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Micro Final

Terms in this set (570)

Bacteria and Archaea have nuclear material roaming free in the
cytoplasm
Eukaryotes have a
nucleus
Bacteria's cell wall is made up of
peptidoglycan
Archaea's cell wall is
distinct from bacteria and eukaryotes
Bacteria and Archaea have
no membrane bound organelles
All bacteria contain
-Cell (cytoplasmic) membrane
-Bacterial chromosome or nucleoid
-Ribosomes
-Cytoplasm
Bacteria cells all carry out the necessary life activities such as
Reproduction, Metabolism, and Nutrient Processing
Bacteria acts as a group through
Colonies and Biofilms
Three shapes of Bacteria
-Coccus: spheres, oval, bean shaped, pointed
-Bacillus: cylindrical
-Spirillum: rigid helix
Pleomorphism
is a variation in size and shape among cells of a single species
Arrangement and group of cocci
-Tetrads: group of four
-Staphylococci: irregular clusters
-Streptococci: chains of a few to hundreds of cells
-Sarcina: cubical packet of 8, 16, or more cells
Arrangement and group of bacilli
-Diplobacilli: pairs of cells with their ends attached
-Streptobacilli: chains of cells
-Palisades: cells of a chain remain partially attached and fold back which creates a side-by-side row of cells.
Spirilla
is occasionally found in short chains
Spirochetes
rarely remain attached after cell division
There are 2 major groups of appendages
-Flagella and Axial Filaments
-Fimbriae and Pili
Flagella and Axial Filaments
provide motility
Fimbriae and Pili
provide attachment points or channels
If flagella are polar that means they are
attached at one or both ends of the cell.
Monotrichous is a
single flagellum
Lophotrichous is flagella with
small bunches or tufts
Amphitrichous is when there is
flagella at both ends of the cell
Peritrichous is when flagella are
dispersed randomly over the surface of the cell
Chemotaxis is movement in response to
chemical signals
Positive chemotaxis is movement of a cell in the direction of a
favorable chemical stimulus
Negative chemotaxis is movement of a cell away from a
repellant or potentially harmful compound
There are different ways the flagella function
-Run
-Tumble
-Phototaxis
Run
Counterclockwise movement of the flagella. The cell swims in a smooth, linear direction toward a stimulus
Tumble
Flagellum reverses direction, causing the cell to stop and change course. Repellants cause numerous tumbles
Phototaxis is when the flagella moves
towards the light
Axial Filament are two or more long coiled threads which are found in
Spirochetes. Where internal flagellum are enclosed between the cell wall and the cell membrane.
Attachment can enhance
pathogenicity in some bacteria.
Pilus and Fimbria both provide
adhesion but not movement.
Fimbriae are small bristle-like fibers sprouting off the surface of certain species of bacteria
There composition varies but most of them contain protein. They have inherent tendency to stick to each other and to all surfaces.
Fimbria are responsible for the formation of
biofilms.
Pili is also known as
sex pilus
Pili are long, rigid tubular structures made of
pilin protein. They are only found in gram-negative bacteria. Used in conjugation, the partial transfer of DNA from one cell to another.
Production of Pili is controlled
genetically
S layer is thousands of copies of a
single protein linked together
S layer provides protection from
environmental condition and only produced in hostile environments.
Glycocalyx Slime Layer
forms loosely around the cell and protects the cell from loss of water and nutrients.
Glycocalyx Capsule
More tightly bound to a cell that a slime layer is and it is denser and thicker than a slime layer.
Capsules are formed by
pathogenic bacteria. Protects the bacteria against phagocytic white blood cells.
Biofilms infect long-term
indwelling artificial devices. Example: Plaque on teeth protect bacteria.
The Cell Envelope is composed of two or three basic layers
-Cell Wall
-Cell Membrane
-Outer Membrane (in some bacteria)
The Cell Envelope act as a single
protective unit
Gram Stain was developed in
1884 by Hans Christian Gram.
The Gram Stain delineates two major groups of bacteria
Gram-Pos and Gram-Neg
Gram-Positive Cells have a
thick cell wall composed of peptidoglycan and an inner cytoplasmic membrane.
Gram-Negative Cells have an
Outer membrane, Thin cell wall, and an Inner cytoplasmic membrane
Characteristics of the cell wall help to determine the shape
of the bacterium and provides a strong structural support to keep the cell from bursting or collapsing due to osmotic pressure.
Peptidoglycan is found in the cell walls of
most bacteria.
Peptidoglycan is a unique macromolecule composed of
glycan chains cross linked with short peptide fragments and it provides a strong but flexible support framework
The Gram-Positive Cell Wall is a thick, homogenous sheath of
peptidoglycan, 20-80 nm thick.
The function of teichoic and lipoteichoic acid
cell wall maintenance, enlargement during cell division, and acidic change on cell surface
The Gram-Negative Cell Wall
is a single, thin sheet of peptidoglycan, 1-3 nm think. It is a somewhat rigid structure, thinness gives gram-negative bacteria a greater flexibility and sensitivity to lysis.
Mycelia Acid or Cord Factor is found in the
cells walls of Mycobacterium and Nocardia. It is a very long chain of fatty acid and contributes to pathogenicity of these organisms.
Acid Fast Stain is used to diagnose
Tuberculosis and Leprosy
Mycoplasmas naturally lack a
cell wall.
Mycoplasmas membrane is stabilized by
sterols and is resistant to lysis.
Mycoplasmas have a Pleomorphic shape
that ranges from 0.1-0.5, ranging from filamentous to coccus or doughnut shaped.
The Gram-Negative Outer Membrane contains specialized
polysaccharides and proteins.
Polysaccharide chains function as
antigens and receptors
Endotoxin stimulates
fever and shock reactions
Lipoproteins anchor the
outer membrane to peptidoglycan
Porin Proteins completely span the outer membrane and only allow relatively small
molecules to penetrate. The size can be altered to block the entrance of harmful chemicals. They act as a defense against certain antibiotics
The functions of the Cell Membrane (Part 1)
-Energy reactions
-Nutrient Processing
-Synthesis
-Transport: passage of nutrients into the cell and discharge of wastes.
The Functions of the Cell Membrane (Part 2)
-Selective Permeability: water and small uncharged molecules diffuse free and special carrier mechanisms exist for passage of moist molecules.
-Secretion: discharge of metabolic products into the extracellular environment
The Outer Membrane in Gram-Neg Bacteria makes them impervious to
antimicrobial chemicals. It is more difficult to kill than gram-pot bacteria.
Infections with gram-pos are treated differently than
infections with gram-neg bacteria
The cell envelop can interact with human tissues and
cause disease.
Proteins in the outer cell wall of gram-pos bacteria
can be toxic
Lipids in the cell wall of
Mycobacterium can be harmful to human cells
Macromolecules in the cell wall are seen as
foreign and can stimulate antibody production.
Cytoplasm is a
gelatinous solution contained by the cell membrane. It is 70-80% water and has a complex of mixtures of sugars, amino acids, and salts.
Prominent site for the cell's
biochemical and enzymatic activities.
The Cytoplasm also contains
chromatin, ribosomes, granules, and fibers that act as the cytoskeleton
Bacterial Chromosome is a
single circular strand of DNA. It is aggregated in a dense area called the nucleoid.
In the Bacterial Chromosome DNA is tightly coiled around
basic protein molecules to fit into the cell compartment
Plasmids is a non-essential piece of DNA. It is
Separate, double stranded circles of DNA. It is duplicated and passed onto offspring during replication. It can confer protective traits and is important in genetic engineering.
Ribosomes are made up of RNA and protein. It is
dispersed throughout the cytoplasm, often found in chains.
Svedberg (S) units
measurement of the relative size of cell parts through sedimentation during centrifugation
Bacterial ribosomes are
70S
Eukaryotic ribosomes are
80S
Inclusion bodies are storage sites for
nutrients during periods of abundance. It is single-layered membranes and they vary in size, number and content
The cytoskeleton has long polymers of proteins similar to
eukaryotic actin. It is arranged in helical ribbons around the cell just under the cell membrane and contributes to cell shape.
Endospores can withstand
hostile conditions and facilitate survival.
Endospores have a two phase life cycle
-Vegetative Cell: metabolically active
-Endospore: Inert, resting condition
-Sporulation: Spore formation induced by environmental conditions.
Endospores CAN resist
-Heating
-Drying
-Freezing
-Radiation
-Chemicals
Stimulus for endospore formation is
depletion of nutrients, especially carbon and nitrogen sources.
Sporangium is a
sporulating cell and the transformation takes 6-8 hours in most species
Some diseases are related to the
persistence and resistance of their spores. For example:
-Bacillus anthracis: Anthrax
-Clostridum tetani: Tetanus
-C. difficile: Pseudomembranous colitis
-C. perfringens: Gas Gangrene
-C. botulism: Botulism
Endospores are constant intruders where
sterility and cleanliness are important.
Endospores resist ordinary cleaning methods such as
boiling water, soaps and disinfectants. They frequently contaminate cultures and media. Hospitals must protect against endospores in wounds and lastly the destruction of endospores is important in the food-canning industry.
The Archaea is the most primitive of all
life forms. It is most closely related to cells that originated 4 billion years ago. They live in habitats that are similar to the extremes found anciently (heat, salt, acid, pH, pressure, atmosphere). Methane producers, hyperthermophiles, extreme halophiles, and sulfur reducers.
Methanogens
convert CO2 and H2 into methane gas (CH4).
Methanogens are common inhabitants of
anaerobic swaps mud, bottom sediments of lakes and oceans, and the digestive systems of animals. Gas produced in swaps may become a source of fuel and they may contribute to greenhouse gases and global warming
Extreme Halophiles
-Require salt to grow
-Can multiply in 36% NaCl that would destroy most cells.
-Exist in inland seas, salt lakes, salt mines, and in salted fish.
-Use a pigment to synthesize ATP in the presence of light
Psychrophiles
adapted to grow at very low temperatures
Hyperthermophiles
-Flourish at temperatures between 80 degrees and 113 degrees.
-Cannot grow below 50 degrees
-Live in volcanic waters and soils and submarine vents
-Often salt and acid tolerant as well as heat tolerant.
rRNA sequencing is used in identification of archaea. This technique has also
advanced the general understanding of transcription, translation, and cellular evolution
Divisions in the Diagnostic Scheme
-Gram-pos
-Gram-neg
-Bacteria without cell walls
-Cell shape
-Arrangements
-Oxygen usage
Types of oxygen use
-Aerobic: DOES use oxygen in metabolism
-Anaerobic: DOES NOT use oxygen in metabolism
-Facultative: MAY or MAY NOT use oxygen
Bacterial species is a collection of
bacterial cells which share an overall pattern of similar traits.
Subspecies, Strain, or Type
Bacteria of the same species that have differing characteristics
Serotype
Representatives of a species that stimulate a distinct pattern of antibody responses
The first eukaryotic cells appeared on the earth
2-3 billion years ago
Bacteria and eukaryotes evolved from a
precursor called the Last Common Ancestor
The Last Common Ancestor
was neither prokaryotic or eukaryotic and it gave rise to bacteria and eukarya separately.
Organelles originated from more
primitive cells that become trapped in eukaryotic cells
First primitive eukaryotes were
single cells and independent. They become specialized to perform a particular function in a colony. They are complex, multicellular organisms evolved when cells lost the ability to survive apart from the colony
Found in all eukaryotic cells
-Cytoplasmic membrane
-Nucleus
-Mitochondria
-Endoplasmic reticulum
-Golgi apparatus
-Vacuoles
-Cytoskeleton
-Glycocalyx
Eukaryotic vs Bacterial flagella
-10x thicker
-Structurally more complex
-Covered by an extension of the cell membrane
-Long, sheathed cylinder containing regularly spaced hollow microtubules. (9+2 arrangement)
Cilia is similar in overall structure to flagella.
It is shorter and more numerous(up to several thousand in some cells). It is found only in a single group of protozoa and certain animal cells. It functions as feeding and filtering structures on some cells.
The Glycocalyx is the outermost boundary that comes into direct contact with the environment. It is also
called an extracellular matrix which is composed of polysaccharides. It has a network of fibers, slime layer, and a capsule
The Cell Wall is found in
fungi and algae. It is rigid and provide structural support and shape. The cell wall has a chemical composition than bacterial cell walls
The cytoplasmic membrane is a
typical layer of phospholipids embedded with protein molecules. It contains sterols and has selectively permeable barriers. It has sophisticated mechanisms for transporting materials in and waste out.
The Nucleus is the Control Center it is a
compact sphere, the most prominent organelle. It is separated from the cytoplasm by the nuclear envelope.
Nucleolus
stains more intensely due to its RNA content and is a site for ribosomal RNA synthesis
Chromatin makes up
eukaryotic chromosomes. Its units of genetic information is in the cell.
Chromatin is a long, linear DNA molecule that is bound to
histones. It is visible during mitosis.
Meiosis
production of sex cells
Endoplasmic Reticulum is
microscopic series of tunnels used in transport and storage.
Rough Endoplasmic Reticulum
The ribosomes are attached to the surface and the proteins are held for packaging and transport
Smooth Endoplasmic Reticulum
Does not contain ribosomes and synthesizes and stores nonprotein molecules
Golgi Apparatus is the site of protein modification and transportation. It consists of a
stack of flattened, disc shaped sacs and is closely connected to the endoplasmic reticulum.
Golgi Apparatus forms
transitional vesicles and condensing vesicles. Becomes lysosomes or secretory vesicles.
Genetic information originates from the
nucleus
Proteins are synthesized on
ribosomes and deposited into the Rough Endoplasmic Reticulum
Proteins are then transported to the
Golgi Apparatus to be chemically modified and packaged into vesicles
.Lysosomes originate in the
Golgi Apparatus and contain a variety of enzymes. It is involved in intracellular digestion of food and protection against invading microorganisms.
Vacuoles are
membrane-bound sacs that contain fluids or solid particles to be digested, excreted, or stored
Mitochondria (the energy generators of the cell) supply the bulk of the energy of a cell.
Structure is made up by Cristae which are folds on the inner membrane that hold the electron carriers of aerobic respiration and Matrix which holds ribosomes, DNA, and enzymes used in metabolism.
Mitochondria's unique characteristics
They divide independently from the cell, contain circular strands of DNA, and have bacteria-size of 70S ribosomes.
Chloroplasts are the Photosynthesis Machines are capable of converting the energy of sunlight into
chemical energy through photosynthesis.
Photosynthetic role of chloroplasts are the
primary producers of all organic nutrients and are primary producers of oxygen gas.
Ribosomes are distributed throughout the cell and
scattered freely in the cytoplasm and cytoskeleton, they are attached to the RER and are found inside mitochondria and chloroplasts.
Polyribosomes are
short chains of ribosomes
Ribosomes are similar to bacterial ribosomes in structure
They are large and small subunits of ribonucleoprotein. They also have a full size of ribosome 80S and a combination of 60S and 40S subunits.
The Cytoskeleton functions are
Anchoring organelles, moving RNA and vesicles, and lastly permitting shape changes and movement
There are three main types of the cytoskeleton
1.) Actin Filaments
2.) Intermediate filaments
3.) Microtubules
The Kingdon Fungi is made up of
over 100,000 species of fungi can be divided into two groups.

Macroscopic fungi: mushrooms, puffballs, and gill fungi
Microscopic fungi: molds and yeasts
Yeast cell
is a round to oval shape and uses asexual reproduction
Hyphae
is a long, threadlike cell found in filamentous fungi or molds.
Pseudohyphae
chains of yeast
Dimorphic
some fungi can take either form.
Heterotrophic
acquires nutrients from a wide variety of substrates
Saprobes
Obtain substrates from dead plants and animals
Parasites
live on the bodies of living animals or plants.
Most microscopic fungi grow in
loose associations or colonies.
Mycelium
the woven, intertwining mass of hyphae that makes up the body or colony of a mold
Septa
hyphae divided into segments or cross wall
Spores
fungal reproductive bodies
Identification in medical specimens
-Isolation on special media
-Observation microscopically and macroscopically
-Sexual spores difficult to detect
-Asexual spore-forming structures used to identify genus and species
-Hyphal type, colony texture, pigmentation, physiological characteristics, genetic makeup
Pathogenic fungi
Infection occurs through accidental contact, primary pathogens sicken healthy persons, and opportunistic pathogens attack people who are already weakened in some way.
Other medical conditions caused by fungi
Allergies or neurological conditions due to toxin production
Algae and Protozoa have been traditionally combined into the Kingdom Protista
Subkingdom Algae and Subkingdom Protozoa
Protist is any
unicellular or colonial organism that lacks true tissues
Group of photosynthetic organisms
Seaweed and kelp are the most recognizable
The algae exhibit all of the eukaryotic organelles
Chloroplasts contain green chlorophyll and other pigments create yellow, red, and brown coloration
Plankton is a
Floating community of microscopic organisms, essential role in the aquatic food web, and produce most of the earth's oxygen
The protozoa include about 65,000 most members
are harmless inhabitants of the water and soil. A few species are parasites responsible for millions of infections in humans per year
Protozoa are single cells containing all
major eukaryotic organelles except chloroplasts. Organelles can be highly specialized into structures analogous to: mouths, digestive systems, reproductive tracts, legs which means locomotion
Free-living species
scavenge dead plant or animal debris and graze on live cells of bacteria and algae.
Parasitic species
live on fluids of the host such as plasma and digestive juices and may actively feed on tissues
Pseudopods are "false feet" and
serve as feeding structures
Flagella vary in
number from one to several
Cilia are distributed over the entire
surface of the cell in characteristic patterns
Trophozoite
motile and feeding stage. It requires ample food and moisture to remain active
Cyst
dormant, resting stage. Formed when conditions become unfavorable for growth and feeding. Important factor is spread of disease
Life cycles vary from simple to complex
-Some protozoan groups exist only in trophozoite state
-Many types alternate between trophozoite and cyst stage depending on the habitat
-Life cycle dictates the mode of transmission
Protozoan reproduction
-Simple, asexual methods, usually mitosis
-Multiple fission
-Sexual reproduction also occurs
Those that use flagella to move
-Flagella alone or flagella and amoeboid motion
-Single nucleus
-Sexual reproduction by syngamy (the fusion of two cells or of their nuclei in reproduction)
-From cysts and are free-living
Those using amoeboid motion to move
-Primarily amoeba
-Use pseudopods for locomotion
-Asexual reproduction by fission
-Mostly uninucleate
-Usually encyst
-Free-living and not infectious
Those with NO motility (Sporozoa)
-Motility absent in most representative
-Complex life cycles with well-developed asexual and sexual stages
-Entire group is parasitic
Parasitology
Study of protozoa and helminths
Parasite
term most often used to denote protozoan and helminth pathogens
Pathogenic Flagellates
Trypanosomes
Trypanosoma brucei
African Sleeping Sickness
Trypanosoma cruzi
Chagas Disease
Trypanosomes are
long, crescent-shaped cells with a single flagella. It is found both in the blood during infection and is transmitted by blood-sucking vectors
Amoebic dysentery: Entamoeba histolytica
Is the fourth most common protozoan infection in the world. This disease is transmitted through ingestion of food or water contaminated with human feces
Helminths are
Tapeworms, Flukes, Roundworms. Usually large enough to be seen with the naked eye: 1mm-25m in length
Multicellular animals equipped with organs and organ systems have a
reproductive tract that is most developed, a primitive digestive system, excretory system, nervous system, and muscular systems. They have thick cuticle for protection and mouth glands for breaking down the host's tissue
The completed life cycle is a
Fertilized Egg >> Larval Stage >> Adult Stage

Majority of the helminths derive nutrients and reproduce sexually in the host's body
Nematodes
sexes have different morphologies
Trematodes
sexes are separate or hermaphroditic
Hermaphroditic
male and female sex organs in the same worm
Cestodes
generally hermaphroditic
General Life Cycle
-Transmission of an egg or larva to the body of another host, either a different or the same species
-Intermediate (secondary) host: the host in which larval development occurs
-Definitive (final) host: host in which adulthood and mating occur
Sources for human infection
Food, soil, water, and infected animals
Route of infection
Oral intake or penetration of unbroken skin
Humans are the definitive hosts for many species and the
sole biological reservoir for about half of the diseases. Animals or insect vectors also serve as reservoirs.
Enterobius vermicularis
-Causes a very common infestation of the large intestine.
-Worms range from 2-12 mm long
-Tapered, cylindrical shape
-Simple, uncomplicated infection that does not spread beyond the intestine
Pinworm Treatment
mebandazole, pyrantel pamoate or albendazole. Any of these are given in one dose initially and then another single dose of the same drug two weeks later.
Pyrantel pamoate is available without prescription
There are different ways to classify a Helminth
Shape, Size, Degree of development of organs, Presence of hooks, suckers, or other special structures, Mode of reproduction, Kinds of hosts, Appearance of eggs and larvae
Microscopic detection of adult worm, larvae, or eggs are often
distinctive shapes or external and internal structures. Occasionally cultured to verify all life stages
About 50 species of helminths parasitize humans they are
geographically restricted, usually to tropical areas. They are yearly estimated to have case numbers worldwide in the billions. A conservative estimate of 50 million infections in the US alone.
Humans evolved in the constant presence of helminths recently they have
evolved into a "helminth-free" existence and an absence of helminth infections may contribute to autoimmunity and allergy
Pasteur developed a vaccine for rabies
coined the term "virus".
Ivanovski and Beijernick founders of a
tobacco disease caused by a virus
Loeffler and Frosch founded a
foot-mouth disease caused by a virus
Filterable virus
-Infectious fluids were passed through filters designed to trap bacteria
-The cell-free filtered fluid remained infectious
-This proved that an agent smaller than bacteria was the cause of disease
Viruses can infect every type of cell
-Bacteria
-Algae
-Fungi
-Protozoa
-Plants
-Animals
Properties of Viruses
-They are not cells
-They are obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals
-DO NOT independently fulfill outside the host cell and active only inside host cells
-Have basic structure of protein shell (capsid) surrounding nucleic acid core
-Are ubiquitous in nature and have had major impact on development of biological life
-Are ultramicroscopic in size, ranging from 20 nm to 450 nm (diameter)
-Can have either DNA or RNA but not both
-Can have double-stranded DNA, single-stranded DNA, single-stranded RNA, or double-stranded RNA
-Carry molecules on surface that determine specificity for attachment to host cell
-Multiply by taking control of host cell's genetic material and regulating the synthesis and assembly of new viruses
-Lack enzymes for most metabolic processes
-Lack machinery for synthesizing proteins
Viruses are smaller than the average bacterium and the electron microscopes are required to detect them
-Parvoviruses: 20 nm in diameter
-Mimiviruses: 450 nm in length - larger than some small bacteria
-Cylindrical viruses: 800 nm long but 15 nm in diameter
Viruses bear no resemblance to cells because they
lack protein-synthesizing machinery
Viruses need only those parts required to invade and control a host cell
-External coating
-Core containing nucleic acids
Viral components
-Capsid
-Nucelocapsid
-Envelope
-Naked viruses
-Spikes
-Virion
Virion
Fully formed virus able to establish infection in a host
Spikes
Found on both naked and enveloped viruses, project from either the nucleocapsid or envelope, all viruses to dock with their host cells
Naked Viruses
Consist only of a nucleocapsid
Envelope
usually a modified piece of the host cell membrane
Nucleocapsid
Capsid and nucleic acid together
Capsid
Shell surrounds the nucleic acid
Complex Capsids
Found in bacteriophage, the viruses that infect bacteria, have multiple types of proteins, and take shapes that are not symmetrical
The Viral Envelope is composed of the membrane system of the host
-Cell membrane or nuclear membrane
-Regular membrane proteins are replaced with viral proteins
-Spikes: Protruding glycoproteins essential for attachment to the host cell
Genome is a full
complement of DNA and RNA carried by a cell
Viruses contain either DNA or RNA but
NOT BOTH.
The number of viral genes is
small compared to that of a cell. Possess only the genes necessary to invade host cells and redirect their activity
Nucleic Acids
-Positive-sense RNA: single-stranded RNA genomes ready for immediate translation into proteins
-Negative-sense RNA: RNA genomes that need to be converted into the proper form to be made into proteins.
Enzymes for specific operations within the host cell
-Polymerases: synthesize DNA and RNA
-Replicases: copy RNA
-Reverse transcriptase: synthesizes DNA from RNA
Informal classification system
-Animal, plant, or bacterial viruses
-DNA or RNA viruses
-Helical or icosahedral
Criteria of a formal classification system
-Structure
-Chemical composition
-Similarities in genetic makeup
Nucleocytoplasmic large DNA viruses
-Closely related to each other
-Distantly related to other viruses
-May constitute a new order of viruses
General phases in the life cycle of animal viruses
_Absorption
-Penetration
-Uncoating
-Synthesis
-Assembly
-Release from the host cell
Viral Multiplication
enters the nucleus >> transcribed in two phases. In the early phase, viral DNA that codes for enzymes needed to replicate DNA is transcribed. In the late phase, viral DNA that codes for structural proteins is transcribed >> The RNA transcripts move to cytoplasm >> viral mRNA is translated into structural proteins, proteins enter the nucleus >> Viral DNA is replicated repeatedly in the nucleus >> Viral DNA and proteins are assembled into a mature virus in the nucleus >> Because it is double-stranded, the viral DNA can insert itself into host DNA (latency)
Invasion begins when the virus encounters a susceptible host and
absorbs specifically to receptor sites on the cell membrane
Adsorb
to attach
Absorb
to soak in
A virus can invade its host cell only through
making an exact fit with a specific host molecule
Restricted host range
hepatitis B only infects liver cells of humans
Intermediate host range
poliovirus infects intestinal and nerve cells of primates
Broad host range
rabies virus infects various cells of all mammals
Endocytosis
entire virus is engulfed by the cell and enclosed in a vacuole or vesicle
Uncoating
enzymes in the vacuole dissolve the envelope and capsid, releasing the virus into the cytoplasm
Viral nucleic acid takes control over the host's synthetic and metabolic machinery
-Mechanisms vary depending on whether the virus is a DNA or RNA virus
-RNA viruses replicate in the cytoplasm
-DNA viruses replicate in the nucleus
Viral budding or exocytosis
-Nucleocapsid bind to the membrane
-A small ouch is formed
-Pinching off of the pouch releases the virus with its envelope
-Viruses are shed gradually without destruction of the cell
Cytopathic Effects (CPEs)
-Virus induced damage to the cell that alters its microscopic appearance
-Cells can become disoriented, undergo major changes in shape or size or develop intracellular damage
Inclusion bodies
Compacted masses of viruses or damaged cell organelles in the nucleus or cytoplasm
Syncytis (singular, syncytium)
Fusion of multiple host cells into single large cells containing multiple nuclei
A carrier relationship that develops in some cells
-Cell harbors the virus and is not immediately lysed
-Provirus: viral DNA incorporated into the DNA of the host
-Chronic latent state: periodic activation after a period of viral inactivity
Oncogenic viruses
Experts estimate that up to 20% of human cancers are caused by viruses
Transformation
-Virus carries genes that directly cause cancer
-Virus produces proteins that induce a loss of growth regulation in the cell
Bacteriophage was discovered in 1915 by Frederick Twort and Felix d'Herelle. It parasitize
every known bacterial species and often make the bacteria they infect more pathogenic for humans
"T-even" bacteriophage infect E. coli
-T2 and T4
-Most widely studied bacteriophage
-Go through similar stages as animal viruses
Primary Purposes of Viral Cultivation
-Isolate and identify viruses in clinical specimens
-Prepare viruses for vaccines
-Do detailed research on viral structure, multiplication cycles, genetics, and effects on host cells
Using live animal inoculation specially bred strains of animals used for animal cultivation of viruses
White mice, rats, hamsters, guinea pigs, rabbits. There are special injection sites for viral exposure: brain, muscle, body cavity, skin, and footpads
Benefits of using bird embryos
-Embryonic development occurs in a protective shell
-Intact and self-supporting unit with its own sterile environment and nourishment
-Furnished several embryonic tissues that support viral multiplication
Cell culture or tissue culture: in vitro virus cultivation systems
-A simple effective way to grow populations of isolated animal cells in culture dishes
-Most viruses are propagated through cell culture
-Much of a virologist's work involves developing and maintaining cultures
Primary cell cultures
-Freshly isolated animal tissue is placed in a growth medium
-Cells undergo mitotic division, producing a monolayer
-Retain the characteristics of the original tissue from which they were derived
Continuous cell cultures
-Have altered chromosome numbers
-Grow rapidly
-Show changes in morphology
-Can be continuously subcultured if they are given fresh nutrient media
Detecting viral growth in culture is done through
-Degeneration and lysis of infected cells
-Plaques
Plaques
-Clear, well-defined patches in the cell sheet
-Develops when viruses released from an infected cell radiate out of surrounding cells and infect them
-Infection spreads gradually and symmetrically from the original point of infection
Spongiform encephalopathies
-Implicated in chronic, persistent disease in humans and animals
-Brain tissue removed from affected animals resembles a sponge
Prions
-Common feature of spongiform encephalopathies
-Distinct protein fibrils deposited in the brain tissue of affected animals
Creutzfeldt-Jakob Disease (CJD)
-Affects the central nervous system of humans
-Causes gradual degeneration and death
-Transmissible by an unknown mechanism
-Several animals are victims of similar diseases: Scarpie are sheep mink, and elk. Bovine spongiform encephalopathy: cows.
Prion infection
-Exact mode of infection is unknown
-Protein composition of prions has revolutionized ideas of what can constitute an infectious agent
-Questions about how prions replicate given that they have no nucleic acid
Satellite viruses
-Dependent on other viruses for replication
-Adeno-associated virus (AAV)
Aden-associated virus (AAV)
-Originally thought that it could only infect cells infected with the adenovirus
-Now found to infect cells infected with other viruses or had their DNA disrupted through other means
Viroids
is a virus like agent that parasitizes plants and is about one-tenth the size on an average virus. It is composed only of naked strand of RNA and it lacks a capsid or other type of coating. Significant pathogens in economically important pants: tomatoes, potatoes, cucumbers, citrus trees, and chrysanthemums
Viruses and Human health is impossible to measure the number of viral infections worldwide
The most common cause of acute infections that do not result in hospitalization are colds, chickenpox, influenza, herpes, and warts. Viral infections that only occur in certain regions are Dengue fever, Rift Valley fever and Yellow fever
Some viruses have high mortality rate such as
Rabies and Ebola.
While other viral infections lead to long-term disability
Polio and Neonatal rubella
Viruses mutate at a rapid rate and are difficult to
design therapies against viruses. Scientists focus on developing vaccines against viruses since so few antiviral drugs are available and antibiotics are ineffective
Interferon (IFN)
Are naturally occurring human cell product and are used with some success in preventing and treating viral infections
Nutrients
are acquired from the environment and used for cellular activities
Essential nutrient
Any substance, whether in elemental or molecular form that must be provided to an organism
Macronutrients
Are required in relatively large quantities and play a principal role in cell structure and metabolism
Micronutrients (trace elements)
Are present in smaller amounts and are involved in enzyme function and maintenance of protein structure
Inorganic nutrients
Simple molecule that contains a combination of atoms other than carbon and hydrogen
Organic nutrients
Contain carbon and hydrogen atoms and usually the product of living things
Heterotroph
is an organism that must obtain its carbon in organic form and is dependent on other life forms. Most carbon sources exist in a form that is simple enough for absorption. Many carbon sources must be digested by the cell in order to be absorbed
Autotroph
is a "self-feeder" and its an organism that uses inorganic CO2 as its carbon source. They have the capacity to convert CO2 into carbon compounds and it is not dependent on other living things
Nitrogen sources are indispensable to DNA, RNA and ATP.
Primary nitrogen source for heterotrophs and must be degraded into basic building blocks in order to be utilized
Regardless of the source, nitrogen must be converted to NH3 before it enters the cell.
This is the only form that can be directly combined with carbon to synthesize amino acids and other compounds
Oxygen plays an important role in the structure and enzymatic functions of the cell
Major component of carbohydrates, lipid, nucleic acids and proteins
Oxygen plays an important role in the structural and enzymatic functions of the cell
Major component of carbohydrates, lipids, nucleic acids, and proteins. Common component of inorganic salts.
Hydrogen sources are overlapping roles in the biochemistry of cells
Like maintaining pH, forming hydrogen bonds between molecules, and serving as the source of free energy in oxidation-reduction reactions of respiration
Phosphorous (Phosphate) Sources
Main inorganic source is phosphate (PO4) which is derived from phosphoric acid (H3PO4) and is found in rocks and oceanic mineral deposits
Key component of nucleic acids
essential to genetics of cells and viruses
Sulfur sources are widely distributed throughout the environment in rocks and sediments
They are essential component of vitamins and amino acids methionine and cysteine. They form disulfide bridges that help determine the shape and structural stability of proteins
Growth factor is an organic compound such as an amino acid, nitrogenous base, or vitamin that
cannot be synthesized by an organism and must be provided by the environment
Aerobic respiration is a principal energy-yielding pathway in animals, protozoa, fungi, and aerobic bacteria.
Glucose and oxygen are reactants and carbon dioxide is given off. The earth's balance of energy and metabolic gases is dependent on this reaction. It is complementary to photosynthesis
Parasitic Microorganisms live on or in the body and cause some degree of harm to the host
It is considered pathogens because they can damage tissues and cause death
Ectoparasites
live on the body
Endoparasites
live in organs and tissues
Intracellular parasites
live within cells
Obligate parasites
unable to live outside of a living host
Nutrient Absorption is when
necessary nutrients must be taken into the cell and waste material must be transported out of the cell.
Transport occurs across the cell membrane
Structure is specialized for transport and the cell wall is too nonselective to screen the entrance or exit of molecules
Diffusion
The movement of molecules in a gradient from an area of higher density/concentration to an area of lower density/concentration
Diffusion across a cell membrane is determined by the
concentration gradient and the permeability of the substance
Osmosis is the
movement of water across a selectively permeable membrane
The membrane is selectively or differentially permeable
has passageways that allows the passage of water but not other substances
Isotonic conditions pose
little stress on cells
Hypotonic environments
-Bacteria and Amoeba living in fresh pond water
-Bacteria: cell wall protects cells from bursting
-Amoeba: utilize a contractile vacuole that constantly moves excess water out of the cell and requires energy
Hypertonic environments
Cells must restrict the loss of water to the environment or increase the salinity of the internal environment
Halobacteria
absorb salt to make their cells isotonic with the environment. Have a physiological need for a high salt concentration in their environments
Saturation
The rate of transport of a substance is limited by the number of binding sites on the transport proteins.
In saturation the rate of transport increases as the
rate of substance concentration until all of the binding sites are occupied
Competition is when
two molecules of the same shape can bind to the same binding site on the carrier protein. and the chemical with the higher binding affinity or the chemical in higher concentration will be transported at a greater rate
Features of Active Transport
it transports nutrients against a concentration gradient or with a concentration gradient at a faster rate. Presence of specific membrane proteins: permeates and pumps and lastly Expenditure of energy
Endocytosis
transport of large molecules, particles, or liquids across the cell membrane by certain eukaryotes. It requires the expenditure of energy
Phagocytosis
endocytosis by amoebas and certain white blood cells that ingest whole cells or large solid matter
Pinocytosis
energy of oils or molecules in solution into the cell
Environmental factors that microbes experience
Heat, cold, gases, acid, radiation, osmotic pressure, hydrostatic pressure, and other microbes
Cardinal temperatures
range of temperatures for a given microbial species.
Minimum, Maximum and Optimum Temperature
Optimum temperature
the intermediate temperature range between minimum and maximum. it promotes the fastest rate of growth and metabolism. It is small chemical differences in bacterial membranes which affect their fluidity allow them to thrive at different temperatures
Psychrophiles
Organisms that have an optimum temperature below 15 degrees and is capable of growth at 0 degrees. It CANNOT grow above 20 degrees.
Psychotrophs or facultative psychrophiles
grow slowly in the cold but have an optimum temperature between 15-30 degrees
Mesophiles
majority of medically significant organisms. Individual species can grow from 10-50 degrees. Optimum growth temperature is 20-40 degrees. Most human pathogens 30-40 degrees
Thermoduric microbes survive short exposure to
high temperatures. common contaminants of heated or pasteurized foods
Thermophiles
grow optimally at temperatures above 45 degrees. They live in soil and water associated with volcanic activity, compost piles, habitats directly exposed to the sun. They range from 45-80 degrees
Microbes fall into one of three categories
1.) those that use oxygen and can detoxify it
2.) those that can neither use oxygen nor detoxify it
3.) those that do not use oxygen but can detoxify it
Singlet Oxygen
-Is extremely reactive molecule produced both by living and nonliving processes
-Produced by phagocytes to kill invading microbes
-Buildup of singlet oxygen and the oxidation of membrane lipids and other molecules can damage or destroy a cell
Superoxide ion, Hydrogen Peroxide and Hydroxyl radicals
-Destructive metabolic byproducts of oxygen
-Cells use enzymes to scavenge and neutralize them (Catalase and Superoxide dismutase)
Aerobe (aerobic organism)
-Can use gaseous oxygen in its metabolism
-Possesses the enzymes needed to process toxic oxygen products
Obligate aerobe
an organism that cannot grow without oxygen
Facultative anaerobe
-An aerobe that does not require oxygen for its metabolism
-Capable of growth in the absence of oxygen
-Metabolizes by aerobic respiration when oxygen is present
-Adopts anaerobic metabolism (fermentation) when oxygen is absent
Microaerophile
-Does not grow at normal atmospheric conditions of oxygen
-Requires a small amount of oxygen in its metabolism
-Usually live in a habitat that provides a small amount of oxygen but is not directly exposed to the atmosphere.
Anaerobe
-Lacks the metabolic enzyme systems for using oxygen in respiration
Strict or obligate anaerobes cannot
tolerate free oxygen and will die in its presence. They live in highly reduced habitats such as lakes, oceans, and soil
Aerotolerant anaerobes
-DO NOT utilize oxygen
-Can survive and grow to a limited extent in its presence
-Not harmed by oxygen because they possess alternative mechanisms for breaking down peroxides and superoxide
Capnophiles
-Grow best at a higher CO2 tension than is normally present in the temperature
-Important in the isolation of some pathogens
-Incubation is carried out in a CO2 incubator that provides 3-10% CO2
pH
the degree of alkalinity (or basicity) of a solution expressed on a scale from 0-14
Pure water is
neutral at pH 7.0
As the pH value decreases toward 0
acidity increases
As the pH value increases toward 14
alkalinity increases
Obligate acidophiles
-Require an acidic environment for growth
-Molds and yeasts tolerate acid and are common spoilage agents of pickled foods
Alkalinophiles
-Live in hot pools and soils that contain high levels of basic minerals
-Bacteria that decompose urine create alkaline conditions
Obligate Halophiles
-Require high concentrations of salt for growth
-Have significant modifications to their cell walls and membranes and will lyse in hypotonic habitats
Facultative halophiles
Resistant to salt, even though they do not normally reside in high-salt environments
Protective measures against radiation
-Yellow carotenoid pigments absorb and dismantle toxic oxygen
-Other microbes use enzymes to overcome the damaging effects of UV radiation on DNA
Barophiles
-Deep sea microbes that exist in pressures up to 1000x atmospheric pressure
-So strictly adapted to high pressures that they rupture when exposed to normal atmospheric pressure
Parasitism
-Host: provides the parasitic microbe with nutrients and a habitat
-Parasite: multiplication of the parasite usually harms the host to some extent
Antagonism
-Arises when members of a community compete
-One microbe secretes chemical substances into the surrounding environment that inhibit or destroy other microbes
Biofilms are mixed communities of different kind of bacteria and other microbes
-Pioneer colonizer initially attaches to a surface
-Other microbes attach to the pioneer or to the polymeric or protein substance secreted by the colonizers
Quorum sensing
cells are stimulated to release chemicals as the population grows to monitor its size
Normal microbiota
microbes that normally live on the skin, alimentary tract, and other sites.

It participates in commensal, parasitic and synergistic relationships with a human host
Binary fission
-Parent cell enlarges
-Chromosomes are duplicated
-Cell envelope pulls together in the center of the cell to form a septum
-Cell divides into two daughter cells
Generation time or doubling time
-The time required for a complete fission cycle
-Each new fission cycle doubles the population
-As long as the environment remains favorable, the doubling effect can continue at a constant rate
-The length of the generation time is a measure of the growth rate of an organism
Exponential growth
-The growth pattern of microbes
-Useful of express the populations of microbes as exponents or logarithms
Plotting data from a growing bacterial population
-Number of cells as a function of time
-Can be represented logarithmically or arithmetically
Lag phase
-Flat period on the graph when the population appears not to be growing
-Newly inoculated cells require a period of adjustment, enlargement, and synthesis
Exponential growth or log phase
-Period during which the growth curve increases dramatically
-Phase will continue as long as cells have adequate nutrient and the environment is favorable
Stationary growth phase
-Population enters survival mode
-Cells stop growing or grow slowly
Death phase
-Limiting factors intensify and cells begin to die at an exponential rate
-Curve dips down
Antimicrobial agents rapidly accelerate the death phase
Microbes in the exponential phase are more vulnerable to these agents than those in the stationary phase
Growth patterns can account for stages of infection
Bacterial shedding during the early and middle stages of infection is more likely to spread it to others
Chemostat
Is a continuous culture system that admits a steady stream of nutrients, siphons off used media and old cells to stabilize growth rate. It maintains the culture in a biochemically active state
New methods to analyze population growth
-Polymerase chain reaction (PCR)
-Tests that measure ATP
Polymerase chain reaction (PCR)
Quantifies bacteria and other microbes in environmental tissue samples without isolating and culturing them
Tests that measure ATP
They are used in food and pharmaceutical industries and may be used for rapid quantification of microbes in other environmental samples
Metabolism
All chemical reactions and working of a cell
Anabolism
Builds small things up into big ones
Biosynthesis
synthesis of cell molecules and structures
Catabolism
Breaks the bonds of larger molecules to release energy
Metabolism accomplishes the following
Assembles smaller molecules into large macromolecules for the cell, utilizing ATP. Degrades a macromolecules into smaller molecules, a process that yields energy and it conserves energy in the form of ATP or heat
Simple enzymes
consist of protein alone
Conjugated enzymes (holoenzyme)
Contain protein and some other nonprotein molecule
Apoenzyme
protein portion of the enzyme
Cofactor
nonprotein portion
Coenzyme
organic cofactors
Active site or catalytic site
The actual site where the substrate binds, it is a three-dimensional crevice or groove formed by the way amino acid chains are folded. Each enzyme has a different: primary structure, variations in folding, and unique active site
There are 6 classes of enzymes
1.) Oxidoreductases
2.) Transferases
3.) Hydrolases
4.) Lyases
5.) Isomerases
6.) Ligases
Oxidoreductases
transfer electrons from one substrate to another and dehydrogenase transfer a hydrogen from one compound to another
Transferases
transfer functional groups from one substrate to another
Hydrolases
Cleave bonds on molecules with the addition of water
Lyases
Add groups or remove groups from double bonded substrates
Isomerases
change a substrate to its isomeric form
Ligases
catalyze the formation of bonds with the input of ATP and the removal of water
Oxidation
Loss of electrons. A compound that loses electrons is oxidized
Reduction
Gain of electrons. A compound that gains electrons is reduced
NAD and FAD are
coenzyme carriers
Pathogens secrete unique envy,es that help them avoid host defenses or promote multiplication in tissues
Considered virulence factors or toxins because they contribute to disease. Examples are: streptokinase, streptomycin, elastase, collagenase, lipase, penicillinase
Denaturation
-Weak bonds that maintain the shape of an enzyme are broken caused by heat, low or high pH or certain chemicals
-Disruption causes distortion of the enzyme's shape
-Prevents the substrate from from attaching to the active site
-Nonfunctional enzymes block metabolic reactions and can lead to cell death
Exergonic reactions
Release energy as they go forward and the energy is available for doing cellular work
Endergonic reactions
Require the addition of energy to move forward
Redox reactions always occur in pairs
called redox pairs and contains an electron donor and an electron acceptor
Oxidoreductases are important in cellular redox reactions
Coenzyme carriers: NAD and FAD
Phosphorylation
The energy captured in the electron carrier is used to phosphorylate (add inorganic phosphate to) ADP or another compound and it stores energy in a high energy molecule (ATP)
NAD
Most common electron carrier. It carries hydrogens and electrons from dehydrogenation reactions.
Adenosine Triphosphate is a three part molecule
Adenine: nitrogen base. Ribose: 5 carbon sugar
Three phosphate groups bonded to the ribose
Its bulky and has a negative charge. Repelling electrostatic charges imposes a strain between the last two phosphate groups. Removal of phosphates releases free energy
Substrate-Level phosphorylation
Generate of ATP through a transfer of a phosphate group from a phosphorylated compound directly to ADP
Oxidative phosphorylation
A series of redox reactions occurring during the final phase of the respiratory pathway
Photophosphorylation
ATP formed through a series of sunlight-driven reactions in phototrophs
There basic catabolic pathways
1.) Aerobic respiration
2.) Anaerobic respiration
3.) Fermentation
Glycolysis
most commonly used to break down glucose
The Krebs Cycle
NADH formed is shuttled to the electron transport system to produce ATP
All reactions that occur in the Krebs cycle happen
twice for each glucose molecule because two pyruvate are formed during glycolysis
The Krebs Cycle serves to transfer the
energy stored in acetyl CoA to NAH+ and FAD y reducing them.
Main products of the Krebs cycle
-Reduced NADH and FADH2
-2 ATP produced through substrate-level phosphorylation
Chemiosmosis
As the electron transport carriers shuttle electrons, hydrogen ions are actively pumped into the periplasmic space or the space in-between the cell wall and cytoplasmic membrane.
Chemiosmosis sets up the concentration gradient of
hydrogen ions called the proton motive force
Proton motive force
-Consists of a difference in charge between the outside of the membrane (+) and the inside (-)
-Seperation of changes temporarily stores potential energy
-H+ can only diffuse into the membrane through ATP synthase, which sets the stage for ATP synthesis
ATP synthesis in eukaryotes occurs through the same overall process
-ETS is state in mitochondrial membranes between the mitochondrial matrix and the outer inter membrane space
-This difference affects the amount of ATP produced
Nitrate and Nitrite reduction systems
-Found in E. coli
-Nitrate reductase catalyzes the removal of oxygen from nitrate reducing it to nitrite and water
-A test for this reaction is one of the physiological tests used in identifying bacteria
Denitrification
-Enzymes that further reduce nitrite to nitric oxide (NO), nitrous oxide (N2O) and even nitrogen gas (N2)
-Found in Pseudomonas and Bacillus
-Important step in recycling nitrogen in the biosphere
Fermentation
-The incomplete oxidation of glucose or other carbohydrates in the absence of oxygen
-Uses organic compounds as the terminal electron acceptors
-Yields a small amount of ATP
Mixed acid fermentation
-Members of the family Enterobacteriaceae possess enzyme systems for converting pyretic acid to several acid simultaneously
-Acetic, lactic, succinic, formic acids, as well as CO2
-This fermentive actively accounts for the accumulation of some types of gas in the intestine
-Some bacteria reduce organic acids to neutral butanediol and other solvents
Lipases
Break apart fatty acids joined glycerol
Glycerol is converted to
dihydroxyacetone phosphate which can enter step 4 of glycolysis
Beta oxidation
-Oxidation of fatty acids
-2 carbon units transferred to coenzyme A, creating acetyl CoA, which enters the Krebs cycle
-Oxidation of a 6-carbon fatty acid yields 50 ATP, compared to 38 for a 6-carbon sugar
-Also the complete oxidation of fats yields enormous amounts of water for those organisms that do not have adequate access to drinkable water such as camels and killer whales
Proteases
-Break down proteins to their amino acid components
-Amino groups removed through domination
-Remaining carbon compound can be easily converted to one of several Krebs cycle intermediates
Amphibolism
-Most catabolic pathways contain strategic molecular intermediates that can be diverted into anabolic pathways
-A given molecule can serve multiple purposes to derive maximum benefit from all nutrients and metabolites
-Catabolic an anabolic pathways are integrated to improve efficiency
Light-dependent reactions
-Proceed only in the presence of sunlight
-Catabolic, energy producing reactions
Light-Independent reactions
-Proceed regardless of the lighting conditions
-Anabolic, synthetic reactions
-Carbon atoms from CO2 are added to the carbon backbones or organic molecules
Anoxygenic photosynthesis
-Occurs in green and purple bacteria that utilize bacteriochlorophyll
-Have only cyclic photosystem 1
-Generate a small amount of ATP
-Use H2, H2S, or elemental sulfur as an electron source
-Strict anaerobes
Genetics
the study of inheritance or heredity that explores: the transmission of biological properties (traits) from parents to offspring, the expression and variation of those traits, the structure and function of genetic material and how this material changes
Genome
is the sum total of genetic material of an organism and most exists in the form of chromosomes. Some may appear in non chromosomal sites
Plasmids
tiny extra pieces of DNA.

Extrachromosomal DNA adept at moving between cells.
Organelles
mitochondria and chloroplasts
Genomics
the study of an organism's entire genome
Chromosome
A discrete cellular structure composed of a neatly packaged DNA molecule
Eukaryotes frequently have multiple types of chromosomes with many more base pairs.
Humans have 23 pairs of chromosomes, the maternal and paternal sets, containing about 2.9 billion base pairs in total
Genes
Basic informational packets
Classical genetics
a functional unit of heredity
Molecular and biochemical genetics
site on the chromosome that provides information for a certain cell function
Preferred definition
a segment of DNA that contains the necessary code to make a protein or an RNA
Genotype
the sum of all types of genes constituting an organism's distinctive genetic makeup
Phenotype
the expression of the genotype that creates certain structures or functions
Basic unit of DNA is a
nucleotide.
Nucleotide is composed of
-Phosphate
-Deoxyribose sugar
-Nitrogenous base
Nitrogenous bases
purines (Adenine and Guanine) and pyrimidines (Thymine and Cytosine)
Antiparallel arrangement
When one side of the helix runs in the opposite direction of the other. It has 5' to 3' in one direction and 3' to 5' in the other direction
Antiparallel arrangement has a significant factor in
DNA synthesis and protein production
Semiconservative replication
Each daughter molecule is identical to the parent in composition and neither is completely new. The template strand is an original parental DNA strand
Leading Strand
The strand of the new DNA that is synthesize continuously in a 5' to 3' direction
Lagging Strand
The strand of new DNA that must be synthesized in short segments. It is later sealed together to form a strand in the 3' to 5' direction
Replication of eukaryotic DNA is similar to replication of bacterial and archaeal DNA
It uses a variety of DNA polymerases. Replication proceeds in both directions but from multiple origins. Topoisomerases are used to relieve tension in the strand and to recompact the molecule when it is fully replicated
The "central dogma" of genetics
-Transcription: DNA is used to synthesize RNA
-Translation: RNA used to produce proteins
The "central dogma" is incomplete
-A wide variety of RNAs are used to regulate gene function
-The DNA that codes for these crucial RNA molecules was once called "junk" DNA
Connection between DNA and an organism's traits
-A protein's primary structure determines its characteristic shape and function
-Proteins ultimately determine phenotype
-DNA is mainly a blueprint that tells the cell which kinds of proteins to make and how to make them
Proteomics
The study of an organism's complete set of expressed proteins
Participants in transcription and translation
-Messenger RNA (mRNA)
-Transfer RNA (tRNA)
-Regulatory RNA (rRNA)
-Ribosomes
-Several types of enzymes
-Many raw materials
Differences in RNA structure
-Single-stranded molecule that exists in helical form. Can assume secondary and tertiary levels of complexity
-Contains Uracil (U) instead of Thymine (T) as the complementary base pair to adenine
-Sugar is ribose rather than deoxyribose
mRNA
-A transcript of a structural gene or genes in the DNA
-Synthesized in a process similar to synthesis of the leading strand during DNA replication
Codons
a series of triplet bases that hold the message of the transcribed mRNA
tRNA
contains sequences of bases that form hydrogen bonds with complementary sections of the same tRNA strand
Anticodon
Found at the bottom loop of the cloverleaf. It designated the specificity of the tRNA and complements the mRNA codon
rRNA
Long polynucleotide molecule. It forms complex three-dimensional figures that contribute to the structure and function of ribosomes. The interaction of rRNA and protein create the two subunits of the ribosome
Central principle of translation
mRNA nucleotides are read in codons or groups of three. The codon dictates which amino acids are added to the growing chain, except for a very few cases, this code is universal for bacteria, archaea, eukaryotes, and viruses
More than one codon can exist for an amino acid
True
All the elements needed to synthesize a protein are brought together
-mRNA
-Amino acids
-Ribosomes
Three stages of translation
-Initiation
-Elongation
-Termination
Start codon
the first three RNA nucleotides that signal the beginning of the message
Stop codon
Nonsense codons: one of three codons that has no corresponding tRNA and causes translation to be terminated
Translocation
the process of shifting the ribosome down the mRNA strand to read new codons
Posttranslaatoinal modifications
-Proteins begin to fold upon themselves to achieve their tertiary conformation even before the peptide chain is released
-Formyl methionine may be clipped off
-Cofactors may be added
-Some join with other proteins to form a quaternary structure
Differences between prokaryotic and eukaryotic transcription and translation
Cotranslation translation, AUG codes, and Eukaryotic mRNAs only code for one protein
Cotranslational translation
only occurs in bacteria and archaea
AUG codes
for a different form of methionine in eukaryotes