# DBT JRF 2022 — Question 135

Exam: DBT JRF 2022 · Section: B · Topic: Bioinformatics › PAM Scoring Matrix · Difficulty: Medium

## Question

Which one of the following is true for PAM250 Scoring Matrix?

## Options

- **A.** It is used for structural database search.
- **B.** It is based on an evolutionary model that predicts the types of amino acid changes over long periods of time.
- **C.** It can be used to score alignments for nucleotide changes over long periods of time.
- **D.** It can distinguish synonymous and non-synomynous mutations.

## Answer

Option B

## Explanation

PAM250 scoring matrix — evolutionary model for distant sequences: PAM (Point Accepted Mutation) matrices were developed by Margaret Dayhoff based on evolutionary models: • PAM1: model matrix for 1 accepted point mutation per 100 amino acids (very recent divergence). • PAM250: mathematical extrapolation of PAM1 raised to the 250th power → represents the expected amino acid substitution frequencies after 250 million years of evolution (distant relationships). Key properties: • Based on an EVOLUTIONARY MODEL: how amino acids change over LONG evolutionary time periods. • Appropriate for aligning DISTANTLY RELATED protein sequences. • For nucleotide sequences or synonymous/non-synonymous distinction: use different tools (e.g., dN/dS analysis, nucleotide substitution matrices). • Structural database searches: structure-based matrices (e.g., GONNET, BLOSUM) may be preferred. Contrast: BLOSUM62 is derived empirically from aligned conserved blocks; PAM250 is derived from evolutionary models. Both are used for protein alignment. Answer: PAM250 is based on evolutionary models predicting amino acid change frequencies over long evolutionary distances (250 accepted mutations per 100 aa).

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