the offspring are tall. If one of these tall offspring is allowed to self-pollinate, it produces a mixture of tall and short offspring, three-quarters of them tall and one-quarter of them short.


Similar patterns are observed for large numbers of traits from pea plants to oak trees. Because of the widespread application of Mendel’s work, the study of genetic traits by controlled mating is often referred to as Mendelian genetics.

In 1909 German botanist Karl Erich Correns discovered a trait in the four-o’clock plants (Mirabilis jalapa) that appeared to be inconsistent with Mendelian inheritance patterns.

He discovered that four-o’clock plants had a mixture of leaf colors on the same plant: Some were all green, many were partly green and partly white (variegated), and some were all white.

If he took pollen from a flower on a branch with all-green leaves and used it to pollinate a flower on a branch with all-white leaves, all the resulting seeds developed into plants with white leaves.

Likewise, if he took pollen from a flower on a branch with all-white leaves and used it to pollinate a flower on a branch with all-green leaves, all the resulting seeds developed into plants with green leaves.

Repeated pollen transfers in any combination always resulted in offspring whose leaves resembled those on the branch containing the flower that received the pollen, that is, the maternal parent. These results could not be explained by Mendelian genetics.

Since Correns’s discovery, many other such traits have been discovered. It is now known that the reason these traits do not follow Mendelian inheritance patterns is that their genes are not on the chromosomes in the nucleus of the cell where most genes are located. Instead, the gene for the four o’clock leaf color trait is located on the single, circular chromosome found in chloroplasts.

Because chloroplasts are specialized for photosynthesis, many of the genes on the single chromosome produce proteins or ribonucleic acid (RNA) that either directly or indirectly affect synthesis of chlorophyll, the pigment primarily responsible for trapping energy from light.

Because chlorophyll is green and because mutations in many chloroplast genes cause chloroplasts to be unable to make chlorophyll, most mutations result in partially or completely white or yellow leaves.

Identity of Chloroplast Genes

Advances in molecular genetics have allowed scientists to take a much closer look at the chloroplast genome. The size of the genome has been determined for a number of plants and algae and ranges from 85 to 292 kilobase pairs (one kb equals one thousand base pairs), with most being between 120 kb and 160 kb. The complete DNA sequences for several different chloroplast genomes of plants and algae have been determined.

Although a simple sequence does not necessarily identify the role of each gene, it has allowed the identity of a number of genes to be determined, and it has allowed scientists to estimate the total number of genes. In terms of genome size, chloroplast genomes are relatively small and contain slightly more than one hundred genes.

Roughly half of the chloroplast genes produce either RNA molecules or polypeptides that are important for protein synthesis. Some of the RNA genes occur twice in the chloroplast genomes of almost all land plants and some groups of algae.

The products of these genes represent all the ingredients needed for chloroplasts to carry out transcription and translation of their own genes. Half of the remaining genes produce polypeptides directly required for the biochemical reactions of photosynthesis.

What is unusual about these genes is that their products represent only a portion of the polypeptides required for photosynthesis. For example, the very important enzyme ATPase, the enzyme that uses proton gradient energy to produce the important energy molecule adenosine triphosphate (ATP), comprises nine different polypeptides.

Six of these polypeptides are products of chloroplast genes, but the other three are products of nuclear genes that must be transported into the chloroplast to join with the other six polypeptides to make active ATPase.

Another notable example is the enzyme ribulose biphosphate carboxylase (RuBP carboxylase), which is composed of two polypeptides. The larger polypeptide, called rbcL, is a product of a chloroplast gene, whereas the smaller polypeptide is the product of a nuclear gene.

The last thirty or so genes remain unidentified. Their presence is inferred because they have DNA sequences that contain all the components found in active genes. These kinds of genes are often called “open reading frames” (ORFs) until the functions of their polypeptide products are identified.

Impact and Applications

The discovery that chloroplasts have their own DNA and the further elucidation of their genes have had some impact on horticulture and agriculture.

Several unusual, variegated leaf patterns and certain mysterious genetic diseases of plants are now better understood. The discovery of some of the genes that code for polypeptides required for photosynthesis has helped increase understanding of the biochemistry of photosynthesis.

The discovery that certain key chloroplast proteins, such as ATPase and RuBP carboxylase, are composed of a combination of polypeptides coded by chloroplast and nuclear genes also raises some as yet unanswered questions.

For example, why would an important plant structure like the chloroplast have only part of the genes it needs to function? Moreover, if chloroplasts, as evolutionary theory suggests, were once free-living bacteria-like cells, which must have had all the genes needed for photosynthesis, why and how did they transfer some of their genes into the nuclei of the cells in which they are now found?

Of greater importance has been the discovery that the DNA sequences of many chloroplast genes are highly conserved; that is, they have changed very little during their evolutionary history. This fact has led to the use of chloroplast gene DNA sequences for reconstructing the evolutionary history of various groups of plants.

Traditionally, plant systematists (scientists who study the classification and evolutionary history of plants) have used structural traits of plants, such as leaf shape and flower anatomy, to try to trace the evolutionary history of plants.

Unfortunately, there are a limited number of structural traits, and many of them are uninformative or even misleading when used in evolutionary studies. These limitations are overcome when gene DNA sequences are used.

A DNA sequence of a few hundred base pairs in length provides the equivalent of several hundred traits, many more than the limited number of structural traits available (typically much fewer than one hundred).

One of the most widely used sequences is the rbcL gene. It is one of the most conserved genes in the chloroplast genome, which in evolutionary terms means that even distantly related plants will have a similar base sequence.

Therefore, rbcL can be used to retrace the evolutionary history of groups of plants that are very divergent from one another. The rbcL gene, along with a few other very conservative chloroplast genes, has already been used in attempts to answer some basic plant evolution questions about the origins of some of the major flowering plant groups.

Less conservative genes and ORFs show too much evolutionary change to be used at higher classification levels but are extremely useful in answering questions about the origins of closely related species, genera, or even families. As analytical techniques are improved, chloroplast genes show promise of providing even better insights into plant evolution.

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8:57 PM
Chloroplasts
Chloroplasts
Plastids are highly specialized, double membrane-bound organelles found within the cells of all plants and algae. A type of plastid called the chloroplast is the cellular location of the process of photosynthesis.

Plastids exhibit remarkable diversity with respect to their development, morphology, function, and physiological and genetic regulation. Chloroplasts, a type of plastid, are arguably largely responsible for the maintenance and perpetuation of most of the major life-forms on earth through photosynthesis.

The process of photosynthesis uses visible light as an energy source to power the conversion of atmospheric carbon dioxide into organic molecules that can be used by living organisms.

As a by-product of photosynthesis, oxygen is released into the atmosphere and is used by living organisms in the energy-obtaining process of cellular respiration. Other plastid types are specialized for synthesis and storage of pigments, starch, and other secondary metabolites.

Plastid Structure


The typical plastid from the cell of a flowering plant is surrounded by a double membrane system consisting of an inner and outermembrane, with an intermembrane space between the two.

In chloroplasts, the photosynthetic pigments that are responsible for absorbing sunlight are located in the thylakoid membrane system. This continuous internal membrane system is found throughout the chloroplast stroma, an internal fluid matrix analogous to the cellular cytosol.

Granal thylakoids are organized into stacks, and the stromal thylakoids are unstacked and exposed to the stromal matrix. The internal space within the thylakoid membrane system is called the lumen.

The pigments and proteins involved in the light reactions of photosynthesis, the processes whereby light energy is converted into chemical energy, are embedded in the thylakoid membrane system. The dark reactions, or Calvin cycle, which is the carbon fixation pathway that leads to the formation of simple carbohydrates, occurs in the stroma.

Small starch granules and oil bodies, termed plastoglobuli, are often found in chloroplasts. These serve as energy storage reserves for the plant cell. Plastids other than chloroplasts typically lack thykaloids.

Proplastids

Plastids
Plastids
The developmental precursor to all plastid types is the proplastid. Proplastids are relatively undifferentiated plastids typically found in young, undifferentiated meristematic cells and tissues.

Under the appropriate cellular and environmental conditions, proplastids can undergo development and differentiation to any of three main plastid types: chloroplasts, chromoplasts, or leucoplasts.

Chloroplasts

Chloroplasts typically contain one or more of the three types of plastid chlorophylls (chlorophyll a, b, or c) and, often, members of the two classes of photosynthetic accessory pigments: carotenoids and phycobilins.

The most obvious and essential physiological process unique to chloroplasts is photosynthesis. In the energy transduction reactions (the light reactions), radiant energy in the form of visible light (mostly of the violet, blue, and red wavelengths) is harnessed primarily by the green pigment chlorophyll.

The harnessed energy is then used to phosphorylate adenosine diphosphate (ADP) to produce adenosine triphosphate (ATP) in a process termed noncyclic photophosphorylation and reduce the electron carrier nicotinamide adenine dinucleotide phosphate (NADP) to NADPH. Oxygen is liberated through the light-dependent oxidative splitting of water.

In the carbon-fixation reactions (often called the dark reactions, although they can occur in the presence of light) the ATP is used as an energy source for the attachment of atmospheric carbon dioxide to the simple sugar ribulose 1,5-bisphosphate (RuBP). The NADPH is used to facilitate the reduction of RuBP through a series of simple sugars in a biochemical set of reactions known as the Calvin cycle.

One of the products of this cycle, glyceraldehydes-3-phosphate (G3P), is used by the chloroplast to make glucose and other carbohydrates. G3P is also needed to perpetuate the Calvin cycle, so only one of every three produced is used for carbohydrate synthesis.

Chloroplasts
Chloroplasts
Chloroplasts are also the site of synthesis for the three aromatic amino acids: phenylalanine, tyrosine, and tryptophan.

The precursor compound aspartate is imported into chloroplasts from the cell cytosol and is used for the synthesis of the amino acids lysine, threonine, and isoleucine. An intermediate in the synthesis of threonine, called homoserine 4-phosphate, is exportedfromthe chloroplast into the cytosol as a precursor formethionine.

Thus, there is a strong integration of function among the chloroplast, cytosol, and nucleus, in that the enzymes involved in these amino acid biosynthetic pathways are nuclear-encoded, their mRNAs are translated using cytosolic ribosomes, and most of the biosynthetic enzymes are imported into the chloroplast.

Fatty acid biosynthesis is another biochemical function that occurs in chloroplasts. Fatty acids, as lipid precursors, might be either incorporated directly into chloroplast lipids via a plastid-localized biochemical pathway or exported into the cytoplasm for conversion into endoplasmic reticulum lipids.

Lipids found in the inner plastid membrane are plastid-synthesized, whereas those of the outer plastid membrane are synthesized in the endoplasmic reticulum.

Other Plastids

Other plastid types include chromoplasts, which typically contain carotene or xanthophyll pigments and are responsible for the colors of many fruits, flowers, and roots. Under some conditions chromoplasts can differentiate into chloroplasts. Leucoplasts are colorless and lack complex inner membranes.

One type of leucoplast, the amyloplast, synthesizes and stores starch. Other leucoplasts synthesize a wide range of products, including oils and proteins. Proplastids that are arrested during their normal development into chloroplasts are termed etioplasts. These typically are formed when developing plant tissues are deprived of light.

Evolutionary History

Plastids possess a number of features that provide insights into their remarkable evolutionary history. The chloroplasts of eukaryotic cells photosynthesize in a manner similar to the more ancient prokaryotic cyanobacteria by using membrane-bound chlorophyll to capture radiant energy.

Some plastids even bear a strong morphological similarity to cyanobacteria, being similar in size and having similar internal structures. Plastids divide by binary fission in a manner similar to bacterial reproduction.

Plastids also have a certain degree of autonomy in terms of their genetic system. Typically, the majority of flowering plant plastids contain multiple copies (50-100) of a circular chromosome, ranging in size from 130 to 180 kilobase pairs (kb) in higher plants. Chromosome size in algae is much more variable, ranging all the way from 57 kb to 1,500 kb.

The plastid chromosome contains genes for RNAs, such as rRNA(ribosomal RNA) and tRNA(transfer RNA), and structural genes that code for polypeptides involved in photosynthesis, transcription, protein synthesis, energy transduction, and several other functions. Many of the genes on the chloroplast chromosome are organized into clusters termed operons in a manner similar to that found in eubacteria.

The nucleotide sequences of many plastid genes, especially the ribosomal RNA genes, are highly similar to those in eubacteria, and the ribosomes found within plastids have a similar composition and size to eubacterial ribosomes.

The plastid-encoded genes are transcribed either by a nuclear-encoded or plastid-encoded RNA polymerase, and the resultant mRNAs are translated by plastid ribosomes found within the stroma. The majority of plastid biochemical processes rely on both nuclear-and plastid-encoded genes.

Some proteins, such as RuBP carboxylase/oxygenase (Rubisco), are composed of both nuclear- and plastid-encoded protein subunits, again demonstrating the remarkable coordination of biogenesis anddevelopment between organelle and cytosol.

This evidence lends strong support to the endosymbiotic theory of the origin of plastids. This theory, in essence, states that plastids were once free-living, autotrophic (having the ability to obtain carbon from carbon dioxide), prokaryotic cells that were engulfed through phagocytosis by an ancestral heterotrophic nucleated cell (a cell having a metabolism where carbon must be obtained from organic molecules) termed a protoeukaryote.

Typically this engulfment would result in the ingestion and subsequent destruction of the engulfed prokaryotic cell. However, in one—or perhaps several—independent incidents, a symbiotic relationship was gradually established between the engulfed photosynthetic bacterium and the protoeukaryote.

The captured bacterium provided an internal source of food production for the heterotrophic eukaryotic cell through photosynthesis. The bacterium, in turn, was provided with protection and a stable external environment in the cytosol of the eukaryotic cell.

To coordinate further the physiological and genetic interactions between the two, massive transfer of genes took place over time from the genome of the photosynthetic bacterium to the nuclear genome of the protoeukaryote, leading to the genetic capture and control of the photosynthetic endosymbiont.

Recent investigations have shown that this gene transfer event is an ongoing process, with examples of transfer documented in recent evolutionary time for both plastids and mitochondria in several different evolutionary lineages of flowering plants.
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11:34 AM
Chromatin
Chromatin
Chromatin is an inclusive term referring to DNA and the proteins that bind to it, located in the nuclei of eukaryotic cells. The huge quantity of DNA present in each cell must be organized and highly condensed in order to fit into the discrete units of genetic material known as chromosomes. Gene expression can be regulated by the nature and extent of this DNA packaging in the chromosome, and errors in the packaging process can lead to genetic disease.

Scientists have known for many years that the hereditary information within plants and other organisms is encrypted in molecules of deoxyribonucleic acid (DNA) that are themselves organized into discrete hereditary units called genes and that these genes are organized into larger subcellular structures called chromosomes.

James Watson and Francis Crick elucidated the basic chemical structure of the DNA molecule in 1952, and much has been learned since that time concerning its replication and expression.

At the molecular level, DNA is composed of two parallel chains of building blocks called nucleotides, and these chains are coiled around a central axis to form the well-known double helix.


Each nucleotide on each chain attracts and pairs with a complementary nucleotide on the opposite chain, so a DNA molecule can be described as consisting of a certain number of these nucleotide base pairs.

The entire human genome consists of more than six billion base pairs of DNA, which, if completely unraveled, would extend for more than 2 meters. It is a remarkable feat of engineering that in each human cell this much DNA is condensed, compacted, and tightly packaged into chromosomes within a nucleus that is less than 10–5 meters in diameter.

Plants typically have larger genomes than humans; for example, wheat has fifteen billion base pairs of DNA. By contrast, the most widely studied plant among current scientists is Arabidopsis. The species Arabidopsis thaliana was selected as a model organism in plant research because of its comparatively simple structure: Its 26,000 genes make up “only” 125 million base pairs.

Chromatin
Chromatin
What is even more astounding is the frequency and fidelity with which this DNA must be condensed and relaxed, packaged and unpackaged, for replication and expression in each individual cell at the appropriate time and place during both development and adult life. The essential processes of DNA replication or gene expression (transcription) cannot occur unless the DNA is in an open or relaxed configuration.

Chemical analysis of mammalian chromosomes reveals that they consist of DNA and two distinct classes of proteins, known as histone and nonhistone proteins. This nucleoprotein complex is called chromatin, and each chromosome consists of one linear, unbroken, double-stranded DNA molecule that is surrounded in predictable ways by these histone and nonhistone proteins.

The histones are relatively small, basic proteins (having a net positive charge), and their function is to bind directly to the negatively charged DNA molecule in the chromosome.

Five major varieties of histone proteins are found in chromosomes, and these are known as H1, H2A, H2B, H3, and H4. Chromatin contains about equal amounts of histones and DNA, and the amount and proportion of histone proteins are constant from cell to cell in all higher organisms, including the higher plants.

In fact, the histones as a class are among themost highly conserved of all known proteins. For example, for histone H3, which is a protein consisting of 135 amino acid “building blocks,” there is only a single amino acid difference in the protein found in sea urchins as compared with the one found in cattle.

This is compelling evidence that histones play the same essential role in chromatin packaging in all higher organisms and that evolution has been quite intolerant of even minor sequence variations between vastly different species.

Nonhistones as a class of proteins are much more heterogeneous than the histones. They are usually acidic (carrying a net negative charge), so they will most readily attract and bind with the positively charged histones rather than the negatively charged DNA.

Each cell has many different kinds of nonhistone proteins, some of which play a structural role in chromosome organization and some of which are more directly involved with the regulation of gene expression. Weight for weight, there is often as much nonhistone protein present in chromatin as histone protein and DNA combined.

Nucleosomes and Solenoids

The fundamental structural subunit of chromatin is an association of DNA and histone proteins called a nucleosome. First discovered in the 1970’s, each nucleosome consists of a core of eight histone proteins: two each of the histones H2A, H2B, H3, and H4.

Around this histone octamer is wound 146 base pairs of DNA in one and three-quarters turns (approximately eighty base pairs per turn). The overall shape of each nucleosome is similar to that of a lemon or a football.

Nucleosomes and Solenoids
Nucleosomes

Each nucleosome is separated from its adjacent neighbor by about fifty-five base pairs of linker DNA, so that in its most unraveled state they appear under the electron microscope to look like tiny beads on a string. Portions of each core histone protein protrude outside the wound DNA and interact with the DNA that links adjacent nucleosomes.

The next level of chromatin packaging involves a coiling and stacking of nucleosomes into a ribbonlike arrangement, which is twisted to form a chromatin fiber about 30 nanometers in diameter, commonly called a solenoid.

Formation of solenoid fibers requires the interaction of histone H1, which binds to the linker DNA between nucleosomes. Each turn of the chromatin fiber contains about twelve hundred base pairs (six nucleosomes), and the DNA has now been compacted by about a factor of fifty.

The coiled solenoid fiber is organized into large domains of 40,000 to 100,000 base pairs, and these domains are separated by attached nonhistone proteins that serve both to organize and to control their packaging and unpackaging.

Loops and Scaffolding

Physical studies using the techniques of X-ray crystallography and neutron diffraction have suggested that solenoid fibers may be further organized into giant supercoiled loops.

The extent of this additional looping, coiling, and stacking of solenoid fibers varies, depending on the cell cycle. The most relaxed and extended chromosomes are found at interphase, the period of time between cell divisions.

Interphase chromosomes typically have a diameter of about 300 nanometers. Chromosomes that are getting ready to divide (metaphase chromosomes) have the most highly condensed chromatin, and these structures may have a diameter of up to 700 nanometers.

One major study on the structure of metaphase chromosomes has shown that a skeleton of nonhistone proteins in the shape of the metaphase chromosome remains even after all of the histone proteins and the DNA have been removed by enzymatic digestion. If the DNA is not digested, it remains in long loops (10 to 90 kilobase pairs) anchored to this nonhistone protein scaffolding.

Impact and Applications

Studies on chromatin packaging continue to reveal the details of the precise chromosomal architecture that results from the progressive coiling of the single DNA molecule into increasingly compact structures. Evidence suggests that the regulation of this coiling and packaging within the chromosome has a significant effect on the properties of the genes themselves.

In fact, errors in DNA packaging can lead to inappropriate gene expression and developmental abnormalities. In humans, the blood disease thalassemia, several neuromuscular diseases, and even male sex determination can all be explained by the altered assembly of chromosomal structures.

The unifying lesson to be learned from these examples of DNA packaging and disease is that DNA sequencing studies and the construction of genetic maps will not by themselves provide all the answers to questions concerning genetic variation and genetic disease.

An understanding of genetics at the molecular level depends not only on the primary DNA sequence but also on the three dimensional organization of that DNA within the chromosome. Compelling genetic and biochemical evidence has left no doubt that the packaging process is an essential component of regulated gene expression.

10:51 AM
Chromatography
Chromatography
Chromatography is a method of separating the components of a mixture over time. Chromatography has allowed for the discovery of many specialized pigments, including at least five forms of chlorophyll.

Chromatography was first described in 1850 by a German chemist, Friedlieb Ferdinand Runge. It was not until the early twentieth century, however, that Mikhail Semenovich Tsvet became the first to explain the phenomenon and methods of this analytical tool.

Chromatography and Photosynthesis

Tsvet’s chromatography of plant leaf pigments prompted scientific investigations of photosynthesis—the all-important biochemical reaction that transforms inorganic to organic energy and therefore is at the base of most life. Chromatography has revealed that many different pigments, not only green ones, are simultaneously present in leaves.

Each pigment absorbs only certain colors of light from sunlight, rather than absorbing all the incident light energy that falls upon it. Each pigment behaves as though it has a tiny “window” that allows the energy of certain wavelengths of light to be harvested.


These little bundles of energy are quantized, or set, amounts of energy, and they are unique for each different type of pigment. (White sunlight is actually composed of a broad range of wavelengths, with the visible wave lengths appearing as a rainbow of colors when passed through a prism.)

Paper chromatography has allowed for the discovery of many specialized pigments, including at least five forms of chlorophyll. Chlorophyll pigments are now known to include chlorophylls a through e.

Also, many different forms of carotenes and xanthophylls exist. Paper chromatography reveals that red and yellow pigments are always present in the leaves of deciduous trees and shrubs and not just during the fall color change.

paper chromatography
paper chromatography

Because of the high abundance of the green chlorophyll pigments, as compared with the bright reds of carotenes or yellows of xanthophyll, only the dominant green hues are generally seen. In the fall, deciduous trees show a loss of chlorophyll pigments, thereby revealing the brilliant foliage associated with an autumn forest.

Once pigments are separated from one another, they can be chemically characterized and further studied. Carotenes and xanthophylls have been discovered to be of similar chemical composition, with each being made of forty carbon atoms covalently bonded to one another. Different arrangements of these covalent bonds produce the different colors of red and orange.

paper chromatography
paper chromatography

Chromatography has allowed scientists the opportunity to trace the path that carbon atoms follow through every tiny increment of the photosynthetic process.

Paper chromatography, coupled with radioisotopic studies of carbon-labeled (with radioactive carbon 14) compounds, eventually led to the ability to describe the carbon-containing products of each step in the series of reactions of photosynthesis.Today this pathway is called the Calvin cycle.

Methodology

A classical demonstration of chromatographic principles utilizes techniques that allow plant pigments to be isolated. Spinach leaves are an excellent tool for the identification of four pigments: chlorophyll a, chlorophyll b, carotene, and xanthophyll.

The stationary phase is a piece of chromatography paper with a dried spot of the plant extract near one end. The mobile phase is an acetone-ligroin mixture, a nonpolar (hydrophobic) solvent mixture.

The paper is placed with a small portion of the end with the pigment spot in the solvent, the mobile phase. As the acetone-ligroin mobile phase comes into contact with the paper, capillary action allows the liquid to travel upward, against gravity.

The mobile phase has a migrating moisture line, or leading line of wetness, which is called the solvent front. As the solvent travels over the spot, each of the pigments will travel with the mobile phase at different rates from the original spot. Some pigments will adhere to the paper more strongly than others, and thus travel shorter distances along the paper.

Yellow-green chlorophyll b travels the least distance with the mobile phase. Chlorophyll b is a more polar (water-loving) pigment than the other pigments found in spinach extracts and is therefore more strongly attracted to the polar surface of the paper than to the nonpolar solvent.

The remaining pigments travel increasing distances with respect to chlorophyll b, beginning with blue-green chlorophyll a, followed by yellow-orange xanthophyll and, finally, the orange pigment of carotene.

Carotene moves the farthest because it is the most nonpolar of the pigments and it is attracted more strongly to the acetone-ligroin mixture (mobile phase) than to the paper. This stronger, nonbonded interaction with the mobile phase indicates that carotene is the most nonpolar pigment found in spinach chloroplasts.

Once the solvent front is about half an inch from the top of the paper strip, the strip is removed from the chamber. A pencil line must be drawn immediately across the top of the strip to indicate how far up the paper the mobile phase traveled. The paper strip is then referred to as a chromatogram.

The Rf value is a numerical constant that is unique for each of the four pigments identified in spinach. The ratio of the distance each pigment travels, as compared with the distance traveled by the mobile phase (from the start to finish lines),will be unique to that pigment alone.

Thus, chlorophyll b will not switch places with carotene on the chromatogram because of the unique interactions it has with the stationary and mobile phases. For this reason, the Rf values determined by the method described above can be generated repeatedly by anyone using this method.

Types of Chromatography


As performed by Runge and Tsvet, chromatography has evolved from the days of paper, chalk, and dyes into a computerized and versatile instrumentation requiring expert training and a significantly larger budget.

Thin-layer chromatography (TLC) is useful in protein chemistry. The stationary phase of this method consists of thin gel applied to a plastic or glass plate (strip). Various gels can be used to coat the plate. Some coatings may be polar, while others may be nonpolar.

Column chromatography can look for the amounts and types of vitamins in food or diet supplement tablets. Pigments, steroids, alkaloids, and carbohydrates all can be identified and measured using an appropriate column-chromatographic system. Many recent advances in column chromatography now allow for isolation and purification of proteins, DNA, RNA, and many other biological molecules.

High-pressure liquid chromatography (HPLC) can purify biologically important enzymes from living systems without destroying the biological activity of the enzyme. In gas chromatography (GC), an inert gas such as helium or nitrogen flows through several feet of a packed and coiled column. The gas acts as the mobile phase by sweeping the sample through the column.

The packing is often a solid material, but liquid-coated solid particles are also used. Paper chromatography continues be a popular method for analysis of plant pigments, dyes, inks, and food colorings. It is largely used, however, in academic settings to demonstrate the principles of chromatography.
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9:34 AM
Chromosomes
Chromosomes

Chromosomes contain the genetic information of cells. Replication of chromosomes assures that genetic information is correctly maintained as cells divide.

The genome of an organism is the sum total of all the genetic information of that organism. In eukaryotic cells, this information is contained in the cell’s nucleus and organelles, such as mitochondria and plastids. In prokaryotic organisms (bacteria and archaea), which have no nucleus, the genomic information resides in a region of the cell called the nucleoid.

A chromosome is a discrete unit of the genome that carries many genes, or sets of instructions for inherited traits. Genes, the blueprints of cells, are specific sequences of deoxyribonucleic acid (DNA) that code for messenger ribonucleic acids (monas), which in turn direct the synthesis of proteins.

Each eukaryotic chromosome contains a single long DNA molecule that is coiled, folded, and compacted by its interaction with chromosomal proteins called histone. This complex of DNA with chromosomal proteins and chromosomal RNAs is chromatin.


DNA of higher eukaryotes is organized into loops of chromatin by attachment to a nuclear scaffold. The loops function in the structural organization of DNA and may increase transcription of certain genes by making the chromatin more accessible.

To maintain the genetic information of a cell, it is essential that chromosomes correctly replicate and divide as a cell divides. After DNA replication, chromosomes separate in a process called mitosis.

During this process, the nuclear envelope breaks down and chromosomes condense into compact structures. A cellular structure known as the mitotic spindle forms, pulling pairs of replicated chromosomes apart so that the two cells receive identical sets of chromosomes.

Chromosomes are readily visualized when they condense during cell division. All the chromosomes of a cell visualized during mitosis constitute that cell’s karyotype.

Each chromosome has a centromere—a constricted area of the condensed chromosome where the mitotic or meiotic spindle attaches to assure correct distribution of chromosomes during cell division—and a telomere, the end or tip of a chromosome, which contains tandem repeats of a short DNA sequence.

The number of chromosomes in a gamete (either egg or sperm) is the haploid number, n. The haploid number of chromosomes in humans is 23; in corn, 10; in peas, 7; in Arabidopsis (the model organism used in much botanical research), 4.

Some carp and some ferns have more than 50 chromosomes in the haploid genome. Pollen grains of some plants, such as pear, contain three haploid cells: One directs the growth of the pollen tube down the style to the ovary; the other two are sperm.

In flowering plants (angiosperms), there is a unique double fertilization where by one sperm nucleus fuses with the egg nucleus to form the diploid (2n) zygote, and the other sperm nucleus fuses with two polar nuclei to form the triploid nutritive tissue, or endosperm, which will nourish the embryo in the seed.

The zygote then increases in cell number by mitosis, a type of cell division during which chromosomes in a nucleus are replicated and then separated to form two genetically identical daughter nuclei.

schematic of chromosome
schematic of  a chromosome

This is followed by cytokinesis, the process of cytoplasmic division, which results in two daughter cells, each having the same number of chromosomes and genetic composition as the parent cell. The mature 2n plant forms the haploid (n) gametes by meiosis, a type of cell division that reduces the number of chromosomes to the haploid number.

A distinctive feature of plant cell division is the plant cell has three genomes (the nuclear, mitochondrial, and plastid genome) to replicate and divide. The chromosomes of eukaryotes consist of unique genes among a complex pattern of repeated DNA sequences. Arabidopsis has only 4 chromosomes containing about 120 million base pairs.

There are typically between twenty and one hundred copies of the mitochondrial genome per mitochondrion, ranging in size from two hundred to twenty-four hundred kilobase pairs (or kb; one kilobase pair equals one thousand base pairs).

Plant mitochondrial genomes are much larger than the mitochondrial genomes of yeast or animals. Chloroplast genomes range in size from 130 to 150 kb, with 50 to 150 copies of that genome per plastid.

In cell division in plant cells, the two daughter nuclei are partitioned to form two separate cells by a cell plate that grows at the equator of the mother cell. In animal cells, this separation involves the constriction of the cell at a central contractile ring. DNA replication is strictly controlled during the cell cycle.

DNA synthesis occurs in the synthesis (S) phase, beginning at origins of replication distributed around the genome, occurring on average every 66 kb in dicotyledonous plants and on average every 47 kb in monocotyledonous plants.

Heterochromatin is the term for regions of chromosomes that are permanently in a highly condensed state, are not transcribed, and are late-replicating.

chromosomes made out of
chromosomes made out of

Heterochromatin contains highly repeated DNA sequences. Euchromatin is the rest of the chromosomes that is extended, accessible to RNA polymerase, and at least partially transcribed.

Some plants and animals have extra chromosomes that do not seem to be essential. These are called accessory or supernumerary chromosomes. They have been most studied in corn where these extra chromosomes are called B-chromosomes. B-chromosomes are usually highly condensed heterochromatin that may or may not be present in an individual of that species.

An increase in the copy number of the genome is common in plants and animals, occurring during the development of individuals. Polyploids have three or more complete sets of chromosomes in their nuclei instead of the two sets found in diploids. For example, in Arabidopsis, tissues of increasing age have an increase in polyploidy, reaching up to sixteen duplications.
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