Last minute Prok. exam 2

Which of the following viral structures is simply a modified version of the host cell

a. capsomers

b. spikes

c. envelopes

d. the head and tail of the phage

e. none of the above

c. envelopes

viral genome can be which of the following configurations

a. dsDNA

b. dsRNA

c. ss(+) RNA

d. ss(-) RNA

e. all of the above

e. all of the above

a retrovirus much have which of the following enzymes

a. RNA polymerase

b. reverse transcriptase

c. lysosome

d. DNA-dependent DNA polymerase

e. all of these

b. reverse transcriptase

you are walking through the woods and see a fungus with a club-like spore-producing structure growing out of a dead log. What fungal phylum does it most likely belong to

a. microsporidia

b. chtridiomycota

c. glomeromycota

d. ascomycota

e. basidiomycota

e. basidiomycota

which organism is known for creating slug like pseudo plasmodium that are composed multiple individual cells, but behaves as a single organism

a. ascomycota

b. zooflagellates

c. oomycetes

d. plasmodial slime molds

e. cellular slime molds

e. cellular slime molds

The oomycetes are called water molds because both oomycetes and fungi

a. have a chitin based cell wall

b. have hyphae

c. are protozoans

d. are algae

e. have basidia

b. have hyphae

which of the following groups can fix nitrogen from the atmosphere

a. bacteria

b. archea

c. animals

d. plants

e. fungi

a. bacteria

which of the following is a gammaproteobacteria

a. yersinia pestis

b. rhizobium radiobacter

c. streptococcus mutans

d. bacillus subtills

e. ralstonia pickettii

a. yersinia pestis

which fungal phylum has members known for forming symbiotic associations with plants via mycorrhiza

a. microsporidia

b. chtridomycota

c. glomeromycota

d. ascomycota

e. basidiomycota

c. glomeromycota

which virus has dna that returns to the nucleus for assembly and translation

a. DNA animal virus

b. RNA virus

c. Lysogenic virus

d. lytic virus

a. DNA animal virus

what describes a retrovirus

a. turns DNA into RNA

b. RNA to protein

c. RNA to DNA

d. protein to ribosome

c. RNA to DNA

what intergrates into a bacterial cell

a. porin

b. retrovirus

c. lytic

d. lysogenic

d. lysogenic

which of these contain mycorrhiza

a. mycelia

b. gloomeromycotya

c. hyphae

d. yeast

b. gloormeromycotya

sequencing protozoan phyla is done by

common traits

Cell wall composition of bacteria

possess peptidoglycan in their cell walls

Cell wall composition of archaea

lack peptidoglycan entirely, many possess pseudomurein

Chromosomal structure and proteins of archaea

possess a single circular chromosome bound with histone (similar to eukaryotes)

Chromosomal structure and proteins of bacteria

lack eukaryotic like histones

physiological and ecological diversity or archaea

include aerobes, anaerobes, autotrophs, heterotrophs, extremeophiles, and psychrophiles; are part of human microbiome their roles as human pathogens remains unclear

hemidallarchaeota

is identified as the achaeal phylum from which eukaryotes evolved

gram positive bacterial phyla

primarily chemoheterotrophs divided into distinct phyla based on DNA G+C content

two phylum of gram positive phyla

Low GC content, phylum Firmicutes

High GC content, phylum Actinobacteria

what does the phylum firmicutes break into

endospore forming and nonendospore forming

what does the phylum actinobacteria break into

filamentous mycelia and non filamentous pathogens

Phylum Firmicutes- low GC content, genus clostridium:

endospore forming

obligate anaerobes that lack an ETC

common soil inhabitants

produce potent exotoxins that include C. botulinum (botulism), C. tentani (tetanus), C. perfringens (gastroenteritis) C. difficile (severe diarrhea)

Phylum Firmicutes- low GC content, genus Bacillus:

endospore forming

aerobes or facultative anaerobes, chemoheterotrophs

motile via peritrichous flagella (flagella projected in all directions)

major source of clinical antibiotics (bacitracin and polymyxin)

relatively few human pathogens, B. anthracis (causative agent of anthrax)

Phylum Firmicutes- low GC content, genus Lactobacillus:

non endospore forming

rod-shaped (bacilli)

belongs to lactic acid bacteria

aerotolerant anaerobes (lack ETC rely on lactic acid fermentation)

used in food productions like yogurt cheese and pickled food

Phylum Firmicutes- low GC content, genus Streptococcus:

non endospore forming

spherical chains (cocci)

aerotolerant anaerobes (lack etc)

many species produce hemolytic exotoxins (lyse red blood cells)

major pathogens include, S. pyogenes (strep throat, rheumatic fever), S. pneumoniae (pneumonia), S. mutans (tooth decay)

Phylum Firmicutes- low GC content, genus Staphylococcus

non endospore forming

spherical clusters

facultative anaerobes highly resistant to drying and salt tolerant

S. aureus is common component of the human skin and respiratory microbiome it can cause

• dermatological infections

• respiratory infections in immunocompromised

• TSS and Food poisoning

• antibiotic-resistant infections (MRSA)

Phylum Actinobacteria- High GC content

gram positive, mostly aerobic, filamentous bacteria that form branching mycelia

Phylum Actinobacteria- High GC content, genus Streptomyces

GC content exceptionally high (69-73%)

aerobic soil inhabitants, produce extracellular enzymes to degrade complex organic compounds

produces reproductive spores (distinct from firmicute endospores)

primary source of essential antibiotics: streptomyocin tetracycline, and erythromycin

Other pathogenic genera in actinobacteria

Myobacterium (112 species) Corynebacterium (56 species) Nocardia (53) actinomyces (26)

Gram negative bacterial phyla, includes what phylums

Proteobacteria, bacteroidetes, cyanobacteria

Phylum proteobacteria

Gram negative bacterial phyla

the largest bacterial phylum, 1/3 of all known bacterial species, grouped strictly by their 16s rRNA gene homology rather than phenotypic traits

divided into six classes including Alphaproteobacteria and Gammaproteobacteria

Phylum Proteobacteria key genera and groups

Genus Rickettsia (Alphaproteobacteria)

Genus Rhizobium & Genus Agrobacterium (Alphaproteobacteria)

Genus Neisseria

Enteric Proteobacteria (Enterobacteriaceae)

Genus Pseudomonas

phylum bacteroidetes

gram negative bacterial phyla

gram negative chemoheteroptrophs: includes major human intestinal microbiom genera like bacteroides and prevotella

phylum cyanobacteria

gram negative bacterial phyla

oxygenic photosynthetic bacteria responsible for converting light energy into chemical energy while producing oxygen

Fungla Phyla overview

fungi are eukaryotic heterotrophs categorized by their reproductive structures and spore generation mechanism

1. ascomycota

2. basidiomycota

3. glomeromycota

4. chytridiomycota

Fungal Phyla Ascomycota phylum

characterized by sexual reproduction, where meiosis occurs to produce ascospores enclosed within an ascus structure

Fungal Phyla Basidiomycota phylum

includes traditional club fungi, rusts, and smuts

forms sexual basidiospores on external basidia structures

Fungal phyla Glomeromycota phylum

obligate endomycorrhizal fungi that form arbuscular structures within the root cells of terrestrial plants

Fungal phyla Chytridiomycota phylum

primitive aquatic fungi characterized by glagellated motile zoospores

Protist groupings overview

Comprise a polyphyletic collection of eukaryotic microorganisms divided into four main functional categories:

1. algae

2. protozoa

3. oomycetes

4. slime molds

Protist- Algae

photosynthetic plant like protists possessing chloroplasts, critical primary producers in aquatic ecosystems

protist- Protozoa

unicellular, heterotrophic, animal-like protists that exhibit motility via pseudopodia, cilia, or flagella

Protist- oomycetes

water molds, filamentous fungus like organisms with cell walls composed of cellulose rather than chitin

Protist- slime molds

fungus like protists that feed on microorganisms via phagocytosis and form multinucleate plasmodia or cellular aggregates under starvation conditions

Prokaryotes polycistronic

Polycistronic mRNA is very common; a single transcribed mRNA molecule contains multiple open reading frames coding for distinct functional proteins that share a single promoter and terminator

Eukaryotes Monocistronic

monocistronic mRNA is standard, single mRNAs code for single proteins

gene architecture prokaryotes vs eukaryotes

P: lack introns and coding sequences are continuous

E: Possess exons (coding regions) interrupted by introns (noncoding regions) that are spliced out prior to translation

Lac Operon Mechanics (inducible system)

the lac operon controls lactose metabolism in E. coli, it consists of a promoter P operator O and regulatory gene lac 1 and three structural genes

Lac operon structural genes

1. lacZ: encodes beta-galactosidase, an enzyme that hydrolyzes the disaccharide lactose into glucose and galactose

2. lacY: encodes permease, a membrane transport protein that facilitates lactose entry into the bacterial cell

3. lacA: encodes transacetylase, an enzyme that transfers an acetyl group to beta- galactosidase

Chart of Lac Operon and what comes in what order

general idea: glucose used first and then lactose is used after 

what is the role of the operator

a specific DNA sequence adjacent to the promoter that physically binds the active repressor to block RNA polymerase transcription

Baltimore Classification, Class 1

dsDNA (+), no packaged virion enzymes required, its primary replication site host nucleus, transcribed directly to mRNA by host RNA plymerase

Baltimore Classification, Class 2

ssDNA (+ or -), no packaged virion enzymes required, its primary replication site host nucleus, converted to dsDNA intermediate via host DNA; ploymerase —> transcribed to mRNA

Baltimore Classification, Class 3

dsRNA, RNA-dependent RNA polymerase is the packaged virion enzyme required, its primary replication site is the cytoplasm, segmented genome; (-) strand acts as template for RNA-dependent RNA polymerase to make (+) mRNA

Baltimore Classification, Class 4

(+) ssRNA, no packaged virion enzyme required it encodes enzyme in genome, primary replication site is cytoplasm, Genome functions directly as mRNA —> translated into polyprotein; forms (-) ssRNA template for replication.

Baltimore Classification, Class 5

(-) ssRNA, RNA dependent RNA polymerase (packaged virion enzyme required) , primary replication site is cytoplasm, (-) strand serves as template for packaged RNA dependent RNA poly to synthesize (+) mRNA

Baltimore Classification, Class 6

(+) ssRNA retrovirus, reverse transcriptase (packaged virion enzyme required) primary replication site is cytoplasm to the nucleus, Diploid (+) ssRNA —> Reverse transcribed to RNA/DNA hybrid —> dsDNA —> integrated into host genome by integrase.

DNA Viruses Baltimore replication path

Class 1 and 2, replicate in nucleus use host DNA/RNA ploymerase

RNA viruses Baltimore replication path

Class 3, 4 and 5 replicate in cytoplasm, requiring viral RNA-dependent RNA polymerase

Retrovirus Baltimore replication path

Class 6, reverse transcribe RNA to dsDNA —> integrates into host chromosome

Lytic Cycle case study

virulent T4 phage

Lytic cycle stages

1. absorption

2. penetration

3. replication

4. assembly

5. release

6. latent period

lytic cycle stage 1. absorption

tail fiber bind host cell wall receptors

lytic cycle stage 2. penetration

tail lysozyme degrades peptidoglycan; the sheath contracts, injecting viral DNA with the help of a viral pilot protein

Lytic cycle stage 3. replication

host DNA is degraded by viral enzymes; host protein/nucleic acid synthesis halts, host machinery replicates phage DNA and translates capsid proteins

Lytic cycle stage 4. assembly

heads and tails assemble independently, viral DNA is packaged into heads before tail attachment

Lytic cycle stage 5. release

phage lysozyme weakens the cell wall including inducing osmotic lysis

Lytic cycle stage 6. ish the latent period

about 22 minutes burst size: 50-200 viral particles per cell

lysogenic cycle case study

temperate lambda phase

lysogenic cycle stage 1

phage injects DNA instead of replication viral DNA intergrates into host chromosome becoming a prophage

lysogenic cycle stage 2

viral repressor proteins suppress viral gene expression

lysogenic cycle stage 3

the prophage replicates passively alongside the host cell during division

lysogenic cycle: induction

environmental stress or DNA damage inactivates the repressor protein, the prophage excises from the chromosome, circularizes in the cytoplasm, and initiates the lytic cycle

Which one does not cause genetic diversity in microbes

a. Transduction,

b.conjugation,

c. Transformation,

d. translation errors

e. random mutations

d. translation errors

which ones use the hosts DNA polymerase in viral replication (select all).

1. dsDNA viruses

2. ssDNA viruses

lac operon growth when it comes to glucose and lactose

Diauxic growth (two phase growth)

phase 1: glucose utilization:

• Glucose is consumed first because it is the most energy-efficient, and then

phase 2: the lag phase metabolic switch:

• population grown temporarily stops and then at a slight slower rate lactose supply is used

what can lyse red blood cells

Phylum Firmicutes- low GC content, genus Streptococcus, Gram-positive, called the hemolytic exotoxins

How do domain archea and domain bacteria differ structurally and genetically

Archaea lack peptidoglycan in their cell walls (have pseudomurein), they have histones on their circular chromosomes (like eukaryotes) and have unique 16s rRNA gene signatures.

Bacteria have peptidoglycan in their cell walls and distinct bacterial 16s rRNA signatures

Why is Protista considered an artifical group rather than a true kingdom

Protista is not a monophyletic taxon or true kingdom, rather, it is an artificial collection of eukaryotic lineages grouped historically by physical traits rather than shared evolutionary ancestry revealed by 18s rRNA sequencing

what are the primary distinguishing traits of algae within protists

Eukaryotic phototrophs that perform oxygenic photosynthesis using chlorophyll (a, b, c, or d), contain cellulose cell walls, use CO2 or HCO3- and may have flagella (never cilia)

What are the primary distinguishing traits of Protozoa within the Protists

Unicellular, motile heterotrophs (first animal) that absorb or engulf food. Most live in aquatic environments and possess contractile vacuoles to pump out excess water for osmoregulation

How do oomycetes (water molds) differ from true fungi

oomycyetes have cellulose cell walls (fungi have chitin) and are phylogenetically related to diatoms and brown algae rather than true fungi, they form hyphae and act as freshwater decomposers or plant/animal parasites

What is an F+ cell versus an F- cell in bacterial conjugation

An F+ cell contains a self-replicating fertility (F) plasmid that codes for the sex pilus, an F- cell lacks the F plasmid and acts as the recipient during conjugation

How is an HFr cell formed (high frequency recombination)

an Hfr cell is formed when a free F plasmid integrates directly into the host bacterial chromosome via homologous recombination, the integrated plasmid replicares along with the host genome

What happens during Hfr conjugation when an Hfr cell mates with an F- cell

conjugation begins at the origin of replication on the integrated F plasmid, ssDNA containg F plasmid genes followed by donor chromosomal DNA is transferred into the recipient cell through the sex pilus

Why does the recipient cell usually remain F- after Hfr conjugation?

The entire bacterial chromosome takes 90–100 minutes to transfer13. Because the trailing end of the F plasmid enters last, conjugation is almost always interrupted before complete transfer13. The recipient stays F- because it doesn't receive the complete F plasmid, but it gains new chromosomal genes through homologous recombination13.

What organism is this?

1. Has cell wall

2. no cellulose in the cell wall

3. No peptidoglycan in the cell wall

4. Does not have hyphae

5. Unicellular
   a. Algae
   b. Protozoa
   c. Archaea
   d. Fungi
   e. Bacteria

c. archea

members of the genus Pseudomonas rely on

aerobic repiration and are incapable of fermentation, the respiration is done via the entner dourdoroff pathway