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Domains & Domain Classification

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Structural Basis for Biological Function (Basics) Quiz on Domains & Domain Classification, created by gina_evans0312 on 13/12/2013.
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Quiz by gina_evans0312, updated more than 1 year ago
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Created by gina_evans0312 over 10 years ago
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Question 1

Question
Of known structures (60-80% of genes) how many are multidomain proteins?
Answer
  • 40
  • 50
  • 60
  • 30

Question 2

Question
Different combinations of domains are advantageous because they allow the organism to specialise
Answer
  • True
  • False

Question 3

Question
How can we recognize domains?
Answer
  • DNA sequencing
  • Amino acid sequencing
  • Structure
  • Topology (fold)

Question 4

Question
Why are DNA/amino acid sequencing of little use when investigating relationships between proteins?
Answer
  • As diversion occurs, sequence patterns are lost even as the fold remains the same
  • They can detect short evolutionary relationships only
  • The techniques for reading the sequences are unreliable
  • Identical sequences can give different aa sequences/folds

Question 5

Question
When investigating using structure, how do we identify domains?
Answer
  • Amino acid sequence
  • Domains have the same fold
  • The interaction of the protein with other proteins

Question 6

Question
There is a limited number of folds in nature (10^3-4)
Answer
  • True
  • False

Question 7

Question
Structural similarity occurs from what kind of evolution?
Answer
  • Divergent
  • Convergent

Question 8

Question
Sequence is more highly conserved than protein structure
Answer
  • True
  • False

Question 9

Question
Define convergent evolution
Answer
  • The independent evolution of similar features in different lineages
  • The carrying of a feature from a common ancestor into two lines, which allows the reconvergence of the two lines into a single species again
  • The dependent evolution of similar features in two species that interact/co-operate closely

Question 10

Question
How does the CATH system establish taxonomy?
Answer
  • Cut proteins into domains and use computor analysis to group domains
  • Uses structure based analysis

Question 11

Question
Which of the following classifications would be in the Class portion of the CATH system
Answer
  • Connectivity of fold
  • Barrel
  • Mostly alpha

Question 12

Question
Which of the following would be in the Architecture domain of the CATH system
Answer
  • Mostly beta
  • Both
  • Two layer sandwitch
  • Connectivity of fold
  • Barrel

Question 13

Question
Put the following in order of their use in the CATH system A- Class B- Sequence Superfamily C- Homologous Superfamily D-Architecture E- Topology
Answer
  • A-D-E-C-B
  • B-A-C-E-D
  • D-E-A-B-C

Question 14

Question
There are 3 classes, 32 architectures and 820 topologies in the CATH system
Answer
  • True
  • False

Question 15

Question
The SCOP classifications, in descending order, are Class-Superfamily-Family-Fold-Species
Answer
  • True
  • False

Question 16

Question
What is the specification after Superfamiy in the Pfam system?
Answer
  • Fold
  • Architecture
  • Clade

Question 17

Question
All the systems agree in _% of cases
Answer
  • 30-40
  • 40-50
  • 50-60
  • 60-70

Question 18

Question
To be homologous, two proteins must have two of which of the following in common?
Answer
  • Structural Similarity
  • Sequence Similarity
  • Functional Simiarity
  • Species Similarity
  • Genus Similarity

Question 19

Question
What is the following describing- a protein contained in two different species with a similar function due to divergent evolution
Answer
  • Orthologues
  • Paralogues

Question 20

Question
What is the following describing- changes to a sequence following gene duplication leads to a variant copy with an additional (usually similar) function in the same species
Answer
  • Orthologues
  • Paralogues

Question 21

Question
Give the two defining features of orthologues
Answer
  • RMSD of >4
  • High SI
  • Low SI
  • SI may be high or low

Question 22

Question
NAD is a co-enzyme found in all living cells that accepts and donates electrons
Answer
  • True
  • False

Question 23

Question
NAD is made of three nucleotides and a phosphate group
Answer
  • True
  • False

Question 24

Question
Which of the following binds NAD when present in a protein?
Answer
  • A Rossman Fold
  • A Sherman Fold
  • A Fieldman Fold

Question 25

Question
The Rossman Fold has it's 6 beta sheets arranged in what order?
Answer
  • 654123
  • 123456
  • 615243

Question 26

Question
In a Rossman fold, the crossover of the strands form the binding site
Answer
  • True
  • False

Question 27

Question
In lactate dehydrogenase, which terminal domain contains the Rossman fold?
Answer
  • C
  • N

Question 28

Question
What is the role of the C-terminal domain in dehydrogenases?
Answer
  • Enzyme specificity
  • Enzyme regulation
  • Enzyme catalytic activity

Question 29

Question
Lactate dehydrogenase catalyses lactate --> oxaloacetate
Answer
  • True
  • False

Question 30

Question
Malate dehydrogenase is structually identical to LADH, so why do they have different substrates?
Answer
  • An SI of 17%
  • They operate in cells where only one or the other is avalible
  • Lactate and malate are structurally identical, but have different components

Question 31

Question
How can we tell two proteins are not homologues?
Answer
  • They have a different function
  • They have a different S.I
  • They're found in different species
  • They're structurally different

Question 32

Question
What is the following descrbing- the existence of a shared ancestry between two structures (in this case proteins)
Answer
  • Homology
  • Divergent evolution
  • Convergent evolution

Question 33

Question
Alcohol dehydrogenase contains a Rossman fold
Answer
  • True
  • False

Question 34

Question
ADH and LDH have an RMSD of 2.2 & an S.I of 17%- what relationship do they share?
Answer
  • Orthologues
  • Paralogues

Question 35

Question
In the case of sequence diversity between proteins, surface residues change less than core/functional site residues
Answer
  • True
  • False

Question 36

Question
Where do residue insertions usually occur?
Answer
  • In the functional site
  • In loops connecting secondary structures
  • In alpha helices

Question 37

Question
The functional diversity of a domain superfamily depends on the fold
Answer
  • True
  • False
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