Question 1

How are sequence alignments made?

Accepted Answer

Two sequences are aligned, and the best

Question 2

Analysis of substitution matrices indicates that cysteine (C) and __________________ residues tend to be conserved more than other amino acid residues.

Accepted Answer

The answer of Analysis of substitution matrices indicates that cysteine...

Question 3

Which of the following would be classified as paralogs due to development of a new function from a duplication and subsequent mutation of a gene?

Accepted Answer

A)  hemoglobin and myoglobin. 
B)  actin and keratin. 
C)  DNA polymerase and trypsin. 
D)  actin and myosin. 
E)  None of the answers is correct. 
A)  hemoglobin and myoglobin. 
B)  actin and keratin. 
C)  DNA polymerase and trypsin. 
D)  actin and myosin. 
E)  None of the answers is correct.

Question 4

What is a conserved region of a protein that is used to search for homologs?

Accepted Answer

A)  conservative sequence 
B)  conservative domain 
C)  conservative template 
D)  sequence template 
E)  None of the answers is correct. 
A)  conservative sequence 
B)  conservative domain 
C)  conservative template 
D)  sequence template 
E)  None of the answers is correct.

Question 5

What are the three criteria necessary for evolution to occur?

Accepted Answer

There are three distinct steps

Question 6

What is the difference between a simple scoring system for alignment and the
Blosum-62 matrix?

Accepted Answer

A simple scoring system looks only at al

Question 7

Define the terms homologs, paralogs, and orthologs.

Accepted Answer

Any two proteins which are evolutionaril

Question 8

Homologs that exist in the same species are called _____.

Accepted Answer

A)  holologs 
B)  multilogs 
C)  autologs 
D)  paralogs 
E)  orthologs 
A)  holologs 
B)  multilogs 
C)  autologs 
D)  paralogs 
E)  orthologs

Question 9

Which of the following molecules is the most stable?

Accepted Answer

A)  mRNA 
B)  hemoglobin 
C)  carbohydrates 
D)  rRNA 
E)  mitochondrial DNA 
A)  mRNA 
B)  hemoglobin 
C)  carbohydrates 
D)  rRNA 
E)  mitochondrial DNA

Question 10

Why is it more effective to compare protein sequences, rather than DNA sequences, in evolutionary studies?

Accepted Answer

More effective statistical com

Question 11

Briefly describe the ATP-RNA binding experiment showing that a structure had evolved that was capable of specific binding to ATP.

Accepted Answer

RNA sequences, synthesized by combinator

Question 12

Homologs are two molecules

Accepted Answer

A)  related by sequence similarity. 
B)  derived from a common ancestral protein. 
C)  with similar domains. 
D)  with similar function. 
E)  None of the answers is correct. 
A)  related by sequence similarity. 
B)  derived from a common ancestral protein. 
C)  with similar domains. 
D)  with similar function. 
E)  None of the answers is correct.

Question 13

Which of the following is an example of a conservative amino acid change?

Accepted Answer

A)  glycine to tryptophan 
B)  aspartate to glutamine 
C)  alanine to leucine 
D)  serine to lysine 
E)  glutamine to asparagine 
A)  glycine to tryptophan 
B)  aspartate to glutamine 
C)  alanine to leucine 
D)  serine to lysine 
E)  glutamine to asparagine

Question 14

What is a substitution matrix?

Accepted Answer

A substitution matrix is a means to rate

Question 15

What is the process by which different evolutionary paths end up at a similar structure or mechanism?

Accepted Answer

A)  divergent evolution 
B)  convergent evolution 
C)  confluent evolution 
D)  analogous evolution 
E)  homologous evolution 
A)  divergent evolution 
B)  convergent evolution 
C)  confluent evolution 
D)  analogous evolution 
E)  homologous evolution

Question 16

________________ amplification of well-preserved samples allows the determination of nucleotide sequences from extinct organisms.

Accepted Answer

The answer of ________________ amplification of well-preserved samples allows the...

Question 17

An example of proteins that evolved similar mechanisms by convergent evolution is

Accepted Answer

A)  DNA polymerase and elastase. 
B)  chymotrypsin and subtilisin. 
C)  neuramidase and glycolase. 
D)  actin and myosin. 
E)  None of the answers is correct. 
A)  DNA polymerase and elastase. 
B)  chymotrypsin and subtilisin. 
C)  neuramidase and glycolase. 
D)  actin and myosin. 
E)  None of the answers is correct.

Question 18

Evolutionary trees are constructed with the assumption that the number of sequence differences is related to the time since the two sequences ________________________.

Accepted Answer

The answer of Evolutionary trees are constructed with the assumption...

Question 19

What are some of the inherent difficulties of using DNA from ancient samples?

Accepted Answer

Contamination of the DNA sourc

Question 20

What graphical depiction shows how protein sequences are related in evolutionary terms?

Accepted Answer

A)  evolutionary tree 
B)  evolutionary funnel 
C)  evolutionary shrub 
D)  evolutionary map 
E)  None of the answers is correct. 
A)  evolutionary tree 
B)  evolutionary funnel 
C)  evolutionary shrub 
D)  evolutionary map 
E)  None of the answers is correct.

Exam 6: Exploring Evolution and Bioinformatics

How are sequence alignments made?

Analysis of substitution matrices indicates that cysteine (C) and __________________ residues tend to be conserved more than other amino acid residues.

Which of the following would be classified as paralogs due to development of a new function from a duplication and subsequent mutation of a gene?

What is a conserved region of a protein that is used to search for homologs?

What are the three criteria necessary for evolution to occur?

What is the difference between a simple scoring system for alignment and the Blosum-62 matrix?

Define the terms homologs, paralogs, and orthologs.

Homologs that exist in the same species are called _____.

Which of the following molecules is the most stable?

Why is it more effective to compare protein sequences, rather than DNA sequences, in evolutionary studies?

Briefly describe the ATP-RNA binding experiment showing that a structure had evolved that was capable of specific binding to ATP.

Homologs are two molecules

Which of the following is an example of a conservative amino acid change?

What is a substitution matrix?

What is the process by which different evolutionary paths end up at a similar structure or mechanism?

________________ amplification of well-preserved samples allows the determination of nucleotide sequences from extinct organisms.

An example of proteins that evolved similar mechanisms by convergent evolution is

Evolutionary trees are constructed with the assumption that the number of sequence differences is related to the time since the two sequences ________________________.

What are some of the inherent difficulties of using DNA from ancient samples?

What graphical depiction shows how protein sequences are related in evolutionary terms?

Biochemistry: an Evolving Science

Protein Composition and Structure

Exploring Proteins and Proteomes

DNA, RNA, and the Flow of Genetic Information

Exploring Genes and Genomes

Hemoglobin: a Portrait of a Protein in Action

Enzymes: Basic Concepts and Kinetics

Oxidative Phosphorylation

Catalytic Strategies

Regulatory Strategies

Carbohydrates

Lipids and Cell Membranes

Membrane Channels and Pumps

Signal-Transduction Pathways

Metabolism: Basic Concepts and Design

Glycolysis and Gluconeogenesis

The Citric Acid Cycle

The Light Reactions of Photosynthesis

The Calvin Cycle and the Pentose Phosphate Pathway

Glycogen Metabolism

Fatty Acid Metabolism

Protein Turnover and Amino Acid Catabolism

The Biosynthesis of Amino Acids

Nucleotide Biosynthesis

Biosynthesis of Membrane Lipids and Steroids

The Integration of Metabolism

DNA Replication, Repair, and Recombination

Rna Synthesis and Processing

Protein Synthesis

The Control of Gene Expression in Prokaryotes

The Control of Gene Expression in Eukaryotes

Sensory Systems

The Immune System

Molecular Motors

Drug Development

Filters