Lecture 3&4: Seidler AA-bioinformatics Flashcards Preview

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Flashcards in Lecture 3&4: Seidler AA-bioinformatics Deck (12)
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1

What form AA are found in proteins

L-AA

2

Peptide bond is what type of bond

Covalent

3

Essential AA

PVT TIM HALL

4

Homolog

A gene related to a second gene by descent from a common ancestral DNA sequence

5

Orthologs

Homologs that perform SAME/ SIMILAR functions in different species. Ex: comparing zebrafish to human

6

Paralogs

Homologs that perform DIFFERENT functions w/ in one species. Ex: comparing proteins in eye to liver

7

3 ways to compare Amino acid sequences:

Sliding, Shuffling, and blosum 62

8

Sliding analysis

Pair-wise comparison- stacking on top of one another for a numerical number of sameness. Multiply the number of same residues by 10. Helps top identify Gaps. USes a chart that has peak generally in the middle d/t highest number of matches d/t sliding mechanism.

9

Gaps

Identify where certain portions of sequence have Been removed or added. Can occur w/ gene duplication and insertions / deletes

10

Shuffling

Scrambling the sequences multiple times to see the number of alignments (/10 d/t the X 10 of Same residues)

11

Blosum 62

Scores differences in Amino acid properties (highly variant, invariant, and conservative groups). Positive score=positive mutations. Net scores=mutation that changes property of amino acid.

12

BLAST search can be used to:

Search online database to compare sequences for already documented amino acids