Lecture 3&4: Seidler AA-bioinformatics

Question 1

What form AA are found in proteins

Answer 1

L-AA

Question 2

Peptide bond is what type of bond

Answer 2

Covalent

Question 3

Essential AA

Answer 3

PVT TIM HALL

Question 4

Homolog

Answer 4

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

Question 5

Orthologs

Answer 5

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

Question 6

Paralogs

Answer 6

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

Question 7

3 ways to compare Amino acid sequences:

Answer 7

Sliding, Shuffling, and blosum 62

Question 8

Sliding analysis

Answer 8

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.

Question 9

Gaps

Answer 9

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

Question 10

Shuffling

Answer 10

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

Question 11

Blosum 62

Answer 11

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.

Question 12

BLAST search can be used to:

Answer 12

Search online database to compare sequences for already documented amino acids