Conservative Amino Acid Substations in Proteins

Question 1

How we use our knowledge of amino acid structure in genetics

Answer 1

• important in genomic sequencing an analysis

- function and evolution of proteins due to comparative sequences of nucleic acids to deduce sequences of proteins.

Question 2

Conservative

Answer 2

unlikely to result in major change of the characteristics of a protein.

Question 3

Acidic R group conservations

Answer 3

• Asp (D) and Glu (E)

Question 4

Basic R group conservations

Answer 4

• Lys (K), Arg (R), and His (H)

Question 5

Hydrophobic R group conservations

Answer 5

• Leu (L), Ile (I), Val (V)

- about the same size

Question 6

Amide R group conservations

Answer 6

• Asn (N) and Gln (Q)

Question 7

Aromatic group conservations

Answer 7

• Phe (F), Tyr (Y), and Trp (W)

Question 8

Conservation on a genetic basis

Answer 8

• Many (but not all) amino substations that are conservative on a structural basis and also conservative on a genetic basis.
• They can result from the change of a single nucleotide in the third position of the codon.

Question 9

Conservation on a genetic basis example

Answer 9

• Asp (D) GA U/C

- Glu (E) GA A/G

Question 10

Aligning conserved sequences

Answer 10

• clone
• sequence
• BLAST
• align with CLUSTAL

Question 11

BLAST

Answer 11

• find homology of protein

- determine hypothetical gene or actual gene

Question 12

DNA polymerases

Answer 12

• proofread

Question 13

Taq polymerases

Answer 13

• makes more mistakes

- fidelity

Question 14

conservative substations on the frequency of substitution basis

Answer 14

• if one AA substitutes for another at a frequency higher than expected by chance = conservative
• determined statistically

Question 15

BLAST

Answer 15

peptide or nucleic acid sequence and want to find what known proteins or nucleic acids have the sequence or related sequences.

Question 16

CLUSTAL

Answer 16

• 2 or more proteins or nucleic acid sequences and you want to align them with the best fit.

Question 17

strongly conserved versus structurally conserved substitutions

Answer 17

• are the same but 5 additional indications of homology in weakly conserved substitutions

Question 18

Effect of non-conservative amino acid substitutions

Answer 18

• Normal erythrocytes versus sickle-cell anemia erythrocytes
• a homozygous mutation that changes Glutamic Acid (a very hydrophilic amino acid) to Valine (a very hydrophobic amino acid)