Chapter 26 and 27

Question 1

What is phylogeny

Answer 1

Phylogeny is the evolutionary history of a species or group of related species .

show evolutionary relationships

Question 2

What is systematics

Answer 2

Systematics is the scientific discipline focused on classifying organisms and determining their evolutionary relationships.

Question 3

What is taxonomy

Answer 3

Taxonomy is the scientific discipline concerned with naming and classifying the diverse forms of life .

2 part binomial scientific name scheme

First word is the genus to which species belong to followed by the epithet .

Binomial italicized and genus name capitalized

Question 4

Taxon

Answer 4

Taxonomic unit at any level of the hierarchy

There is genetic diversity within a taxon

Question 5

What is a phylogenetic tree and what is it used for ?

Answer 5

A phylogenetic tree a branching diagram to represent a hypothesis about the evolutionary history of a group of organisms

• shows patterns of descent
• shows common ancestors
• shows evolutionary relationships
• shows info about similar characteristics in closely related species.

Question 6

What is the pholygenic tree vocab

Answer 6

• Each branch point represents the divergence of two species
• Sister Taxa are groups that share a common immediate ancestor

• Rooted tree- branch to represent the last common ancestor of all taxa in a tree
• Basal taxon- diverges early in the history of a group and originates from the common ancestor of the group

• Polytomy a branch from which more than two groups emerge

Question 7

What are homologies

Answer 7

Homologies are phenotypic and genetic similarities due to shared ancestry

Question 8

Difference between homology and analogy

Answer 8

Homology is similarity due to ancestry but analogy is similarity due to convergent evolution aka homoplasies

Example of homologies bat wing and bird wing have forelimbs from a common ancestor.

should consider the explanation that
reflects the most likely sequence of evolutionary events, given rules
about how DNA changes over time

Example of analogs have functional wings developed differently not in a common ancestor between a bat and a bird.

Question 9

What are molecular homologies

Answer 9

Computers and mathematics are used to compare DNA sequences.

Question 10

What are clasidistics and clades?

Answer 10

Clade is a group of species that includes an ancestral species and all it’s descendants
clades can be nested to other clades.

Claudistics is a method of grouping organisms to a common descent.
identified using shared derived characters.

Question 11

What are the clade types ?

Answer 11

•
Clade types
Monophyletic group- has an ancestor species and ALL its descendants- most valid
• Paraphyletic group- has an ancestral species and SOME of the descendants

Polyphyletic group- Group includes distantly related species but does not include their most recent common ancestor

Question 12

give an example of the clade types

Answer 12

monophyletic group is a clade saying we know that common ancestor and what derived from all the descendants. meaning you have ancestors and descentants

paraphyletic group is when a common ancestor known and knows groups a,b,c,d,e but hasn’t studied for g descendants. there is a hole in knowlege.

polyphletic group - A group composed of a collection of organisms in which the most recent common ancestor of all the included
organisms is not included.

group includes distantly related species but dies not include their recent most common
ancestor so there is two or more different
ancestors.

Question 13

what is an example of shared ancesteral chaarcter and shared derived character ?

Answer 13

example of shared ancestor character is all mammals have a backbone and the backbone pre dates mammals branching from all other veterbrates.

example of shared derived characteristics is all mammals have hair but the hair is not found in the ancestors and is unique to mammalian clade.
hair on mammals when compared to other veterbrates .

Question 14

what is the difference and similarities between maximum parisomy and maximum likelihood.

Answer 14

maximum parisomy assumes the fewest evolutionary events and appearance of shared derived characters is most likely. first investigate the simplest explanation that is consistent with the facts.

maximm likelihood should consider the explanation that
reflects the most likely sequence of evolutionary events, given rules
about how DNA changes over time

both help scientists narrow the options when it comes to making a phylogenetic tree.

Question 15

difference between shared ancesteral and shared derived character ?

Answer 15

shared ancesteral character is shared by members of a clade orginated in an ancestor that is not a member of the clade.

shared derived character is an evolutionary novelty unique to a particular clade.

Question 16

difference between ingroup and outgroup?

Answer 16

ingroup is the group of species being studied and shares common traits/ characteristics.

Outgroup is the group that completely unlike all the other organisms . ( outside of a group of taxi being studied) excluded

Question 17

analogous morphology versus homologous morphology ?

Answer 17

analogous morphology structures that have similar functions but with dissimilar evolutionary changes.

homologous morphology is a structure found in two or more different species but derived from a common ancesteral structure.

differences due to heterochrony an evolutionary change in the rate or timing or development of events.

Question 18

molecular homology vs molecular homoplasies ?

Answer 18

molecular homology is when the sequence of genes or DNA is similiar if descended from a common ancestor.
Sequence nucleotides and align comparable genes/DNA regions
Humans and chimpanzees share a similarity in the sequence of amino acids in haemoglobin

molecular homoplasies is a nucleotide or base sequence within two different organisms that may align due to concidental matches but not common ancestor.

Question 19

the difference between gene duplications and gene families

Answer 19

gene duplications increase the number of genes in the genome.

repeated duplications in gene families.
groups of related genes within an organism’s genome, and two types of homologous genes

duplications can be used to share ancestry.
paralogs similiar genes in one species and orthologs similar genes in two species.

Question 20

what is a biological community ?

Answer 20

A biological community is a group of populations living close enough to interact.
all organisms living in asia.

Question 21

interspecific communities vs intraspecific communities ?

Answer 21

Interspecific interactions define the relationship between individuals of species in a community

Competition
Predation
Symbiosis

intraspecific interactions is between members of a species.

Question 22

what is interspecific competition and give an example of it.

Answer 22

occurs when indivisuals of different species compete for a resource that affects their growth and survival.

competitive exclusion is populations with 2 same species compete for the same resources and one species eventually is eliminated .

Question 23

what are the types of competiton

Answer 23

ecological niche is the sum of species use of the abiotic and biotic resources in their environment.

The species’ fundamental niche is the niche potentially occupied by that species

The realized niche is the portion of its fundamental niche actually occupied by the species.

Resource partitioning is the division of environmental resources by coexisting species such that a niche of each species differs significant factors from the niches of all coexisting species.

Question 24

what is character displacement

Answer 24

character displacement is the tendancy or charcteristics to be more divergent in sympatic populations of two species than allopatric.

Question 25

what is predation

Answer 25

prediation is when a predator eat and kills their prey.

predator ambushes, claws, and pursues
preys adaptations behaivoral defenses, alarm calls, morphological and physiological adaptions.

Question 26

what are the types of coloration ?

Answer 26

cryptic coloration is camoflauge blending in.

aposematic coloration is bright warning coloration of animals with effective chemical defenses.

Question 27

what are the types of mimicry.

Answer 27

batesian mimicry a harmless species mimics a harmful one.
mullerian mimicry two unplatable species mimic each other. you avoid all wasps because you know one type of wasps sting.

Question 28

what is symbiosis

Answer 28

an elogical relationship between organisms of 2 different species that live together in direct and intimate contact.

paratism a parasite derives nourishment from the host.

mutualism both species benefits

Obligate mutualism: At least one species has lost the ability to survive without the partner

Facultative mutualism: Both species can survive independently

Commensalism (+/0): Interaction benefits one species but neither helps nor harms the partner species

Question 29

What is species diversity

Answer 29

Species diversity is the number and relative abundance of species in a biological community.

Composed of species richness which is the number of species present in a biological community .

Composed of relative abundance the proportional abundance of different species in a community .
Example vast majority of your species is made up of species A is 80%.

Question 30

What is the difference between tropic structure ( food chain) and food web

Answer 30

Food chains is the pathway along which food energy is transferred.

Food web is the interconnected feeding relationships found in an ecosystem .

Trophic structures is the entirety of how you have feeding relationships amongst different organisms.

Question 31

Keystone species

Answer 31

Species that exert strong control on a community structure by the nature of its ecological roles or niches .

Holds a community together
Not the most abundant

Question 32

Types of Motility

Answer 32

Taxis - directed movement which is the Ability to move away or towards a stimulus.

Chemotaxis- Specifically the movement towards or away from a chemical substance.

away from toxins is negative chemotaxis, ( high level )
towards nutrients, oxygen positive chemotaxis.

Question 33

Dominant species

Answer 33

Dominant species are species that are most abundant or that collectively have the highest biomass and exert powerful control over occurrence and distribution of species.

Question 34

Classification of prokaryotes bs eukaryotes

Answer 34

3 domain classification
Bacteria
Archaea
Eukarya

There are differences between bacteria and archea at the DNA molecular level and differences in the way that they build cellular structure.
Analogous structure of the cell wall has similar functions but different in the way it was built together ( building blocks) in bacteria and archea.

Question 35

Cell wall in prokaryotes

Answer 35

Maintains shape and protection

Prevents cell from bursting in hypotonic environments ( water entering the cell ).

In hypertonic environment prokaryotes lose water shrink away from cell wall inhibit reproduction .

Question 36

Cell wall in bacteria vs archaea

Answer 36

In bacteria it contains peptidoglycan a polymer composed of modified sugars cross linked by short polypeptides.
- encloses entire bacterium
- anchors molecules that extend from cell surface.

In archaea contains polysaccharides and proteins.

Similar outcomes but fundamental building blocks are different.
analogus structures coming from different lineages.

Question 37

What is the purpose of gram staining?

Answer 37

To be able to determine the composition of the cell wall.

Question 38

Gram positive

Answer 38

Delivery of other antibiotics into the cell.

Virulent strains emerge that are resistant to one or more antibiotics.

Sensitive to antibiotics that inhibit peptidoglycan cross linking cell wall no longer functional.

Question 39

Gram negative

Answer 39

Outer membrane impedes entry of antibiotics.

Outer membrane helps protect it from host immune defenses.

Lip-polysaccharides in cell wall are toxic cause fever or shock.

Question 40

fimibriae versus pilli

Answer 40

fimbriae is like an appendage that helps a prokaryotic cell adhere to substrate (surface) or other prokaryotic cells.

pilli are appendages that pull 2 cells together to dna transfer during conjugation. (lasso effect)

Question 41

prokaryotes internal organization

Answer 41

lack organelles ( complex compartmenzilation)

can perform metabolic functions
invaganitation and infolding of plasma membrane

Question 42

motility (flagella)

Answer 42

may be scattered over entire celluar surface or concentrated at both ends .
ATP driven pumps in the motor transport protons out of cell diffusion of protons into cell turned curved hook filament rotates to propel cell.

beacterial and archeal flagella similar in size and mechanism made up of different proteins analogous structures.

Question 43

capsule and slime layer

Answer 43

a capsule is a dense and well defined layer of polysaccharide or protein

slime layer fufills the same role which is adherence and preventing dehydration but the way it’s constructed is different.

Question 44

cell wall sticky layer functions

Answer 44

adhere to the substrate or other individuals in the colony

prevent dehydration
stay protected from host immune diseases .

Question 45

genome

Answer 45

located in a nucleoid a nonmembrane bounded region in the cell where DNA is concentrated .
have plasmids smaller rings of independantly replicating DNA usually carries few genes

f plasmid ( fertility)
r plasmiid ( resistance)

Question 46

reproduction is limited by

Answer 46

exhaustion of nutrient supply
consumed by other organisms
compettition from other microorganisms
accumulation of metabolic wastes ( toxic )

rapid production is key to variation.

Question 47

types of genetic diversity

Answer 47

genetic recombination creates additional diversity by combining DNA from 2 individual cells ( within the same species)

horizontal gene transfer refers to the transfer of genes across species through mechanisms such as transposable elements plasmid exchange, plasmid exchange, viral activity, and perhaps fusion of organisms .

Question 48

types of genetic recombination

Answer 48

transfer is a change in genotype or phenotype due to assimilation of external DNA by a cell.

transduction is a process in which phages (viruses) carry bacterial DNA from one bacterial cell to another

conjugation prokaryotes) is the direct transfer of DNA between two cells that are temporarily joined

Bacteria: Movement in one direction from donor to recipient (not a bi-directional process)

E. coli:

Pilus from donor cell attaches to recipient
Pilus retracts, pulling two cells together

“Mating bridge” formed between two cells; DNA transfers from donor to recipient

Question 49

compare and contrast conjugation, transformation, and transduction.

Answer 49

Conjugation is similar to transduction in that DNA is moved directly from one bacterial cell to another.

In transformation, a bacterium takes up a piece of DNA floating in its environment. In transduction, DNA is accidentally moved from one bacterium to another by a virus. In conjugation,is where genetic matieral is transferred between prokaryotic cells.

there are a few similarities between transformation and transduction: -Both are involved in horizontal gene transfer from one bacterium to another.

Question 50

conjugation

Answer 50

Ability to act as donor cell during conjugation results from presence of DNA called the F factor (f for fertility)

Question 51

conjugation f plasmid

Answer 51

mating bridge forms between f plus (donors) and f minus ( recipents)

One strand of F+ cell plasmid DNA
breaks at arrowhead.
Broken strand peels off and enters F− cell.
Donor and ecipient cells synthesize
complementary DNA strands.
Recipient cell is now a recombinant
F+ cell for each.

f minus recipent —- gets a new f plus donor

f donor gets a f donor.

Question 52

conjugation f factor in chromosome hfr

Answer 52

An Hfr cell forms a
mating bridge with an F− cell.

A single strand of the F factor
breaks and begins to move
through the bridge.

Crossing over can result in exchange of homologous genes.

Enzymes degrade and
DNA not incorporated.
Recipient cell is now a recombinant F− cell.
hfr donor —–> hfr donor
f- recipent goes to a f - recipent cuz it lacks infertility.

Question 53

What is a virus

Answer 53

•A virus is an infectious particle incapable of replicating outside of a cell

Question 54

what are unique types of archaea

Answer 54

Extreme halophiles live in highly saline environments
Extreme thermophiles live in very hot environments
Methanogens are archaea that release methane as a byproduct

Question 55

what are prokaryotes metabolic diversity ?

Answer 55

Phototrophs: Organisms that obtain energy from light

Chemotrophs: Organisms that obtain energy from chemicals

Autotrophs: Organisms that need only CO2 in some form as a carbon source

Heterotrophs: Organisms that require at least one organic nutrient, such as glucose, to make other organic compounds

Question 56

R plasmid antibiotic resistance

Answer 56

• R plasmids carry antibiotic resistance genes
  – The ability to survive treatment with antibiotics

Mutation in a chromosomal gene can confer resistance  altered protein may no longer transport an antibiotic into the cell

Resistance genes carried on R plasmids  enzymes that specifically destroy/hinder effectiveness of certain antibiotics

Natural selection: Cells without resistance die in presence of antibiotic; cells with R plasmid persist

Many R plasmids contain genes which allow DNA transfer by conjugation

Question 57

oxygen in metabolism

Answer 57

– Obligate aerobes
* Need oxygen for cellular respiration

– Obligate anaerobes
* Are poisoned by oxygen
* Use fermentation or anaerobic respiration to make ATP

– Facultative anaerobes
* Can survive with
* or without oxygen

vObligate aerobes absolutely require oxygen for cellular respiration and cannot grow without it

Obligate anaerobes cannot tolerate oxygen (toxic) and must live in a niche deficient in O2

Fermentation: A catabolic process that makes a limited amount of ATP from glucose (or other organic molecules) without an electron transport chain, producing a characteristic end product such as ethyl alcohol or lactic acid

Anaerobic respiration: Utilizes an electronic transport chain but uses substances other than O2 (nitrate ions or sulfate ions) as electron acceptors

Facultative anaerobes use O2 if it is present, but can also utilize fermentation or anaerobic respiration in an anaerobic environment

Question 58

types of symbiotic relationships

Answer 58

Mutualism
– Benefits both host and symbiont
* Commensalism
– One organism benefits
– The other organism is not affected in a significant way
* Parasitism
– One organism benefits- the parasite
* Parasites that cause disease are known as pathogens
– One organism is harmed- the host

Question 59

domains of bacteria

Answer 59

Every major mode of nutrition and metabolism represented

Major groups:

Proteobacteria: Gram Negative

Alpha (Ancestor organism from this group = hypothetical origin of mitochondria)

Beta important in nitrogen fixation and strains causes diseases.

Gamma bacteria that cause salmonella.

Delta can produce spores that can survive droughts.

Epsilon contain many pathogens

Chlamydias: Gram “Negative” (no peptidoglycan); parasites

Spirochetes: Gram Negative; internal, flagellum-like filaments

Cyanobacteria: Gram Negative, photoautotrophs (Ancestor organism from this group = hypothetical origin of chloroplasts)

Gram-positive bacteria: Extremely diverse; include false-positive Mycoplasma

Question 60

what is the structure of a virus ?

Answer 60

Nucleic acid genome can be either DNA or RNA

DNA virus

RNA virus

Either single-stranded or double-stranded molecule

linear or circular.

Question 61

structure of viruses capsid

Answer 61

capsid is the protein shell that encloses a viral genome

Rod-shaped

Polyhedral

Complex assembly

Composed of protein subunits called capsomeres

Each capsid contains limited number of kinds of proteins

Large number of capsomeres assembled to create capsid

capsid protein coat that covers viruses .

Question 62

structure of viruses - capsid shapes

Answer 62

helical virus is a rigid rod shaped capsoid and encases coiled rna genome ( example tobacco mosaic virus)
adenovirus has glycoprotein spike located at each vertex and encloses dna genome .

t even bacteriophages have a complex capsid structure
Elongated icosahedral head encloses DNA

Protein tail apparatus used to attach to bacterial host cell
viruses that infect bacteria.

Question 63

information about viral envelopes

Answer 63

viral envelopes are derived from the protein cell and also contain viral particles.

envelope can surrond capsules of a viral particle.

Question 64

what is a host range and define a host range.

Answer 64

host range of a virus is the limited number of species whose cells can be infected by a particular virus

Recognition systems: Virus has specific interaction between viral surface proteins and specific receptor molecules on the host cell

Wide range: Infect multiple species

West Nile virus: mosquitos, birds, horses, humans

Narrow range: Infect single species

Measles: humans only

Specific cell type within multicellular eukaryote

HIV: CD4+ T cells

Specific interaction between host cell and virus the result of evolution

Viruses have been found that infect every form of life

Question 65

structure of viral envelope

Answer 65

The viral envelope is derived from the host cell membrane and cloaks the capsid

Host phospholipids and membrane proteins

Viral proteins and glycoproteins

May also help package viral enzyme molecules

example of viral envelope influenza virus

Question 66

the steps of replication ?

Answer 66

Specific attachment

2. Penetration

Tail apparatus injection (T-even phages)

Endocytosis

Fusion of viral envelope with host plasma membrane

3.Synthesis

Viral genome

Capsid proteins

4.Spontaneous assembly

5. Release of new particles

Question 67

lyctic cycle

Answer 67

A phage replicative cycle that culminates in death of the host cell is called a lytic cycle

A phage that replicates using only a lytic cycle is called a virulent phage

Question 68

lysogenic cycle

Answer 68

A lysogenic cycle allows replication of the phage genome without destroying (lysing) the host – but retains the ability to generate active phages via a lytic cycle

A phage capable of replicating within a bacterium using both modes (lytic and lysogenic) is called a temperate phage

Integrated viral DNA is called a prophage

Prophage genes replicated along with host genome

Prior to entering lytic cycle, prophage excised from bacterial chromosome, yields two separate circular DNA molecules

Question 69

plant viruses

Answer 69

vexternal source

Virus must penetrate plant’s outer protective layer of cells

Associated with tissue damage by wind, injury, herbivores (insects also carriers)

Vertical transmission refers to infection inherited from a parent

Asexual propagation (cuttings)

Sexual reproduction (infected seeds)

Infection can spread through plant via plasmodesmata, the cytoplasmic connections that penetrate the walls between adjacent plant cells

Question 70

animal viruses

Answer 70

Animal viruses classified into 6 classes based on genome:

dsDNA double strnded

ssDNA single stranded

dsRNA

ssRNA (serves as mRNA)

ssRNA (serves as template for mRNA synthesis)

ssRNA (serves as template for DNA synthesis)

Question 71

retrovirus replication

Answer 71

Class VI RNA animal viruses are called retroviruses

Replicate by transcribing RNA into DNA and insert the DNA into a cellular chromosome

Utilize an enzyme called reverse transcriptase which transcribes an RNA template into DNA, creating the RNA  DNA (retro) information flow

Reverse transcriptase is packaged into the viral particle along with the viral genome

Human Immunodeficiency Virus (HIV)

Contains two identical molecules of ssRNA and two molecules of reverse transcriptase

Viral infection causes Acquired Immunodeficiency Syndrome (AIDS)

Question 72

compare and contratst the lyctic and lasogenic cycle.

Answer 72

The lytic cycle involves the reproduction of viruses using a host cell to manufacture more viruses; the viruses then burst out of the cell. The lysogenic cycle involves the incorporation of the viral genome into the host cell genome, infecting it from within.

Both lytic cycle and lysogenic cycle are mechanisms of viral reproduction. Both lytic cycle and lysogenic cycle only occur inside a host cell. Both lytic cycle and lysogenic cycle may produce thousands of original copies of the original virus.