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Evolutionary Biology > Final Term Lab Exam > Flashcards

Final Term Lab Exam Flashcards

(65 cards)

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1
Q

A classification of databases applicable both to nucleic acid sequences and protein sequences

A

Sequence Databases

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2
Q

A classification of databases applicable only to protein

A

Structure Databases

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3
Q

A classification of databases which contains information of the sequence or structure alone

A

Primary Database
- Swiss-Prot
- PIR
- GenBank
- DDB
- PDB

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4
Q

A classification of databases which contains derived information from the primary database

A

Secondary Database
- Prosite
- Pfam

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5
Q

A classification of databases which amalgamates a variety of different primary database sources which removes the need to search multiple sources

A

Composite Database
- NCBI
- ExPASy

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6
Q

The 3 protein databases that make up UniProtKB

A
  • Swiss-Prot
  • TrEMBL
  • PIR-PSD
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7
Q

A popular sequence-alignment and database-scanning program

A

FASTA

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8
Q

They created FASTA in 1988

A
  • W.R. Pearson
  • D.J. Lipman
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9
Q

The 4 parts found in a GenBank entry

A
  • Locus Name
  • Reference Section
  • Features Section
  • Sequence Section
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10
Q

A sequence comparison tool that quickly tells you which of the other known proteins out there has a sequence similar to yours

A

BLAST
(Basic Local Alignment Search Tool)

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11
Q

The 3 purposes of BLAST

A
  • prediction of protein function
  • 3D structure and domain organization
  • identification of homologues in other organisms
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12
Q

An assessment of the statistical significance of the score

A

E-value

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13
Q

These involve lining up many similar proteins side by side for the sake of comparison

A

Multiple Alignments

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14
Q

He discovered the skeleton of archaeopteryx in 1861

A

Richard Owen

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15
Q

He argued that archaeopteryx bore a striking resemblance to small dinosaurs like Compsognathus

A

Thomas Henry Huxley

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16
Q

He discovered the fossils of Deinonychus

A

John Ostrom

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17
Q

He and colleagues argued that dinosaurs grew fast and had active metabolisms like extant birds

A

Robert Bakker

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18
Q

He and colleagues used cladistics to place birds within the family tree of dinosaurs

A

Jacques Gauthier

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19
Q

The overarching pattern of evolution observed in birds

A
  • Feathers and flight are only seen in birds with dinosaur ancestors
  • Rapid growth and beaks are absent in the earliest birds
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20
Q

The only taxon with asymmetrical hindlimb feathers

A

Microraptor

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21
Q

The 2 primary groups of birds

A
  • Palaeognathae
  • Neognathae
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22
Q

The 6 camouflage concepts

A
  • Background Matching
  • Disruptive Coloration
  • Self-Shadow Concealment and Obliterative Shading
  • Distractive Markings
  • Masquerade
  • Decoration
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23
Q

The 3 costs and constraints on plant camouflage evolution

A
  • Physiology
  • Camouflage Efficacy
  • Selection Strength
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24
Q

The 5 factors that may promote plant camouflage evolution

A
  • Heterotrophism
  • Open Habitats
  • Small Individual Size
  • Fragile Structure
  • Specialized Enemies
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25
An important evolutionary strategy that allows plants to avoid detection by predators and to better exploit different habitats and resources
Plant Camouflage
26
A mammal that has transitioned from terrestrial to aquatic lifestyle
Whale
27
Fossil records show that early whales [...], but over time they evolved into [...] with [...] and [...] behaviors
- had four legs and walked on land - efficient swimmers - complex communication - social
28
The presence of [...] in whales is considered to be strong evidence for the theory of evolution
vestigial pelvic bones
29
Cetaceans were found to be more closely related to [...] than other groups of mammals
Even-toed ungulates
30
The 3 morphological evolutions of cetaceans
- Limbs > Flippers - Nostrils > Blowholes - Tails > Flukes
31
The discovery of [...] showed how early cetaceans were adapting to an aquatic lifestyle
Ambulocetus
32
A mycoheterotrophic monocot plant discovered in Japan and was presumed to be extinct
*Thismia kobensis*
33
Its rediscovery after three decades has significantly advanced our understanding of fairy lanterns
*Thismia kobensis*
34
A detailed morphological investigation suggested that *Thismia kobensis* is indeed the closest relative of [...]
*Thismia americana*
35
A type of cell that provides physical and chemical support to neurons and maintains their environment
Glial Cells
36
The [...] of the brain is composed of axons to form neural networks
white matter
37
The estimated storage capacity of the brain
1.25 * 10^25 bytes
38
Increase in volume of white matter in the brain from [...] in a monkey to [...] in primates led to improved function
- 22% - 65%
39
[...] in axons increase the transmission across the brain into a near double
Myelination
40
The evolution of the human brain is limited by [...]
energetic constraints and neural processing time
41
The 3 factors that may cause the evolution of the human brain
- Environmental Factors - Natural Selection - Limits
42
The oldest known hominin fossil
*Ardipithecus ramidus*
43
A hominin at 1.8 Ma suggested to be fully bipedal but others argue it had arboreal adaptations
*Homo habilis*
44
A hominin at 4 Ma suggested to be fully bipedal but others argue it had a combination of terrestrial and arboreal locomotion
*Australopithecus afarensis*
45
A hominin at 3.6 Ma suggested to have a mosaic of locomotion
*Australopithecus africanus*
46
The hypothesis on the evolution of bipedalism
- Brachiation - Vertical Climbing - Knuckle-walking - Obligate Bipedal
47
A hominin that showed high sexual dimorphism; smaller individuals were better at climbing while larger individuals were better at walking on two legs
*Australopithecus afarensis*
48
The presence of a [...] is the evolutionary key feature of *Homo sapiens* which separates them from their ancestors
protruding chin
49
The analysis of Australopithecine [...] suggest that there has been a shift in their dietary capacities
teeth
50
The 3 models that explain the reduction phenomenon in the masticatory region of humans
- probable mutation effect - increasing population density effect - selective compromise effect
51
The critical change in human evolution 40,000 years ago which resulted in the development of human civilization, believed to be the result of the appearance of spoken complex language
The Great Leap Forward
52
The evolutionary changes believed to be the cause of sleep apnea
pharyngeal collapse
53
A system that differed from other mammals for having communication as a dominant function
Human Oropharyngeal System
54
The evolution of [...] was closely related to the development of the brain by stressing that language provides communication and coordination
maxilla mandibular system
55
The 3 factors that caused masticatory evolution of humans
- use of tools and fire - changing course of diet - vocabulary and speech
56
Sexual differences in body size or morphology may evolve for [...]
ecological causes
57
The 8 topics discussed
- On the Evolution of Human Jaws and Teeth: A Review - The Origin and Diversification of Birds - Ecological Causes for the Evolution of Sexual Dimorphism: A Review of the Evidence - Plant Camouflage: Ecology, Evolution, and Implications - The Ecological Rise of Whales Chronicled by the Fossil Record - The Rediscovery of an Ethereal Fairy Lantern After Three Decades Brightly Illuminates Their Mysterious Past - A Review on Brain Evolution and Development - Fossils, Feet, and the Evolution of Human Bipedal Locomotion
58
What does the **Summary** box in NCBI show?
Information about the organism and gene ID
59
What does the **Genomic Context** in NCBI show?
What other genes are in the genomic neighborhood and allow inferences about what role a gene plays
60
What does the **Genomic Regions...** in NCBI show?
Information about the transcription (green bar) and translation (red bar) products of the gene
61
What is the function of dihydrofolate reductase?
Involved in tetrahydrofolate biosynthesis; required for respiratory metabolism
62
What is the function of lactate dehydrogenase?
Catalyzes the reduction of lactate into pyruvate using NAD+ as cofactor
63
A bioinformatics tool that gives numerous useful information about a protein based on its sequence
ProtParam - MW - Extinction Coefficient - pI
64
A bioinformatics tool that allows direct comparison of two or more sequences and look for similarities and differences
Multiple Sequence Comparison by Log-Expectation (MUSCLE)
65
How many amino acids are present in: a) *B. subtilis* str. 168 b) *E. coli*
- 321 - 324

Evolutionary Biology (6 decks)

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