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Category Archives: Bacteria
Bacteria DNA Replication
Bacteria DNA Replication
DNA Replication in Bacteria
DNA is synthesized from dNTPs through enzymes termed DNA polymerases. In E.coli there are 5 different DNA polymerases. The five different DNA polymerases in E.coli have distinct roles in DNA replication as well as DNA repair.
DNA polymerases synthesize DNA in the 5′ to the 3′ direction ONLY. Nucleotides are always added to the 3′ OH hydroxyl group on the deoxyribose moiety of the sugar.
DNA polymerases always require a DNA strand, termed the template, in order to synthesize DNA. Added nucleotides are complementary to the template DNA strand.
DNA replication is semi-conservative
DNA replication is semi-conservative, meaning that each new DNA molecule, which is a double-stranded molecule, contains one strand from the original DNA molecule and one newly synthesized strand.
DNA synthesis starts at the DNA sequences called ‘origins,’ “Ori” of replication.
These origin regions and sequences contain the required information that directs the replication machinery where to form and where to start the replication process. The origin is the region which allows the helix to be melted, thereby allowing the replication machinery proteins to bind and interact with one another.
E.coli DNA Replication is Bi-directional
Bacterial DNA is circular and need to replicate in a bi-directional mode. These bidirectionally replicating structures are called theta structures. In a theta structure replication, there a the formation of a replication bubble. The replication bubble is formed at the origin and is subsequently extended in two directions, basically both sides of the bubble. Both ends of the bubble are extended at the replication forks. Some phages and viruses have unidirectional replication however.
DNA Replication is Semi-discontinuous
DNA Replication is semi-discontinuous, meaning that DNA replication occurs uninterrupted or continuous on one DNA strand termed the leading strand and discontinuous on the other strand termed the lagging strand. DNA is synthesized on the lagging strand, discontinuous strand, as a series of DNA fragments, called Okazaki fragments. Okazaki fragments are around 1500 nucleotides long.
DNA Polymerases require RNA or DNA Primers
DNA Polymerases require RNA or DNA primers which they extend. The enzyme primase copies short stretches of DNA to synthesize RNA primers that are subsequently extended through the DNA polymerases. The leading strand requires the synthesis of only 1 primer as it is continuous. However, the lagging strand synthesis requires 1 primer for every Okazaki fragment.
Bacteria
Bacteria
Important Facts to know about Bacteria:
Bacteria Facts
The term for parasitic bacteria is PATHOGEN
GENETIC ENGINEERING is a mechanism used by E. coli to produce insulin and growth hormone.
The relationship between bacteria and the roots of legumes is known as MUTUALISM
Cocci describes the spherical shape of a bacterial organism.
The method of sexual reproduction in which viruses carry bacterial DNA fragments between moneran cells is TRANSDUCTION.
ANAEROBES are bacteria that can live without oxygen
ANTIBIOTIC is a substance that prevents bacteria from forming new cell walls.
The oxygen-rich atmosphere of earth may have been developed from a group of bacteria called CYANOBACTERIA.
Bacteria get their food by means of ABSORPTION.
CONJUGATION is the type of reproduction in which genetic material is transferred from one bacterium to another.
NITROGEN is the substance that some bacteria take in from the air and convert to compounds that living things can use. For ex. In the case of plant growth.
ENDOSPORE is the resistant resting cell of a bacterium
FISSION is the asexual reproduction in monerans.
DECOMPOSERS are bacteria that can break down complex molecules into simple, inorganic materials.
The grainy appearance on bacterial cytoplasm is caused by RIBOSOMES.
CHEMOSYNTHESIS is the process by which bacteria make food using only simple inorganic compounds for energy and raw materials.
Bacteria Structure
Bacteria Capsule
The capsule is the main structure of the bacterium that allows for pathogenesis. It is the outermost part of the bacterium and is composed of polysaccharide sugars and proteins. The capsule protects the bacteria from phagocytosis from macrophages.
Bacteria Flagella
Flagella in bacteria are required for motility. The flagella may be located at one end of the bacterium, termed polar flagulla or around the entire bacterium, termed peritrichous.
Pili
Pili, also known as fimbriae, are protein filaments which allow bacteria to attach and stick to things as well as to one another. The pili most importantly allow for the process of conjugation which is “bacterial mating.” Conjugation is the process of DNA transfer from one cell to another. Conjugation allows one bacterium to give genetic information to another bacterium, as in antibiotic resistance.
Endospore
The endospore of bacteria allows bacteria to live in soil and surround themselves with a hard outer coat. The bacterium at this stage is not growing and also does not need respiration. The endospore is formed by a small fraction of gram-positive bacteria, mainly Clostridium and Bacillus species, such as Clostridium tetani. The enospore allows resistance to heat and drying and contains nuclear material and protein allowing germination and bacteria to divide under optimal conditions.
Nucleoid
The bacteria nucleoid is a nuclear region containing a single circular DNA molecule without a nuclear membrane. Plasmids may often also be present within the nucleoid region of bacteria.
Ribosomes
Ribosomes in bacteria transcribe mRNA, messenger RNA, into proteins, which is similar to other cells.
Cell Membrane
Bacterial cell membranes enclose the bacterium and allow fro selective permeability and transport of soultes, such as sodium and potassium into and out of the cell. The cell membrane contains enzymes that produce the energy for the bacterium cell, through electron transport and oxidative phosphorylation. Bacteria do not have mitochondria that preform energy production as in eukaryotes, such as human cells.
Cell Wall
The cell wall of bacteria is a rigid enclosure that surrounds the cell membrane and creats the shape of the bacterium. The cell wall most importantly protects the bacterium against osmotic lysis. The cell wall is a mixed polymer called peptidoglycan. Peptidoglycan is a mix of sugar and protein, polymers of N-acetylglucosamine and N-acetylmuramic acid.
Cell Wall and Gram Stain
The thickness and inner structure of the cell wall determines the characteristics of the Gram stain. Bacteria that stain positive with a Gram stin have thick, dense, rigid layers of peptidoglycan and teichoic acid. Teichoic acid is not present within gram negative bacteria.
Gram negative bacteria have a much thinner peptidoglycan layer. Gram negative bacteria have an outer membrane layer that is much thicker than the layer of peptidoglycan. This outer membrane layer is composed of lipopolysaccharides and lipoproteins, such as LPS and endotoxin.
LPS Lipopolysaccharides
LPS, lipopolysaccharides, is a toxin. When bacteria die, the LPS is released from their membrane into the circulation and can lead to outcomes, such as sepsis and vascular collapse and the body reacts to the antigen.
Bacteria Classification
Bacteria may be classified according to many of their different properties.
Most common:
Gram stain properties
Gram positive bacteria stain blue.
Gram negative bacteria stain pink.
The gram stain is very important as it can divide most bacteri, allows for direction in further testing as to what bacteria is causing the disease and also gives direction to management and treatment of the disease.
Morphology
Cocci which are round bacteria.
Bacilli which are rod shaped bacteria.
Growth Conditions
Bacteria have different preferred growth conditions.
Strict aerobic
Aerobic bacteria, strict, have an absolute requirement for oxygen gas within air and cannot grow without oxygen. There are very few strict aerobic bacteria.
Strict obligate anaerobes
Obligate anaerobes, strict, can grow only in complete or nearly complete absence of oxygen. Oxygen will halt these bacteria’s growth or kill them. Clostridium is an obligate anaerobe.
Facultative anaerobes
Faultative anaerobes are bacteria that can flip between the two above mentioned states. Facultative anaerobes can use oxygen if it is present and can grow also if it is not present. Most bacteria are of the facultative anaerobe type.
Bacteria Structure and Growth Conditions
| Gram positive | Gram positive | Gram negative | Gram negative | |
| Cocci | Rods | Cocci | Rods | |
| Aerobes | Staphylococcus | Listeria | Nesseria | E.coli |
| Streptococcus | Clostridium | Moraxella | Bacteroides | |
| Micrococcus | Corynebacterium | Haemophilus | ||
| Peptococcus | Bacillus | Pseudomonas | ||
| Anaerobes | Peptostreptococcus | Propionibacterium | Fusobacterium |
Posted in Bacteria
Tagged , Bacteria, Bacteria Capsule, Bacteria Classification, Bacteria Facts, Bacteria Flagella, Bacteria Structure, Cell Membrane, Cell Wall, Cell Wall and Gram Stain, Endospore, Growth Conditions, Lipopolysaccharides, LPS, Morphology, MUTUALISM, nucleoid, Pili, Ribosomes
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Bacteria Nutrition
Bacteria Nutrition
Classifying Bacteria according to Modes of Nutrition
Types Of Bacterial Organisms Mode Of Nutrition (How do they live?)
Heterotrophs live from other organisms
Parasites are disease causing bacteria
Saprophytes live from utilizing dead and decomposing matter
Autotrophs survive through photosynthesis or chemosynthesis (inorganic matter)
Bacterial Nutrition
Autotrophic Bacteria:
Some bacteria only
They make their own food from raw material
a) Photosynthetic Autotrophic Bacteria:
Carry out process of photosynthesis
b) Chemosynthetic Autotrohpic Bacteria:
Obtain energy for making food from chemicals in the environment
Heterotrophic Bacteria:
Most bacteria
Cannot make own food and hence obtain food from an outside source
a) Symbiotic Heterotrophic Bacteria:
Live on or in other living things
b) Saprophytic Heterotrophic Bacteria:
Live off dead organic matter or wastes
Bacteria Shape
Bacteria Shape
How to examine and identify bacterial organisms through the light compound microscope:
Because of their small size it is a bit of a challenge to examine and identify bacterial organisms.
Bacteria has been divided into three groups on the basis of shape:
Cocci (spherical)
Bacilli (straight rod)
Spirilla (spiral rod)
Shape is used as one means of bacterial identification.
The size of bacteria range from 0.1-0.5 microns where (1 micron = 1 x 10^-6m)
Therefore this shows that bacteriologists depend on biochemical and physiological characteristics for classifying and identifying bacterial organisms.
Bacterial organisms can be further classified with respect to colonization:
Type Number In Colony Group Name
Diplo Group of two Diplococci, Diplobacilli
Staphylo Clusters of many grapes Staphlococci
Strepto Long chains Streptococci, Streptobacilli
Posted in Bacteria
Tagged , bacilli, Bacteria, Bacteria Shape, cocci, colonization, rod, shape, spirilla
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Good Bacteria
Good Bacteria
Helpful Bacteria:
They cause the fertilizers to rot in order to transfer their minerals to the soil where plants can take in the nourishment they need to grow. Beneficial to plants.
Bacteria are often helpful in breaking down foods in the intestine of humans. This is helpful because it enables the body to get its nourishment from the food that is eaten.
Bacteria also help I the formation of wine; changing the juice of grapes into wine.
Bacteria living in small lumps or on roots of certain plans such as clover, peanuts and beans are helpful bacterial because they enable the plant in which they live in/on to take in Nitrogen in the form of NO3-.
Bad Bacteria
Bad Bacteria
Harmful Bacteria:
Some bacteria give off poison as waste. For example, Diphtheria bacteria which is the cause of a sore throat.
Bacteria can live in water and in foods we eat. Harmful bacteria found in water or food we eat can cause the occurrence of a fever.
Two red rods which are slightly bent, are deadly germs which attach lungs and other organs causing tuberculosis and the coughing up of mucus.
Harmful bacteria get into food and grow in large numbers, spreading rapidly. As they develop, these bacteria give off a waste which is a powerful poison; food poisoning called botulism.
Bacteriophage
Bacteriophage
Bacteriophages are not a cell themselves, but a simple acellular organization which can consist of only one molecule of nucleic acid covered in a protein coat. Some bacteriophages are complex, however most are simple. Bacteriophages can have either DNA or RNA, but never both. There is much variation in the genetic material of bacteriophages. Bacteriophages can have linear or circular genetic material, which can be single stranded or double stranded.Bacteriophages can survive alone outside of a cell, but require to infect a cell in order to replicate. Replication requires a cell and the cells machinery and components.
Bacteriophage Plaque Assay
Bacteriophage Life Cycle
Bacteriophage Functions
Bacteriophages protect nucleic acid material from external chemicals and physical agents that could damage and alter the genetic material, by mutation or breakage. Bacteriophages do this through containing a protein capsule. Bacteriophages main function is to delivery functional and undamaged nucleic acids into the interior of a bacterium in order to proceed with the bacteriophage life cycle. The genetic material once inside the bacterium will produce large numbers of new, progeny bacteriophages which will then be released from the infected bacterium.
Some definitions:
Prophage
Prophage is bacteriophage DNA found in lysogens. Prophage may stay in the cell and never enter a lytic cycle, for example if it is mutated.
Lysogen
Lysogen is a bacterium containing a complete set of bacteriophage genes, either as a plasmid or chromosome.
Temperate phage
A temperate phage can enter into the lysogenic or lytic life cycle.
Integration
Integraion is the process of DNA insertion into a chromosome.
Lysogens
Lysogens contain bacteriophage genetic material. Interstingly, lysogens are unable to be reinfected by the same bacteriophage that infected the cell initially. Lysogens can go through the lyitc bacteriophage life cycle, however, lysogens can also initiate the lytic cycle after many cell cycles. This is termed induction.
Plasmid
Plasmid
Plasmids DNA Molecules
Plasmids are small, circular, supercoiled DNA molecules containing often around 30 genes or less. Plasmids are present in most bacterial species and there may be 1 to a 1000 copies of a plasmid within a cell. Plasmids utilize the DNA replication machinery of the cell to replicate. Plasmids have there own replication origin and can replicated autonomously. Because of this, plasmids are stably inherited through time. Plasmids can confer cells many advantages by giving the cell that inherits them the function of the genes that they carry. Under certain external changes and stresses, these plasmids can give a cell the needed genetic diversity to grow and overcome natures obstacles. These plasmids are selected as they carry a particular function. If not selected for, the plasmid will be lost, however if selected for, as with antibody resistance genes, the plasmid with be favored and selected for and spread.
Plasmid Replication
Plasmid replication may be bidirectional, but also unidirectional. The replication proteins required for plasmid replication vary, and include both plasmid-encoded proteins and host encoded proteins.
Respiration
Bacteria Respiration
Classifying Bacteria on the basis of respiration mechanisms:
Anaerobic Bacteria vs. Aerobic Bacteria
Obligate Aerobes
Obligate aerobes: must have Oxygen in lungs
Ex. Bacterial organisms that produce pneumonia
Obligate Anaerobes
Obligate anaerobes: Absence of Oxygen
Ex. Fermentation to carbon dioxide, alcohol, lactic acid, CH4-
Facultative Anaerobes
Facultative anaerobes: with or without Oxygen (Host)
Note: These bacterial organisms are the most dangerous because they have the ability to live with or without oxygen.
Posted in Bacteria
Tagged , Bacteria, Bacteria Respiration, bacterium, Facultative Anaerobes, obligate, obligate aerobes, Obligate Anaerobes, respiration
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