protein function

Question 1

What is protein function?

Answer 1

Protein function refers to the different roles and activities that proteins perform in biological processes.

Question 2

What are the different aspects of protein function?

Answer 2

The different aspects of protein function occur in different scales of space and time, ranging from almost instantaneous enzymatic reactions to slower biological processes.

Question 3

How can we know which functional aspect of protein is being investigated?

Answer 3

We can know which functional aspect of protein is being investigated through the establishment of a standardized machine-readable vocabulary, such as the Gene Ontology (GO).

Question 4

What is the Gene Ontology (GO)?

Answer 4

The Gene Ontology (GO) is a standardized machine-readable vocabulary that describes the different aspects of protein function.

Question 5

What are the three ontology trees in the Gene Ontology (GO)?

Answer 5

The three ontology trees in the Gene Ontology (GO) are molecular function, biological process, and cellular location.

Question 6

Why is the standard vocabulary for GO important?

Answer 6

The standard vocabulary for GO allows annotations to be computationally processed and provides a standard approach for programs to output their functional predictions.

Question 7

What is homology-based transfer?

Answer 7

Homology-based transfer is a method used to assign unannotated proteins with the function of their annotated homologs.

Question 8

What is the rationale for homology-based transfer?

Answer 8

The rationale for homology-based transfer is based on the assumption that two sequences with a high degree of similarity most likely evolved from a common ancestor and therefore must have similar functions.

Question 9

Is homology-based transfer a form of experimental function prediction?

Answer 9

No, homology-based transfer is not a form of experimental function prediction, but rather a computational function-prediction method.

Question 10

Why is homology-based transfer the most widely used form of computational function-prediction method?

Answer 10

Homology-based transfer is the most widely used form of computational function-prediction method because it is relatively accurate and has a strong theoretical basis.

Question 11

What is a homolog?

Answer 11

A homolog is a gene or protein that has evolved from a common ancestor with another gene or protein, often sharing similar functions.

Question 12

What is the importance of homology in the study of protein function?

Answer 12

Homology is important in the study of protein function because it allows us to infer the function of unannotated proteins based on the function of their annotated homologs.

Question 13

What are the two most commonly used programs for comparing an unknown sequence against a sequence database?

Answer 13

FASTA and BLAST.

Question 14

What is a heuristic approach in sequence alignment?

Answer 14

A heuristic approach is a computationally efficient strategy that, if it doesn’t find the optimum solution, will at least find a solution very close to the optimum.

Question 15

What does FASTA stand for?

Answer 15

FASTA stands for Fast-All.

Question 16

What is the difference between FASTA and BLAST in terms of sensitivity?

Answer 16

Although it is more sensitive than BLAST for DNA sequences, FASTA sometimes misses weak protein matches.

Question 17

What is the FASTA format?

Answer 17

Some servers require the sequence to be entered in FASTA format. This means that the line of the sequence should start with a title line which must start with a >, followed by the sequence, as a single uninterrupted line.

Question 18

what does BLAST stand for

Answer 18

Basic Local Alignment Search Tool

Question 19

What do the color codes in a Graphic Display indicate?

Answer 19

The quality of the match, with red being good, green being acceptable, and black being bad.

Question 20

What is the Bit score in a Hit List?

Answer 20

It measures the statistical significance of the alignment, with a higher Bit score indicating a good match.

Question 20

What is the Bit score in a Hit List?

Answer 20

It measures the statistical significance of the alignment, with a higher Bit score indicating a good match.

Question 21

What is the E-Value in a Hit List?

Answer 21

It is the expected number of chance alignments and indicates the likelihood that the similarity between the query sequence and database sequence occurred by chance.

Question 22

What is the % identity in Alignments?

Answer 22

It is the number of identical residues divided by the number of matched residues, ignoring gaps.

Question 23

What is the difference between similarity and identity?

Answer 23

Similarity is a measure of how close two amino acids are to identical, while identity is a measure made on an alignment.

Question 23

What is the difference between similarity and identity?

Answer 23

Similarity is a measure of how close two amino acids are to identical, while identity is a measure made on an alignment.

Question 24

What is homology?

Answer 24

It implies an evolutionary relationship and is a property that either exists or does not exist between two sequences.

Question 25

What is homology?

Answer 25

It implies an evolutionary relationship and is a property that either exists or does not exist between two sequences.

Question 26

How is homology established between DNA and protein sequences?

Answer 26

Two DNA sequences with more than 70% identity (over 100 nucleotides) are homologs, and two protein sequences with more than 25% identity (over 100 amino acids) are homologs.

Question 27

What is the twilight zone

Answer 27

when 2 proteins (at least 100 residues long) share less than 25% identity