Question 1

Two molecules are said to be _________________ if they have been derived from a common ancestor.

Accepted Answer

homologous

Question 2

In the Blosum-62 substitution matrix, a large ________________ score corresponds to substitution that occurs only rarely.

Accepted Answer

negative

Question 3

A BLAST search provides

Accepted Answer

A)  three-dimensional motifs. 
B)  a list of sequence alignments. 
C)  an estimate that an alignment occurred by chance. 
D)  three-dimensional motifs and a list of sequence alignments. 
E)  a list of sequence alignments and an estimate that an alignment occurred by chance. 
A)  three-dimensional motifs. 
B)  a list of sequence alignments. 
C)  an estimate that an alignment occurred by chance. 
D)  three-dimensional motifs and a list of sequence alignments. 
E)  a list of sequence alignments and an estimate that an alignment occurred by chance. E

Question 4

Evolutionary trees provide relative scales of divergence. How can these be reconciled with real times?

Accepted Answer

A)  by comparing the amount of sequence divergence 
B)  by comparing proteins from convergent evolution 
C)  by comparing proteins from both convergent and divergent evolution 
D)  by using fossil records when possible 
E)  None of the answers is correct. 
A)  by comparing the amount of sequence divergence 
B)  by comparing proteins from convergent evolution 
C)  by comparing proteins from both convergent and divergent evolution 
D)  by using fossil records when possible 
E)  None of the answers is correct.

Question 5

Comparison of three-dimensional structures indicated that heat shock protein 70 is a paralog of ____________, despite only 16% sequence identity.

Accepted Answer

The answer of Comparison of three-dimensional structures indicated that heat...

Question 6

What is used during sequence alignments to better align two sequences?

Accepted Answer

A)  insertion of Gly residues 
B)  removal of $\alpha$-helical regions 
C)  insertion of gaps 
D)  removal of methionine and tryptophan due to their low prevalence in proteins 
E)  None of the answers is correct. 
A)  insertion of Gly residues 
B)  removal of $\alpha$-helical regions 
C)  insertion of gaps 
D)  removal of methionine and tryptophan due to their low prevalence in proteins 
E)  None of the answers is correct.

Question 7

Why are protein comparisons of three-dimensional shape more revealing than primary sequences?

Accepted Answer

The amino acid sequence can provide clue

Question 8

What technique produces large populations of molecules and selects for a biochemical property?

Accepted Answer

A)  peptide mass fingerprinting 
B)  two-dimensional gel electrophoresis 
C)  template-directed peptide synthesis 
D)  combinatorial chemistry 
E)  None of the answers is correct. 
A)  peptide mass fingerprinting 
B)  two-dimensional gel electrophoresis 
C)  template-directed peptide synthesis 
D)  combinatorial chemistry 
E)  None of the answers is correct.

Question 9

Based on their three-dimensional structures, actin and Hsp-70 are BEST described as

Accepted Answer

A)  homologs. 
B)  orthologs. 
C)  paralogs. 
D)  holologs 
E)  None of the answers is correct. 
A)  homologs. 
B)  orthologs. 
C)  paralogs. 
D)  holologs 
E)  None of the answers is correct.

Question 10

How are three-dimensional structures useful in evolutionary comparisons?

Accepted Answer

The structural details can be correlated

Question 11

__________________ are homologous molecules that are found in a given species.

Accepted Answer

The answer of __________________ are homologous molecules that are found...

Question 12

) An example of a conservative substitution would be

Accepted Answer

A)  Ala to Trp. 
B)  Gly to Ser. 
C)  Asp to Glu. 
D)  Val to Cys 
E)  Lys to Met. 
A)  Ala to Trp. 
B)  Gly to Ser. 
C)  Asp to Glu. 
D)  Val to Cys 
E)  Lys to Met.

Question 13

Which of the following is a database search procedure that is used to find homologous sequences in proteins?

Accepted Answer

A)  DisEMBL 
B)  Heliquest 
C)  BLAST 
D)  APSSP 
E)  REPRO 
A)  DisEMBL 
B)  Heliquest 
C)  BLAST 
D)  APSSP 
E)  REPRO

Question 14

Which of the following sequences would retain the base-pairing necessary to form a hairpin loop? The original sequence is UUGCUCAGUAAGAGCAA.

Accepted Answer

A)  UAGCUCAGUAAGAGCUA 
B)  UACCUCAGAGAGCUA 
C)  UUGUUUCAGAGAGCAA 
D)  All of the answers are correct. 
E)  None of the answers is correct. 
A)  UAGCUCAGUAAGAGCUA 
B)  UACCUCAGAGAGCUA 
C)  UUGUUUCAGAGAGCAA 
D)  All of the answers are correct. 
E)  None of the answers is correct.

Question 15

What is the population of molecules in which it is easy to study evolutionary processes using combinatorial chemistry?

Accepted Answer

A)  proteins 
B)  nucleotides 
C)  lipids 
D)  All of the answers are correct. 
E)  None of the answers is correct. 
A)  proteins 
B)  nucleotides 
C)  lipids 
D)  All of the answers are correct. 
E)  None of the answers is correct.

Question 16

If a protein contains a repetitive region, what might be assumed, and what should be done next to test the hypothesis?

Accepted Answer

Similar sequences imply a gene duplicati

Question 17

Homologs from different organisms that perform similar functions are called _____.

Accepted Answer

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

Question 18

In a combinatorial study of RNA described in the text, what functional feature(s) was/were of interest?

Accepted Answer

A)  ATP binding 
B)  loop formation 
C)  replication ability 
D)  All of the answers are correct. 
E)  None of the answers is correct. 
A)  ATP binding 
B)  loop formation 
C)  replication ability 
D)  All of the answers are correct. 
E)  None of the answers is correct.

Question 19

__________________ are homologous molecules that are found in different species and have similar or identical functions.

Accepted Answer

The answer of __________________ are homologous molecules that are found...

Question 20

In an evolutionary tree, what is the relationship between the length of the branches connecting each pair and the sequence differences?

Accepted Answer

The length of the branches con

Exam 6: Exploring Evolution and Bioinformatics

Two molecules are said to be _________________ if they have been derived from a common ancestor.

In the Blosum-62 substitution matrix, a large ________________ score corresponds to substitution that occurs only rarely.

A BLAST search provides

Evolutionary trees provide relative scales of divergence. How can these be reconciled with real times?

Comparison of three-dimensional structures indicated that heat shock protein 70 is a paralog of ____________, despite only 16% sequence identity.

What is used during sequence alignments to better align two sequences?

Why are protein comparisons of three-dimensional shape more revealing than primary sequences?

What technique produces large populations of molecules and selects for a biochemical property?

Based on their three-dimensional structures, actin and Hsp-70 are BEST described as

How are three-dimensional structures useful in evolutionary comparisons?

__________________ are homologous molecules that are found in a given species.

) An example of a conservative substitution would be

Which of the following is a database search procedure that is used to find homologous sequences in proteins?

Which of the following sequences would retain the base-pairing necessary to form a hairpin loop? The original sequence is UUGCUCAGUAAGAGCAA.

What is the population of molecules in which it is easy to study evolutionary processes using combinatorial chemistry?

If a protein contains a repetitive region, what might be assumed, and what should be done next to test the hypothesis?

Homologs from different organisms that perform similar functions are called _____.

In a combinatorial study of RNA described in the text, what functional feature(s) was/were of interest?

__________________ are homologous molecules that are found in different species and have similar or identical functions.

In an evolutionary tree, what is the relationship between the length of the branches connecting each pair and the sequence differences?

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