chapter 5 section 4

Question 1

What are homologous proteins?

Answer 1

Proteins with significant sequence similarity and structural resemblance

Question 2

What do homologous proteins often share across species?

Answer 2

Similar function and nearly identical chain lengths

Question 3

What is strong evidence for evolutionary relationships?

Answer 3

Comparing amino acid sequences of homologous proteins.

Question 4

What are orthologous proteins?

Answer 4

Homologous proteins in different species with similar sequences and often similar function.

Question 5

What are paralogous proteins?

Answer 5

Homologous proteins within a species that arose from gene duplication.

Question 6

Example of paralogous proteins in humans?

Answer 6

Hemoglobin α and β chains.

Question 7

What tool is commonly used to detect sequence homology?

Answer 7

BLAST (Basic Local Alignment Search Tool).

Question 8

How does BLAST find similarity?

Answer 8

By aligning sequences and scoring identical or similar residues.

Question 8

What evolutionary events naturally cause gaps

Answer 8

Insertions and deletions (indels).

Question 8

What are gap penalties in sequence alignment?

Answer 8

Negative scores that prevent overuse of gaps when aligning sequences.

Question 9

What matrix is often used to score sequence substitutions in BLAST?

Answer 9

BLOSUM (Blocks Substitution Matrix).

Question 10

How are BLOSUM scores determined?

Answer 10

From observed amino acid substitutions in related protein blocks.

Question 11

What do high BLOSUM scores mean?

Answer 11

Substitution is likely and common.

Question 12

What do low or negative BLOSUM scores mean?

Answer 12

Substitution is unlikely.

Question 13

What happens when alignment has mismatched regions?

Answer 13

Gaps are introduced to optimize alignment.

Question 14

what protein is a classic example of orthology studied across species?

Answer 14

Cytochrome c.

Question 15

What do invariant residues in cytochrome c indicate?

Answer 15

They are crucial for protein function and cannot tolerate substitutions.

Question 16

How does sequence difference in cytochrome c relate to species differences?

Answer 16

The number of amino acid differences is proportional to evolutionary distance.

Question 17

What is identical between humans and chimpanzees in cytochrome c?

Answer 17

The full amino acid sequence.

Question 18

What tool is often built from cytochrome c sequence comparisons?

Answer 18

Phylogenetic trees showing evolutionary relationships

Question 19

What does molecular evolution study rely on?

Answer 19

Sequence comparisons like cytochrome c across organisms.

Question 20

What type of proteins are myoglobin, α-globin, and β-globin

Answer 20

Paralogous proteins.

Question 21

What is the function of myoglobin?

Answer 21

Oxygen binding in muscle.

Question 22

What is the structure of hemoglobin?

Answer 22

A tetramer with 2 α-chains and 2 β-chains.

Question 23

What evolutionary event gave rise to myoglobin and hemoglobin genes?

Answer 23

Duplication of an ancestral globin gene.

Question 24

What event later separated α- and β-globin genes?

Answer 24

Another gene duplication.

Question 25

Which proteases are examples of homologous proteins with different substrate preferences

Answer 25

Trypsin, chymotrypsin, elastase, and thrombin.

Question 26

Why do all globins retain oxygen-binding ability?

Answer 26

They all bind heme groups.

Question 27

What key residue defines serine proteases?

Answer 27

A serine in the active site critical for catalysis.

Question 28

What unusual protein pair shows strong structural homology despite different functions?

Answer 28

Hen egg-white lysozyme and human α-lactalbumin.

Question 29

What is lysozyme’s function?

Answer 29

Hydrolyzes bacterial cell walls.

Question 30

What is α-lactalbumin’s function?

Answer 30

Regulates lactose synthesis in milk.

Question 31

Why are lysozyme and α-lactalbumin considered related?

Answer 31

Their tertiary structures are strikingly similar.

Question 32

What effects can mutations in proteins have

Answer 32

Neutral, loss of function, or harmful (depending on substitution).

Question 33

What are some functional changes mutations can cause in hemoglobin?

Answer 33

Altered oxygen affinity, heme binding, solubility, or stability.

Question 34

Why do some mutations cause little effect on protein function

Answer 34

Substituted residues do not affect crucial structural or functional regions.

Question 35

Why is HbS harmful?

Answer 35

It changes hemoglobin’s properties, causing red blood cells to sickle.

Question 36

What broader concept do mutant proteins highlight?

Answer 36

that some amino acid changes are tolerated, while others disrupt protein function severely.