Glossary of microbio 2

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What types of cells are considered eukaryotic
The cells of animals, plants, algae, fungi, and protozoa are eukaryotic
What are the major differences between prokaryotic and eukaryotic cells?
Euk are 1 bigger,
2 have a nuclear membrane and nucleoli,
3 more than one chromosome, 4 Mitochondria, endoplasmic reticulum, Golgi apparatus, and lysosomes are present. Chloroplasts may be present.
What size ribosomes do eukaryotes have?
. They have 80S ribosomes in their cytoplasm, composed of a 60S subunit and a 40S subunit. These are composed of rRNA and protein.
How do eukaryotic cells divide?
by mitosis
What is the eukaryotic cytoskeleton composed of?
They have a cytoskeleton composed of tiny rods called microfilaments and intermediate filaments, and cylinders called microtubules.
What are cell walls made of?
Cell walls, when present, are usually cellulose (plants) or chitin (fungi).
What are flagella and are they membrane bound?
Flagella (cilia), when present have a complex structure and are membrane-bounded
What are resting cells called in protozoa and what are they restistant to?
Some protozoa produce resting cells called cysts which are resistant to environmental conditions such as heat and drying
What do fungi produce as reproduction? What is special about them?
Fungi may produce spores which are a means of reproduction. Fungal spores may be somewhat resistant to environmental conditions.
What is found on the cell surface? What is it made of and what does it do?
Cell-surface proteins and extracellular secreted proteins are glycosylated (called glycoproteins). Aids in identification
What are examples of prokaryotic cells?
The cells of bacteria and cyanobacteria are prokaryotic.
What are some differences between eukaryotes and prokaryotes?
1. No nuclear membrane is present.

2. All vital genetic information is usually encoded on one chromosome.

3. They have no membrane-bounded organelles such as mitochondria, endoplasmic reticulum, Golgi apparatus, or lysosomes.

4. There are no cytoskeletal elements.

5. Cell division is by binary fission.
How do prokaryotes reproduce?
binary fission
What are the sizes of prokaryotic ribosomes?
70S ribosomes formed of 30S and 50S subunits
What does the bacterial cell wall contain?
Almost all bacteria of medical importance have a chemically complex cell wall containing peptidoglycan (murein).
What is another name for peptidoglycan?
Are bacterial flagella membrane bound?
When they have flagella, they are almost always unsheathed
What kind of projections come from a bacterial cell?
flagella or pili are possible
Are bacterial proteins glycosylated?
no, not normally
Is the surface to volume ratio high or low in bacteria? What does this allow for?
high surface to volume ratio, allows for a high metabolic rate.
What do eukaryotic cell membranes contain?
What makes up the cytoskeleton?
cytoskeleton in eukaryotes only. Made of mircrofilaments and intermediate filaments and microtubules
What is the purpose of petidoglycan or murein?
In BACTERIA only allows for rigidity of the cell wall. Gives bacterial shape and is involved in binary fission
What are the three shapes of bacteria?
coccus, spiral, rod/bacillius

can also be pleomorphic, or variable in size and shape
How big are most bacteria?

Are they visible in the light microscope?
0.5-1.0 μm in width and up to several μm in length

yes, visible by light microscope
What are the 6 most important factors of the bacterial cell wall (peptidoglycan)?
1. It protects cells against osmotic lysis, imparts rigidity, and confers their characteristic shape to bacteria.

2. It determines the Gram staining characteristics.

3. It can cause some of the symptoms of disease.

4. It possesses antigenic properties.

5. Some of its subunits are unique to bacteria.

6. it is the site of action of some antibiotics.
Is the outer part of the bacterial cell includign the cytoplasmic membrane or envelope used more in gram positive or negative organisms?
gram negative
What makes up peptidoglycan (murein)?
alternating units of AMINO SUGARS--
N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).
Short peptides are attached to NAG or NAM?
to NAM

they NAME the residue,don't nag it
How are adjacent glycan chains held together?
by cross linkages between peptides.
Which amino acids are unique to bacterial cell walls?
D amino acids and D, L-diaminopimelic acid (DAP)
What are the characteristics of gram positive cell walls?
relatively thick, multiple layers of densely cross linked peptidoglycan, may have added peptide bridges, teichoic acids, may have polysaccharides or proteins whihc contribute to antigenicity of cells
What type of bacteria have polysaccharides in their cell membranes?

What is interesting about mycobacterium?
Gram positive might. More specifically, streptococcus do.

These gram positive bacteria produce a waxy substance which makes them more resistant to harsh environments
What makes up teichoic acids?
ribitol or glycerol connected by phosphate bonds
What are lipooteichoic acids?
Acids which are linked to the cytoplasmic membrane and span the peptidoglycan layer.
What is the charge on teichoic acids? What do they do (4 things)?
negative charge, so they bind cations to regulate movement into and out of the cell. Also they mediate adherance to mucosal cells and provide antigenic specificity. Have a weak endotoxin like activity.
What are the features of a gram negative cell wall?
1 more complex than gram positive.

2 peptidoglycan layer is thin and sparsely cross

What is the outer membrane of a gram negative cell envelope made of? What is imbedded in it?
asymmetric lipid bilayer of phospholipid and lipopolysaccharide.

Proteins and lipoproteins are embedded in the lipid bilayer
What are porins? Where are they found? What do they do?
porins are proteins in the gram negative cell envelope which allow for the influx of nutrients and the efflux of waste products across the outer membrane.

They are nonspecific channels that permit the passage of small hydrophilic molecules up to a molecular weight of about 700.

Keeps out enzymes and other larger molecules
Are porins specific or non-specific?
What do specific channel proteins do?
Allow passage of certain substances that are too LARGE for porins

Ex. B12, matodextrins, nucleosides, iron
What types of pathways are responsible for differential penetration and effectiveness of certain beta-lactam antibiotics?
hydrophobic pathways across the outer membrane

note beta lactam antibiotics are active against gram NEGATIVE bacteria
What are the three components of the lipopolysaccharide?
LPS is made of--Lipid A, core oligosaccharide, and the O antigen
Where is lipopolysaccharide (LPS) found and what is its classification?
found in the outer membrane of gram negative envelope. Makes up most of the otuer membrane lipid bilayer.

Where is Lipid A found?

What's its claim to fame?
embedded in the membrane.

toxic to animals

major virulence factor of most gram negative bacteria
What does the core oligosaccharide do?
connects the O antigen to lipid A
What does the O antigen do and where is it found?

What if the O antigen is missing?
important antigenic determinant of gram negative bacteria.

Found as a repeating polysaccharide which extends into the environment.

Without the O anitgen then LPS is LOS lipooligosaccharide
What are 3 functions of the outer membrane?
(i) Its strong negative charge is an important factor in evading both phagocytosis and the action of complement.

(ii) barrier to certain antibiotics, some hydrolytic enzymes, and other environmental chemicals.

(iii) prevents loss of metabolite-binding proteins and hydrolytic enzymes found in the periplasmic space.
Where is the periplasmic space found? What does it contain?
Found between the outer membrane and cytoplasmic membrane of a gram negative organism.

The space is aqueous and contains proteins, oligosaccharides and lipoproteins.
What is the function of the protien, oligosaccharide, and lipoprotein in the periplasmic space?
The protein include degradative, detoxifiying, and binding (for membrane transport)proteins

oligosaccharide is for osmoregulation

lipoprotein connects the peptidoglycan to the outer membrane of the gram neg cell
What do autolysins do?
Autolysins create sites for insertion of newly synthesized peptidoglycan precursors.
What three enzymes prepare for biosynthesis of peptidoglycan?
glycosidases--break glycoside backbone

amidase--releases tetrapeptide from NAM

endopeptidases--attack peptide bonds of side chains and cross links
What are the 7 steps of peptidoglycan biosynthesis?
1. form soluble precursor monomers as UDP-NAG and UDP-NAM

2. add AA's to UDP-NAM to build a UDP-NAM-pentapeptide. Transfer NAM-pentapeptide via udecaprenol

3. then add NAG to get NAG-NAM-pentapeptide (AKA disaccharide pentapeptide)

4. undecaprenol in membrane flips from the inner surface of the cytoplasmic membrane to the outer periplasmic surface.

5. undecaprenol transfers the disaccharide pentapeptide (AKA NAG-NAM-pentapeptide)to the glycan backbone

6. glycosydic bonds are formed

7. transpeptidation forms peptide cross links

COMPLETE cell wall!
What part of peptidoglycan biosynthesis does penicillin disrupt?
The transpeptidation rxn's thus preventing formation of a stable cell wall.
Where are outer membrane precursors formed? How are they transported?

How is the outer membrane formed in gram negative bacteria (e.coli)?

What holds the inner and outer membrane of the gram neg bacteria together?
outer membrane precursors are made in the cytoplasm of the cell, then transferred to the membrane carrier lipid.

the inner and outer membranes are fused to each other at several hundred sites.

The lipopolysaccharide (LPS)molecules are assembled at the inner membrane and then inserted into the inner-outer membrane adhesion sites
Do all bacteria have cell walls?
What group of bacteria do not have cell walls?

What do they have in the cytoplasmic membrane? Where does it come from?
mycoplasma group

have sterols in their cytoplasmic membrane

sterols are acquired from host or environment--they are NOT made by the bacteria
How does the bacterial cytoplasmic membrane compare with the eukaryotes? What's the main difference?

What is the bacterial cytoplasmic (inner) membrane like?
It is structurally similar to the cytoplasmic membrane of eukaryotic cells, except for the absence of sterols in most bacteria

composed of a phospholipid bilayer with proteins embedded in it. The phospholipids and proteins are not static, but move quite freely within the plane of the membrane.
Name 5 functions of the bacterial cytoplasmic membrane which in eukaryotes would each be done by separate membrane bound organelles?
1. enzymes for energy conversion via ATP synthesis (electron transport/oxidative phosphorylation).

2. enzymes for cell wall component synthesis.

3. secretion of extracellular proteins.

4. cell division and an anchoring site for DNA.

5. transport control

It is a selectively permeable membrane, and possesses specific transport activities to allow particular molecules to enter and exit the cell.
What does bacterial DNA look like and how many genes does a chromosome have?
single, continuous circular piece of double-stranded DNA (nucleoid or bacterial chromosome).

Bacterial chromosomes vary in size from about 1000 genes to 6000 genes.
Where is the nucleoid in relation to the cytoplasmic membrane?

Why is this believed to be the case?
nucleoid appears to be attached to the cytoplasmic membrane.

Proteins in the membrane are believed to be responsible for the replication of the bacterial DNA and for the segregation of the new chromosomes to daughter cells during cell division.
What is a plasmid?

How do they replicate?

Are they associated with the membrane proteins?

How many genes do they contain? Are the genes necessary for life? What do the genes protect against?

Can plasmids be tra
small circular double- stranded DNA molecules.

plasmids replicate independently of chromosomal DNA.

They are also associated with cytoplasmic membrane protein.

They usually contain from 5 to 100 genes which are not crucial for the survival of the bacterium under normal environmental circumstances.

The genes may be for antibiotic resistance, tolerance to toxic metals, production of toxins, or synthesis of enzymes.

Plasmids may be transferred from one bacterium to another.
What does a bacterial ribosomal subunit contain?
Each subunit is composed of one or two molecules of ribosomal RNA (rRNA) and numerous protein molecules
How can you distinguish a growing bacterial cell based on ribosomes?
There are many ribosomes in each bacterial cell. In rapidly growing cells they usually occur as polysomes (polyribosomes) which indicates protein synthesis is occurring.
Are bacterial and eukaryotic ribsomes the same? What uses this to its advantage?
No, they're not the same so some antibiotics expliot this.
What are bacterial flagellum made of?

How is the protein arranged?
globular protein, flagellin

the filament is arranged in several chains that coil together to form a helix around a hollow core.
Where does the flagellum filament anchor?

Anchors in the cell envelope via a 2 part structure--the hook and the basal body.

Basal body = motor
Can bacterial flagella be seen under the light microscope?
Bacteria flagella are ordinarily too slender to be seen in the light microscope, but can be visualized by special stains or by electron microscopy.
Besides movement why are flagella important?
The arrangement of flagella is characteristic of the taxonomic group to which the organisms belong. Not all groups of bacteria have flagella.
What is interesting about the bacteria spirochetes' flagella?
present in the periplasmic space as axial filaments, which are also involved in motility.
What type fo response do motile bacteria show?
Motile bacteria show both positive and negative chemotactic responses
What are flagellar antigens commonly called?
H antigens
Which type of bacteria are much more likely to have pili?
Gram negative

very rare in gram positive
Can bacterial pili be seen with the light microscope?
no--to slender
What are pili (fimbriae) made of?
pilin--forms the shaft of the pilus and a thin tip called the fibrillum
What are the 4 functions of the pili?
1. adhesion pili
2. antiphagocytic
3. disguises that enable them to avoid the immune system
4. sex pili--F pilus which transfers DNA during conjugation
What is the purpose of a common pili?

Where are gonococci found?

How do other bacteria adhere?
helps bacteria to adhere to mucosal surfaces

gonococci in epithelial cells of genitourinary tract

others have pili that attach to surfaces that will be colonized.

E.Coli in urinary tract
Which bacteria has a number of genes co=ding for variants fo pilin? Why is this important?
Neisseria gonorrhoeae

pilin polymerizes to form pili. the bacteria can change enough to fool the immune system and remain.
What are two types of viscous polymers external to the cell wall in bacteria?

What is the difference between the two.
slime layer and capsule.

The capsule is organized and attached firmly. While the slime layer is not.
What are 5 functions of the capsule?
virulence, prevent phagocytosis, promote attachment, protect against dehydration, antigenic
Name a bacteria that uses a capsule as a virulence factor.
Streptococcus pneumoniae
Are capsules necessary for viability?

How can capsules be lost?

can be lost by mutation
What is an example of a bacteria that secretes exotoxins?
Clostridium tetani
What are exotoxins?
secretes toxic proteins
Are exotoxins heat-labile? antigenic?
yes and yes!
What are exotoxins usually reponsible for in disease?
The particular symptoms
Where is DNA located which codes for exotoxins?
On a plasmid
What are the characteristics of an endospore?
highly resistant, metabolically dormant, primarily found in gram positive bacteria genera bacillus and clostridium. They have a core, cortex, and coat
What type of bacteria are more likely to have endospores?
Gram positive Bacillus and Clostridum
What are the three components of an endospore and what do they contain?
1 core-- (consisting of a complete nucleoid, ribosomes, and energy-generating components) enclosed within a cytoplasmic membrane,
2. cortex-composed of peptidoglycan
3. coat--made of protein, and is highly cross-linked with disulfide linkages.
When are spores formed (sporulation)?

Is sporulation used as a means of reproduction?
occurs when nutrients are exhausted or when water is unavailable

may also be part of the developmental process as in vegatative cells

No, in fact one bacterial cell forms ONE spore. used for protection, NOT reproduction
Are spores hydrated or dehydrated?
Where are spores most important? Why?
Spores are important clinically and in the food industry, because they may resist the usual means of infection control or sterilization
Can spores be stained normally?
No, Spores are resistant to the usual bacterial stains but can be stained with special stains
What is the reverse of sporulation? How is it activated?
germination--activated by presence of nutrients or environmental conditions

Then endospore enzymes breakdown layers surrounding endspore, water enters, metabolism resumes, spre converted to a vegetative cell.
What important use can spores serve for a baceria?
storage of intracelluar granules in a polymerized form--metabolic reserves

polymerize in order to minimize osmotic effect

Ex. 1 glucose as glycogen
2 beta hydroxybutyric acid as poly beta hydroxybutyrate 3 phosphate as inorganic polyphosphate (volutin)
What are the two classical methods of microbiology? What are the two newer ones?
older--culture and light microscopy

newer--gene cloning and molecular probes
What minimal ingredients must be in a sterile culture media?
Na, K, Cl--salts
C, N, P, S--energy sources
Mg, Fe--trace elements
Should culture medium be solid or liquid?
Both depends on what you want
What is the best technique for obtaining pure cultures from a mixture of different bacterial species?
solid medium
What is the most common solidifying or gelling agent?

Is it a nutrient?

No, not a nutrient.
What technique is used to find isolated colonies on an agar plate.

What kind of cultures are obtained?

How does it work?

Pure cultures are obtained

This is a method in which the original mixed inoculum is serially diluted, by sequential streaking and spreading with a sterile metal loop.
What steps are necessary in order to quantify bacterial cultures?
serial liquid dilutions on solid media, incubating, counting the resulting colonies, and then calculating the viable titer of the original culture.
What are the units of titers?

Is this the same as cells/ml?
colony-forming units per milliliter (CFU/ml), which may or may not be equivalent to viable cells/ml.
What are bacteria that can synthesize all the organic molecules they need from a simple carbon source called?
Bacteria that require amino acid or other growth requirement in addition to Carbon are called _____?
Bacteria require a multitude of complex organic molecules are called _____?
What kind of medium contains only a carbon source and the minerals required for bacterial growth?
minimal nutrient medium
What kind of medium contains many additional nutrients, such as vitamins, amino acids, etc, but every aspect of the chemical composition of the medium is known in detail
chemically defined medium
How are rich media prepared? Are they chemically defined?
Rich media are prepared by making an infusion, broth, or extract from organic material such as fish, meat, yeast, etc by boiling in water.

They are chemically undefined.
What may be added to media in addition to basic growth requirements?
particular metabolizable compounds (e.g. lactose), inhibitors (e.g. high salt, antibiotics), indicators (e.g. pH-sensitive dyes).
What is a differential media?
Media which will allow the growth of most kinds of bacteria, but which will allow the various colonies to be distinguished from each other by a color change (or some other aspect of their appearance)
What is a selective media?
Media which will allow some bacterial species to grow while inhibiting the growth of most others
What are the 4 main environmental factors important in bacterial viability?
heat, pH, presence or absence of O2, osmolarity
What are the three types of temperature preferences?

For each where is the optimal temp?
psychrophiles--like cold temps
mesophiles--like moderate temps like the human body
thermophiles--grow best at elevated temps

The upper mid portion of their growth range. They slow down toward the extremes

Obligate anaerobes

facultative bacteria


obligate aerobes

obligate anaerobes--no oxygen.

facultative bacteria can use o2 or not, either way they'll live

microaerophilic--needs low o2

obligate aerobe must have o2

capnophilic--requires increased CO2
what is an aerotolerant anaerobe? What is a strict anaerobe?
A strict anaerobe will die in the presence of O2 and aerotolerant anaerobe will not.
Are bacteria usually osmotically tolerant?
Yes, soem can grow in the presence of saturated 6M NaCl
How can increase in cell MASS as a fx of time be determined?

Which is most common and what equipment does it require?
1. Dry weight of cells.
2. Amount of a particular marker, e.g. an enzyme activity or metabolic process.
3. Amount of a particular cell component, e.g. protein or DNA.
4 . Incorporation of a radioactive precursor into cells.
5. MOST COMMON The turbidity of the culture, i.e. the amount of light scattered from or absorbed by the cell suspension. It uses a spectrophotometer
How can an increase in cell number as a function of time be measured?

Which is most common?
1. Direct microscopic
2. Electronic counting in a Coulter counter, or similar device. In this method a defined volume of culture is drawn through a tiny orifice across which an electrical field exists. Each cell that passes through the hole causes a transient increase in the impedance (resistance) and is counted electronically. This method is technically difficult and counts both viable and dead cells.

3. Plate count or viable titer is the most common method.
What does direct microscopic counting require?

Does it count dead or alive bacteria?
small known volume, requires large #'s of bacteria and

counts dead and alive bacteria
What does electronic counting require?

Does it count dead or alive bacteria?
a coulter counter, defined volume thru an electric field, resistance is measured to count.

technically difficult

counts dead and alive cells
Plate count or viable titer is the most common method of counting bacterial cells. how does it work? Does it measure dead or alive cells?
1. bacterial culture is serially diluted so that about 100 colonies are available.

2. Incubate

Only measures viable cells. Slow and sensitive technique
What factors indicate how fast a bacterial population will double? What is this known as?
species, culture medium, temperature

generation time or doubling time
What is the generation time or doubling time inversely proportional to?
The growth rate
Do bacterial cells grow exponentially or arithmetically?
What isthe equation that gives the number of cells present in successive generations (Nn)
Nn = 2^n No

where n is the number of generations of growth
Will a semilog plot have a straight or curved line?
straight--the slope of the line gies alpha or the growth rate constant
What are the four principle phases of growth in a bacterial culture w/o nutrients?
Lag phase--preparation, slow growth

Exponential phase--log phase, constant growth

Stationary phase--exhausts nutrients

Death phase--decline in viable population, decreases exponentially
What must be in effect for a continuous culture technique to work?
must keep at least one nutrient in limiting amount so cells don't reach the stationary phase

Volume is kept constant and is continuously diluted with fresh medium
What is the limit of resolution on a light microscope?
200 nm or 0.2um
What are the two types of magnifying lenses on a light microscope?
ocular and objective
What is true of the 100X lens on the light microscope
oil immersion--increases resolving power
What do microbiologist commonly use to look at specimins?
What is the most common staining method how does it work?
Gram stain,

1. Begin with crystal violet--primary stain

2. Iodine--the mordant (fixer)

3. Organic solvent to decolorize

4. Safranin--pink counterstain
What color do gram negative bacteria stain? Why?
stain pink--the purple primary is washed out with the organic solvent because of the weak bonds of the cell wall.
What color do the gram positive bacteria stain? Why?
primary stays in the cell wall because of strong bonds. It is not washed out by the organic solvent.
Do Gram-positive or Gram-negative organisms take up the crystal violet and the Gram's iodine which form a purple complex inside the cells?
Both do. It is a matter of which is washed out with the organic solvent. (gram neg is washed out because of weaker bonds in peptidoglycan cell wall)
Why are aged cells tricky?
Thy may appear gram negative when they are in fact gram positive because of degradation of cell wall due to autolytic enzymes
How do bacteria look under a light microscope when unstained? How can this be overcome? How can living bacteria be seen?
Appear transparent

overcome by changing optics, use phase contrast or narrow the cone of illumination

Can see living bacteria in wet mount. or by dark field optics.
Which bacteria is often observed by dark field optics? How does it work?
Treponema pallidum appear bright and luminous against the dark background but can't be seen under normal circumstances.

use a special condenser with a stop to block light in the center field
What's the difference between transmission and scanning electron microscopy?
scanning views the outer surface while transmission can see inside the cell. Both use beams of electrons to do their work
How do bacteria divide?
by binary fission
What must be duplicated in order for a bacterial cell to divide?
All the components of the cell must be duplicated before the cell can divide. This means that the cell must regulate and coordinate the biosynthesis of all its components. This includes the bacterial chromosome, which must be replicated
What does a bacterial chromosome look like?
single large circular DNA molecule
What is a nuceleoid?
bacterial wanna be nucleus- supercoiled chromosome forms a compact structure called the nucleoid.
How does DNA repliation proceed?
bidirectional, with two replication forks diverging from the origin. They meet at the terminus to complete replication.
How many replication forks exist at once?
Thus multiple replication forks may exist at one time.
How is frequency of initiation of DNA replication regulated?
regulated in response to increases in cell mass AND regulatory proteins which act at the origin of replication to prevent or allow formation of replication forks.
What is a replicon model?
regulatory mechanism which controlls regulatory proteins at origin of replication. Allows or prevents replication
What must follow each new round of DNA replication?
cell division
How does a bacterial cell divide?
invagination of the cell membrane forming a division septum.

Segragation of daughter chromosomes, probably doen by origin of replication sites on the cell membrane; an aspect of replicon model
Do bacterium grow synchonously?
No asynchronous. Each bacteria species has its own natural range of growth rates, which can be further influenced by availability of nutrients and oxygen, temperature, and other environmental factors.
Cell size is a function of ___?
growth rate. lager cells are rapidly growing
Which is more metaboically diverse: prokaryote or eukaryote? Why?
prokaryote, Use of oxygen, products for potential use more diverse than eukaryotes. Used in classification of bacteria
What are the two types of metabolism?
anabolism and catabolism.
What do exoenzymes do?
facilitate uptake of nutrients
Which type of cells have a periplasmic space?
Gram negative cells
Where do exoenymes work?
In the periplasmic space of gram -, and they degrade large molecules OUTSIDE of the cell
Cna hydrophobic molecules pass directly thru the cell membrane
Yes, membrane is lipid
How do water and ammonia get thru the cell membrane?
simple diffusion
What type of bacteria use carriers?
Both gram + and - use active transport, group traslocation, facilitated diffusion
Is a transport molecule modified in active transport?
Is group translocation energy dependent? Is the nutrient modified?
Yes and Yes. Need energy and modifiy nutrient in group translocation. The modified molecule is UNABLE to leave the cell
Does facilitated diffusion require energy and does it move against or down its concentration gradient?
facilitated diffusion does NOT use energy and moves down its gradient. Requires facilitation o f a specific protein carrier in the membrane
What does rapid hydrolysis achieve?
lower concentration inside the cell, to allow a molecule to enter cell spontaneously. Can also TRAP molecule inside by converting it to a form that cannot bind with a carrier protein
What is an autotrophic bacteria?
use oxidized carbon (carbon dioxide) as their MAIN carbon source, and PHOTOSYNTHESIS OR OXIDATION of reduced inorganic compounds as a source of energy and reducing power.
What is the difference between an autotroph and a heterotroph?
a heterotroph uses organic molecules as an ENERGY and C source

An autotroph uses oxidized C (CO2) as main C source, and photosynthesis or ox of inorganic cmpds as energy source
Are most bacteria auto or heterotrophs? What about pathogens?

ALL pathogens are heterotrophs
What molecules act as energy carriers?
ATP, GTP, UDP, reduced pyridines: NADH AND NADPH
How is energy captured?
as ATP, pH gradient, etc
Are high energy precursosr reduced or oxidized?
Are the following reduced or oxidized? Methane? Carbon dioxide? Fatty acid? Glucose? Pyruvate? Lactate?
methane--reduced; carbon dioxide--oxidized; Fatty acid--reduced; Glucose--50/50 reduced/oxidized; Pyruvate--oxidized; Lactate--reduced
What are the two types of metabolism? Which uses oxygen?
respiration and fermentation

respiration uses oxygen (or N) as terminal e acceptor(glucose to pyruvate to TCA to ETC etc), fermentation doesn't (lactate)ATP generated directly
How many ATP produced via respiration? fermentation?
What is the Pasteur effect?
When fermenting bacteria, which have a high consumption rate of glucose, are given O2, the rate of glucose consumption drops abruptly
The hexose monophosphate shunt uses what instead of NADH? What is its function?

reduces lipids and yields pentose phosphates for nucleic acid biosynthesis. Also converts glucose to pyruvate kind of like glycolysis
What is the Entner-Doudoroff pathway?
thrid way to get from glucose to pyruvate in some bacteria. ONLY YIELDS 1 ATP PER GLUCOSE
What is the Strickland rxn?
fermentation of aa instead of sugar
What are products of catobolsm used for?
Where is the cells supply of ATP? What happens when it is needed elsewhere?
The cell's supply of ATP is located in the cytoplasm, and can be used to energize the synthesis of macromolecules which occurs in the cytoplasm or in the nucleoid (which is intimately associated with the cytoplasm).

But ATP cannot be directly used to drive the synthesis of macromolecules such as peptidoglycan, lipopolysaccharide, or capsular polysaccharide, which are synthesized outside the cell membrane where there is no ATP. Such extracellular biosynthesis is driven by energy stored in a membrane carrier lipid called UNDECAPRENOL PHOSPHATE
What form of energy does undecaprenol phosphate use?
What types of extracellular proteins are secreted from the cell?
1. toxins 2. components of cellular appendages(flagella or pili) 3. periplasmic proteins
How do extracellular proteins get to their destination?
syntesized on ribosomes like peptidoglycan etc, then get to extracellular location by: ex. Type III, IV hypodermic needlike action, which increases virulence. OR directed by signal sequence, ie. N terminal (1st synthesized) passes thru membrane while C end synthesized.
How is Fe metabolized by bacteria? Is Fe necessary for bacterial life?
Hard to get at in human body b/c trapped by hemoglobin, myglobin, transferrin, ferritin etc. Bacteria w/ SIDEROPHORES have high affinity for Fe and take it away. Also have transporters for the Fe complex and Fe is released into the bacterium.

Yes Fe is a nutritional requirement for bacteria.
What is a critical item? Semicritical? Non-critical?
• Critical items-items introduced into the body-should be sterile.
• Semi critical items-items which have contact with mucous membranes and items such as respiratory therapy equipment-sterilize if possible; if not possible, use high level of disinfection preceded by proper physical cleaning.
• Noncritical items- use cleaning and low level disinfection (Items such as face masks, EKG electrodes, bedpans, walls). Even stethoscopes can carry bacteria from one patient to another.
What is the difference between sterilization and disinfection?
Sterilization kills endospores, disinfection does not.
What types of antimicrobial agents are used on living tissue? Non-living?
Living--anticdeptic and antibiotic

Non-living--sterilant, disinfectant, sanitizer
Does decontamination ensure that an item is safe for patient use?
Which is more effective: 100 or 70% ethanol?
70% ethanol is more effective; used as a disinfectant (not sterilant)
Are detergents disinfectants? What about quaternary ammonium compounds? How do they work?
No, they remove organisms from survace. Quaternary ammonium compounds are used for skin antisepsis. Work by disrupting cell membranes.
How do phenols work? What cleaner contains phenols?
damage membranes and denature proteins. Found in lysol. Very hydrophobic and good at killing.
How does chlorine work?
hypochlorite is a strong oxidizing agent kills sulfhydryl cross links and inactivates microbe proteins. Kills anthrax,
How does iodine work?
iodine is an oxidizing agent, like Cl. Betadine commonly used.
How do heavy metals work?
Heavy metals act on sulfhydryl groups as do Cl, and I
Which antimicrobial agents work by disrupting the sulfhydryl groups?
h202, I, Cl, heavy metals
Which chemical is used as a skin antiseptic?
Which microbes are resistant to h202?
those that produce catalases--inactivates H202.
How does formaldehyde and gluteraldehyde work?
denatures proteins and nucelic acids AND alkylates proteins
What type of disinfectant is used to clean bronchoscopes?
formaldehyde and gluteraldehyde
Which chemicals denature proteins and nucleic acids?
ethylene oxide, formaldehyde, gluteraldehyde, acids, alkalis, alcohol, detergents, phenols
What is ethylene oxide used for?
gas sterilization in hospital for heat sensitive equipment
In addition to denaturing proteins how do acids and alkalis work?
alter pH and homeostasis
How do dyes work? Which type of bacteria are more suceptible to malacate green?
inhibit growth by binding to nucleic acids.

Gram negative bacteria--LJ slants
Which is a better killer: moist or dry heat?

Why isn't boiling a good enough killer? What should be used instead?
moist aids in denaturation by allowing h20 to bind and stabilize denatured structure.

Boiling won't inactivate spores. But autoclaves will.
What level of UV light is necessary to kill microbes? What microbes are sensitive to UV light and what must be taken into consideration as far as UV light is concerned?
250-260 nm

Myobacterium tuberculosis

distance from UV source is important--should be short distance
How can microbes be separated from a liquid? What is the benefit over autoclave?
By filtration.

Immunogenic lysed bacteria are absent, but may be present in autoclave
What is efficacy dependent on?
• Nature of ITEM being disinfected or sterilized- more porous = harder to disinfect or sterilize.

• Nature of ORGANISM

• Type of GERMICIDE used

• CONCENTRATION OF GERMICIDE (each has its optimum) - In general a higher concentration results in more killing. There are exceptions: ethanol is actually more effective at 70% than at 100%.

• CONCENTRATION OF ORGANISMS: more organisms = less efficient killing

• DURATION, TEMP, AND pH of exposure- many times longer duration, higher temperature, and lower pH enhances killing

• PHYSIOLGOICAL STATE OF ORGANISM, actively growing organisms are easier to kill while stationary phase cells and spores are harder to kill.

• Presence of extraneous organic matter
From greatest to least resistance of disinfection or sterilization rate the following: nonlipid or small viruses, mycobacteria, fungi, bacterial spores
bacterial spores, mycobacteria, nonlipid or small viruses, fungi
What is the phenol coefficient and what does it mean if >1 or <1?
phenol coefficient rates how well a germicide sterilizes. Greater than 1 is more active and less than 1 is less active.

Not used much and not very accurate
How frequent are bacterial mutations?
Mutations occur spontaneously at a frequency of about one in a million per gene, per generation.
What is a transposon?
Mutatoin caused by transposing DNA
Are frameshift mutations always troublesome?
No, frameshift mutations may cause no problems
Are bacteria haploid or diploid? What does this implicate?
haploid--single chromosome. It means that every gene that if there is a mutationi it will be expressed. there is no such thing as dominant and recessive in bacteria
How many base pairs are in a bacterial gene? Codons? MW of typical protein?
1KB= 100 base pairs

300 codons

30,000 daltons MW
What is a bacteriophage? What kind of parasite is it?
virus that uses bacteria as a host. dependent on bacteria. AKA phage. OBLIGATE INTRACELLULAR PARASITES--completely dependent on bacteria for reproduction
Can a phage perform metabolism outside of a bacterial cell? How does it get inside a bacterial cell?
No, must be inside bacteria. Gets wrapped in a protein coat--CAPSID.
What does the phage genome consist of ? What is the capsid structure?
ss or ds DNA or RNA. Linear or circular. Might contain unusual nucleotides.

Capsid--filamentous and helical OR icosahedral (soccer ball). May have tail to inject genome to bacterial host
Is the capsid injected into the bacterium? What is a virion?
Never! A virion is a phage particle
What are the steps of the lytic cycle?
adhere, inject, express, produce gene products (capsid etc), self assembly of virions, lysis of host cell to release progeny phage.
What is a phage called that can ONLY perform the lytic cycle? What is the other option?
virulent phage.

Temperate phages can do the lytic cycle, but can turn it off and intermittently perform the lysogenic cycle.
What is the lysogenic cycle?
A phage produces a repressor to stop the lytic stage. The stop may last for decades. Prevents cell from being killed AND prevents the production of phage. The phage genome is integrated into the bacterial DNA linerally and passively replicates.
What effect do lysogenic or temperate phages often produce? What is lysogenic conversion?
Transfer coding for toxins, which are expressed by the host,i.e., non-toxic can become toxic--lysogenic conversion
What is a prophage?
phage genome
What are the three methods of bacterial genetic exchange? Describe each.
TRANSFORMATION (transfection)--naked DNA is introduced into the bacterium, which must be COMPETENT
TRANSDUCTION--when dna is transferred via a phage w/ in the capsid-accidental. There is generalized and specialized
CONJUGATION--2 cells get close enough together and then directly transfer by sex pilius (F factor)etc.
By conjugation is ss or ds DNA passed?
ss transferred made into ds inside
When DNA is transferred what important fragement is not available? What must be done?
origin of replication. Need to do genetic recombination, spec. HOMOLOGUS RECOMBINATION--incoming DNA fragment lines up with resident chromosome and substitutes its DNA for resident's DNA--incorporate permanently
What can the three methods of genetic transfer do for science?
Can create a genetic map. sequence DNA . Have complete sequence of 20, 50 more in progress
What is a plasmid? What is its size? What is its most important characteristic?
A plasmid is a circular piece of DNA--kind of a small chromosome. < 1% size of bacterial chromosome. CAN REPLICATE AUTONOMOUSLY--HAVE OWN ORIGIN OF REPLICATION
How do plasmids transfer? What is R factor? What type of genes are often found in plamsids?
by conjugation.

Resistance factor, many plasmids have--antibiotic resistance, often multiple.

Toxin genes often found in plasmids
Does a plasmid need to recombine with bacterial dna?
no, it can replicate autonomously, so there is no need
What are the types of transposable elements?

Which is smallest?
insertion sequences, transposons, and certain temperate phages which integrate at random into the chromosome

Smallest is isertion sequence (20-40 BP)
What does an intertion sequence look like? What do they encode for?
Has inverted repeats on each end (2 total). Encode for transposase.
What does transposase do?
recognizes inverted repeats at two ends of the element AND catalyzes transposition to new site
What happens if an insertion sequence hops into the middle of a gene?
most likely disrupt activity and cause a mutation
What is a transposon? What important function does it have?
segment of DNA containing an antibiotic resistance gene and having an insertion sequence on each end. When it transposes to a new site (e.g. onto a plasmid) it carries the antibiotic resistance gene with it. This is how R factors come to exist.
When was gene cloning developed? Describe the process.
1970's. fragment(s) of DNA from any organism can be incorporated into a cloning vector which is then put inside a bacterium to be replicated, so that the cloned DNA fragment will be replicated as well.
Where do cloning vectors usually come from? What is the absolute requirement for the vector??
Come from plasmids, some from phages.

MUST be a replicon, ie have a origin of replication
What is used to cut DNA? What other function do they serve?
restriction endonucleases. Cut AND convert circular TO linear
What does DNA ligase do?
links the ends of linear dna, to form circular
What is the end product of gene cloning?
large amounts of cloned gene, and large amounts of protein encoded by that gene
What is the major difference of gene expression in bacteria and eukaryotes?
Eukaryotes have introns that need to be spliced out. Code for nothing
How does most gene regulation take place?
By binding of a regulatory protein either activating or repressing gene expression
Describe the lac operon. Is this an ex. of positive or negative control?
lac operon. Lactose controls regulatory protein. The protein is bound to the operon when lactose is NOT present. When lactose IS available it binds to the regulatory protein, which is then removed from the operon, and expression can occur. NEGATIVE control.
What is an operon?
group of adjacent genes which are co regulated

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