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Evolution 2 > Lecture 18 - Sequence Similarity > Flashcards

Lecture 18 - Sequence Similarity Flashcards

1
Q

What is an open reading frame?

A

Part of the reading frame that has the potential to be translated.

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2
Q

How can the function of unknown proteins be inferred?

A

By similarity of sequence to known proteins.

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3
Q

What was the first protein database?

A

Protein Information Resource (PIR)

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4
Q

Give some protein sequence databases.

A
  • Swiss-Prot
  • TrEMBL
  • Uniprot
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5
Q

Which protein database is manually annotated?

A

Swiss-Prot

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6
Q

Give three DNA sequence databases in order from early to late.

A
  • Genbank
  • European Molecular Biology Laboratory
  • DNA Databank of Japan
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7
Q

What is sequence alignment?

A

A way of arranging the primary sequences of DNA, RNA or protein to identify regions of similarity.

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8
Q

What is pairwise alignment?

A

Comparing two sequences.

A query sequence is compared to every sequence in a database to find the best match.

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9
Q

What is global alignment?

A

An attempt to match every residue in two sequences.

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10
Q

When is global alignment most useful?

A

When sequences are of equal lengths.

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11
Q

When is local alignment more useful?

A

For dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.

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12
Q

What is local alignment?

A

Trying to match regions of two sequences.

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13
Q

What alignment method does BLAST use?

A

Local alignment

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14
Q

What has BLAST been designed for?

A

Speed

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15
Q

What are the following BLAST programmes for?

a) blastn
b) blastp
c) blastx
d) tblastn
e) tblastx

A

a) blastn = nucleotide query vs. nucleotide database
b) blastp = protein query vs. protein database
c) blastx = nulecotide query vs. protein database
d) tblastn = protein query vs. nucleotide database
e) tblastx = nucleotide query vs. nucleotide database

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16
Q

What is it best to compare between the species?

A

Protein sequences, because they evolve more slowly.

17
Q

Which BLAST programme should you use when mapping mRNA or gene sequences to genomic DNA from the same organism?

A

blastn

18
Q

What is a score?

A

A value calculated from number of matching or similar amino acids in alignment.

19
Q

What is an expect?

A

A probability that alignment could happen by change; depends on score, length of query sequence and size of database.

20
Q

What are identities?

A

The number of identical amino acids in alignment.

21
Q

What are positives?

A

The number of similar amino acids in alignment.

22
Q

What is a protein family?

A

A group of evolutionarily-related proteins.

23
Q

What do members of a protein family share?

A

Similar 3-dimensional structures, functions and sequence similarity.

24
Q

What can create gene families?

A

Gene duplication

25
Q

What are Cytochrome p450s?

A

A group of enzymes involved in the oxidative metabolism of a large number of natural compounds.

26
Q

What kingdoms are Cytochrome P450s found in?

A
  • Animals
  • Plants
  • Fungi
  • Bacteria
27
Q

Give some functions of cytochrome p450.

A
  • Detoxification of drugs and toxins
  • Biosynthesis of steroids, fatty acids
  • Biosynthesis of toxins
  • Alkane assimilation
28
Q

What is Magnaporthe oryzae?

A

Rice blast fungus.

29
Q

What is Neurospora crassa?

A

Red bread mould. (lives on dead organic matter)

30
Q

What are the number of cytochrome p450s in

a) M. oryzae?
b) N. crassa?

A

a) M. oryzae = 122

b) N. crassa = 37

31
Q

Why are cytochrome P450s important for pathogens?

A

Need to detoxify anti-fungal chemicals produced by the host, and to synthesise toxins to help it invade the host.

32
Q

What are Cytochrome P450s classified into families based on?

A

Sequence homology

33
Q

Are amino acid sequences well conserved or not well conserved between cytochrome P450 families?

A

Not well conserved.

34
Q

What is Pfam?

A

Protein family database based on hidden Markov models.

35
Q

What is HMM?

A

A statistical model that considers all of the possible combinations of matches, mismatches and gaps to generate an alignment of a set of sequences.

36
Q

What is a domain?

A

A segment of polypeptide chain that can fold into a three-dimensional structure irrespective of the presence of other segments of the chain.

37
Q

What is Myosin V involved in?

A

Actin-dependent transport of vesicles.

38
Q

What is TPA?

A

An extracellular protein that prevents blood clotting.

39
Q

How many domains does TPA have?

A

Four, each coded for by a different exon.

Evolution 2 (11 decks)

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