Bio 132 Exam One

What is a taxonomy based one?

phylogeny

What is a phylogenetic tree?

a diagram evolutionary relationships among organisms

What are the two ways phylogenetic trees can be drawn?

rooted and unrooted

What is a clade (monophyletic group)?

a group containing an ancestor and all of its descendants

What is modern taxonomy based on?

clades, computational analysis of gene/protein sequences

What is paraphyletic group?

a clade minuses one or more subgroups

What is a polyphyletic group?

a set of organisms not directly evolutionarily related

What is the order of taxonomic classification from most inclusive to least inclusive?

domain, kingdom, phylum, class, order, family, genus, species

What is a taxon?

any taxonomic level

What re the three domains?

bacteria, Archaea, eukarya

What two categories' make up an organism’s scientific name?

genus and species

What is binomial nomenclature?

the two-word naming system for organisms

How is binomial nomenclature written?

always italicized or underlined; first word capitalized only

What is a homologous trait?

a physical feature derived from a common ancestor

What can make comparison of physical traits confusing?

analogous traits

What are analogous traits?

traits with similar function but different evolutionary origins

What is convergent evolutions?

when different species independently evolve similar traits

What can confuse gene-based taxonomy?

horizontal gene transfer

Are viruses cellular or noncellular?

noncellular

Are viruses alive?

no

What do viruses act as?

parasitic macromolecules / obligate intercellular parasites

Why are viruses difficult to detect?

they are much smaller than cells

What are viruses composed of?

genetic material (DNA or RNA) inside a protein capsid

What is a capsid?

the protein shell surrounding viral genetic material

What are the three common capsid shapes

helical, icosahedral, and binal

What is helical virus shape?

a rod or tube structure

What is a icosahedral virus shape?

a 20-sided geometric shape

What is a binal virus shape?

a combination of an icosahedral head and helical sheath

Why are viruses difficult to classify evolutionarily?

they don’t have genes in common with one another for comparison

What three things can viruses be classified based on?

genome structure, capsid morphology, and how they make mRNA

What does “obligate intracellular parasite” mean?

a virus must enter a host and use its resources to replicate

What do viruses require for replication?

a host cell

What is the first step of the lytic cycle?

attachment

What happens during viral attachment?

specific protein-protein interactions occur

What happens during entry in the lytic cycle?

viral genetic material enters the cytoplasm, the capsid is taken up, or the viral envelope fuses with the host membrane

What happens during replication in the lytic cycle?

host enzymes and energy make viral proteins and genomes

What happens during assembly?

capsid assembles and genome is inserted

How does egress occur in the lytic cycle?

by lysis or budding

What happens during integration in the lysogenic cycle?

viral genome integrates into the host chromosome

What is a provirus?

integrated viral DNA with gene expression turned off

What happens during propagation?

viral DNA replicates along with the host cell

What triggers induction?

stress, which reactivates the lytic cycle

What is bacteriophage?

a virus that infects bacteria

Why are plant viruses important?

they cause diseases with major economic impacts

Why are viral infections significant in humans?

they have major health implications

Why are antiviral drugs not widely available?

most viruses are hard to target without harming host cells

How can viral infections be prevented?

vaccines

What are the three prion diseases mentioned?

BSE (mad cow disease), Scrapie (sheep), Creutzfeldt-Jakob disease (Kuru)

What are prions?

infectious misfolded proteins

What normal protein do we all have that prions affect?

PrPC

How does PrPSC cause dieases?

it contains PrPC and converts it into PrPSC, which forms brain lesions

How are prions transmitted?

through infected nerve tissue

Why is prion infectivity unusual?

is persists even when infected tissues is irradiated (DNA/RNA destroyed)

What are viroids?

infectious agents like viruses but lacking a capsid or envelope; consist only of RNA

How do viroids replicate?

they replicate inside a host cell

What do viroids infect?

they infect host cells (primarily plants)

What groups are included under prokaryotes?

bacteria and archaea

Are prokaryotes a clade?

no, they are paraphyletic group

What characteristic defines prokaryotes?

cells that lack a nucleus

Where are prokaryotes found?

they are ubiquitous, found basically everywhere

What were the oldest living things on Earth?

prokaryotes

How did prokaryote evolution affect Earth’s atmosphere?

photosynthesis dramatically altered the atmosphere

What are extremophiles?

prokaryotes that live in extreme environments (temperature, pH, salt)

Why are bacteria cultured in labs?

for use as a diagnostic tool

Do all bacteria grow easily in lab conditions?

no, many bacteria will not grow under standard conditions are considered “unculturable”

Are most archaea culturable?

no, almost all archaea are unculturable and poorly understood

What is the major difference in the cell wall of bacteria vs. archaea?

bacteria have peptidoglycan; archaea do not have peptidoglycan

How many RNA polymerases do have compared to archaea?

bacteria have one; archaea have multiple (Pol. 1-3)

What determines whether an organism is an autotroph or heterotroph?

its method on obtaining its energy

What is a photoautotroph?

uses light for energy and CO2 for carbon

What is a chemoautotroph?

uses chemicals for energy and CO2 for carbon

What is a photoheterotroph?

uses light for energy and organic molecules for carbon

What is a chemoheterotroph?

uses chemical energy and organic molecules for carbon

What roles do many bacteria play in ecosystems?

primary produces and decomposers in the carbon cycle

What bacterial processes are part of the nitrogen cycle?

nitrogen fixations and denitrification

What are bacteria that cause disease in humans called?

pathogenic bacteria

What does antibiotic use create in bacterial populations?

selective pressure favoring resistant individuals

What has overuse of antibiotics caused?

strains resistant to multiple antibiotics

What are solutions to antibiotic resistance?

develop new antibiotics and vaccines

What are three common bacterial cell shapes?

coccus (sphere), bacillus (rod), spirillum (spiral)

What structures may some bacterial cells have for movement or attachement?

pili and/or flagella

What are monoderm bacteria?

single membrane, thick peptidoglycan wall, Gram-positive

What are diderm bacteria?

inner membrane, thin peptidoglycan, outer membrane, Gram-negative

What is transformation?

a cell takes up DNA from environment and may incorporate it into its genome

What is transduction?

a virus transfers DNA between bacteria

What are commensal bacteria?

microbes that don’t harm and may benefit the host

What are two benefits commensal bacteria provide?

crowd out opathogens on skin; help digest food in the gut

When can commensal bacteria cause harm?

if they enter other body parts or gain toxin genes

What foods rely on bacterial activity?

cheese, wine, bread, yogurt

How many bacterial phyla are currently recognized?

50+

What are viroids similar to?

viruses

What do viroids lack that viruses have?

a capsid and an envelope

What are viroids made of?

just RNA

Where do viroids replicate?

inside a host cell

What do viroids infect?

host cells

What defines a prokaryotic cells?

they lack a nucleus

What were the oldest living things on Earth?

prokaryotes

Where did early prokaryotes obtain energy from?

hydrothermal vents

What major change did the evolution of photosynthesis cause?

it dramatically altered Earth’s atmosphere

What des “unculturable” mean?

will not grow under common lab conditions