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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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Domains & Domain Classification

Question 1 of 37

1

Of known structures (60-80% of genes) how many are multidomain proteins?

Select one of the following:

  • 40

  • 50

  • 60

  • 30

Explanation

Question 2 of 37

1

Different combinations of domains are advantageous because they allow the organism to specialise

Select one of the following:

  • True
  • False

Explanation

Question 3 of 37

1

How can we recognize domains?

Select one or more of the following:

  • DNA sequencing

  • Amino acid sequencing

  • Structure

  • Topology (fold)

Explanation

Question 4 of 37

1

Why are DNA/amino acid sequencing of little use when investigating relationships between proteins?

Select one or more of the following:

  • 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

Explanation

Question 5 of 37

1

When investigating using structure, how do we identify domains?

Select one of the following:

  • Amino acid sequence

  • Domains have the same fold

  • The interaction of the protein with other proteins

Explanation

Question 6 of 37

1

There is a limited number of folds in nature (10^3-4)

Select one of the following:

  • True
  • False

Explanation

Question 7 of 37

1

Structural similarity occurs from what kind of evolution?

Select one of the following:

  • Divergent

  • Convergent

Explanation

Question 8 of 37

1

Sequence is more highly conserved than protein structure

Select one of the following:

  • True
  • False

Explanation

Question 9 of 37

1

Define convergent evolution

Select one of the following:

  • 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

Explanation

Question 10 of 37

1

How does the CATH system establish taxonomy?

Select one of the following:

  • Cut proteins into domains and use computor analysis to group domains

  • Uses structure based analysis

Explanation

Question 11 of 37

1

Which of the following classifications would be in the Class portion of the CATH system

Select one of the following:

  • Connectivity of fold

  • Barrel

  • Mostly alpha

Explanation

Question 12 of 37

1

Which of the following would be in the Architecture domain of the CATH system

Select one or more of the following:

  • Mostly beta

  • Both

  • Two layer sandwitch

  • Connectivity of fold

  • Barrel

Explanation

Question 13 of 37

1

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

Select one of the following:

  • A-D-E-C-B

  • B-A-C-E-D

  • D-E-A-B-C

Explanation

Question 14 of 37

1

There are 3 classes, 32 architectures and 820 topologies in the CATH system

Select one of the following:

  • True
  • False

Explanation

Question 15 of 37

1

The SCOP classifications, in descending order, are Class-Superfamily-Family-Fold-Species

Select one of the following:

  • True
  • False

Explanation

Question 16 of 37

1

What is the specification after Superfamiy in the Pfam system?

Select one of the following:

  • Fold

  • Architecture

  • Clade

Explanation

Question 17 of 37

1

All the systems agree in _% of cases

Select one of the following:

  • 30-40

  • 40-50

  • 50-60

  • 60-70

Explanation

Question 18 of 37

1

To be homologous, two proteins must have two of which of the following in common?

Select one or more of the following:

  • Structural Similarity

  • Sequence Similarity

  • Functional Simiarity

  • Species Similarity

  • Genus Similarity

Explanation

Question 19 of 37

1

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

Select one of the following:

  • Orthologues

  • Paralogues

Explanation

Question 20 of 37

1

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

Select one of the following:

  • Orthologues

  • Paralogues

Explanation

Question 21 of 37

1

Give the two defining features of orthologues

Select one or more of the following:

  • RMSD of >4

  • High SI

  • Low SI

  • SI may be high or low

Explanation

Question 22 of 37

1

NAD is a co-enzyme found in all living cells that accepts and donates electrons

Select one of the following:

  • True
  • False

Explanation

Question 23 of 37

1

NAD is made of three nucleotides and a phosphate group

Select one of the following:

  • True
  • False

Explanation

Question 24 of 37

1

Which of the following binds NAD when present in a protein?

Select one of the following:

  • A Rossman Fold

  • A Sherman Fold

  • A Fieldman Fold

Explanation

Question 25 of 37

1

The Rossman Fold has it's 6 beta sheets arranged in what order?

Select one of the following:

  • 654123

  • 123456

  • 615243

Explanation

Question 26 of 37

1

In a Rossman fold, the crossover of the strands form the binding site

Select one of the following:

  • True
  • False

Explanation

Question 27 of 37

1

In lactate dehydrogenase, which terminal domain contains the Rossman fold?

Select one of the following:

  • C

  • N

Explanation

Question 28 of 37

1

What is the role of the C-terminal domain in dehydrogenases?

Select one of the following:

  • Enzyme specificity

  • Enzyme regulation

  • Enzyme catalytic activity

Explanation

Question 29 of 37

1

Lactate dehydrogenase catalyses lactate --> oxaloacetate

Select one of the following:

  • True
  • False

Explanation

Question 30 of 37

1

Malate dehydrogenase is structually identical to LADH, so why do they have different substrates?

Select one of the following:

  • 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

Explanation

Question 31 of 37

1

How can we tell two proteins are not homologues?

Select one or more of the following:

  • They have a different function

  • They have a different S.I

  • They're found in different species

  • They're structurally different

Explanation

Question 32 of 37

1

What is the following descrbing- the existence of a shared ancestry between two structures (in this case proteins)

Select one of the following:

  • Homology

  • Divergent evolution

  • Convergent evolution

Explanation

Question 33 of 37

1

Alcohol dehydrogenase contains a Rossman fold

Select one of the following:

  • True
  • False

Explanation

Question 34 of 37

1

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

Select one of the following:

  • Orthologues

  • Paralogues

Explanation

Question 35 of 37

1

In the case of sequence diversity between proteins, surface residues change less than core/functional site residues

Select one of the following:

  • True
  • False

Explanation

Question 36 of 37

1

Where do residue insertions usually occur?

Select one of the following:

  • In the functional site

  • In loops connecting secondary structures

  • In alpha helices

Explanation

Question 37 of 37

1

The functional diversity of a domain superfamily depends on the fold

Select one of the following:

  • True
  • False

Explanation

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