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BIO115 > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

Phylogeny

A

shared common ancestry

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2
Q

Why do we need a species system?

A

Organization Communication Different contexts and languages

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3
Q

What are the requirements for life?

A

Carbon source, energy source, water, nitrogen, phosphorus, cell membrane

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4
Q

What are the environmental characteristics for life?

A

Temperature, O2 level, pressure, salt concentration, pH

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5
Q

Steps to life

A
  1. Abiotic synthesis of organic molecules 2. Building polymers from monomers 3. Packaging polymers, separating self from non-self (cell membrane) 4. Self-replication and inheritance
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6
Q

Miller-Urey experiment

A

using electricity and atmospheric gasses to produce amino acids

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7
Q

shock synthesis

A

comet impact creating organic molecules

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8
Q

montmorillonite

A

clay that may have catalyzed the formation of RNA polymers

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9
Q

RNA World Hypothesis

A

early forms of life used RNA as their genetic material

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10
Q

What did protocells use to protect their RNA?

A

Phospholipids

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11
Q

Vesicle vs. Micelle

A
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12
Q

What is a cell membrane important for?

A

Establishing protein gradients

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13
Q

RNA replicase

A

makes RNA from a template

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14
Q

Why does the use of DNA for long term storage make sense?

A

More chemically stable than RNA (chemically selected), mutates less

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15
Q

Where could life have started?

A

Surface, deep sea vent, geyser

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16
Q

Who could have been the first replicates?

A

Viruses

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17
Q

What are the oldest fossils we have?

A

Cyanobacteria Not the oldest form of life

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18
Q

Are prokaryotes simple?

A

Nope just specialists

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19
Q

What is the difference between metabolic processes in prokaryotes and eukaryotes?

A

Eukaryotes do things pretty much the same (chemoheterotroph and/or photoautotroph) Prokaryotes’ processes are diverse and complicated

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20
Q

What is the size difference between prokaryotes and eukaryotes?

A

Prokaryotes are 1/10 the size of eukaryotes

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21
Q

How do prokaryotes and eukaryotes move molecules inside the cell?

A

eukaryotes: endomembrane system prokaryotes: diffusion

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22
Q

Organelles

A

membrane-bound sub-cellular structure eukaryotes have a common set, prokaryotes don’t

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23
Q

Why can’t the biological species concept be applied to prokaryotes?

A

Asexual reproduction

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24
Q

How do we ID bacteria in clinical labs?

A

metabolic tests, not very useful for novel species

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25
Q

Carl Woese

A

proposed using 16S rRNA gene for molecular phylogenies Led to discovery of archaea domain

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26
Q

What are genetic changes caused by?

A

(A)sexual reproduction mutations horizontal gene transfer

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27
Q

Why are rRNA genes useful?

A

Every cell has them There are regions that are highly conserved and regions that are highly variable

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28
Q

MLST

A

Multi-locus sequence typing analyze several housekeeping genes

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29
Q

At the molecular level, archaeal proteins are more similar to:

A

eukaryotes, not bacteria

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30
Q

Difference in membrane lipids in archaea?

A

Archaea have ether linkages, can have bi- or monolayer Eukaryotes and bacteria have bilayer ester linkages

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31
Q

Difference between G+ and G- bacteria?

A

G+ has thick peptidoglycan layer and thin lipid layer G- has thin peptidoglycan layer and thick lipid layer

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32
Q

Do archaea have a cell wall?

A

Some do, they are highly variable with diverse components and no outer membrane

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33
Q

Why don’t we know more about archaea?

A

Little research money since they aren’t infectious

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34
Q

How did the G+ state come about?

A

Convergent evolution, evolved independently

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35
Q

Why don’t we change the names of microorganisms?

A

Healthcare Consistency Keeping track of where microbes go

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36
Q

Archaea shapes

A

round, rod, spiral

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37
Q

Swarmers and stalkers

A

Caulobacter crescentes In swarmer form, uses motile flagella to move Once it finds a surface, attaches via stalk and loses flagella Stalk cell divides to produce new swarmers

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38
Q

Akinete

A

cyanobacteria dormant cell type thick cell wall storing lots of food vegetative cells actively conduct photosynthesis and reproduce, akinetes don’t

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39
Q

endospores

A

dormant cell type extremely resistant to environmental damage formed when conditions go bad when dividing, makes 1 new endospore instead of 2 new cells usually G+

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40
Q

heterocysts

A

cyanobacteria, not dormant Nitrogen-fixers anaerobic cell in an aerobic environment since oxygen inhibits n-fixing enzymes 3 layered cell wall and degradation of photosystem 2

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41
Q

Mycococcus Xanthus

A

hunts in predatory wolfpack forms fruiting bodies when they run out of food

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42
Q

Magnetoglobus Multicellularis

A

Found in groups of 10-40 cells Removing one cell kills the rest Each cell contains about 80 bullet-shaped magnetosomes Displays negative phototaxis

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43
Q

Anammoxosome

A

membrane-bound organelle that uses ammonia for energy special lipids in membrane (“ladderanes”) protect rest of cell from harmful chemicals

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44
Q

Do eukaryotes outweigh prokaryotes?

A

No, prokaryotes also outnumber eukaryotes

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45
Q

Termite digestive system

A

termites can’t digest cellulose protists break down wood into smaller pieces bacteria (endosymbiotes) secrete digestive enzymes to break down cellulose Archaean methanogens produce methane as a food source for bacteria

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46
Q

Humane Microbiome Project

A

National Institute of Health project aimed at developing a reference set of microorganisms, disease state vs. healthy state

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47
Q

How do we sample diversity?

A

Metagenomics, meta-metabolomics

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48
Q

How do we acquire our microbiomes?

A

Caregivers Environment (breathing in, eating) Medications can disturb it

49
Q

Steps to biofilm formation

A

adherence to surface monolayer formation and production of slime microcolony formation, other species join formation of polysaccharide “mushroom”, some cells split off and revert to planktonic cells

50
Q

Methanogens

A

obligate anaerobes, only need CO2, N2, and H2O

51
Q

What is the electron donor in oxygenic photosynthesis?

A

H2O

52
Q

What is the electron donor in anoxygenic photosynthesis

A

H2S

53
Q

Difference between chlorophyll a and b?

A

Chlorophyll a is found in all photosynthetic eukaryotes and cyanobacteria Chlorophyll b is the synapomorphy for viridiplantae

54
Q

Phycobilins

A

pigments that help absorb wavelengths not absorbed by chlorophyll a and b, useful in low light situations like deep underwater

55
Q

Chlorosomes

A

organelle found in green sulfur bacteria Obligate anaerobes, live in extremely low light Photoheterotrophs that use light for energy and carbon to build cells

56
Q

Types of gene transfer

A

vertical - parent to offspring horizontal - transfer between cells of the same generation

57
Q

Types of horizontal gene transfer

A

transformation, conjugation, transduction

58
Q

Transformation

A

cell picks up DNA from environment that was released when a cell died Can be forced in the lab by damaging a cell, will cause it to pick up DNA near it need way of killing those that didn’t pick up new DNA, antibiotic resistance usually included

59
Q

Conjugation

A

One cell directly transfers DNA to another using Fertility pilus Copy plasmid and send to recipient

60
Q

Transduction

A

virus infects cell A, DNA from cell becomes part of viral particle and spreads with it virus infects cell B which incorporates DNA from cell A into genome

61
Q

Why is horizontal gene transfer important?

A

foundation of genetic engineering medicine, research viral transfer of DNA results in 15-20% of cancers

62
Q

Who and what disproved spontaneous generation?

A

Louis Pasteur and Germ Theory of Disease

63
Q

Robert Koch

A

developed organized method for demonstrating link between microbe and illness (Koch’s postulates)

64
Q

Koch’s postulates

A
  1. Organism must present in all states of disease 2. Isolate pure culture of microbe 3. Observe disease characteristics in test subject 4. Isolate same pure culture from test subject
65
Q

How did Koch’s postulates hold back virology?

A

They were followed too strictly

66
Q

How was tobacco mosaic virus isolated?

A

First thought to be toxin, crushed and filtered leaves resulted in filtered water harming plants but not leaves, thought that filter stopped bacteria Then realized that it replicated in plants when any dose produced same results, didn’t follow dose response curve

67
Q

Are viruses living organisms?

A

No cell membrane No growth or metabolism Do replicate and evolve Require a host organism to replicate

68
Q

Components of virus

A

DNA or RNA genome Capsid - protein coat Envelope - typically protein, not always present, glycoprotein spikes for attachment

69
Q

Types of viral envelopes

A

Helical Polyhedron Enveloped Complex

70
Q

How do viruses limit host cell diversity?

A

Kill 1/2 of all bacterial cells each day Keep diseases at bay

71
Q

Emerging viruses with a threat to humans

A

SARS from Asia MERS from middle east

72
Q

Steps to viral replication

A

Attachment Entry (Integration) of viral genome into host genome Synthesis of viral proteins and genome Assembly Release

73
Q

Helper-T cells

A

Cause body to produce antibodies, activates cytotoxin cells to destroy infected cells, attacked by HIV

74
Q

Acute infection

A

short-lived, get sick and get better, common cold

75
Q

chronic infection

A

get sick and never get cured, Hepatitis C

76
Q

latent infection

A

get sick, symptoms get better, symptoms show up again later, can last for a lifetime, Herpes, HIV

77
Q

Phage therapy

A

using bacteriophages to fight infection

78
Q

What causes chronic and latent infections to show up?

A

Injury or harm to host cell can trigger replication

79
Q

How can viruses cause cancer?

A

If they integrate their DNA close to genes controlling growth, cells can replicate uncontrollably

80
Q

oncogenes

A

genes that normally are tightly controlled and related to growth, viruses can cause them to lose control and cause cancer

81
Q

Similarities and differences between bacteria, archaea, and eukaryotes in:

Chromosome structure

Nucleosome structure

Chromosome segregation

Introns in genes

Ribosome number

Initiator tRNA

Operons

Capping of mRNA

RNA Polymerases

Promotion of Structural Genes

Cell compartmentalization

Membrane Lipids

A
82
Q

What is the defining characteristic of eukaryotes?

A

nucleus

83
Q

nucleus

A

membrane bound organelle containing DNA, site of RNA synthesis

must have ribosomes to be true nucleus

exists only in eukaryotes

84
Q

What is the difference in RNA synthesis between prokaryotes and eukaryotes?

A

Prokaryotes have simulataneous transcription and translation all in cytoplasm, no introns/exons

Eukaryotes transcribe RNA in nucleus, then introns stay and exons recombine and go to cytoplasm to create proteins

85
Q

Cons of using nucleus for protein synthesis

A

DNA takes up a lot of space, can be problematic with many or large chromosomes

86
Q

Endosymbiosis

A

theory that mitochondria and chloroplasts originated from bacteria that took up residence in a primordial eukaryotic cell

87
Q

Anagenesis

A

Straight line from A to B

New species from many small accumulations over time

88
Q

Cladogenesis

A

Divergence between species over time, Darwin’s finches with geographical division

89
Q

Reticulate evolution

A

Sharing of genetic material results in new species

90
Q

Types of reticulate evolution

A

Horizontal gene transfer - a few genes move

Hybridization - entire genome moves

endosymbiosis - entire cell moves

91
Q

Sites of DNA in a cell

A

nucleus, mitochondria, chloroplasts

92
Q

Sites of RNA synthesis in a cell

A

cytoplasm, mitochondria

93
Q

Mitochondria function

A

oxidize food residues to produce usable energy

94
Q

Chloroplast function

A

reduce CO2 molecules to produce sugar

95
Q

Pros and Cons of Mitochondria

A

Pros:

More energetic organisms, gave rise to predators

19x more energy, metabolic efficiency

Cons:

Habitat restrictions, need oxygen

96
Q

Pros and cons of chloroplasts

A

Pros:

Energy independence

Less energetic demands

More resources for reproduction, more offspring produced

Cons:

Makes you into food

Habitat restrictions, need sunlight

97
Q

T/F: eukaryotic plastids are more closely related to their cell’s nucleus than bacteria

A

False

98
Q

Cyanobacteria and plastids form a:

A

monophyletic grouping (clade)

99
Q

What group are we a member of? What else is in that group?

A

Opisthokonta, fungi and metazoa

100
Q

Where did the first endosymbiotic capture occur?

A

Archaeplastida

101
Q

Parasymbiosis

A

Two organisms undergo symbiotic relationship side by side

102
Q

Who controls each membrane in archaeplastida plastids?

A

Nucleus controls outer

Plastid controls inner

103
Q

Glaucophyte

A

Plastid contains peptidoglycan (cell wall of bacteria) in membrane

Only chlorophyll a

104
Q

Requirements for endosymbiosis

A
  1. Obligate relationship, mixing of DNA caused by horizontal gene transfer
  2. Cell, not organism, living inside another cell
  3. Passed through vertical transmission
105
Q

Cryptomonads

A

Provide evidence for secondary endosymbiosis

cyanobacteria inside eukaryote inside eukaryote

3 sets of genetic material in one cell

106
Q

Dinoflagellates

A

Show secondary and tertiary levels of endosymbiosis

Plastid can’t survive without cell, cell can’t survive without plastid (obligate relationship)

107
Q

Hatena

A

When they divide, 50% of cells are photosynthetic and 50% are heterotrophs

In the wild, they eat nephroselmis and use their chloroplasts and eyespot for energy

If digested, swells up feeding hole so it can only be photosynthetic

108
Q

synapomorphy

A

evidence for a monophyletic group

presence of a plastid in archaeplastida

feature that only that group has from a common ancestor

109
Q

3 clades of archaeplastida

A

viridiplantae

rhodophyta

glaucophyta

110
Q

What is the synapomorphy for chlorophytes?

A

Chlorophyll b

111
Q

Chlamydomonas

A

Vegetative, normal states are haploid

Enters a sexual reproductive state when environment toughens, 2 haploids combine to form diploid zygote

Undergoes meiosis to produce 4 new cells

112
Q

Isogamy

A

two identical, undifferentiated gametes

113
Q

Oogamy

A

two different gametes come together to form zygote

114
Q

iteroparity

A

ability to reproduce more than once

115
Q

semelparity

A

organisms that only reproduce once in lifetime

116
Q

genetic load

A

recessive, harmful alleles building up in a population’s gene pool

117
Q

two primary synapomorphies of streptophytes and what they allow

A

phragmoplasts

rosette proteins

allowed for the development of life on land

118
Q

Phragmoplasts

A

microtubular assemblages that move chromosomes, guide movement in cell, arrange material

119
Q

Difference between phragmoplasts and phycoplasts

A

Phragmoplasts let cells fully divide, true multicellularity

Phycoplasts keep cells connected but still individuals so only allows unicells and colonies

BIO115 (6 decks)

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