MCAT Study Guide Biology Ch. 4 – Micro Organisms 2017-08-15T06:45:06+00:00

I.          4.1:  VIRUSES

Obligate intracellular parasite, not living organisms, require cellular machinery to copy themselves

A.     VIRAL STRUCTURE AND FUNCTION

1.     Genome – either DNA or RNA, either ss or ds, either linear or circular

a)     Genome is small but often uses >1 reading frame to code for proteins, so genes overlap

2.     Size – much smaller than bacteria, 100-300 nm

3.     Structure

a)     Capsid – protein coat surrounding the genome (can be helical, rod-shaped, polyhedral)

b)     Bacteriophage – virus that infects bacteria; more complex structure:

(1)   Capsid head – stores genome

(2)   Tail fibers and base plate – both attach to the surface of the host cell

(3)   Sheath – middle portion that contracts (using ATP) and injects the genome into the host cell

c)     Envelope – a membranous component that sometimes surrounds a virus, composed of host cell membrane (with viral proteins) to allow fusion with a cell for future infection

(1)   These enveloped viruses are produced by budding through the host cell membrane

4.     Naked viruses – viruses that do not have envelopes (all phages and plant viruses)

5.     Binding site – very specific to a particular cell type

B.     BACTERIOPHAGE LIFE CYCLE

1.     Step 1:  Attachment (adsorption) – binding to the exterior of a bacterial cell

2.     Step 2:  Penetration (eclipse) – Injection of the viral genome into the host cell

3.     Step 3:  Either Lytic Cycle or Lysogenic Cycle

a)     Lytic Cycle – all host cells destroyed

(1)   Host cell polymerases and/or ribosomes begin to transcribe/translate viral genome

(a)   Hydrolase – early gene product (1st made), enzyme that degrades the host genome

(2)   Multiple copies of the viral genome are produced using remnants of host genome

(3)   Capsid proteins are also produced

(4)   Next, capsids automatically assemble themselves around genomes

(5)   Finally, lysozyme (late gene) is produces, which destroys bacterial cell walls

(6)   Bacterium bursts, releasing about 100 progeny viruses

b)     Lysogenic Cycles – host  cells remain intact

(1)   Upon infection, the phage genome is incorporated into bacterial genome and is now referred to as a prophage (host cell is now called a lysogen)

(2)   Prophage is silent, repressor proteins made by phage bind to operators

(3)   Everytime the host cell reproduces itself, the prophage is reproduced too

(4)   Eventually the prophage becomes activated and then removes itself from the host genome (via excision) and enters the lytic cycle

(a)   Transduction – during excision, the prophage may take a chunk of host cell DNA with it, and integrate stolen DNA into new cells

(b)   This may enable the cells to have a trait it did not originally possess (e.g., the ability to metabolize galactose)

C.    REPLICATION OF ANIMAL VIRUSES – similar life cycle as described above, with some differences

1.     Viruses bind to specific proteins on cell membranes

2.     Viruses often enter cell through endocytosis

3.     Once inside, they are uncoated (genome is released from capsid), or, viruses fuse with the plasma membrane to release genome into the cytoplasm

4.     Next, viruses enter lytic cycle, the productive cycle (a lytic-like cycle), or a lysogenic cycle

a)     Lytic cycle – same as bacterial lytic cycle

b)     Productive cycle – same as lytic cycle, but instead of lysis of host cell, viruses are released by budding through the cell membrane

c)     Lysogenic cycle – dormant form of the genome is called a provirus (analogous to prophase)

D.    VIRAL GENOMES

1.     (+) RNA viruses – must encode RNA-dependent RNA pol

a)     SS-RNA genome, very simple, serves as mRNA

[called (+) RNA]

b)     (+) RNA enters cell and host ribosomes begin translating it, making viral proteins

(1)   Infective – describes this viral genome where injecting 1 genome will result in virus production

(2)   RNA-dependent RNA polymerase – a protein that must be encoded for that copies the RNA genome for viral replication (first produces a (-) strand intermediate to serve as a template for generating new (+) RNA strand genomes

c)     EX:  common cold, polio, rubella

2.     (-) RNA viruses – must carry RNA-dependent pol (and encode for it)

a)     The genome is complementary to the RNA that codes for the proteins (is a template)

b)     When the virus enters the cell, the RNA-dependent pol creates a (+) strand from the genome

c)     The viral lifecycle then proceeds

d)     EX:  rabies, measles, mumps, influenza

3.     Retroviruses – must encode reverse transcriptase

a)     (+) RNA viruses that integrate into host genome as proviruses

b)     RNA-dependent DNA polymerase (aka reverse transcriptase) – enzyme that allows reverse transcription, which makes DNA from an RNA template

c)     3 main retroviral genes are gag (viral capsid proteins), pol (reverse transcriptase), and env (viral envelope proteins)

4.     DS-DNA viruses – often encode enzymes required for dNTP synthesis and DNA replication

a)     This is necessary because host cells, although they possess these enzymes, only produce them when they are preparing for replication

b)     RNA viruses don’t need this because RNA pol is always around (cells are always producing proteins)

II.          4.2:  PROKARYOTES

Do not contain membrane-bound organelles (including nucleus)

A.     BACTERIAL STRUCTURE AND CLASSIFICATION

1.     Contents of the cytoplasm

a)     Genome – DS circular DNA chromosome; transcription and translation occur at the same time in the same place

(1)   Transcription occurs in the 5’ → 3’ direction (but tracks along template DNA 3’ → 5’)

b)     Plasmids – circular pieces of ds-DNA found in prokaryotic cells, often encode for gene products that may confer an advantage to the bacteria; capable of autonomous replication

(1)   Important because they orchestrate bacterial exchange of genetic information (conjugation)

2.     Cell membrane and wall

a)     Membrane – phospholipid bilayer

b)     Wall – made of peptidoglycan, prevents lysis due to increased osmotic pressure

(1)   Peptidoglycan is unique to prokaryotes, polymer made of sugars and AAs (including D-alanine, which is different than eukaryotic L configurations)

(2)   Lysozyme (enzyme in tears, saliva) destroys bacterial wall

c)     Gram staining of wall

(1)   Gram positive – dark purple stain, stains the thick peptidoglycan wall (nothing else beyond this wall)

(2)   Gram negative – light pink, doesn’t stain well; thin peptidoglycan wall, surrounded by outer layer of lipopolysaccharide (LPS)

(a)   Periplasmic space – area between peptidoglycan wall and LPS, sometimes contains abx-destroying enzymes

(b)   More difficult to kill with antibiotics

(c)   Endotoxins – normal component of LPS membrane, cause extreme immune reaction if all these bacteria are killed at once

(d)   Exotoxins – toxic substances secreted by G+ and G- bacteria (like botulism, tetanus, TSS)

3.     Capsule (glycocalyx) – present in some bacteria, is the “goo” that makes it more difficult to eradicate infection and also enables bacteria to adhere to smooth surfaces

4.     Flagella

a)     Whip-like filaments involved in bacterial mobility

b)     Motile – used to describe bacteria with flagella

c)     Monotrichous – bacteria with flagellum at one end

d)     Amphitrichous – bacterial with flagellum at both ends

e)     Peritrichous – multiple flagella

f)       Structure:  made of hook, filament, and basal structure

(1)   Basal structure – contains a number of rings that anchor the flagella to the inner and outer membrane and serve to rotate the flagellum either CW or CCW

g)     Requires significant ATP

h)     Chemotaxis – a process where bacteria can be directed toward attractants or away from toxins

5.     Pili

a)     Large projections on the bacterial surface involved in attaching it to different surfaces

b)     Sex pilus attach male and female bacteria together to form conjugation bridges

c)     Fimbrae – smaller structures not involved in conjugation bridges, just in adhering

B.     BACTERIAL GROWTH REQUIREMENTS AND CLASSIFICATIONS

1.     Temperature

a)     Mesophiles – moderate temperature lovers

b)     Thermophiles – heat lovers (can survive up to 100º C)

c)     Psychrophiles – cold lovers (thrive at 0º C)

2.     Nutrition

a)     Chemoautotrophs –  use CO2 as carbon source, and oxidize inorganic molecules as energy source

b)     Chemoheterotrophs – require organic molecules for their carbon source and for energy

c)     Photoautotrophs – use CO2 as carbon source and energy from the sun

d)     Photoheterotrophs – require organic molecules as carbon source, but use sun for energy

3.     Growth media

a)     Agar – clear gel made from seaweed to grow bacteria (no nutritional value)

b)     Minimal medium – contains nothing but gulcose and agar

c)     Lawn – dense growth of bacteria on petri dish

d)     Plaque – clear area in the lawn

e)     Wild-type – strain which possess all the characteristics normal to the species

f)       Auxotroph – bacterium which cannot survive on minimal medium because it cannot synthesize a molecule it needs to live (requires auxillary trophic substance to live)

(1)   Arg- is the denotation used to describe an auxotroph requiring arginine and minimal medium

(2)   Lac+ is a bacteria that can metabolize lactose as only carbon source

(3)   Lac- is a bacteria that cannot use lactose as its only carbon source

4.     Oxygen utilization and tolerance

a)     Obligate aerobes – bacteria which require oxygen

b)     Facultative anaerobes – bacteria which use oxygen when its around, but do not need it

c)     Tolerant anaerobes – can grow in the presence of oxygen, but do not use it in their metabolism

d)     Obligate anaerobes – poisoned by oxygen (they lack enzymes that detoxify free radicals)

5.     Fermentation vs. Respiration

a)     Respiration – glucose catabolism with use of electron acceptor (O2)

b)     Fermentation – no electron acceptor, waste product is either lactate or ethanol

c)     Anaerobic respiration – \use of electron acceptor other than O2 (like SO42-, H2S, CO2, CH4, NO3)

C.    BACTERIAL LIFE CYCLE

1.     Binary fission – asexual reproduction, takes place after a bacteria has grown sufficiently to produce enough material to split and form 2 cells

2.     Conjugation – a way for prokaryotes to exchange genetic material

3.     Growth of bacterial populations:

a)     Lag phase – phase prior to exponential growth, where cell division does not occur even if growing conditions are ideal

b)     Log phase – phase of exponential growth

c)     Stationary phase – phase in which cells cease to divide for lack of nutrients

(1)   Carrying capacity – maximum population at the stationary phase for that environment

D.    ENDOSPORE FORMATION

1.     Endospores are produced by some G+ bacteria under unfavorable growth conditions

2.     Endospores – pieces of bacteria comprised of a tough, thick external shell made of peptidoglycan surrounding the genome, ribosomes, and RNA, all of which are required for the cell to become metabolically active when conditions are favorable

a)     Can survive in T > 100º, which is why pressure is required to kill bacteria

b)     Germination – reactivation of endospores

E.     GENETIC EXCHANGE BETWEEN BACTERIA

1.     Transduction (see 4.1, lysogenic cycle)

2.     Transformation – if pure DNA material is added to bacterial culture, bacteria can internalize the DNA under certain conditions and gain any genetic information from it

3.     Conjugation – most likely related to normal bacterial function

a)     One cell copies DNA and this copy is transferred through a bridge to another cell

b)     F (fertility) factor – a key to bacterial conjugation; is a small circular piece of DNA that contains many genes for conjugation

(1)   Male (F+) – contain the fertility factor and transmit to female (F) cells, which then become male

(2)   The male first forms a sex pili and comes into contact with a female cell and forms a conjugation bridge

(3)   F factor is replicated then transmitted from male to female only

(4)   F factor sometimes becomes integrated into the bacterial chromosomes through recombination

(a)   These cells are called Hfr (high frequency of recombination) cells

(b)   When Hfr cell performs conjugation, replication of the F factor DNA occurs just as it would in an F+ cell

4.     CONJUGATION MAPPING

a)     Hfr bacteria can provide a mechanism for mapping bacterial genome

 

III.          4.3:  FUNGI

A.     FUNGAL STRUCTURE

1.     Most are nonmotile, multicellular eukaryotes (except yeast, which is unicellular)

2.     Chitin – material that fungal cell walls are composed of (also found in insects)

3.     Chemoheterotrophs

a)     Saprophytes – feed off dead animals/plants

b)     Parasites – feed off living organisms, doing harm to the host

c)     Mutualists – part of a symbiotic relationship where both organisms benefit (lichens)

4.     Nutrition

a)     Most are obligate anaerobes (yeasts are facultative anaerobes

b)     Absorptive – digestion of nutrients takes place outside fungal cell

5.     Levels of structure, in order

a)     Cell

b)     Hyphae (long filament of cells joined end-to-end

(1)   Septate hyphae – cells are separated by cell walls called septae

(2)   Aseptate hypae – cells are joined together in a long tube where the cytoplasmic contents and nuclei are shared among the many cells (multinucleate)

(3)   Haustoria – hyphae that are specialized to digest and absorb nutrients in a parasitic fashion

c)     Mycelium – meshwork of hyphae

d)     Thallus – large fungal structure visible to the naked eye

(1)   Vegetative portion – involved in obtaining nutrients

(2)   Fruiting body – functions in reproduction (make spores)

B.     FUNGAL LIFE CYCLES

1.     Asexual reproduction

a)     Budding – new smaller hyphae (or cell) grows out from existing one

b)     Fragmentation – Mycelium can be broken into smaller pieces, each of which develops into a separate mycelium

c)     Asexual spore formation – occurs through mitosis to generate many spores from one cell (formed on sporangia)

(1)   Spores are covered by tough resistant wall and when conditions are favorable, spores will germinate

2.     Sexual reproduction

a)     Fungal adults are haploid (only one copy of chromosomes)

b)     Two haploid cells fuse to produce a diploid zygote; this zygote quickly enters meiosis to produce haploid cells again

c)     Gametangia – regions that specialize in sexual reproduction

(1)   These can produce gametes that will fuse with other gametes, serve as a site for gamete fusion, or fuse with gametangia from other fungi of the same species

d)     Dikaryon – a cell with two nuclei, which happens after cells fuse but before the nuclei fuse to form a diploid gamete

MCAT Study Guide Biology - Kim Matsumoto


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Ch. 2 Thermodynamics and Cellular Respiration

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Ch. 3 Transcription + Translation

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Ch. 4 Microbiology

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Ch. 5 Cell Biology

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Ch. 6 Genetics

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Ch. 7 Nervous System

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Ch. 8 Circulatory System

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Ch. 9 Renal + Digestive System

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Ch. 12 Reproductive System

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