Notes 

Chap 19 Genetics of Viruses and Bacteria /Chap 20 Developmental Genetics. (p.391-433)

  Certain nonliving things also have genomes. Viruses are nonliving particles with nucleic acid genomes. Why viruses are considered nonliving? They do not exhibit all seven properties associated with living organisms.  Viruses are not composed of cells, and by themselves, they do not carry out metabolism, use energy, maintain homeostasis, or even reproduce. A virus or its genetic material must be taken up by a living cell to replicate.

Pathogens are agents that cause disease symptoms in their host. 

   The first virus to be found was TMV or Tobacco Mosaic Virus

A virus is a small infectious particle that consists of nucleic acid enclosed in a protein coat.

Researchers have identified over 4,000 viruses

  Vary in Host range, structure, and genome composition.

GROUP QUESTIONS

  Brain and CNS: Flavivirus-yellow fever Rhabdovirus-rabies.

  Skin: Herpes simplex I-cold sores Variola virus-smallpox.

  Respiratory tract: influenza virus-flu Rhinovirus-common cold.

  Immune system: Rubella virus-measles Human immunodeficiency virus-AIDS Epstein-Barr virus-mononucleosis.

  Digestive system: Hepatitis B virus-viral hepatitis Rotavirus-viral gastroenteritis Norwalk virus-viral gastroenteritis.

  Reproductive system: herpes simplex II-genital herpes Papillomavirus-warts, cervical cancer.

  Blood: Ebola virus-hemorrhagic fever Hantavirus-hemorrhagic fever with renal syndrome.

  A cell that is infected by a virus is called a host cell, and a species that can be infected by a specific virus is called a host species for that virus. Viruses differ greatly in their host range-the number of species and cell types the can infect

Host Range is the number of species and cell types a virus can infect.

Difference in Host Range:

TMV is known to infect over 150 species of plants but by comparison many viruses have a narrow host range

A virus may infect only a specific cell type in a host species

Most viruses are smaller than the wavelength of visible light (20-400nm in diameter)

Difference in structures:

All viruses have a protein coat called a capsid that encloses a genome consisting of one or more molecules of nucleic acid

Capsids are composed of several protein subunits called capsomers

Many viruses that infect animal cells, such as influenza, have a viral envelope enclosing the capsid

Bacteriophages (phages) are viruses that infect bacteria

Differences in genome:

The genetic material of a virus is called a viral genome

The composition of a viral gnome varies mostly among different types of viruses

Viruses reproduce by mobilizing their host cells to produce new viruses

When a virus infects a host cell, the expression of viral genes leads to a series of steps, called a viral reproductive cycle that produces new viruses

Step 1: Attachment

Attaches to specific cells or binds to molecules on the cells surface

Step 2: Entry

Once attached the virus injects the capsid and its contents into the cytosol. Once it has entered it can either move to step 3 or 4.

Step 3: Integration

Viruses that are capable of integration carry a gene that encodes and enzyme called integrase.  For integration to occur, the gene is expressed soon after entry so that integrase protein is made. Integrase cuts chromosomal DNA and inserts the viral genome into the chromosome. Once integrated, the phage DNA in a bacterium is called a prophage. While it’s a prophage, this type of viral reproductive cycle is called the lysogenic cycle. New phages are not made during this cycle and the host cell is not destroyed. For an RNA virus to integrate the viral genome must be copies into DNA by means of a viral enzyme called reverse transciptase. Reverse transcriptase is carried within the capsid along with the viral RNA. Reverse transcriptase uses the viral RNA strand to make a complimentary copy of DNA, and then it uses the DNA as a template to make double-stranded viral DNA. This process is called reverse transcription. Once the RNA enters the host cell nucleus and is inserted into the chromosome via integrase it becomes a eukaryotic cell called a provirus. Viruses that follow this mechanism are called retroviruses.

Step 4: Synthesis of Viral Components

The production of new viruses by a host cell involves the replication of the viral genome and the synthesis of viral proteins which make up the protein coat. For bacteriophages that have been integrated into the host chromosome, the prophage must be excised before synthesis of new virus components. An enzyme called excisonase is needed for this process.

Step 5: Viral Assembly

Viruses with a simple structure self assemble while others need help from a noncapsid proteins not found in the complete phage particle.

Step 6: Release

The release of the bacteriophage is a dramatic event because the phages must burst, or lyse, their host cell in order to escape. The enzyme lysozyme digests the bacterial cell wall, causing it to burst. Lysis releases many new phages into the environment where they can infect other bacteria. Collectively steps 1,  2, 4, 5, and 6 are called the Lytic cycle because they lead to cell lysis. The release of enveloped viruses is less dramatic and it escapes by a mechanism called budding. This happens when the membrane enfolds the viral capsid and eventually buds from the surface of the cells, this does not lyse the cell.

Latency of bacteriophages:

When viruses integrate into their genomes the prophage or provirus may remain inactive, or latent, for a long time. Most of the viral genes are silent during latency. Latency in bacteriophages can also be called lysogeny. When this occurs the prophage and its host cell are said to be called lysogenic. When lysogenic bacterium prepares to divide it copies the prophage DNA and also its DNA so each daughter cell can have a copy of the prophage. The prophage can be replicated this way repeatedly without harming the host cell or making new phage particles. This is called the lysogenic cycle. Bacteriophages can alternate between lysogenic and lytic cycles. When a bacteriophages spends some of its time in the lysogenic cycle it is called a temperate phage. Virulent phages have only lytic cycles.

Latency in human viruses:

This can happen in two ways. Latency occurs because the virus has integrated into the host genome and may remain dormant for long periods of time. In, addition the genomes of other viruses can exist as an episome—a genetic element that can replicate independently of the chromosomal DNA but also can occasionally integrate into chromosomal DNA

Emerging viruses—are viruses that have arisen recently or are likely to have a greater probability of causing infection. The most devastating example has been human immunodeficiency virus (HIV), the causative agent of acquired immune deficiency syndrome (AIDS) 

Viroid—an infectious particle made solely of RNA

Prions—composed solely of proteins

START HERE

Nucleoid-a tight package of bacterial chromosomes

Loop domains—chromosomal segments that are folded into loops

DNA supercoiling is a second important way to compact the bacterial chromosome

Plasmids—small circular pieces of DNA that exist separately from the bacterial chromosome

Bacterial colony—cells that undergo repeated circular divisions and form a clone of genetically identical cells

Binary fission—a much simpler process during which a cell divides into two daughter cells

Strain—refers to a lineage that has genetic differences compared to another strain

Gene transfer—genetic material is transferred from one bacterial cell to another

Bacterial Conjunction—a process that involves a direct physical interaction between two bacterial cells

Transformation—a process where DNA that is released into the environment is taken up by another bacterial cell

Transduction—occurs when a virus infects a bacterial cell and the transfers some of that cell’s DNA to another bacterium

F factor—fertility factor

Sex pili—made up of F+ cells that bind specifically to F- cells

Competent—bacterial strains that have the ability to take up DNA

Horizontal gene transfer—refers to the process in which an organism incorporates genetic material from one organism without being the offspring of that organism

Acquired antibiotic resistance—refers to the common phenomenon of a previously susceptible strain becoming resistant to a specific antibiotic

Chapter 20 Developmental Genetics. (p. 391-410)

  The process, called pattern formation, gives rise to the formation of a body with a particular morphology. Pattern formation in animals is usually organized along three axes: the dorsoventral axis, the anteroposterior axis, and the left-right axis. In plants there is a root-shoot axis and a radial pattern.

  Positional information. For an organism to develop the correct morphological features or pattern, each cell of the body must become the appropriate cell type based on its position relative to other cells.

  A cell may respond to positional information in one of four ways: cell division, cell migration, cell differentiation, and cell death.

         Developmental genetics is science concerned with understanding how gene expression controls the process of development.

  Apoptosis is a necessary event during normal animal development. Apoptosis is known to play a key role in sculpting the bodies of animals. In plants, programmed cell death is also important during development.

  Cell division with accompanying cell growth increases the size of the limb. Cell migration is also important in this process, embryonic cells that eventually form muscles in the arm and hand must migrate long distances to reach their correct location within the limb.

  Cell differentiation produces the various tissues that will eventually be found in the fully developed limb.

  Finally, apoptosis is important in the formation of fingers. If apoptosis did not occur, a human hand would have webbed fingers.

  Morphogens impart positional information and promote development changes at the cellular level. A morphogen influences the fate of a cell by promoting cell division, cell migration, cell differentiation, or apoptosis.

  At a high concentration, a morphogen will restrict a cell into a particular development pathway, whereas at a lower concentration, it will not.

  Threshold concentration above which the morphogen will exert its effects. Morphogens typically are distributed asymmetrically along a concentration gradient.

         Oocyte is a cell that matured into an egg cell.

  The process by which a cell or group of cells governs the development fate of other cells is known as induction.

  Cell adhesion is how each animal cell makes its own collection of surface receptors that enable it to adhere to other cells and to the extracellular matrix (ECM). Such receptors, known as cell adhesion molecules (CAMs).

  Four general phases of pattern formation in an animal. The first phase organizes the body along major axes. The anteroposterior axis determines the organization from head to tail; the dorsoventral axis governs the structure from back (dorsal) to front/abdomen side to side. During the second phase, the body becomes organized into smaller regions that will eventually contain organs and other structure such as legs.

  In the third phase, the cells within the segments organize themselves in ways that will produce particular body parts.

  Forth phase, the cells themselves change their morphologies and become differentiated.

  A hierarchy of transcription factors control whether or not certain genes are expressed at a specific phase of development in a particular cell type, a phenomenon called differential gene regulation. Many morphogens, particularly those that act at an early phase of development, function as transcription factors. Such transcription factors regulate the expression of genes in a way that controls the formation of the body axes.

  Phase 1: transcription factors determine the formation of the body axes and control the expression of transcription factors of Phase 2.

  Phase 2: transcription factors cause the embryo to become subdivided into regions that have properties of individual segments. They also control transcription factors of phase 3.

  Phase 3: transcription factors cause each segment and groups of segments to develop specific characteristics. They also control transcription factors of phase 4.

  Phase 4: transcription factors cause cells to differentiate into specific cell types such as skin, nerve, and muscle cells.

  The oocyte is critical to establishing the pattern of development that will ultimately produce an adult organism. It is an elongated cell that contains positional information.

  In Drosophila, the segments can be grouped into three general areas: the head, the thorax, and the abdomen.

  A larva which is a free-living organism that is morphologically very different from the adult. After the third larval stage, the organism becomes a pupa.

  Through a process known as metamorphosis, the organism transforms into a mature adult and emerges from the pupal case. From beginning to end, this process takes about 10 days.

  Pattern formation is the establishment of the body axes, which occurs before the embryo becomes segmented.

  Certain morphogens, which are important in early development stages, are deposited asymmetrically within the egg as it develops. Later, after the egg has been fertilized and development begins, these morphogens will initiate developmental programs that govern the formation of the body axes of the embryo.

  Bicoid: during normal oocyte development, the bicoid gene product accumulates in the anterior region of the oocyte. This gene product later acts as a morphogen to cause the development of the anterior end of the embryo.

  How does the bicoid gene product accumulates in the anterior region of the oocyte? The answer involves specialized nurse cells that are found next to the oocyte, which matures in a follicle within the ovary of a female fly, nurse cells supply the products (for example, mRNA) of maternal effect genes to the developing oocyte.

  In drosophila, the bicoid gene is transcribed in the nurse cells, and bicoid mRNA is then transported into the anterior end of the oocyte and trapped there concentrated near the anterior end of the oocyte. After fertilization, the bicoid mRNA is translated, and a gradient pf Bicoid protein is established across the zygote.

  The Bicoid protein is a morphogen that function as a transcription factor to activate particular genes at specific times. The ability of Bicoid to activate a given gene depends on its concentration.

  A high concentration of Bicoid stimulates the expression of a gene called hunchback (that also encodes a transcription factor) in the anterior half of the embryo, but its concentration is too low in the posterior half to activate the hunchback gene.

  The second phase of pattern formation is the development of segments. The normal Drosophila embryo is subdivided into 15 segments: three head segments, three thoracic segments, and nine abdominal segments, the second thoracic segment (T2) produces a pair of legs and a pair of wings.

  Segmentation genes, genes that alter the segmentation pattern of the Drosophila embryo and larva.

  Three classes: gap genes, pair-rule genes, and segment-polarity genes adjacent segments are missing in the larva-a gap occurs.

  Pair-rule gene may cause alternating segments or parts of segments to be absent.

  Segment-polarity gene mutations cause portions of segments to be missing and cause adjacent regions to become mirror images of each other.

  In general, the products of maternal effect genes such as bicoid, which promote the formation of body axes, activate gap genes.

  You follow the progression from maternal effect genes to segment-polarity genes, notice that a body pattern in emerging in the embryo that matches the segmentation pattern found in the larva and  adult animal.

  During the third phase of pattern formation, each segment begins to develop its own unique characteristics, fate to describe the ultimate morphological features that a cell or group of cells will adopt.

  In Drosophila, the cells in each segment of the body have their fate determined at a very early stage of embryonic development, long before the morphological features become apparent.

  Homeotic genes, each homeotic gene specifies the fate of a particular segment or region of the body.

  Homeotic mutation, in a normal fly, two wings are found on the second thoracic segment, and two halters, which together function as a balancing organ that resembles a pair of miniature wings, are found on the third thoracic segment. In this mutant fly, the third thoracic segment has the characteristics of the second, so the fly has no halters and four wings. The term bithorax refers to the duplicated characteristics of the second thoracic segment.

  Drosophila has eight homeotic genes that are found in two clusters called the Antennapedia complex and the bithorax complex. Both of these complexes are located on the same chromosome, but a long stretch of DNA separates them, the order of homeotic genes along the chromosome correlates with their expression along the anteroposterior axis of the body. This phenomenon is called the colinearity rule; lab is expressed in the anterior segment and governs the formation of mouth structures.

  The role of homeotic genes in determining the identity of particular segments has been revealed by mutations that alter their function, a mutation in the Antp genes has been identified in which the gene is incorrectly expressed in an anterior segment. A fly with this mutation has the bizarre trait in which it develops legs where antennae are normally found.

  Homeotic genes encode homeotic proteins that function as transcription factors. The coding sequence of homeotic genes contains a 180-bp sequence known as a homeobox.

  The homeobox is also found in other genes affecting pattern formation. The homeobox encodes a region of the protein called a homeodomain, which can bind to DNA. The arrangement of α helices in the homeodomain promotes the binding of the protein to the DNA.

     The primary function of homeotic proteins is to activate the transcription of specific genes that promote developmental changes in the animal.

     Designated HoxA, HoxB, HoxC and HoxD. Hox genes, an abbreviation for homeobox-containing genes. Thirty-eight genes are found in the four clusters, which represent 13 different genes types. As shown.

     During the fourth phase of pattern formation, the emphasis shifts to cell differentiation.

     Though muscle and nerve cells contain the same set of genes, they regulate the expression of their genes in very different ways.

     Muscle and nerve cells express different proteins that affect the characteristics of the respective cells in distinct ways.

MONDAY!

     Stem cells, undifferentiated cells that divide and supply the cells that constitute the bodies of all animals and plants. Stem cells have two common characteristics. First, they have the capacity to divide, and second, their daughter cells can differentiate into one or more specialized cell types. The two daughter cells that are produced from the division of a stem cell can have differentiated into a specialized cell type. For example, in mammals, this mechanism is needed to replenish cells that have a finite life span, such as skin cells and red blood cells.

     The ultimate stem cell is the fertilized egg. A fertilized egg is considered to be totipotgent because it can produce all of the cell types in the adult organism. Blastocyst, contains embryonic stem cells (ES cells), which are found in the inner cell mass. Embryonic stem cells are pluripotent, which means they can also differentiate into every or nearly every cell type of the body. However, a single embryonic stem cell by itself has lost the ability to produce an entire, intact individual.

     The cells that later give rise to sperm or eggs cells, known as the embryonic germ cells (EG cells), also are pluripotent.

     Adults have multipotent and unipotent stem cells. A multipotent stem cell can differentiate into several cell types, but far fewer than an embryonic stem cell. For example, hematopoietic stem cells (HSCs) found in the bone marrow give rise to multiple blood cell types.

     A unipotent stem cell produces daughter cells that differentiate into only one cell type.

     Why are researchers so interested in stem cells? A compelling medical reason is their potential to treat human diseases or injuries that cause cell and tissue damage.

     Nerve: implantation of cells into the brain to treat Parkinson disease; treatment of spinal cord injuries.

     Skin: treatment of burns and skin disorders.

     Cardiac: repair of heart damage associated with heart attacks.

     Cartilage: repair of joints damaged by injury or arthritis.

     Bone: repair or replacement of damaged bone.

     Liver: repair or replacement of liver tissue damaged by injury or disease.

     Skeletal muscle: repair or replacement of damaged muscle.

Determined, differentiated, morphology and function, pattern formation, cell division, cell migration, cell differentiation, and apoptosis, cell migration does not occur in plants.

Morphogens and cell adhesion are ways that cells obtain positional information.

Fertilized oocyte, embryo, larvae, pupa, and an adult.

Maternal effect genes control the formation of body axes, development of segmentation.

Homeotic genes control the development of a particular segment or group of segment.

TUESDAY!

PLANTS

Meristems are organized groups of actively dividing stem cells.

Apical Region produces leaves and flowers of a plant.

Central Region creates the stem of a plant.

Basal Region produces the roots of a plant.

Organizing Center ensures proper organization of the meristem and preserves the correct number of actively dividing cells.

Central Zone is an area where undifferentiated stem cells are always maintained.

Peripheral Zone contains dividing cells that eventually differentiate into plant structures.

Apical-Basal-Patterning Genes are a category of genes important in early stages of plant development.

Sepal protect the flower bud before it opens. Part of the first whorl.  Four of them

Petals are part of the second whorl. There are four of them.

Stamens are part of the third whorl. There are six.

Carpels are part of the fourth whorl. Produce enclose and nurture the female gametophytes. There are two of them.

ABC Model proposed by Elliot Meyerowitz and Enrico Coen that models flower development.