Taxonomy, Cell Types, prokaryotes, viruses

Taxonomic Divisions

• Domain

• Kingdom

• Phylum

• Class

• Order

• Family

• Genus

• Species

3 domains in nature

• archaea

• eubacteria

• eukarya

type of cells: archaea and eubacteria

prokaryotic

prokaryotic cells are _____ celled organisms

single

do prokaryotic cells have organelles?

No

What type of DNA to prokaryotes have?

circular DNA, and they have no introns

what are prokaryotic cell walls made of?

peptidoglycan

how do prokaryotes reproduce?

binary fission, because they are single chromosome and haploid

What are pili and fimbriae

Used by prokaryotic cells for adhesion to the outside environment

What is flagella made up of in prokaryotic cells?

flagellin

What type of ribosomes do prokaryotic cells have?

70S - svedvirg

What type of DNA do eukaryotes have?

DNA is bound to histone proteins that is linear

Introns

none translated regions or sequences that are cut out and left within the nucleus

What is cilia or flagella made of in eukaryotes?

tubulin

What type of ribosomes in eukaryotes?

80S ribosome

heterotrophs

obtain energy by the consumption of organic molecules produced by autotrophs

Autotrophs

make their own organic molecules

Types of heterotrophs

• parasites

• saprophytes

What are saprophytes?

they live off of dead, decaying matter, also referred to as decomposers

types of autotrophs

• photoautotrophs

• chemoautotrophs

Photoautotrophs

organisms that use light for their organic molecules

Chemoautotrophs

use inorganic molecules for their energy (chemosynthesis)

Parasite

Lives inside of a host, and gains its energy from that host

obligate aerobes

must live in the presence of oxygen

obligate anaerobe

can only survive in the absence of oxygen

faculative anaerobe

grows in the presence of oxygen but can also undergo anaerobic metabolism if oxygen is absent

Archaea

oldest domain of life, the most primitive species

Archaea characteristics

• prokaryote

• no peptidoglycan

• phospholipids with ether linkages to glycerol and hydrocarbons are branched

• histone proteins

• DNA has introns

• not pathogenic

3 common archaea

• Methanogens

• Thermophiles

• Halophiles

Methanogens

• obligate anaerobes

• produce methane

• found in GI tract of humans, cows, the mud, and swamps

Thermophiles

• Heat lovers

• Sulfur based chemoautotrophs (most of them)

• think yellowstone national park, found in heated pools

Halophiles

• salt lovers

• live in environments with high salt concentration

• most are aerobic, some are anaerobic

• some or photosynthetic autotrophs and others are heterotrophic

Eubacteria

• prokaryotic cells

• cell wall made of peptidoglycan

• no histone proteins

• ribosome composition can be inhibited by antibiotics

• endospores

What are endospores

hard, tough, and dormant in external environment, similar to a seed/egg

What is bacteria classified based on?

its shape

Bacillus/bacilli

rod shaped

Coccus/cocci/diplococcus, triplococcus

spherical shape

sprillium/spirilla

spiral shaped

strepto—

multiple cells in a chain

staphyl—

cluster of cells

Gram positive

• thick layer of peptidoglycan

• no LPS outer membrane

• teichoic acids between peptidoglycan and plasma membrane

• dark purple when stained

Gram negative

• thin layer of peptidoglycan

• LPS (lipopolysaccharide) outer membrane, Endotoxins when killed

• NO teichoic acids

• pink when stained

Nitrogen-fixing and nitrigying bacteria

• key players in the nitrogen cycle

what do nitrogen-fixing bacteria do?

Take atmospheric nitrogen (N2) and make it into ammonium (NH₄⁺)

What do nitrifying bacteria do?

Take ammonium (NH₄⁺) and make it into Nitrates (NO₂^-)

Cyanobacteria (Blue-green Algae)

• NOT EUKARYOTIC ALGAE

• photoshynthetic bacteria

Types of bacteria genetic recombination

• conjugation

• transformation

• trandsuction

conjugation

• horizontal gene transfer

• involves transfer of a plasmid

• involves a pilus

• prokaryotes only

transformation

• prokaryotes only

• heat or CaCl₂ causes bacteria cell wall to uptake plasmids in the environment

transduction

• involves viruses

• transfer of bacterial DNA via viruses

• prokaryotes only

viruses

non-living, parasites that infect the host’s cells

bacteriophages

viruses that infect bacteria

viruses are made up of either…

double or single stranded RNA or DNA (never both)

capsid

protein cover that encloses viruses genetic information

capsomere

polymers that make up capsids

phospholipid envelope

obtained from the host cell membrane (takes some of phospholipid bilayer from host)

Lytic

• virus injects genetic material into host cell

• hijacks the cell’s machinery (enzymes) to produce more virus

• new virus erupts from the cell membrane, it obtains its phospholipid bilayer and kills the cell

Retroviruses

ssRNA viruses that use reverse transcriptase to make DNA from its RNA.

• RNA → DNA

Lysogenic cycle

• virus hides out in a host’s genome

• viral DNA is incorporated into the DNA of the hosts cell

• knowns as “prophage” in bacteria or “provirus” when it is dormant

• after dormant virus receives a signal from external environment, it undergoes the lytic cycle and kills the cell

What are viruses?

• infectious particles

• incredibly small

• non-living

Basic structure of viruses

• nucleic acids (DNA or RNA)

• capsid (protein coat that surrounds nucleic acids

Bacteriophage structure

• sheath: helps to eject viral DNA into a cell

• tail fibers: allow it to recognize and attach to those bacterial host cells

Viral envelope

can enhance a viruses ability to infect a host, its also the membrane

• composed of viral glycoproteins, host cell membranes, membrane proteins

viral lifecycle

1. attachment

2. entry

3. uncoating

4. synthesis/replication

5. self-assembly

6. release

attachment

binding to host cell via an interaction of host cell and viral surface proteins

entry

viral particle enters cell - mode depends on virus type and host cell

uncoating

genome is exposed via breakdown of viral capsid

synthesis/replication

replication of genome + creation of viral proteins

• specific to type of virus

self-assembly

process of assembling of genome + viral proteins

release

process of exiting the host cell - viral shedding

• budding, apoptosis, exocytosis

budding

virus exits by budding off a portion of host’s membrane to use. as a viral envelope

apoptosis

• programmed cell death

• viruses forces the host to self-destruct

exocytosis

virus released by vesicles fusing with the host cell membrane

retroviruses

use reverse transcriptase to create ENA from RNA genome

bacteriophages

viruses that specifically infect bacteria

What is the lytic cycle

the phage infects and then actively replicates in the host cell before lysing the host to release its viral progeny

What is the lysogenic cycle?

the phage integrates its genome into the host genome and replicates until it is triggered to enter the lytic cycle

Prophage

viral genomes that integrate into bacterial genomes

provirus

viral genomes that integrate into eukaryotic genomes

How do Bacteria defend themselves against viruses?

• cell surface mutations

• restricion enzymes

• CRISPR-Cas system

Cell surface mutations

mutations on the bacterial cell surface have prevented phages from identifying bacterial cell surface

Restriciton enzymes

cut the phage DNA at specific recognized sequences, preventing it from being duplicated or replicated

CRISPR-Cas system

phage DNA added into own genome → subsequent infection will activate CRISPR-Cas → phage DNA transcribed and processed to small RNA → small RNA binds Cas proteins → Cas + RNA complex tracks down viral genome → viral genome is cleaved and destroyed

Viral infections in human

• acute viral infections

• chronic viral infections

• latent viral infections

• slow progressing infections

acute viral infection

• quick onset of symptoms - rapid replication of virions

• viral load shortly decreases after infection is high

chronic viral infections

• period of high initial viral load - virus can spread to other sites

• immune system is eventually able to control infection

• low viral load which can last several years to a life time

latent viral infections

• similar to chronic - can last years to a lifetime

• includes intermittent phases of high viral load after the initial acute phase

slow progressing infections

• similar to latent infections

• after period of latency, the illness continues to progress

What are the types of viral outbreaks?

• emerging viruses

• epidemic

• pandemic

emerging viruses

suddenly become prominent in a population

epidemic

viral outbreak in a large population

pandemic

global viral outbreak

What are vaccines?

weakened agents that mimic a disease-causing organism to stimulate the immune system

How effective are vaccines?

affected by random mutation of viral surface proteins (antigens) that vaccines recognize

Antigenic drift

infects same host species

antigenic shift

increases viral host ranges

prions

infections mis-folded proteins that cause other proteins to mis-fold

viroids

simple molecules of ssRNA that infect plants

prions are characterized by

• long incubation period

• acts slowly - can incubate for 10+ years

• slowly-progressing infections

• resistance to deactivation

• not killed of at standard cooking temperatures

• can result in human transmission