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BIS 2C Midterm 1 > Lecture Slides 1-10 > Flashcards

Lecture Slides 1-10 Flashcards

1
Q

phylogeny

A

unifying principle that all organisms are linked to one another through their shared evolutionary history

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2
Q

how old is the tree of life?

A

~3.8 billion years

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3
Q

What do phylogenetic trees allow us to do?

A

Trace the history of changes in morphology, behavior and geographical distribution of a group of organisms

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4
Q

What is speciation?

A

process where one species gives rise to two descendant species

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5
Q

What is a bifurcating tree?

A

Trees where each internal node gives rise to two descendant branches

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6
Q

What is a polytomy?

A

Nodes that have three of more descendant branches. Often reflect uncertainty about phylogenetic relationships

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7
Q

what is the relationship between the number of monophyletic groups and number of internal nodes in a tree?

A

x=y

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8
Q

What are homologous traits?

A

those that are inherited from a common ancestor

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9
Q

What is phylogeny classification?

A

the naming of taxa and their placement in a hierarchical arrangement

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10
Q

Modern biological classification

A

species: binomial name (genus and species)
groups of species: single name and placed in a ranked hierarchy

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11
Q

What is a cladogram?

A

only the relative branch order is depicted. no meaning to branch lengths

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12
Q

What is a phylogram?

A

Branch length is proportional to amount of character change

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13
Q

What is a chronograph?

A

Branch length is proportional to time

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14
Q

What is parsimony?

A

The least amount of change in character states

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15
Q

What is a transition?

A

A to G, C to T
purine to purine, pyrimidine to pyrimidine

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16
Q

What is a transversion

A

A to C, A to T, G to C, G to T
purine to pyrimidine

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17
Q

What is synonymous substitution?

A

no change in the encoded amino acid

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18
Q

What is non-synonymous substitution?

A

change in the encoded amino acid

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19
Q

what is net diversification?

A

number of extant species
a function of the speciation and extinction rate

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20
Q

If sister species (A and B) are 6% divergent in their DNA and the DNA diverges at 1.5% per million years, how long ago did these two species split from their most recent common ancestor?

A

2 million years
(3%/ 1.5= 2 million years)

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21
Q

phylogeny and applied biology: medicine

A

can learn about the origins of disease, process of disease transmission

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22
Q

phylogeny and applied biology: conservation

A

identify previously unsuspected diversity, reveal major lineages within a larger clade

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23
Q

Darwin

A

Tree of life

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24
Q

Ernst Haechel

A

Three kingdoms

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25
Robert Whittaker
five kingdoms
26
microsporidium characteristics
intracellular parasite no mitochondria nucleus
27
What are some microbe problems?
some traits not clear if homologous other traits of limited utility universal homologies
28
LUCA
last universal common ancestor
29
Why use rRNA
- everybody has it - contains both highly conserved and variable regions - not laterally transferred between organisms - large and growing database
30
What did Carl Woese contribute?
discovery of archaea and three domains of life
31
Eocyte tree
hypothesis that eukaryotes evolved from a group called eocytes
32
Prokaryotes are considered
paraphyletic
33
prokaryotes are
unicellular lack a nucleus and cytoskeleton have no membrane enclosed organelles
34
The primary form of cell division and reproduction in prokaryotes is known as
binary fission
35
What is binary fission?
Asexual reproduction and produces two identical daughter cells
36
What are plasmids?
extra chromosomal DNA. small circular DNA molecules
37
3 ways to introduce genetic variation
mutations and selection plasmids lateral gene transfer
38
What are the three processes of lateral gene transfer?
conjugation transformation transduction
39
What is conjugation?
plasmid or piece of chromosome can be transferred
40
What is transformation?
organisms takes and incorporates exogenous DNA, resulting in a genetic alteration
41
What is transduction?
transferring genetic material from one cell to another using a virus
42
LGT vs sexual reproduction
LGT usually involves only a part of a genome LGT often not linked to reproduction LGT has multiple mechanisms LGT can occur across large phylogenetic distances
43
How does LGT affects phylogeny?
LGT complicates phylogenetic analysis
44
Diversity in form: shape
coccus: spherical rod: cylindrical spirillum: spiral
45
gram positive
have a uniformly dense cell wall consisting primarily of peptidoglycan
46
gram negative
very thin peptidoglycan layer and an outer membrane, together make up the cell envelope
47
gram stain
application of - crystal violet - iodine - alcohol wash - counterstain
48
diversity of form: membrane lipids
archaeal phospholipids: ether linked and branched prokaryotic or eukaryotic phospholipids: ester linked and unbranched
49
anaerobes
do not use and may even be killed by oxygen
50
aerotolerant anaerobes
can tolerate the presence of oxygen, even though they cannot use it
51
facultative
organisms can live with or without oxygen
52
aerobes
require oxygen to live
53
microaerophiles
aerobes that can use oxygen only when it is present at levels reduced from that in the air
54
photoautotrophs
energy: light carbon: carbon dioxide
55
photoheterotrophs
energy: light carbon: organic compounds
56
chemoautotrophs
energy: inorganic substances carbon: carbon dioxide
57
chemoheterotrophs
energy: organic compounds carbon: organic compounds
58
primary productivity
photosynthesis- plants and microbes
59
elemental cycles
microbes control global elemental cycles
60
agriculture
microbes important in agriculture
61
What are extremophiles?
organisms that can thrive in extreme environments
62
What domains are thermophiles found in?
bacteria and archaea
63
example of extremophiles
temperature (thermophile) radiation (radiophile) pressure (barophile)
64
adaptation require changes in most/ all genes in the genome
result of convergent evolution
65
presence of specific metabolic processes
results of convergent evolution or lateral gene transfer
66
great plate count anomaly
of microbial cells under a microscope is much greater than the # of colonies in a Petri dish from that same sample
67
What is a virus?
noncellular infectious agents that can replicate only inside living cells of organisms
68
What is a virion?
extracellular form of a virus that contains either a DNA or RNA genome
69
What is a capsid?
proteins that surround or protect the genetic element
70
What is a nucleocapsid?
complete complex of nucleic acid and protein packaged in the virion
71
What is an enveloped virus?
virus that contains additional layers around the nucleocapsid
72
main morphological types
helical icosahedral complex
73
tobacco mosaic virus
codes for 4 genes helical symmetry
74
covid-19
approximately 50 genes
75
mimivirus
codes for ~1000 genes
76
What are plaques?
clear zones that develop on lawns of host cells
77
What is the virus life cycle?
attachment penetration replication self assembly exit
78
host entry: fungal and plant viruses
enter the cell through wounds
79
host entry: bacterial viruses
inject their nucleic acids directly into the host cell
80
host entry: animal viruses
attach to the cell and enter through endocytosis
81
What is a lytic cycle?
involves destruction of the host cell. virus replication occurs independent from the host
82
What is a lysogenic cycle?
viral DNA is incorporated into the host cell's chromosome. virus DNA replication is dependent of the host
83
3 main hypotheses of viruses
relics from a pre-cellular world escaped portions of cellular organisms extremely derived and reduced cellular organisms
84
impact of viruses in the ocean
10^23 viral infections occur every second amount of carbon in viruses is ~75 million blue whales
85
What is symbiosis
range of interactions between two or more organisms
86
What is a parasite?
an organism living on or in another organism and obtaining its nutrients and energy at the expense of the second organism
87
What is a pathogen?
biological agent that causes disease to its host
88
What is a disease?
injurious physiological activity caused by the continuous irritation by a primal causal factor and expressed in characteristic pathological conditions called symptoms
89
What is an infectious disease?
disease caused by a pathogen which can spread from a diseased to a healthy host
90
What is a noninfectious disease?
disease that is caused by an environmental or host factor
91
high income countries
low % of deaths related to infectious diseases
92
low income countries
high % of deaths related to infectious diseases
93
zoonotic disease
infectious disease that can be transmitted from animals to humans
94
cholera outbreak
sequence of 1588 conserved genes
95
mutualism
both species benefit
96
commensalism
one species benefits, the other remains neutral
97
What percentage of cells in our body are human cells?
50%
98
Where are the human microbial communities?
skin conductive oral cavity intestinal tract upper respiratory tract urogenital tract
99
human microbiome
variation between person to person body sites are similar in everyone when classified by bacterial species: they look very different when classified by functional capabilities: look more similar
100

BIS 2C Midterm 1 (3 decks)

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