Final Term Lab Exam Flashcards
A classification of databases applicable both to nucleic acid sequences and protein sequences
Sequence Databases
A classification of databases applicable only to protein
Structure Databases
A classification of databases which contains information of the sequence or structure alone
Primary Database
- Swiss-Prot
- PIR
- GenBank
- DDB
- PDB
A classification of databases which contains derived information from the primary database
Secondary Database
- Prosite
- Pfam
A classification of databases which amalgamates a variety of different primary database sources which removes the need to search multiple sources
Composite Database
- NCBI
- ExPASy
The 3 protein databases that make up UniProtKB
- Swiss-Prot
- TrEMBL
- PIR-PSD
A popular sequence-alignment and database-scanning program
FASTA
They created FASTA in 1988
- W.R. Pearson
- D.J. Lipman
The 4 parts found in a GenBank entry
- Locus Name
- Reference Section
- Features Section
- Sequence Section
A sequence comparison tool that quickly tells you which of the other known proteins out there has a sequence similar to yours
BLAST
(Basic Local Alignment Search Tool)
The 3 purposes of BLAST
- prediction of protein function
- 3D structure and domain organization
- identification of homologues in other organisms
An assessment of the statistical significance of the score
E-value
These involve lining up many similar proteins side by side for the sake of comparison
Multiple Alignments
He discovered the skeleton of archaeopteryx in 1861
Richard Owen
He argued that archaeopteryx bore a striking resemblance to small dinosaurs like Compsognathus
Thomas Henry Huxley
He discovered the fossils of Deinonychus
John Ostrom
He and colleagues argued that dinosaurs grew fast and had active metabolisms like extant birds
Robert Bakker
He and colleagues used cladistics to place birds within the family tree of dinosaurs
Jacques Gauthier
The overarching pattern of evolution observed in birds
- Feathers and flight are only seen in birds with dinosaur ancestors
- Rapid growth and beaks are absent in the earliest birds
The only taxon with asymmetrical hindlimb feathers
Microraptor
The 2 primary groups of birds
- Palaeognathae
- Neognathae
The 6 camouflage concepts
- Background Matching
- Disruptive Coloration
- Self-Shadow Concealment and Obliterative Shading
- Distractive Markings
- Masquerade
- Decoration
The 3 costs and constraints on plant camouflage evolution
- Physiology
- Camouflage Efficacy
- Selection Strength
The 5 factors that may promote plant camouflage evolution
- Heterotrophism
- Open Habitats
- Small Individual Size
- Fragile Structure
- Specialized Enemies
An important evolutionary strategy that allows plants to avoid detection by predators and to better exploit different habitats and resources
Plant Camouflage
A mammal that has transitioned from terrestrial to aquatic lifestyle
Whale
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
The presence of […] in whales is considered to be strong evidence for the theory of evolution
vestigial pelvic bones
Cetaceans were found to be more closely related to […] than other groups of mammals
Even-toed ungulates
The 3 morphological evolutions of cetaceans
- Limbs > Flippers
- Nostrils > Blowholes
- Tails > Flukes
The discovery of […] showed how early cetaceans were adapting to an aquatic lifestyle
Ambulocetus
A mycoheterotrophic monocot plant discovered in Japan and was presumed to be extinct
Thismia kobensis
Its rediscovery after three decades has significantly advanced our understanding of fairy lanterns
Thismia kobensis
A detailed morphological investigation suggested that Thismia kobensis is indeed the closest relative of […]
Thismia americana
A type of cell that provides physical and chemical support to neurons and maintains their environment
Glial Cells
The […] of the brain is composed of axons to form neural networks
white matter
The estimated storage capacity of the brain
1.25 * 10^25 bytes
Increase in volume of white matter in the brain from […] in a monkey to […] in primates led to improved function
- 22%
- 65%
[…] in axons increase the transmission across the brain into a near double
Myelination
The evolution of the human brain is limited by […]
energetic constraints and neural processing time
The 3 factors that may cause the evolution of the human brain
- Environmental Factors
- Natural Selection
- Limits
The oldest known hominin fossil
Ardipithecus ramidus
A hominin at 1.8 Ma suggested to be fully bipedal but others argue it had arboreal adaptations
Homo habilis
A hominin at 4 Ma suggested to be fully bipedal but others argue it had a combination of terrestrial and arboreal locomotion
Australopithecus afarensis
A hominin at 3.6 Ma suggested to have a mosaic of locomotion
Australopithecus africanus
The hypothesis on the evolution of bipedalism
- Brachiation
- Vertical Climbing
- Knuckle-walking
- Obligate Bipedal
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
The presence of a […] is the evolutionary key feature of Homo sapiens which separates them from their ancestors
protruding chin
The analysis of Australopithecine […] suggest that there has been a shift in their dietary capacities
teeth
The 3 models that explain the reduction phenomenon in the masticatory region of humans
- probable mutation effect
- increasing population density effect
- selective compromise effect
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
The evolutionary changes believed to be the cause of sleep apnea
pharyngeal collapse
A system that differed from other mammals for having communication as a dominant function
Human Oropharyngeal System
The evolution of […] was closely related to the development of the brain by stressing that language provides communication and coordination
maxilla mandibular system
The 3 factors that caused masticatory evolution of humans
- use of tools and fire
- changing course of diet
- vocabulary and speech
Sexual differences in body size or morphology may evolve for […]
ecological causes
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
What does the Summary box in NCBI show?
Information about the organism and gene ID
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
What does the Genomic Regions… in NCBI show?
Information about the transcription (green bar) and translation (red bar) products of the gene
What is the function of dihydrofolate reductase?
Involved in tetrahydrofolate biosynthesis; required for respiratory metabolism
What is the function of lactate dehydrogenase?
Catalyzes the reduction of lactate into pyruvate using NAD+ as cofactor
A bioinformatics tool that gives numerous useful information about a protein based on its sequence
ProtParam
- MW
- Extinction Coefficient
- pI
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)
How many amino acids are present in:
a) B. subtilis str. 168
b) E. coli
- 321
- 324
