exam 1 Flashcards
Microorganisms
are minute living things that are too small to see with the naked eye - Bacteria - Archaea - Fungi - Protozoa - Algae - Viruses - Helminths
Microbiology
is the study of microorganisms.
Eubacteria
“true-bacteria” – Small unicellular organisms. – Its genetic material is not enclosed in a nuclear membrane. – are prokaryotes (“prenucleus”) – Most common shapes of cells are: 1. bacillus (rod) 2. coccus (spherical or ovoid) 3. spiral or corkscrew – Have cell wall composed primarily of peptidoglycan. – Generally reproduce by binary fission
prokaryotes
(“prenucleus”)Its genetic material is not enclosed in a nuclear membrane
bacillus shape
(rod)
coccus shape
(spherical or ovoid)
Archaea:
“exteme-ophile” - are prokaryotes - cell walls lack peptidoglycan - are found in extreme environments - There are 3 main groups of Archaea 1. Methanogens: produce methane gas as waste product 2. Extreme halophiles: salt-loving 3. Extreme thermophiles: heat-loving; live in hot sulfurous water such as hot springs in Yellowstone National Park.
Methanogens:
produce methane gas as waste product
Extreme halophiles:
salt-loving
Extreme thermophiles:
heat-loving; live in hot sulfurous water such as hot springs in Yellowstone National Park.
Fungi
- are eukaryotes. - are members of the kingdom Fungi. - are unicellular (yeasts) or multicellular (mushrooms). - True fungi have cell walls composed of chitin. - Yeasts are oval-shaped microorganisms larger than bacteria. - Molds are typical fungi. - reproduce sexually (meiosis) or asexually (mitosis).
meiosis)
reproduce sexually
(mitosis)
asexually
Yeasts
are oval-shaped microorganisms larger than bacteria
Protozoans:
- unicellular eukaryotes - are members of the kingdom Protista - are classified according to their means of locomotion 1. cytoplasmic streaming (amoebas) 2. flagella 3. cilia - shapes vary - can live free or as parasites. - reproduction is sexual or asexual. (Fig. 1.1c)
Algae:
DIVERSITY OF MICROORGANISMS - are photosynthetic eukaryotes. - wide varieties of shapes. - are members of the kingdom Protista. - reproduction is sexual or asexual.
Viruses :
- are so small that they can only be seen with an
electron microscope.
- are not cellular.
- are parasites which require a host cell to replicate itself.
- simple structure:
- Core contains the nucleic acid (DNA or RNA)
- Protein coat surrounds core
- Lipid envelope may surround coat
Multicellular Animal Parasites
2 major groups collectively called helminths
- flatworms
- roundworms
- During some stage of their life
cycle the helminths are microscopic in size.
Robert Hooke
1665 observed and made drawing of “cells” from a cork
M. J. Schleiden & T. Schwann
(1838) established the cell theory
cell theory
- “all living things are composed of cells” -Modern tenets of the cell theory:
1. all known living things are made of cells
2. cell is the basic structural & functional unit of all living things
- all cells come from pre-existing cells by division
- cells contains hereditary information
- all cells are basically the same in chemical composition
- metabolism and biochemistry of life occurs within cells
Anton van Leeuwenhoek
1674
observed microorganisms through magnifying lenses.
Made numerous drawings of bacteria and protozoa and sperms
Spontaneous generation:
life could arise spontaneously from non-living matter.
People thought that toads, snakes, and mice could be born from moist soil and that flies could emerge from manure, and that maggots, the larvae of flies could arise from decaying corpses.
Francesco Redi
Opposition to spontaneous generation: 1668
expirament:
3 jars with decaying meat and sealed them tightly, no maggots
• 3 jars with decaying meat and left them open, maggots • There were doubter still…magical substance in fresh
air was needed for spontaneous generation to occur…
John Needham
Proponent of spontaneous generation 1745
He heated nutrient fluids (chicken broth and corn broth), cooled it, and then poured it into covered flasks, the solutions were teeming with microorganisms.
Needham claimed that the microbes developed spontaneously from the fluids.
Lazzaro Spallanzani
1765
disproved Needham conclusion
- suggested that microorganisms from the air probably entered the solutions from the air after they were boiled.
- showed that nutrient fluids heated after being sealed did not develop microbial growth.
Rudolf Virchow
1858 Theory of biogenesis: living cells can arise only from preexisting living cells
Theory of biogenesis:
living cells can arise only from preexisting living cells
Louis Pasteur
1861 demonstrated that microorganisms are present in the air and that they can contaminate sterile solutions, but air itself does not create microbial life.
During a job on understanding why wine and beer sour, discovered that microorganisms called yeasts convert sugars to alcohol in the absence of air.
This is called FERMENTATION (1857).
Discovered pasteurization (1864)…process of
heating to kill bacteria to reduce/prevent spoilage
This was the first link that microorganisms can cause changes in organic materials.
that microorganisms might cause disease
introduced germ theory of disease
Vaccination
is the process of conferring immunity using a vaccine which is a preparation of killed, inactivated, or attenuated microorganisms or toxoids to induce artificially acquired active immunity
Edward Jenner
1798
developed the first vaccine for smallpox
milkmaid couldn’t get smallpox because she had already been sick with cowpox, a much milder disease
Jenner decided to test this story:
collected scrapings from cowpox blisters and made inoculations with this material by scratching the arm of a healthy volunteer with the cowpox contaminated needle.
The person became mildly sick but recovered and never
contracted either cowpox or smallpox
Simple stain
is an aqueous or alcohol solution of a single basic dye
- is used to highlight the entire microorganism so that cellular shapes and structures are visible.
- A mordant may be added to the simple stain to:
increase the affinity of a stain for the specimen
coat a structure (such as a flagellum) to make it thicker.
- Examples of simple stains: 1. methylene blue (blue) 2. carbolfuchsin (red)
3. crystal violet (purple) 4. safranin (pink)
mordant
may be added to the simple stain to:
increase the affinity of a stain for the specimen
coat a structure (such as a flagellum) to make it thicker.
Differential Stains
react differently with different bacteriacan be used to distinguish them
- 2 types of differential stains 1. Gram Stain
2. Acid-Fast Stain
Gram Stain
was developed in 1884 by the Danish microbiologist
Hans Christian Gram
- differentiates/classify bacteria into 2 large groups
a. gram positive (+) purple
b. gram negative (-) pink
gram stain procedure
- Apply crystal violet which colors all bacteria purple (primary stain)
• Wash off w/ddH O. 2
- Apply iodine, a mordant, all bacteria still purple.
- Wash with ethanol or ethanol- acetone solution, a decolorizing agent
- Gram + bacteria will be purple; Gram - bacteria will be colorless
- wash off w/ddH2O
- stain with safranin, a counterstain.
- Gram (-) will be pink; Gram (+) will be purple - wash off w/ddH2O
- blot dry 19
- examine microscopically
Gram-positive
no membrane covering peptidoglycan wall
Gram (+) bacteria have a thicker cell wall composed of peptidoglycan than gram (-) bacteria
Gram-negative
outer membrane covers peptidoglycan wall
Gram (-) bacteria have a thin layer of peptidoglycan and outside of that, a layer of lipopolysaccharide
- Gram stain: Procedure why it works
rystal violet and iodine can go through the thick cell wall, but once inside form a complex (CV-I) which can not go out of the cell.
- gram (+) bacteria stain purple because of the trapped CV-I complex
- gram (-) bacteria will be colorless because the alcohol wash disrupts the lipopolysaccharide and allow the CV-I complex to be washed out of the cell
- gram (-) bacteria are pink because of the counterstain with safranin
- Gram stain is most consistent when used on young, growing bacteria.
result of gram staining provide information for proper treatment of disease
- Generally, gram (+) bacteria are easily killed by penicillin and sulfonamide drugs.
- Gram (-) bacteria are resistant to these drugs, but are more susceptible to streptomycin, chloramphenicol, and tetracycline.
Acid-Fast Stain
stain binds to bacteria that have a waxy materia(mycolic acid and evades immune system and phagocytosis happens) l in their cell walls
- used to identify all bacteria in the genus Mycobacterium Ex. Mycobacterium tuberculosis causes tuberculosis. Ex. Mycobacterium leprae causes leprosy.
- used to identify the disease-producing strains of the genus Nocardia
Acid-fast stain: Procedure
a. Apply carbolfuchsin to heat-fixed smear and gently heat to enhance penetration and retention of the dye. (All organisms will be red.)
b. Wash
c. Decolorize with acid-alcohol.
- Acid-fast organisms will be red since carbolfuchsin is soluble in the waxy material of the cell wall
- Non-acid-fast organisms will be colorless since these organisms do not have the waxy material in their cell walls to retain the carbolfuchsin
d. Counterstain with methylene blue.
- Acid-fast organisms will be red.
- Non-acid-fast organisms will be blue.
Negative Staining for Capsules
- capsule: a gelatinous covering of some microbes;
confers virulence(polysacharide or polysacharide protine)
- is more difficult than other types of staining procedures because capsules are soluble in water and may be removed during washing.
Negative staining for capsuls: Procedure
a. Mix bacteria with Nigrosine, an acidic dye which provides a
dark purple background.
b. Spread dye as in negative staining.
c. Stain slide with crystal violet, basic dye to stain bacteria (purple)
d. Capsules will appear as colorless halos surrounding purple bacterial cells against a dark purple background.
Endospore (Spore) Staining
Endospores are resistant, dormant structures within a cell which protects the microbe from adverse environmental conditions.
- are formed by 7 genera of bacteria (including Bacillus and Clostridium)
- do not stain with ordinary stains because the dyes do not penetrate the wall of the endospore.
- 2 methods used:
- A. Schaeffer-Fulton endospore stain - B. Dorner endospore stain
Schaeffer-Fulton Endospore Stain
a. Apply malachite green to heat-fix smear on slide and steam heat for 5 minutes. Spores will stain green and cells will be colorless.
b. Wash
c. Counterstain with safranin, which will stain the cells
pink. Spores will be green. d. Wash
Dorner Endospore Stain
a. Put carbolfuchsin, red, in a test tube
b. Add several loopfuls of organism
c. Boil in a beaker of water for 10 minutes
- *Spores will be red, cells colorless.**
d. Add several loopfuls of the carbolfuchsin- bacteria
mixture to a drop of nigrosine on a slide e. Smear mixture
- Bacterial cells will be colorless against dark purple background (Negative Staining).
- Endospores inside the cells will be red.
- Flagella Staining
Flagella are structures of locomotion.
- Staining flagella involves using a mordant and carbolfuchsin to build up the diameters of the flagella until they become visible under the light microscope.
- It is a tedious and delicate staining procedure.
GOLDEN AGE OF MICROBIOLOGY
1857- 1914
A period of explosion of discoveries in
microbiology which led to the establishment of microbiology as a science.
1867 - Joseph Lister
English surgeon
initiates aseptic surgical techniques.
He began soaking surgical dressings in a mild solution of carbolic acid (phenol) which kills bacteria.
This reduced the incidence of infections and deaths in surgical patients.
Founder of aseptic surgery
1876 -83 Robert Koch
proved the germ theory of disease
discovered a rod-shaped bacteria now known as Bacillus anthracis in the blood of cattle that had died of anthrax.
He cultured the bacteria and injected samples of the culture into healthy animals which became sick and died.
Koch isolated the bacteria in the blood and found it to be the same as the original bacteria isolated.
Experimental procedure used to relate specific microbe to a specific disease is known as Koch’s postulate
1881 - developed pure culture and staining techniques.
• 1882 - discovered Mycobacterium tuberculosis, the causative agent of
tuberculosis.
• 1883 - discovered Vibrio cholerae, the
causative agent of cholera.
1879 - Albert Neisser
1880 - Louis Pastuer
developed immunization techniques based on Edward
Jenner’s work with smallpox (vaccination)
• Avirulent form of bacterium causing fowl cholera can induce immunity against subsequent infections by virulent counterpart.
Vaccine: cultures of avirulent microorganism used for preventative inoculations
also discovered Streptococcus pneumoniae (1881), the causative agent of pneumococcal pneumonia.
1884 - Hans Christian Gram
developed a differential staining technique
called the Gram stain which differentiates bacteria into 2 groups, gram (-) and gram (+).
1885 - Theodor Escherich
of Germany discovered Escherichia coli, the
causative agent of urinary tract infections and traveler’s diarrhea.
1887 - Richard Julius Petri
of Germany introduced a covered dish for growing microorganisms on a solid medium. (petri dish)
1890 - Paul Ehrlich
of Germany proposed a theory of immunity in which antibodies are responsible for immunity.
- Discovery of chemotherapy—treatment of disease by use of chemical substances (i.e. synthetic drugs & antibodies)
- Magic bullet — substance that could target and destroy the pathogen without harming the host
- Salvarsan (arsenic derivative; 1910)— chemotherapeutic agent against syphillis
1892 - Dmitri Iwanowski
of Russia discovered a filterable organism (virus) caused tobacco mosaic disease.
1928 - Alexander Fleming
Scottish physician and bacteriologist
discovered the antibiotic, penicillin, by accident
Thus he discovered a mold (fungus), Penicillium chrysogenum which could inhibit the growth
of bacteria.
1735 – Carolus (Carl) Linnaeus
established the system of nomenclature (naming) for organisms which assigns each organism 2 names…
A. Genus is the 1st name and is always Capitalized and underlined or italicized.
B. Specific epithet or species is the 2nd name and is not capitalized, but is underlined or italicized.
Example:
1. Staphylococcus aureus or
- Staphylococcus aureus*
2. Escherichia coli or Escherichia coli
Beneficial Activities of Microorganisms
1. Microorganisms degrade dead plants and animals and recycle chemical elements such as nitrogen, carbon, oxygen, sulfur, and phosphorus.
Example - bacteria and fungi return carbon dioxide to the atmosphere when decomposing organic matter…carbon cycle
Example - Nitrogen fixation - converting nitrogen gas into ammonia (i.e. Rhizobium species)
2. Microorganisms are used to decompose
organic matter in sewage…recycle water and prevent pollution (bioremediation) of rivers and oceans
Bioremediation: use of microorganisms to remove environmental pollutant
(Zoogloea ramigera).
3. Microorganisms (i.e. Bacillus thuringiensis) cause disease in insects and thus can be used as a biological control in insect pests (instead of pesticides which harm the environment).
-
Microorganisms can be used to produce food such as:
a. soy sauce (Aspergillus oryzae (fungi) b. yogurt (Streptococcus thermophilus)
for acid production,
Lactobacillus bulgaricus for flavor and aroma).
- Using biotechnology and recombinant DNA technology, bacteria, can be used to produce human proteins:
a. insulin
b. factor VIII
c. tissue plasminogen activator d. growth hormone
e. use in gene therapy
Microbes and Human Disease
- The body has a normal flora of microorganisms
inside and on its surface that usually are a benefit to the body. - The important factors which determine whether a person will contract a disease include:
a. the disease producing properties of the microorganism
b. the resistance of the body.
- Only a minority of microorganisms are pathogenic (disease producing).
Biofilms: community/aggregate of microorganisms that are usually attached to a surface through secretion of a matrix. Ex. dental plaque
Emerging Infectious Diseases (EID): diseases that are new or changing and are increasing or have potential to increase in the near future
i.e. H1N1 influenza, S. aureus – MRSA, VISA, Ebola virus, Zika virus
Atom
smallest particle of an element that still retains its distinctive chemical properties
Isotopes
Atoms that contain the same number of protons and electrons
but different number of neutronsdifferent atomic mass.
Radioisotopes
sotopes that can decay and emit electromagnetic radiation, which can damage DNA/protein.
– It can be detected by X-ray film or other methods.
– Is widely used in molecular biology studies to label molecules.
– Can be detected by:
- a Geiger counter (monitor)
- exposure to X-ray film (autoradiography)
Molecules
made up of two or more atoms joined together by covalent chemical bonds
Covalent bonds:
– Involves the sharing of electrons between two atoms
– Bond strength is ~12- kcal/mol (the energy needed to break a bond)
– Single bond: 2 atoms sharing 1 pair of electrons
– Double bond: 2 atoms sharing two pairs of electrons
Polar bonds:
electrons are shared unequally by bonded atoms
Non-polar:
Electrons are shared equally by bonded atoms
Electronegativity
the power of an atom to draw electrons to itself
Non-covalent bonds:
– Interaction between atoms that do not involve sharing of electrons
– Weak bonds, but many non-covalent bonds working together can stabilize the 3D structure of a large molecule (intra- molecular interactions)
– Important for biomolecules; help molecules bind to other molecules (intermolecular interactions)
Types of non-covalent bonds:
Ionic interaction
Hydrogen bonds
Van der Waals interaction
Hydrophobic interaction
Hydrophobic
“water-fearing”
Non-polar molecules do not form hydrogen bonds with water.
Hydrophobic interaction is formed because all parties that “hate” water are pushed together.
why are Non-covalent bonds are critical for inter-molecular interactions
Individually, they are weak
Together, they are strong
Confers stability of a molecule
Confers specificity of binding
macromolecules
Small organic molecules combine to form large molecules
macromolecules are usually polymers (made of repetitive monomers)
Biomolecules
molecules produced by the cell
All cells produce similar biomolecules…
monomers
“small” molecules
Nucleotides
Simple sugar
Amino acids
Fatty acids
macromolecules
“Large” molecules
Nucleic acids
Polysaccharides
Proteins
Lipids
Condensation
(dehydration synthesis
reaction)
dehydration synthesis reaction)
water producing reaction
Hydrolysis
water obsorbing reaction
Carbohydrates
- Are sugars and starches (chain of glucose)
- Basic building block = Monosaccharide (simple sugars) - General composition: (CH2O)n
- 3 major groups:
- monosaccharides: contains 3-7 C atoms;
i. e. glucose, fructose, galatose, deoxyribose, ribose - disaccharides: formed by the bonding of 2 monosaccharides in a dehydration synthesis reaction
i. e. glucose + fructosesucrose glucose + galactoselactose
glucose + glucosemaltose
monosaccharides
contains 3-7 C atoms;
i.e. glucose, fructose, galatose, deoxyribose, ribose
disaccharides
Formed by the bonding of 2 monosaccharides in a dehydration synthesis reaction
i.e. glucose + fructosesucrose glucose + galactoselactose
glucose + glucosemaltose
Polysaccharides:
consist of three or more monosaccharides; can have side chains branching from main structure
i. e. glycogen, starch, & cellulose are composed of many glucose molecules
- glycogen: found in animal cells and some bacteria. - starch: found in plant cells and is used as food
by some animals.
- cellulose: is component of plant and most algae cell walls
glycogen
found in animal cells and some bacteria.
starch
found in plant cells and is used as food
by some animals.
cellulose
is component of plant and most algae cell walls
Functions of carbohydrates:
a. provide a source to produce energy, mainly ATP, for the cell.
b. function as food reserves
c. Deoxyribose sugar is backbone of DNA (deoxyribose nucleic acid).
d. are components of cell walls of bacterial cells
Lipids
Are “fat”
- Lipids
- Are composed of C, H, O
- Are nonpolar molecules; can’t dissolve in water
- F(x)s: energy source
- constituent of plasma membranes and cell walls
Types of lipids:
Triglycerides = simple lipids or fats
Complex lipids
- Steroids
Triglycerides
are formed by the dehydration reaction of one glycerol with 3 fatty acids.
- glycerol have 3 hydroxyl (-OH) groups attached to 3 C atoms
- fatty acids are composed of long hydrocarbon (H-C) chains ending with carboxyl (-COOH) group.
Saturated fatty acids
have no double bonds between the carbon atoms; thus, the carbons have the maximum number of hydrogens attached (saturated with hydrogens).
- Most animal fats are saturated fats.
Unsaturated fatty acids
have at least one double or triple bond between the carbons.
- Most plant fats are unsaturated fats.
Which type of fatty acid (saturated or unsaturated) is more easily packed together?
saturated
Complex lipids:
- contains elements (i.e. phosphorus, nitrogen, sulfur) in addition to C, H, O
- Examples are waxes and glycolipids.
- cell walls of bacteria belonging to the genus
Mycobacterium contain waxes & glycolipids; provides distinguishing staining characteristic
(acid-fast stain)
- example: phospholipids (glycerol, 2 fatty acid, phosphate group)
has polar and non-polar ends
- is major constituent of cell membranes—phospholipid bilayer
phospholipids
(glycerol, 2 fatty acid, phosphate group)
- has polar and non-polar ends
- is major constituent of cell membranes—phospholipid bilayer
Steroids
Steroids: has 4-ring structure
- 3 six carbon rings and 1 five carbon ring
- the addition of an -OH group makes the steroid a sterol (alcohol; cholesterol).
- sterols are found in plasma membranes of animal, fungi, and plant cells and one group of bacteria (mycoplasmas)
- Examples: cholesterol and hormones and Vitamin D in animals
benifits of Azotobacter
bennifits of Rhizobium
nitrogen fixation
what foord does Aspergillus oryzae produce
produce soy sauce
what food does Streptococcus thermophilus produce
yogurt
Lactobacillus bulgaricus produces what food
yugurt
Propionibacterium produces
holes in swiss cheese by producing corbon dioxide
Saccharomyces exiquus produces
bread
Lactobacillus
sanfrancisco).
sourdough bread
Saccharomyces cervisiae produces
wine
What are the effects of the normal flora of microorganisms in the human body?
protect us against dis- ease by preventing the overgrowth of harmful microbes, and others produce useful substances such as vitamin K and some B vitamin
- What determines whether a person will contract a disease?
a. the disease producing properties of the microorganism
b. the resistance of the body.
What proportion of the microorganims are pathogenic?
Only a minority of microorganisms are pathogenic (disease producing). about 1%
give at least 3 examples of microorganisms and the food product they are make.
a. soy sauce (Aspergillus oryzae (fungi) b. yogurt (Streptococcus thermophilus)
for acid production,
Lactobacillus bulgaricus for flavor and aroma).
c. cheese (Propionibacterium species produce holes in Swiss cheese by producing carbon
dioxide. )
d. bread (San Francisco sourdough bread requires
Saccharomyces exiquus and Lactobacillus
sanfrancisco) .
e. alcoholic beverages (wine requires the yeast
Saccharomyces cervisiae ).
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What are some uses of radioisotopes?
nucleic acids
Nucleotides are the basic building blocks of nucleic acids (DNA and RNA molecules—genetic material)
• Are composed of
– Phosphate group
– Pentose: 5-carbon sugar molecule
-deoxyribose vs ribose – Nitrogenous Base
Deoxyriboucleic Ribonucleic Acid Acid
There are five different nitrogenous bases:
Which nucleotide is present in DNA?
James Watson and Francis Crick
acquired data, some not so “available,” from rosalind franklin to construct a model for the DNA structure: double helix
They won the Nobel Prize in 1962.
Rosalind Franklin
howed that DNA is helical from X-ray diffraction
DNA
Right-handed double helix
DNA molecule has two strands; run
anti- parallel direction
The 2 DNA strands are complementary
Has polarity: 5’3’
Purines and pyrimidines of opposite
strands form H-bonds
C-G (3 H-bonds); A-T (2 H-bonds)
- Double stranded (ds) DNA can denature (melt) to single stranded (ss) DNA at high temperature, lower salt, or extreme pH conditions
- These conditions breakup the H-bonds between complementary bases.
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• DNA can also renature (anneal) under the reverse conditions
Major groove is major binding site for DNA-binding proteins
Bases are stacked perpendicular to axis of helix
Bases face inside; sugar-phosphate backbone on the outside of helix
Helix also held together by: hydrophobic & van der Waals
RNAstructure
Consists of 1 strand of nucleotides
Primary structure: the sequence of nucleotides in RNA
Secondary structure: RNA is usually single stranded; some regions may form double stranded within the molecule.
Tertiary structure: three- dimensional structure of a single RNA molecule
Types of RNAs Produced in Cells
All cellular RNAs are synthesized by the transcription process.
Type of RNA
mRNAs messenger RNAs, code for proteins
rRNAs ribosomal RNAs, form the basic structure of the ribosome and catalyze protein synthesis
tRNAs transfer RNAs, central to protein synthesis as adaptors between mRNA and amino acids
Adenosine Triphosphate = ATP
is the principal energy-carrying molecule (potential form of energy).
- is composed of adenine, ribose, and 3 phosphate groups
- energy is released when a phosphate is removed ATP———–>ADP + Pi + Energy
Amino acids (aa)
are the monomeric building blocks of proteins
There are 20 different aa.
All organisms on earth have the same 20 aa.
Each protein being synthesized are made from the different arrangements of the aa.
Each aa monomer has 4 different groups attached to the central carbon atom (C)
The nature of an aa is based on the composition of its side chain.
- 20 different aa20 different side chains
- Each side chain differ in: – Size
Hydrogen
– Shape
– Charge
– Hydrophobicity
hydrophobic amino acids
- Alanine (ala)
- valine (val)
- Isolucine (ile)
- Lucine (leu)
- Methinonine (met)
- Phenylalanine (phe)
- Tryptophan (Trp)
hydrophilic amino acids
- basic
- lysine (lys)
- argininine (arg)
- Histidine (his)
- acidic
- asparate (asp)
- glutamate (glu)
- polar amino acids
- serine (ser)
- threonine (thr)
- asparagine (asn)
- Glutamine(gln)
- thyrosine (tyr)
special amino acids
cysteine (cys)
glycine (gly)
proline (pro)
Protein chain (polypeptide)
is formed by amino acid monomers joined together by covalent peptide bonds
Peptide bond
joins the amino end of one aa to the carboxyl end of another aa
Protein: Structure
Primary (1o) structure:
– The linear sequence of amino acid
– Also known as the protein sequence
- Secondary (2o)structure:
– It is the regularly repeating conformation of the
peptide backbone
– Helix; Strands sheets; turns
– A polypeptide usually has different secondary structures at different regions
– Is dependent on the amino acid sequence of the different regions.
– Structure is stabilized by H-bonds
- Tertiary (3o) structure:
– Is the 3D arrangement of all the polypeptide’s amino acid residues
– Is formed by packing various combinations of 2o structures
– Structure is stabilized by a variety of non- covalent bonds between aa side chains (i.e. hydrophobic)
- Quaternary structure:
– The overall structure and organization of more than one polypeptide chain
– Each polypeptide chain in this protein is referred to as a subunit.
conjugated proteins
modified protines
ex
- glycoproteins contain sugars
- nucleoproteins contain nucleic acids 3. metalloproteins contain metal atoms 4. lipoproteins contain lipids
Functions of proteins
- Structural proteins
- microfilaments for movement of cells
- cell membranes or cell walls
- carrier proteinstransport molecules into and out of cells - Enzymes: catalyze chemical reactions 3. signaling molecules
- Toxins are produced by certain bacteria;
Bacteriocins: proteins produced by some bacteria that kill other bacteria.
- Hormones for regulatory function (i.e. insulin) 6. Antibodies for immune function
Prions
(Proteinaceous infectious particles) infectious proteins. Unlike bacteria or viruses, prions do not require any DNA or RNA infectious. A prion is a misfolded protein has lost its normal conformation and function while acquiring the ability to convert other molecules of the same protein from the conformation into the abnormal prion form. This form of self propagation explains the infectious nature of prions. In all of the prion proteins
studied, the transformation between the normal and prion forms occurs through a dramatic change in the protein’s three-dimensional structure. Prions cause diseases such as Creutzfeldt-Jakob disease (CJD; Kuru) in humans, in sheep (scrapie), and bovine spongiform encephalopathy (BSE or mad-cow disease).
Bacteriocins
proteins produced by some bacteria that kill other bacteria.
Enzymes
catalyze chemical reactions
TransmissionElectronMicroscopy (tem)
- can resolve objects as close as 2.5 nm
- Magnification is from 10,000X to 100,000X.
- Only a very thin section (about 100 nm) of a specimen can be studied effectively
- can’t obtain 3D image
- Specimens must be fixed, dehydrated, and viewed under vacuum; therefore, shrinkage and distortion may occur; may get artifacts
Compound Light Microscope:
- Resolution
- cannot resolve structures smaller than 0.2 um, therefore,
cannot be used to observe viruses.
- commonly used to observe various stained (killed) specimens and to count microbes.
- Specimen appears colored against a bright background.
- Maximum magnification is about 2000X (200x oil immersion)
Darkfield microscopy:
used for examining live microorganisms that do not stain easily, or are distorted by staining, or are invisible in brightfield microscopy
- uses a special condenser with an opaque disc that blocks light from entering the objective directly.
- Specimen appears light against a black background.
- can be used to detect Treponema pallidum, causative agent for syphilis
Fluorescence microscopy:
- uses an ultraviolet source of illumination that causes fluorescent compounds to emit light.
- Some organisms fluoresce naturally.
- Other organisms can be stained with fluorescent dyes called fluorochromes.
- Specimens appear as luminescent objects against a dark background
Combine a fluorochrome to a
specific antibody for a specific antigen.
Allow the antibody to combine with the specific antigen
Wash to remove non-specific binding
Thefluorochrome-antibody- antigen fluoresces under UV light
- is useful in diagnosing syphilis and rabies or detecting specific cell types, tissues, or structures
(Fig. 3.6a)
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Electron microscopy:
- uses beam of electrons (shorter wave length) instead of light
- Structures smaller than 0.2 um can be resolved (viruses, cellular structures)
- There are 2 types:
1. Transmission electron microscope (TEM) 2. Scanning electron microscope (SEM)
Scanning Electron Microscope: (sem)
- Image is 3-dimensional
- It can study surface structures of intact cells & viruses
- resolves objects as close as
20 nm
- Magnification is 1000X to 10,000X
Power of resolution of human eye, light microscope, and electron microscope:
Chief characteristics:
- Procaryotes
Greek for “prenucleus”
- Includes unicellular bacteria and archaea
- DNA is not enclosed within a nuclear membrane; usually have single circular chromosome.
- DNA is not associated with histone proteins
- Lack membrane-bound organelles and cytoskeleton
- Cell walls almost always contain peptidoglycan
- Usually divide via binary fission
Prokaryotes: Shape
-1. Spherical or coccus (pl. cocci)
- Diplococci = two cocci
- Streptococci = cocci in chains
- Tetrads = cocci that divide in two planes and remain in groups of four
- Sarcinae are cocci that divide in 3 regular planes and produce a cube- like group of 8
- Staphylococci are those that divide at random planes and form grape like clusters or broad sheets
Prokaryotes: Shape
- Rod-shaped, bacillus (bacilli, pl.)
- divide only across their short axis.
- Diplobacilli appear in pairs after division.
- Streptobacilli occur in chains. - Some have tapered ends like
cigars.
- Coccobacilli are oval and may look like cocci.
- Most appear as single rods.
- bacillus means:
a. bacterial shape
b. genus (i.e. Bacillus anthracis)
Prokaryotes: Shape
- Spiral
- have one or more twists; are never straight
- Vibrios are curved rods that look like commas.
- Spirilla have a distinctive helical shape like a corkscrew, fairly rigid bodies, and move by means of a flagella.
- Spirochetes are helical, flexible, and move by means of an axial filament
- Other spiral bacteria have more complex shapes and arrangements.
Prokaryotes: External Structures
- Glycocalyx
- Glycocalyx: general term used to describe substances that
surround bacterial cells
- are also called extracellular polymeric substances (EPS)
- It is a gelatinous polymer composed of polysaccharide, polypeptide, or both
- is viscous (sticky).
- is referred as a slime layer if glycocalyx is unorganized & loosely attached to cell wall
- is referred as a capsule if glycocalyx is organized and firmly attached to cell wall
- Capsules confer bacterial virulence (the degree to which a pathogen causes disease)
- capsules prevent from phagocytosis & dehydration & allow for substrate attachment
Prokaryotes: External Structures
- Flagellum (flagella, pl.): whip
- are long filamentous appendages
that move bacteria
- There are 4 arrangements of flagella:
a. monotrichous - single polar flagellum
b. amphitrichous - single flagellum at both ends of cell
c. lophotrichous - 2 or more flagella at one or both poles of the cell
d. peritrichous - flagella distributed over the entire cell
monotrichous
single polar flagellum
amphitrichous
single flagellum at both ends of cell
lophotrichous
2 or more flagella at one or both poles of the cell
peritrichous
flagella distributed over the entire cell
Flagellum: structure
- Three basic parts:
a. Filament is the long outermost region which is constant in diameter and contains the globular protein flagellin - not covered by membrane or sheath
b. Hook is the structure to which the filament is attached
c. Basal body anchors the flagellum to the cell wall and the plasma membrane.
(Fig. 4.8)
- It is composed of a central rod inserted into a series of rings.
Flagellum:
- Movement
aused by rotation of basal body.
- rotation is either clockwise or counter-clockwise around its long axis
- Eucaryotic flagella undulate in a wave-like motion
- Patterns of motility:
a. “Run” or “Swim” - when a bacterium moves in one direction for a period of time.
b. “Tumble” - abrupt, random changes in direction caused by a reversal of flagellar rotation - Taxis: the movement of a bacterium towards or away from a particular stimulus.
a. If the stimulus is lightphototaxis
b. If the stimulus is chemicalChemotaxis - positive chemotactic stimulus = attractant
- negative chemotactic stimulus = repellent
- ex. Light: a. if attractant → + phototaxis b. if repellent → - phototaxis
- Flagellum: Taxis
the movement of a bacterium towards or away from a particular stimulus.
a. If the stimulus is lightphototaxis
b. If the stimulus is chemicalChemotaxis - positive chemotactic stimulus = attractant
- negative chemotactic stimulus = repellent
- ex. Light: a. if attractant → + phototaxis b. if repellent → - phototaxis
Axial Filaments:aka endoflagellum
- are bundles of fibrils that arise at the ends of the cell
beneath the outer sheath and spiral around the cell.
- used as a form of locomotion by spirochetes such as Treponema pallidum, the causative agent of syphilis.
3. Rotation of filament causes spiral motion that resembles the movement of a corkscrew
Prokaryotes: External Structures
- Pili:
- are hair like appendages attached to bacterial cells
- are shorter and thinner than flagella
- consist of a protein called pilin
- can occur at the poles of the bacterial cell or evenly distributed over the entire surface of the cell
- many gram (-) bacteria have pili - 2 types of pili
a. common pili (aka fimbriae) allows a cell to adhere to surfaces
b. sex pili join bacterial cells to allow transfer of DNA from one cell to anotherconjugation (“bacterial sex”)
Prokaryotes: Cell Wall
- The cell wall is a complex, semi rigid structure that surrounds the plasma membrane.
- Almost all prokaryotes have cell walls - is the site of action of some antibiotics - Functions:
- to prevent rupture of bacterial cells
- to maintain the shape of the bacterium 3. to serve as a point of
anchorage for flagella 4. to produce symptoms of
disease in some species
Prokaryotes: Cell Wall
Composition and Characteristics:
- is composed of called peptidoglycan (disaccharide + polypeptide)
- The disaccharide is composed of:
1. N-acetylglucosamine (NAG) 2. N-acetylmuramic acid (NAM) - alternating NAG and NAM form the carbohydrate backbone
- tetrapeptide side chain (4 amino acids) attach to each NAM
- Parallel tetrapeptide side chains may be linked by a
peptide cross-bridge
Structure of peptidoglycan:
Difference between Gram (+) and Gram (-) cell walls
- Gram (+) bacterial cell walls consists of several layers of
peptidoglycan while gram (-) bacteria contain 1 thin layer 1.
Gram (+) bacteria:
- contain teichoic acids, which consists of an alcohol (glycerol) and phosphate
- Have negative charge due to phosphate
- F(x)s: regulates cation (+) movement in and out of cell
- Preventing extensive wall breakdown and cell lysis - Provide antigenic specificity
- Gram (-) Bacteria Cell Wall:
- consist of an outer membrane, very few layer of
peptidoglycan, and a periplasmic space (gel-like fluid) - peptidoglycan interacts with lipoprotein in the outer
membrane
- does not contain teichoic acids
a. The outer membrane consists of:
- lipoproteins
- lipopolysaccharides (LPS) = lipid + polysaccharide
- polysaccharide: O polysaccharides that function as antigens which can identify species of bacteria - lipid: lipid A (endotoxin) is toxic in host blood, causes fever and shock
3. phospholipids: strong (-) charge help evade phagocytosis
Functions of outer Membrane of Gram (-) Bacteria:
- Evade phagocytosis 2. Provides a barrier to:
a. certain antibiotics (penicillin)
b. lysozyme (enzyme which breaks down cell
walls of gram (+) bacteria) c. detergents
d. heavy metals
e. bile salts
f. digestive enzymes (i.e. lysozyme) g. certain dyes
- Outer membrane is semi-permeable: 1. Porin proteins form nonspecific channels
(< M.W. 800 can enter)
2. Specific channel proteins:
a. permit passage of specific molecules only (i.e. Vit B12, iron, nucleotides, maltose)
b. function as attachment sites for viruses and bacteriocins (proteins produced by some bacteria to kill closely related species).
Atypical Cell Walls
Atypical Cell Walls
a. Members of the genus Mycoplasma have no cell walls; they have unique plasma membranes which contain lipid sterols (probably protect the cells from osmotic lysis).
b. Archaebacteria have cell walls composed of polysaccharide and proteins; NO peptidoglycan!
c. L forms are tiny mutant bacteria with defective cell walls.
Damage to the cell wall
- Lysozyme: digestive enzyme that occurs naturally in eucaryotic cells; found in tears, mucus, and saliva.
• Gram (+) cell walls: lysozyme catalyzes the hydrolysis of the bonds between the NAM and NAG sugars of the peptidoglycan layers, destroying the cell wall.
- protoplast: resulting wall-less gram (+) cell
2. Gram (-) cell walls: not completely destroyed; some of
the outer membrane remains.
- spheroplast: outer membrane and the remaining cell
3. Protoplasts and spheroplasts are very susceptible to changes in the osmotic environment.
- Plasma (Cytoplasmic) Membrane
- Structure consists of:
a. Phospholipids
- 45-50%
- bilayer: polar head
vs. hydrophobic tail
b. Proteins
- Peripheral proteins: located at the inner and outer surface of the membrane
- may function as enzymes that catalyze chemical reactions
- may mediate changes in membrane shape during movement
- Integral proteins: penetrate the membrane; some may form channels for passage of ions and molecules
- Plasma membrane is a fluid mosaic model (dynamic and move)
- Functions of plasma membrane:
a. selectively permeable or semi-permeable: selective barrier for passage of molecules and ions
b. contains enzymes which break down nutrients
c. is involved in ATP production
d. in some bacteria, pigments and enzymes for photosynthesis are found in the thylakoids of the plasma membrane
- Plasma Membrane:
- Substances that destroy the plasma membrane:
a. certain alcohols
b. quartenary ammonium compounds
c. Antibiotics, such as polymyxins, disrupt the phospholipids
Plasma Membrane:
-2 processes to transport molecules across membrane
a. Passive processes: movement of molecules from an area
of high concentration to an area of low concentration - does not require energy (no ATP)
- simple diffusion
- facilitated diffusion
- osmosis
b. Active Process: use energy to move molecules from an area of low concentration to an area of high concentration (against the concentration gradient). - active transport
- group translocation
Passive process:
- simple diffusion: movement of lipid soluble substances such as oxygen, carbon dioxide, and nonpolar organic
molecules from area of high concentration to low concentration
- facilitated diffusion: require the help of carrier protein to transport molecule across the membrane (i.e. glucose)
- osmosis: net movement of water from an
area of high water to low water concentration
• A bacterial cell may be exposed to 3 kinds of osmotic solutions:
a. Isotonic solution: the same solute concentration as the cell
b. Hypotonic solution: less solute and more water than the cell therefore water will move into the cell which is hypertonic
c. Hypertonic solution: more solute and less water than the cell so that water will move out of the cell and the cell will shrink (plasmolysis).
- simple diffusion:
movement of lipid soluble substances such as oxygen, carbon dioxide, and nonpolar organic
molecules from area of high concentration to low concentration
- facilitated diffusion:
require the help of carrier protein to transport molecule across the membrane (i.e. glucose)
osmosis
net movement of water from an
area of high water to low water concentration
• A bacterial cell may be exposed to 3 kinds of osmotic solutions:
a. Isotonic solution: the same solute concentration as the cell
b. Hypotonic solution: less solute and more water than the cell therefore water will move into the cell which is hypertonic
c. Hypertonic solution: more solute and less water than the cell so that water will move out of the cell and the cell will shrink (plasmolysis).
group translocation:
like active transport but the substance is chemically altered while being transported across the membrane
a. is a special form of active transport b. occurs exclusively in prokaryotes
Ex.: glucose transported across the membrane gets phosphorylated, making it not able to move back across the cell membrane.
active transport:
depends on a carrier protein to move substances against the [gradient] across a membrane
Cytoplasm
substance of cell inside plasma membrane - composed of 80% water
- 20% = proteins, carbohydrates, lipids, and inorganic ions - cellular structures within cytoplasm:
- nucleoid
- ribosomes
- inclusions
- protein filaments
- no cytoskeleton, nucleus, and membrane bound organelles
Nucleoid
nuclear area
- contains a single long circular
molecule of double-stranded (ds)
DNA, “chromosome”.
- No histone proteins associate
with chromosome
Plasmid
extra small circular, dsDNA molecules
- replicate independently of chromosome
- usually contain 5 to 100 genes which are usually not essential for survival of the bacteria
- may carry genes for antibiotic resistance, tolerance to toxic metals, production of toxins, synthesis of enzymes
- horizontal gene transfer via conjugation
What is resolution?
Resolution is the ability of lenses to distinguish between
two points at a specific distance apart.
What are the resolution power of the brightfield microscope vs. TEM and SEM?
BF
cannot resolve structures smaller than 0.2 um, therefore,
cannot be used to observe viruses.
TEM - can resolve objects as close as 2.5 nm
SEM- - resolves objects as close as
20 nm
What is the name of the organism that causes syphilis?
Treponema pallidum
What is the CV-I complex?
Crystal violet and iodine can go through the thick cell wall, but once inside form a complex (CV-I) which can not go out of the cell.
Which group of Gram bacteria is sensitive to penicillin and sulfonamide drugs? Which group of Gram bacteria is more sensitive to streptomycin, chloramphenicol, and tetracycline?
- Generally, gram (+) bacteria are easily killed by penicillin and sulfonamide drugs.
- Gram (-) bacteria are resistant to these drugs, but are more susceptible to streptomycin, chloramphenicol, and tetracycline.
What are the 4 functions of water?
- is one of the most important molecules
for living organisms
2. is the medium for most chemical reactions 3. is the most abundant molecule of most
living cells (~65-75%) 4. is a polar molecule, can form H-bonds
What are the 4 major macromolecules?
Proteins.
Carbohydrates.
Lipids.
Nucleic Acids
DNA can dentature in what conditions
Double stranded (ds) DNA can denature (melt) to single stranded (ss) DNA at high temperature, lower salt, or extreme pH conditions
conjugated proteins
modified protien
- glycoproteins contain sugars
- nucleoproteins contain nucleic acids
- metalloproteins contain metal atoms
- lipoproteins contain lipids
What are the functions of proteins
- Structural proteins
- microfilaments for movement of cells
- cell membranes or cell walls
- carrier proteinstransport molecules into and out of cells - Enzymes: catalyze chemical reactions 3. signaling molecules
- Toxins are produced by certain bacteria;
Bacteriocins: proteins produced by some bacteria that kill other bacteria.
- Hormones for regulatory function (i.e. insulin) 6. Antibodies for immune function
Purines and pyrimidines
Purines and Pyrimidines are nitrogenous bases that make up the two different kinds of nucleotide bases in DNA and RNA. The two-carbon nitrogen ring bases (adenine and guanine) are purines, while the one-carbon nitrogen ring bases (thymine and cytosine) are pyrimidines.
Adenosine Triphosphate = ATP
- is the principal energy-carrying molecule (potential form of energy).
- is composed of adenine, ribose, and 3 phosphate groups
- energy is released when a phosphate is removed ATP———–>ADP + Pi + Energy
