CLASSIFICATION OF LIFE

TWO SYSTEMS:

5 KINGDOM CLASSIFICATION

3 KINGDOM CLASSIFICATION

WHAT ARE THE DIFFERENCES BETWEEN EUCARYOTES AND PROCARYOTES?
 

PROCARYOTES	EUCARYOTES
cell wall- Complex, with peptidoglycan (and in gram negatives, lipopolysaccharide)	cell wall- Chemically simple, in plants (the polysaccharides cellulose and pectin as well as the phenol polymer lignin) and fungi (the polysaccharide chitin)
no membrane bound organelles- but there are numerous inclusions and granules. Numerous small ribosomes in cytoplasm.	many membrane bound organelles- lysosomes, mitochondria (with small ribosomes), golgi bodies, endoplasmic reticulum, nucleus. Large ribosomes in cytoplasm and on rough ER.
genetic information- DNA is in the cytoplasm and is organized into the bacterial chromosome and into plasmids. There is mRNA, tRNA and rRNA. Bacteria, of course, have no nucleus and therefore also nuclear membrane.	genetic information- DNA is organized into numerous chromosomes and is packaged in the nucleus. The nucleus is bounded by a membrane mRNA, tRNA and rRNA are made in the nucleus and shipped out into the cytoplasm.
locomotion- rigid flagella. Spirochetes have axial filaments.	locomotion- flexible flagella and cilia based on microtubules. Contractile motion based on actin. Some cells have endocytosis and exocytosis which also uses actin.

Please note that viruses are not included in the above scheme.:

Viruses have either DNA or RNA but not both.

Viruses can only reproduce inside host cells - even bacterial cells. Many bacteria, fungi and protozoa can live outside of host cells (although some of these organisms do live inside host cells.)

View a video describing how a virus -HIV- infects and replicates in cells -Courtesy of the University of Leicester

THE BACTERIA

BACTERIA ARE GIVEN A GENUS AND SPECIES NAME.

THEY ARE CLASSIFIED INTO A PARTICULAR GENUS AND SPECIES ACCORDING TO A VARIETY OF CRITERIA:

1.) MORPHOLOGY - INCLUDING:

• gram stain or acid fast stain characteristics;
• cell shape (coccus, rod/bacillus, spiral),
• cell arrangement (clusters, chains, tetrads etc.)

• type of metabolism (aerobic respiration, anaerobic respiration, fermentation);
• need for enriched co2 (capnophilic);
• which nutrients can be used;
• which products are produced;
• temperature requirements;
• pH optimums;
• salt tolerance.

• guanine + cytosine content. (G+C content)
• DNA fingerprinting (restriction fragment length polymorphism - RFLP)
• 16s ribosome subunit analysis
• polymerase chain reaction (PCR) with selected primers

BACTERIAL STRUCTURE
 
 

CYTOPLASMIC MEMBRANE / PLASMA MEMBRANE:

phospholipid bilayer -- (hydrophobic tails and hydrophilic heads; another way of saying this: polar heads and non-polar tails).

integral membrane proteins are embedded in the bilayer.

they form pores and channels for the diffusion of some substances across the membrane. diffusion does not require any added energy.

other integral membrane proteins serve as transporter molecules for substances that need active transport to get across the membrane. (active transport requires added energy.)

(integral membrane proteins are found in the membranes of all cells. many also serve as receptors for cell-cell communication processes.)

CELL WALL- two major types of bacterial cell walls were recognized through the gram stain.
 
 

GRAM POSITIVE CELL WALL - has a thick peptidoglycan layer. Also contains teichoic acids linked to either the peptidoglycan or to the underlying plasma membrane.

GRAM NEGATIVE CELL WALL - has a thin peptidoglycan layer as well as an outer membrane. this outer membrane of the the gram negative cell wall contains lipopolysaccharide (LPS) or endotoxin. this substance, which contains both lipid A and "O" polysaccharides ("O" antigens), is responsible for much of the pathogenicity seen in infections with gram negative bacteria.

Bacteria of the genus Mycobacteria, (the organisms which cause tuberculosis and Hansen's disease (leprosy) are Mycobacteria), do not stain easily with the gram stain. these organisms are stained with the acid fast stain and they are called acid fast organisms. they contain waxy lipids in their cell walls (mycolic acid). The genus Nocardia is also acid-fast. This stain is also used to identify certain parasites like Crytptosporidium.

Another atypical cell wall, so to speak, would be found in those bacteria which do not have cell walls -- the Mollicutes which include Mycoplasma and Ureaplasma.

THE CAPSULE / SLIME LAYER / EXTRACELLULAR POLYMERIC SUBSTANCE (EPS).

1. this material (structure) often helps bacteria to adhere to tissues. (glucan in the oral streptococci). (this could be called an adhesin).

2. this material often helps bacteria avoid phagocytosis -- as such it is called antiphagocytic.

PILI / FIMBRIAE

the term pilus is usually used to describe structures used in conjugation.

the term fimbria describes hairlike projections used to help the bacterium adhere. as such it could also be called an adhesin. such fimbriae are very important in organisms that infect the intestinal mucosa, the urinary tract and in gonorrhea.

• Streptococcus pyogenes has protein F which binds to fibronectin on the host cell.
• S. pyogenes also has a fuzzy fibrillar layer which contains M protein - a protein shown to be both anti-phagocytic and autoimmune. (rheumatic fever).

Some Bacteriophage attach to bacterial pili.

THE FLAGELLA:

THE ENDOSPORE

HIGHLY RESISTANT STRUCTURES. CAN WITHSTAND HIGH TEMPERATURES, DRYING AND SEVERAL DISINFECTANTS.

USED IN QUALITY CONTROL ON AUTOCLAVES.

BACILLUS sp. AND CLOSTRIDIUM sp. ARE THE IMPORTANT SPOREFORMERS.

BACILLUS = ANTHRAX AND B. CEREUS FOOD POISONING

CLOSTRIDIUM = TETANUS, BOTULISM, GAS GANGRENE, PSEUDOMEMBRANOUS COLITIS.

GENETIC INFORMATION

TWO FORMS OF DNA IN BACTERIAL CELL:

1.) the chromosome also called the genome - which carries all the information needed to make a functional cell. double-stranded and circular.

2.) plasmid(s) - which often carry genes for antibiotic resistance. double stranded and circular.

SOME BACTERIA GROWING UNDER OPTIMAL CONDITIONS CAN DIVIDE EVERY 20 MINUTES. WHICH MEANS THAT THE DNA NEEDS TO REPLICATE AT LEAST EVERY 20 MINUTES.
A TYPICAL BACTERIAL CHROMOSOME IS ABOUT 4,000,000 NUCLEOTIDES LONG, SO HOW MANY NUCLEOTIDES PER MINUTE GET REPLICATED? HOW MANY NUCLEOTIDES PER SECOND GET REPLICATED?
 
 

INFORMATION ON THE DNA IS ARRANGED IN GENES.

SIMPLY PUT, A GENE IS ALL THE INFORMATION NEEDED TO MAKE A PROTEIN.

TATATA........................................TAC..................................ATTorATCorACT
 
 

GENES ARE TRANSCRIBED INTO EITHER rRNA or tRNA or mRNA.
mRNA IS TRANSLATED INTO PROTEIN BY THE RIBOSOMES WHICH READ THE NUCLEOTIDE SEQUENCE OF THE mRNA IN THREE LETTER BLOCKS WHICH WE CALL CODONS.
 
 

PROTEINS

Click Here for an excellent review of the importance of proteins

Click here if you are interested in taking a course in protein structure and chemistry offered by Birkbeck College (University of London).

PROTEINS ARE MADE OF AMINO ACIDS. POLYMERS.

HOW MANY AA's ARE THERE? WHAT IS THE BASIC STRUCTURE? HOW ARE AMINO ACIDS CLASSIFIED?

HYDROPHOBIC (NON-POLAR), HYDROPHILIC (POLAR), BASIC (+ CHARGE), ACIDIC (- CHARGE).

WHAT DO PROTEINS DO? NAME SOME CATEGORIES OF PROTEINS.

35% of the dry weight of bacteria is ribosomes -- big investment in protein synthesis machinery.

proteins have a shape -- a conformation. this is determined by the amino acid sequence.

The shape is sensitive to physical and chemical conditions around the protein molecule: pH, ionic strength and temperature will affect protein conformation.

Binding to and interaction with other molecules (substrate, cofactors, other proteins) will also alter protein conformation.

GENETIC CHANGE : MUTATION AND RECOMBINATION

MUTATION -- A CHANGE IN BASE SEQUENCE OF THE DNA. CAN HAPPEN SPONTANEOUSLY OR THROUGH MUTAGENS. BASES CAN BE DELETED, REPLACED OR INSERTED.

RECOMBINATION -- CUTTING AND JOINING DNA SEGMENTS INTO NEW COMBINATIONS OR ARRANGMENTS.

ENCAPSULATED STRAINS = SMOOTH = S = VIRULENT TO MICE.

NON-ENCAPSULATED STRAINS = ROUGH = R = AVIRULENT TO MICE.

strain inoculated           effect on mouse             strain isolated from mouse  
living R                    mouse lives                 nothing or R                
living S                    mouse dies                  S                           
dead R                      mouse lives                 nothing                     
dead S                      mouse lives                 nothing                     
living R and dead S         mouse dies                  R and S

2. CONJUGATION -- MATING OF BACTERIA WITH THE TRANSFER OF PLASMIDS. BACTERIA HAVE A PILUS (A SEX PILUS) WHICH ALLOWS THE DONOR TO SNAG A RECIPIENT. THE CELLS GET VERY CLOSE TOGETHER AND A MEMBRANE ENCLOSED CYTOPLASMIC BRIDGE FORMS BETWEEN THE TWO CELLS. THE PLASMID PASSES FROM THE DONOR CELL TO THE RECIPIENT.

IN E. COLI, THE F-PLASMID (F-FACTOR) IS THE MOST COMMONLY CITED EXAMPLE. THE F-PLASMID HAS ON IT THE GENE FOR F-PILUS SYNTHESIS. CELLS WITH THE
F-PLASMID ARE CALLED F+ WHILE THE RECIPIENT CELLS ARE CALLED F-.

  Click here to watch E. coli mate

THE F-PLASMID CAN BECOME INTEGRATED INTO THE GENOME OF THE CELL. SUCH CELLS, CALLED Hfr ARE NOT ONLY ABLE TO MATE WITH F- CELLS, BUT THEY ARE NOW ABLE TO TRANSMIT CHROMOSOMAL INFORMATION ALSO.

BECAUSE THEY CARRY GENES FOR ANTIBIOTIC RESISTANCE (R-FACTORS) AND GENES FOR TOXIN PRODUCTION -- (GENES FOR STAPHYLOCOCCAL ENTEROTOXIN, HEMOLYSIN AND FIBRINOLYSIN ARE ON PLASMIDS; E. COLI TOXINS ARE ALSO FOUND ON PLASMIDS).
 
 

3. TRANSPOSONS -- JUMPING GENES.

THESE GENES HAVE NUCLEOTIDE SEQUENCES AT BOTH ENDS WHICH ALLOW THEM CUT THEMSELVES OUT OF OR INTEGRATE THEMSELVES INTO VARIOUS PLACES IN THE CHROMOSOME OR IN PLASMIDS. TRANSPOSONS CAN MOVE BETWEEN PLASMIDS, BETWEEN PLASMIDS AND CHROMOSOME AND TO DIFFERENT PLACES ON THE CHROMOSOME.
 
 

4. TRANSDUCTION -- TRANSFER OF DNA BY A VIRUS.

FIRST, SOME BASIC VIROLOGY: