SA/V & Nutrient uptake
Growth rate is proportional to nutrient uptake
Bacteria Storage Form of Sugar
- Usually glycogen
- Sometimes cellulose
- Never starch
Prokaryote Cell Membrane
Site of many proteins for transport and bioenergetics
Prokaryote Cell Membrane
Membrane is used for proton motif force
Chemical in soap that inhibits enoyl reductase, killing prokaryotes
Use organic molecules (glucose, acetate, etc) to affix O2
Use inorganic molecules (H2, Fe, NH4+) to affix O2
Present instead of sterols in archaea
Used instead of ester linkage for lipid linkage in archaea
Lipid Composition of Bacteria
Lipid Composition of Archaea
- Nonpolar isoprenoid lipids
3 Characteristics of Active Transport
- 1. Saturation Effect
- 2. Highly Specific
- 3. Number of transport proteins is highly regulated
3 Types of Simple Transport
- Driven by energy of proton motif force
- 1. Antiporter
- 2. Uniporter
- 3. Symporter
Transport a molecule across a membrane while simulataneously transporting a second molecule in the opposite direction.
Transports a molecule in a single direction across the membrane
Cotransporters. Transport one molecule along with another substance, usually a proton.
Involves a series of proteins in the transport event. Driven by phosphoenolypyruvate
Drives group translocation
- Transport involving three components:
- 1. A substrate binding protein
- 2. A membrane-integrated transporter
- 3. ATP hydrolyzing protein
All membrane transporters contain 12 alpha helix domains that weave back and forth through the membrane to form a channel
Periplasmic Binding Protein
ATP Binding Protein
- Involved in ABC transport
- Periplasmic Binding Protein is on the outside of the membrane while the ATP binding protein is on the inside
Translocase. Used to transport proteins out of cell or into membrane
How do bacteria (and some archaea) maintain shape and rigidity?
What acids cause cell wall to be negatively charged?
- Teichoic acid
- Lipoteichoic acid
Two Sugar Derivitives of Peptidoglycan
- N-acetylmuramic acid
Amino Acids of Peptidoglycan
- D-glutamic acid
- Lysine or DAP
Techoic Acid of Peptidoglycan
Used to attach bacteria to host cell
Outer membrane of Gram negative bacteria
Outer membrane are anchored to peptidoglycan via lypoproteins
Area between peptidoglycan and other layers of cell wall
Lipopolysaccharide (LPS) layer
- Outer membrane of gram negative bacteria.
- 1. Polysaccharid portion has two components: O antigen and Core Polysaccharide
- 2. Lipid portion called Lipid A: fatty acids connected to amine group
Lipid A of LPS
Causes inflamation when immune system kills bacteria
How many carbons are in Core Polysaccharide of LPS?
7 (this is odd)
Outer membrane has a lot of porins for movement of small hydrophilic molecules
- 1. Non-specific: Water filled
- 2. Specific: Have binding site for specific substance
Loosely associated layer
- Tightly associated amino acid polymer.
- Usually associated with disease causing
- 1. Protects from dessication
- 2. Adherence to cells via biofilms
- 3. Prevention of phagocytosis
(location and binding proteins)
Found in nucleoid. No histones, but have binding proteins. Circular chromosome.
(Shape and function)
Small circular DNA. Don't usually have necessary genes, but have genes that give selective advantage in various environments.
Drugs ending in -mycin
Target bacterial ribosomes. Archaeal ribosomes are not effected. They are too similar to eukaryotes.
Phototrophs have these. They are folds in plasma membrane that function in the light reactions of photosynthesis.
Surrounded by a protein membrane. Contain rubisco which is used for affixing CO2
Protein coat that is permeable to gases, but not liquid. They are used for buoyancy in photosynthetic bacteria
- Found in intestinal (enteric) bacteria
- Metabolize enzymes in the intestine
- Usually found on gram negative bacteria
- Involved in conjugation
- Made of pillin
- Bind viruses
- Composed of flagellin
- Hook- Wide region at base of filament. Connects filament to motor portion of base.
- Motor- Central rod that passes through series of rings.
- L Ring- Gram neg: Anchored to LPS layer
- P Ring- Peptidoglycan layer
- MS & C Rings- Cytoplasmic Membrane and cytoplasm
- Mot Proteins- Generate torque
- Fli Proteins- Motor switch, reverses direction
How Flagella Works
- Rotor: Central rod, L, P, C, and MS Rings- together called the Basal Body
- Stator: Mot Proteins surrounding basal body
Proton movement through Mot Proteins drives rotation.
Shorter than flagella. Used for cell to adhere to surfaces
1. Single Flagella
2. Single Flagella at Each Pole
3. Tuft of Flagella at One or Both Ends
4. Evenly Distributed Flagella All Over Surface
- 1. Monotrichous
- 2. Amphitrouchous
- 3. Lophotrichous
- 4. Peritrichous
- Drawn toward chemicals of food or other bacteria
- 1. Spacial Gradient- Conc. of chem in space
- 2. Temporal Gradient- Is conc. increasing or decreasing
Drawn toward light
Antigens on bacterial surface (3)
- H Antigen- Flagellar antigen
- O Antigen- LPS
- K Antigen- Capsular antigen
- Produced in detrimental environment
- Resist heat, chemicals, radiation
Cycle of Spore Formation
Vegetative Cell -> Sporulating Cell -> Mature Spore -> Germination (repeat)
Seven Stages of Endospore Formation
- 1. DNA becomes dense
- 2. Asymetric Cell Division
- 3. Endospore septum grows around protoplast
- 4. Forespore formation, Primordial cortex formed between two membranes, dehydration
- 5. Calcium incorporation, dehydration, coat layers formed
- 6. Maturation (development of heat resistant chemicals)
- 7. Lysis of cell and release of endospore
4 Properties of Viruses
- 1. Infectious
- 2. Must use host to manufacture components
- 3. Genome codes for proteins host can't provide
- 4. Self assemble
Protein case, arranged in precise repetitive order
Larger capsid. More elaborate with more types of proteins. Smallest thing to be seen with an electron microscope
Complete package of nucleic acids and proteins
- 20 faces, 12 vertices
- Most efficient arrangement of subunits
Enzyme carried by virus to produce hole in cell wall to enter or lyse
Carried by retroviruses to convert RNA into DNA
Measure of virus quantity
- Each plaque is from a single virion
- Plaque- cleared area of plate
5 Steps of Virus Replication
- 1. Attachment (Absorption) into host
- 2. Penetration (entry, injection) of virion or genome
- 3. Synthesis- of viral nucleic acid and proteins
- 4. Assembly- of capsids and pachaging of viral genomes (maturation)
- 5. Release- of mature virions from cell
Eclipse + Maturation
- Eclipse- When viruses attach to host and are unable to affect other cells
- Maturation- Titer increases as new viruses are formed, but they are trapped in host cell
Number of viruses released from host
Attach to specific receptor of host
What does it mean that a cell is "permissive to a virus"?
Cell allowed viral genome to enter
How do they defend cell? How do viruses get around this?
- Destroy double strand viral DNA after it enters.
- Virus can use glucosylation or methylation to mark DNA for protection from restriction enzymes.
- Virus can also encode proteins to inhibit restriction system.
Seven Classes of Viruses
- 1. dsDNA
- 2. ssDNA
- 3. dsRNA
- 4. ssRNA +
- 5. ssRNA -
- 6. ssRNA w/ DNA intermediate
- 7. dsDNA w/ RNA intermediate
Shapes of Viruses & Examples
- 1. Helical (Tobacco mosaic virus)
- 2. Polyhedral (Adenoviruses)
- 3. Spherical (Influenza)
- 4. Bacteriophage (T4)
Naked Virus vs Enveloped Virus
- Naked: Nucleocapsid
- Enveloped: Nucleocapsid inside envelope
- Synthesized soon after infection
- Necessary for replication of virus nucleic acids (poymerases)
- Typically act catalytically
- Synthesized in smaller amounts
- Synthesized later in infection
- Include proteins of virus coat
- Typically structural components
- Synthesized in larger amounts
Retrovirus Structure and Function
- Two identical ssRNA+ molecules
- gag gene: structural proteins
- pol gene: reverse transcriptase and integrase
- env gene: encode envelope proteins
Animal RNA Viruses
- Nonenveloped: ssRNA, dsRNA
- Enveloped: ssRNA only
Effects of Virus on Animal Cell (5)
- 1. Cell fusion
- 2. Virus present but not replicating=lysis
- 3. Slow release of virus w/o cell death
- 4. Lysis
- 5. Tumor Cell
- abnormal protein with a lot of beta sheets.
- transmissible spongiform encephatopathies (TSE)
- Turns other proteins abnormal
- Mad Cow Disease
Generation Time aka Doubling Time
Time it takes for bacteria to reproduce
Graph (log of viable cells)
Exponential growth phase
- Lag Phase- small slow. Bacteria still getting used to medium
- Exponential growth phase- When generation time is measured. Keep growing until resources run out
- Downslope- bacteria consume eachother (cell walls)
Spread Plate Method vs Pour Plate Method
- Spread plate- hockey stick to spread on medium
- Pour plate- bacteria diluted and poured along with medium
Common errors in viable cell counts
- 1. Innoculation size
- 2. Culture medium
- 3. Incubation conditions and length
- Cells reflect light
- turbidity is proportional to the number of cells
Steady state. Cell number and nutrient status remain constant.
Chemostat adds medium, air, and removes dead cells
Concentration of nutrient in limiting amount
Factors Influencing Microbial Growth
- Macronutrients- Carbon, nitrogen, water, etc. (need a lot)
- Micronutrients- cofactors and growth factors (need a little)
- Siderophores excreted to obtain iron
Microbial nutrition chart
Categorized by energy source and carbon source
Chemicall defined media vs Chemically undefined media
- Chemically defined- precise amount of purified chemicals and distilled water
- Chemically undefined- protein and amino acid based (better)
Allows growth of some organisms and inhibits others
Identify organism by biochemical difference between two organisms that grow equally well on certain medium
- Add nutrients that allow organism to grow that wouldn't normally
- ex. bile and crystal violet- selects for gram negative
- ex. lactose fermentation- select for organism that ferments lactose. Read with pH meter
- Psychorophile - 4
- Mesophile- 39
- Thermophile- 60
- Hyperthermophile- 106
Die in oxygen environement
Use oxygen and other electron acceptor. Can survive in oxygen but doesn't need it
Require low oxygen levels
Don't use oxygen but aren't killed by it
Used to reduce oxygen in lab. Gives layers in broth of varied oxygen concentrations
Aerobes vs Anaerobes in flast
- 1. Vigorously shake flask
- 2. Bubbling sterilized air
- 3. Large headspace
- 1. Fill tube so no headspace
- 2. Reducing agent (reduce O2 to H2O) ex. thiogycolate
Adaptations of acidophiles & alkaliphiles
- Obligate- Needs acidic environment
- Tolerant- will survive in acid but doesn't prefer
Acidophiles- adapt membrane stability under high proton concentration
Alkaliphiles- adapt Na+ gradient instead of H+ gradient
- Halophiles- salt
- Osmophiles- sugar
- Xerophiles- dry environment
To maintain osmolarity in salty environment
- 1. pump inorganic ions
- 2. increase synthesis of organic solute (Compatable solutes= don't inhibit biochemistry or cell processes)
- Bacteriocidal- kill bacteria
- Bacteriostatic- inhibit growth of bacteria
- Decontamination- treatment to make inanimate surface safe to handle
- Disinfection- Eliminate all pathogens, but not all microbes
- Sterilization- Eliminate all microbes
Physical Antimicrobial Control (3 methods)
- 1. Heat- high temp for long time to get microbe and endospores
- 2. Radiation
- 3. Filtration
Used to sterilize. use steam heat pressure at temp above boiling point
Thermal Death Times
Time it takes to kill cells at certain temp
Decimal Reduction Time
Time required for ten-fold reduction of population density at a given temperature
Electromagnetic Radiation (3 methods to control microbial growth)
- 1. UV radiation- decontaminate air and water
- 2. Ionizing radiation- penetrate light absorbing materials and break DNA
- 3. heat
Best filter size
- 0.2um filter
- Used especially for heat sensitive mediums (mediums that can't be heated)
- HEPA filter traps bacteria
Which of the following statements about the intracellular state of a virus is NOT correct?
a) The virus particle is referred to as a
b) New copies of the virus genome are produced.
c) The virus replicates.
d)The components that make up the virus coat are synthesized.
a) The virus particle is referred to as a virion.
The smallest morphological unit of a virus that can be seen with the electron microscope is the:
Which of the following statements does NOT describe a factor affecting the efficiency of plating in quantitative virology?
A) The virus successfully infects a host cell and causes the formation of a plaque.
During the first few minutes after a virus infects a cell, the virus is said to undergo:
Restriction enzymes are specific for:
C) double-stranded DNA viruses.
What type of virus requires an enzyme known as reverse transcriptase?
T4 DNA is protected from host defenses by glycosylation of:
Which of the following viruses causes a latent infection?
D) herpes simplex virus
During a retroviral infection, where is the RNA converted into DNA?
D) in the cytoplasm within an uncoated viral core particle
Viroids possess what type of nucleic acid?
C) single-stranded RNA
A prion particle contains:
Which of the following is NOT one of the three distinct mechanisms by which prion disease occurs?
A) endogenous prion disease
Which statement regarding the cytoplasmic membrane is NOT correct?
B) The cytoplasmic membrane is a highly fluid structure in which proteins are free to move among the phospholipids.
In a peritrichous arrangement of flagella, how are the flagella distributed over the organism?
A) Multiple flagella are randomly dispersed over the cell surface.
ABC System refers to:
A) the ATP-binding cassette.
The outer portion of the outer membrane is, for the most part, composed of:
Which cell surface structure can also be used as a receptor by certain viruses?
Which of the following statements regarding the cell wall of bacteria is NOT correct?
C) It is composed of a repeating framework of lipids.
The outermost layer of the outer membrane is composed of:
Species of the Euryarchaeota include all the following EXCEPT:
What is always a product of a methanogenic reaction?
Where does oxidative phosphorylation take place within an aerobic eukaryote?
C) the mitochondrion
hloroplasts are found in all the following organisms EXCEPT:
D) photosynthetic prokaryotes.
Where in a eukaryotic cell are 70S ribosomes found?
D) They are found within the mitochondria of a eukaryotic cell.
The energy to drive motility in
motile eukaryotes is derived from a protein called ________, which is
attached to tubulin and functions as an ATPase.
Which of the following protists are animal parasites?
To obtain iron, some bacteria produce phenolic siderophores called:
In oxidative phosphorylation, ATP is produced:
at the expense of the proton motive force.
Chemolithotrophs use what compound as a carbon source?
D) carbon dioxide
Under which of the following conditions would a lag phase NOT occur?
C) An exponentially growing culture is transferred into the same medium under the same conditions of growth.
The most important environmental factor affecting the growth and survival of microorganisms is:
Organisms capable of causing disease in humans and animals are of which temperature class?
Which of the following statements about thermophiles/hyperthermophiles is NOT correct?
produced at high levels and help to stabilize proteins.
d) Their proteins have an increased number of ionic bonds between basic and acidic amino acids and their often highly hydrophobic interiors.
- A) The amino acid sequence of their enzymes differ greatly from those
- of the heat-sensitive forms of the enzymes that catalyze the same
- reaction in mesophiles.
In which habitat would you expect to find aerobic prokaryotes?
B) the ocean surfaces
To live in the presence of oxygen, an organism must possess:
D) superoxide dismutase and either catalase or peroxidase