BISC 132 001 Exam 1

Dr.Kemege 2023

What is taxonomy?

The science of classifying organisms.

What is taxonomy based on?

Phylogeny

What is phylogeny?

The evolutionary history and relationship of an organism or a group of organisms.

Phylogeny can be diagrammed in…

phylogenetic trees.

What are phylogenetic trees?

A diagram that reflects the evolutionary relationships between organisms or groups of organisms

What do phylogenetic trees show?

Evolutionary relatonships

Unrooted phylogenetic trees look like…

a circle.

How can phylogenetic trees be drawn?

Rooted or unrooted

What are clades?

Complete branches in a phylogenetic tree (e.g., plants meaning all plants)

What does a clade include?

An ancestor and all of its descendants.

Clades are also known as…

monophyletic groups.

What is modern taxonomy based on?

Clades.

However, many traditional groups are…

not actually clades.

What is a paraphyletic group?

A clade minus a few subgroups (ex. reptiles do not include birds despite being a direct ancestor)

What are polyphyletic groups?

A set of organisms lumped together due to common traits (e.g. mammals and birds being warm-blooded) that are not directly evolutionarily related.

The taxonomic classification system is made up of…

at least eight levels.

A single level of the taxonomic classification system is known as what?

A taxon

What are the eight levels of the taxonomic classification system from largest, most inclusive to the smallest, most exclusive?

* Domain
* Kingdom
* Phylum
* Class
* Order
* Family
* Genus
* Species

What is the largest/first taxon?

Domain

What is the smallest/eighth taxon?

Species

What is the second taxon?

Kingdom

What is the third taxon?

Phylum

What is the fourth taxon?

Class

What is the fifth taxon?

Order

What is the sixth taxon?

Genus

Some organisms have…

subtaxa.

Genus and species make up an organism’s what?

Two-word name

What is binominal nomnclature?

The name of an organism that is made up of genus and species.

Binominal nonciatures always have to be…

underlined or in italics.

The first word in a binomial nomenclature has to always be…

capitalized.

The second word in a binomial nomenclature has to always be…

in lowercase.

What are humans?

*Homo* sapiens

What are the three domains that contain all living things?

* Bacteria
* Archaea
* Eukarya

Evolutionary relationships are inferred based on what?

Homologous traits

What are homologous traits?

A similar physical feature derived from a common ancestor

What is another name for homologous traits?

Synapomorphies

Comparing physical traits can be confusing. Why?

* Analogous traits
* Convergent evolution

What are analogous traits?

Traits that fulfill a similar function but are structurally and evolutionarily different

What is convergent evolution?

A process by which groups of organisms independently evolve into similar forms

Modern taxonomy is based on…

computational analysis of gene and protein sequences.

What is a vertical gene transfer?

A gene that parents pass onto their offspring

Modern taxonomy can be confusing because of…

horizontal gene transfer.

What are horizontal gene transfers?

The transfer of genes between unrelated species.

What is missing from the phylogenetic tree of life?

Viruses, because they are not alive.

Viruses are…

* non-cellular
* not alive
* parasitic macromolecules
* difficult to detect due to their small size (smaller than cells)

The origin of viruses is…

not understood. We don’t know where they came from!

Viruses are composed of…

genetic material (DNA or RNA) in a protein cell known as capsid.

What is a capsid?

A protein coating of the viral core

What are the common capsid morphologies?

* Helical
* Icosahedral
* Binal

What is the helical capsid?

A rod or tube.

What is the icosahedral capsid?

A 20-sided shape (DND dice)

What is the binal capsid also known as?

A head and tail

What are binal capsids made up of?

An icosahedral head and a helical sheath

Some viruses have what is known as what?

An eenvlope

What is an envelope?

A lipid bilayer that surrounds some viruses.

Viruses are difficult to classify evolutionarily, why?

They have to have a sequence alignment, something that can only found in LIVING things, and they do not have genes in common to compare.

How are viruses classifed?

By genome structure, capsid morphology, or by how they make their mRNA.

What is considered an obligate intracellular parasite?

Viruses

Viruses require what to replicate?

A host cell

What are the two types of viral infection cycles?

* Lytic cycle
* Lysogenic cycle

What is the lytic cycle?

“Smash and Grab”

A cycle in which the virus gets into the cell, steals resources, makes more of itself, and then leaves the cell.

Attachment in the lytic/lysogenic cycle…

involves specific protein-protein interactions

Entry in the lytic/lysogenic cycle…

involves the injection of genetic material into the cytoplasm OR involves a host cell taking up a capsid OR involves the viral envelope fusing with the host membrane.

What are the types of the lytic cycle?

1) Attachment

2) Entry

3) Replication

4) Assembly

5) Egress

Replication in the lytic cycle…

involves host energy and enzymes being used to make vital proteins and genomes.

Assembly in the lytic cycle…

involves the capsid assembling with the genome inside.

Egress in the lytic cycle…

involves lysis or budding

What is lysis?

The breaking down of the membrane of the cell

What is budding?

A method of exit of the cell used by certain animal viruses where versions leave the cell individually by capturing a piece of the host plasma membrane.

What is the lysogenic cycle?

An offshoot of the lytic cycle (follows the first two steps)

Integration of the lysogenic cycle involves…

a viral genome being integrated into a host’s chromosomes

What are the steps of the lysogenic cycle?

1) Attachment

2) Entry

3) Integration

4) Propagation

5) Induction

6) Replication

7) Assembly

8) Egress

What happens during integration in the lysogenic cycle?

Viral gene expression is shut off, making the virus inside the host chromosome a provirus.

Propagation of the lysogenic cycle…

involves the viral DNA replicating with the host cell.

What happens during induction of the lysogenic cycle?

Stress triggers the lytic cycle and viral gene expression is turned on

The lysogenic cycle is the lytic cycle with…

three added extra steps.

All living things (animals, plants, bacteria, etc.) have viruses that…

parasitize them.

Each virus is specific for a certain what?

Host

What is an example of a virus being specific to a certain host?

Bacteriophage/phage

What are bacteriophages?

Viruses that infect bactiera

Many viruses are responsible for plant disease. What can this cause?

Significant economic impact

Many viruses can infect humans. What can this cause?

A significant impact on public health

What is not widely avaliable for most viruses?

Antiviral compounds

Most viral infections are considered to be what?

Self-limiting

What do vaccines do?

Prevent infections

What is bovine spongiform encephalopathy (BSE/Mad Cow Disease)?

A neurological disease present in cows that increases aggressive tendecies and often proves to be fatal.

What is scrapie?

A neurological disease that affects sheep and causes the animal to scrape themselves to death.

What is kuru (Creutzfeldt-Jakob disease)?

A neurological disease in humans that causes the brain to deteriorate.

Kuru is NOT a toxin or posion. Why?

It can be transmitted from infected individuals, specifically from nerve tissue.

Kuru is NOT a living organism or a virus. Instead, it is…

a disease caused by a misfolded protein called a prion.

If nerve tissue is irradiated, the condition is NOT…

a living organism or a virus.

When nerve tissue is irradiated, it…

destroys DNA and RNA, but can still transmit disease.

All mammals have prion protein, what are the two types?

Normal: PrP^c

Diseased: PrP^sc

When PrP^sc comes into contact with PrP^c, it…

converts the PrP^c into PrP^sc.

What causes lesions in the brain?

PrP^sc

What are viroids?

They are similar to viruses but lack a capsid or an envelope. It is only made up of RNA sequences.

What do viroids do?

Replicate in a host cell and infect plants

What is considered a prokaryote?

* Bacteria
* Archa
* NOT CLADES!!!

What are clades?

A paraphyletic group.

Prokaryotes are a “cell type”. What is important about these cells?

They do not have a nucleus.