BISC132 Exam1

Order

Among the following taxa, which refers to the smallest, most exclusive level of classification? (Kingdom, Order, Domain, or Class)

Horizontal gene transfer

gene can be transferred between unrelated species

protein

the viral capsid is made up of…

phylogeny

taxonomy is based on their evolutionary relationships or…

rooted or unrooted

Phylogenetic Trees can be drawn….

clades

modern taxonomy is based on…

paraphyletic group

clade minus subgroup(s) (reptiles)

polyphyletic group

a set of organisms NOT directly evolutionary related

Phylum

Which of the following is known as the biggest, most inclusive taxonomic classification system? (Species, Family, Order, or Phylum)

Genus and Species

What make up an organism’s 2-word (Binomial Nomenclature)??

Always italics or underlined & first word is always capitalized and second words is never capitalized

What is so specific about Genus and Species??

Bacteria, Archaea, and Eukarya

What are the 3 Domains that contain all living things?

Homologous Traits (aka synapomorphies)

Evolutionary Relationships are inferred based on what?

analogous traits

traits that fulfill a similar function, but they are structurally and evolutionary different. (comparison of physical traits can be confusing due to this*)

gene/protein sequences

Modern Taxonomy is based on computational analysis of what sequences?

Viruses

noncellular (not alive), parasitic macromolecules, difficult to detect because they are much smaller than cells, origin is not understood, and truly composed of genetic material (DNA or RNA) in a protein capsid

Helical, Icosahedral, and Bina

Common Capsid Morphologies:

Helical Capsid Morphologies

rod/tube (wind in a circle)

Icosahedral Capsid Morphologies

Icosahedron (20 sides)

Bina Capsid Morphologies

icosahedral head and helical sheath (aka head-and-tail)

they do not have genes in common with one another to compare

Why are viruses so difficult to classify evolutionary??

Genome structure, capsid morphology, or how they make their mRNA

Viruses can be classified by….

Because they are “obligate intracellular parasites”

Why do viruses require a host cell for replication?

Attachment of the Lytic Cycle

What step involves specific protein-protein interactions

Entry of Lytic Cycle

What step involves injections of genetic material in the cytoplasm OR host cell takes up capsid OR viral envelope fuses with host membrane

Replication of Lytic Cycle

What step has host energy and enzymes used to make viral proteins and genomes

Assembly of Lytic Cycle

What step is when capsids assemble?

Egress of Lytic Cycle

What step gets out of the cell by lysis or budding?

Lytic Cycle

Attachment, Entry, Replication, Assembly, and Egress

Lysogenic Cycle

Attachment, Entry, Integration, Propagation, Induction, Replication, Assembly, and Egress

Lytic Cycle and Lysogenic Cycle

Viral Infections Cycle(s)

Integration of Lysogenic Cycle

What step does viral genome integrate into host chromosome, viral gene expression is shut off, and is turned to provirus?

Propagation of Lysogenic Cycle

What step does viral DNA replicated with the host cell?

Induction of Lysogenic Cycle

What step does stress triggers entry to lytic cycle steps and viral gene expressions are turned on?

Bacteriophage ( aka phage )

What is an example of when each virus is specific for a certain host?

Significant economic impact

Many viruses are responsible for plant diseases and this is …

significant impact on public health and antiviral compound are NOT widely available for most viruses and are self-limiting

Many viruses infect humans and this is …

Bovine Spongiform Encephalopahty ( BSE ; Mad Cow Disease ), Scrapie ( in sheep ), and Creutzfeldt-Jakob disease ( Kuru )

3 Neurological Diseases

The disease can be transmitted from infection nerve tissue

Why are neurological diseases not a toxin or poison?

because irradiated nerve tissue ( DNA and RNA have been destroyed ) still transmits disease

Why are neurological diseases not a virus or a living organism?

Prion

What misfiled protein causes irradiated nerve tissue to transmit diseases?

Prion Protein ( PrP^C )

What do we all have within us?

PrP^SC ( Scrapie )

Disease - causing protein is.. ( causes lesions in the brain )

PrP^SC

When PrP^SC comes into contact with PrP^C, PrP^C converts into…

Virod

like viruses but lack a capsid or an envelope, just RNA, and replicate in the host cell and infect plants

Prokaryotes

known as bacteria and archaea, not a clade ( paraphyletic group ), a “cell type”, ubiquitous (they are everywhere) and one of the oldest living things on Earth

hydrothermal vents ( evolution of photosynthesis dramatically altered atmosphere on Earth ) some of these are extremophiles

Prokaryotes obtained energy from …

diagnostic tool

Bacteria are cultured in a medical lab as a…

Bacteria

What has a very specific requirement for growth and will NOT grow under common conditions “unculturable”

Archaea

What are almost all unculturable because they have little to no understanding about them

Eukaryotic Traits

nucleus, mitochondria, cytoskeleton, may have flagella or cilia for movement, chromosomes packed using histone proteins, mitosis, sexual reproduction, and may have cell wall (NOT a peptidoglycan)

Origin of the Nucleus

infolding of cell membrane

Origin of the Nucleus

endosymbiotic theory

Evidence of the Mitochondria Endosymbiotic Theory

physically resemble alpha-proteobacteria, have their own DNA (similar to that bacteria), and reproduce somewhat independently in cell.

Origin of Plastids (including photosynthetic chloroplast)

comes after mitochondrial endosymbiosis because all cell wall with this also have mitochondria

King of Protista

paraphyletic group (NOT a clade & very diverse members)

Protist Traits

mostly unicellular, autotrophs, heterotrophs, mixotrophs, phagocytosis, most are motile, and many have complex life styles

Phagocytosis

engulf and take up large food particles

pseudopodia

temporary projections of cell

Supergroups of Eukarya (clades)

Archaeplastida, Ameobozoa, Opisthokonta, Rhizaria, Chromalveolata, and Excavata

Archaeplastida

photosynthetic and includes plants and red algae

red algae

different pigments and proteins from photosynthesis

amoeba

refers to cells that create pseudopodia

Amoebozoa

have pseudopodia and do phagocytosis

Gymnamoeba and Entamoeba

include “naked” amoebas and amoebas with tests; some are pathogenic and responsible for amoebic dysentery

Slime Molds

produce spores that resist harsh conditions and plasmodial slime molds are multinucleate mass of cells (move along surfaces feeding)

Cellular Slime Molds

single-celled form aggregates to release spores

Opisthokonta

have unique flagella structures and includes animals and fungi

Choanoflagellates

colonial cells with flagella and closely related to animals

Nucleariids

amoebas with thin pseudopodia

Groups of Amoeboza

Gymnaoeba, Entamoeba, Slime Molds

Groups of Opisthokonta

Choanoflagellates and Nucleariids

Groups of Rhizaria

Forams, Radiolarian Shell, Cercozoans

Forams

amoeba with thin pseudopodia and form complex test( tests of dead ___ are important carbon sinks )

Radiolarian Shell

Amoeba with thin pseudopodia, form complex shells from silica, and useful indicators in fossil records

Cercozoans

Diverse forms with/without test or shells, some are photosynthetic, some are parasites of fungi (steal nutrients from cytoplasm using needle-like pseudopods)

Archaea:

have cell walls of compounds other than peptidoglycan

transfer bacterial DNA by a phage

Transduction is a mechanism for exchange of genetic information in bacteria, it does

peptidoglycan

bacteria cell walls are made up of..

Dinoflagellates

which group of protist are primarily marine plankton, with some releasing toxins in the water and the other members being bioluminescence

Groups of Chromalveolata (Stramonpiles and Alveolates)

Dinoflagellates, Apicomplexans, Ciliates, Diatoms, Golden Algae, Brown Algae, Oomycetes

Chromalveolata

Photosynthetic; however some members that lost this ability

Apicomplexans

parasites with complex life styles and includes plasmodium spp.

plasmodium spp.

causes malaria

Ciliates

covered in cilia and heterotrophs

Stramenoplies

have hairy flagella

Diatoms

photosynthetic, plankton, and have unique complex shells of silica

Golden Algae

photosynthetic, plankton, and can form branching colonies

Brown Algae

(aka seaweed and kelp) photosynthetic, multicellular, not plankton, and superficially similar to plants

Oomycetes

saprobes or parasites, superficial similar to fungus, (eg. Phytophthora infestans)

Excavata

unicellular and named for a feeding groove “excavated”

Groups of Excavata

Diplomonads, Parabasalids, and Euglenozoans

Diplomondas

two non identical haploid (copy of each chromosome) nuclei, mitosomes (eg. Giardia lamblia)

mitosomes

reduced mitochondria

Giardia lamblia

causes hiker’s diarrhea

Parabasalids

mitosomes, flagella, axostyle—for attachment, and eg. Trichomonas vaginalis and Trichhonympha spp.

Trichomonas vaginalis

causes trichomoniasis

Trichonympha spp.

lives in termite gut, digest cellulose

Euglenozoans

have flagella, most are freshwater mixotrophs, some are parasitic, and eg. Trypanosoma brucei

Trypanosoma brucei

African sleep sickness