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Evolutionary Biology > Final Term Lab Exam > Flashcards

Final Term Lab Exam Flashcards

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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
Q

An important evolutionary strategy that allows plants to avoid detection by predators and to better exploit different habitats and resources

A

Plant Camouflage

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26
Q

A mammal that has transitioned from terrestrial to aquatic lifestyle

A

Whale

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27
Q

Fossil records show that early whales […], but over time they evolved into […] with […] and […] behaviors

A
  • had four legs and walked on land
  • efficient swimmers
  • complex communication
  • social
28
Q

The presence of […] in whales is considered to be strong evidence for the theory of evolution

A

vestigial pelvic bones

29
Q

Cetaceans were found to be more closely related to […] than other groups of mammals

A

Even-toed ungulates

30
Q

The 3 morphological evolutions of cetaceans

A
  • Limbs > Flippers
  • Nostrils > Blowholes
  • Tails > Flukes
31
Q

The discovery of […] showed how early cetaceans were adapting to an aquatic lifestyle

A

Ambulocetus

32
Q

A mycoheterotrophic monocot plant discovered in Japan and was presumed to be extinct

A

Thismia kobensis

33
Q

Its rediscovery after three decades has significantly advanced our understanding of fairy lanterns

A

Thismia kobensis

34
Q

A detailed morphological investigation suggested that Thismia kobensis is indeed the closest relative of […]

A

Thismia americana

35
Q

A type of cell that provides physical and chemical support to neurons and maintains their environment

A

Glial Cells

36
Q

The […] of the brain is composed of axons to form neural networks

A

white matter

37
Q

The estimated storage capacity of the brain

A

1.25 * 10^25 bytes

38
Q

Increase in volume of white matter in the brain from […] in a monkey to […] in primates led to improved function

A
  • 22%
  • 65%
39
Q

[…] in axons increase the transmission across the brain into a near double

A

Myelination

40
Q

The evolution of the human brain is limited by […]

A

energetic constraints and neural processing time

41
Q

The 3 factors that may cause the evolution of the human brain

A
  • Environmental Factors
  • Natural Selection
  • Limits
42
Q

The oldest known hominin fossil

A

Ardipithecus ramidus

43
Q

A hominin at 1.8 Ma suggested to be fully bipedal but others argue it had arboreal adaptations

A

Homo habilis

44
Q

A hominin at 4 Ma suggested to be fully bipedal but others argue it had a combination of terrestrial and arboreal locomotion

A

Australopithecus afarensis

45
Q

A hominin at 3.6 Ma suggested to have a mosaic of locomotion

A

Australopithecus africanus

46
Q

The hypothesis on the evolution of bipedalism

A
  • Brachiation
  • Vertical Climbing
  • Knuckle-walking
  • Obligate Bipedal
47
Q

A hominin that showed high sexual dimorphism; smaller individuals were better at climbing while larger individuals were better at walking on two legs

A

Australopithecus afarensis

48
Q

The presence of a […] is the evolutionary key feature of Homo sapiens which separates them from their ancestors

A

protruding chin

49
Q

The analysis of Australopithecine […] suggest that there has been a shift in their dietary capacities

A

teeth

50
Q

The 3 models that explain the reduction phenomenon in the masticatory region of humans

A
  • probable mutation effect
  • increasing population density effect
  • selective compromise effect
51
Q

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

A

The Great Leap Forward

52
Q

The evolutionary changes believed to be the cause of sleep apnea

A

pharyngeal collapse

53
Q

A system that differed from other mammals for having communication as a dominant function

A

Human Oropharyngeal System

54
Q

The evolution of […] was closely related to the development of the brain by stressing that language provides communication and coordination

A

maxilla mandibular system

55
Q

The 3 factors that caused masticatory evolution of humans

A
  • use of tools and fire
  • changing course of diet
  • vocabulary and speech
56
Q

Sexual differences in body size or morphology may evolve for […]

A

ecological causes

57
Q

The 8 topics discussed

A
  • 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
Q

What does the Summary box in NCBI show?

A

Information about the organism and gene ID

59
Q

What does the Genomic Context in NCBI show?

A

What other genes are in the genomic neighborhood and allow inferences about what role a gene plays

60
Q

What does the Genomic Regions… in NCBI show?

A

Information about the transcription (green bar) and translation (red bar) products of the gene

61
Q

What is the function of dihydrofolate reductase?

A

Involved in tetrahydrofolate biosynthesis; required for respiratory metabolism

62
Q

What is the function of lactate dehydrogenase?

A

Catalyzes the reduction of lactate into pyruvate using NAD+ as cofactor

63
Q

A bioinformatics tool that gives numerous useful information about a protein based on its sequence

A

ProtParam
- MW
- Extinction Coefficient
- pI

64
Q

A bioinformatics tool that allows direct comparison of two or more sequences and look for similarities and differences

A

Multiple Sequence Comparison by Log-Expectation
(MUSCLE)

65
Q

How many amino acids are present in:
a) B. subtilis str. 168
b) E. coli

A
  • 321
  • 324

Evolutionary Biology (6 decks)

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