Chapter 6 Exploring Evolution and Bioinformatics Matching Questions Use the following to answer questions 1-10: Choose the correct answer from the list below.Not all of the answers will be used a)BLAST b)glutamine to asparagine c)orthologs d)alignment e)convergent evolution f)paralogs g)gap h)evolutionary tree i)sequence templates j)PCR k)glycine to tryptophan 1)conservative Homologs that perform similar or identical functions. Ans:c Section:Introduction 2 Homologs from the same organism that perform different functions. Ans:f Section:Introduction 3 An amino acid substitution to another of similar size and charge is called a substitution. Ans:I Section:6.2 4 Regions of a protein,critical to three-dimensional structure,that are conserved. Ans:i Section:6.1 5 A database search procedure used to find homologous sequences in proteins. Ans:a Section:6.3
Chapter 6 Exploring Evolution and Bioinformatics Matching Questions Use the following to answer questions 1-10: Choose the correct answer from the list below. Not all of the answers will be used. a) BLAST b) glutamine to asparagine c) orthologs d) alignment e) convergent evolution f) paralogs g) gap h) evolutionary tree i) sequence templates j) PCR k) glycine to tryptophan l) conservative 1 ____________ Homologs that perform similar or identical functions. Ans: c Section: Introduction 2 ____________ Homologs from the same organism that perform different functions. Ans: f Section: Introduction 3 An amino acid substitution to another of similar size and charge is called a ____________ substitution. Ans: l Section: 6.2 4 ____________ Regions of a protein, critical to three-dimensional structure, that are conserved. Ans: i Section: 6.1 5 ____________ A database search procedure used to find homologous sequences in proteins. Ans: a Section: 6.3
Chapter 6 Exploring Evolution and Bioinformatics 2 6 The process by which different evolutionary paths end up at a similar structure or mechanism. Ans:e Section:6.3 Used to present a graphical depiction of how sequences are related in evolutionary terms. Ans:h Section:6.4 P Technique used prior to sequencing to demonstrate the evolutionary relationships between Neanderthals and Homo Sapiens. Ans:j Section:6.5 9 An example of a conservative amino acid change. Ans:b Section:6.2 10 In some sequence alignments it is necessary to include a Ans:g Section:6.2 Fill in the Blank Questions are homologous molecules that are found in different species and have similar or identical functions. Ans:Orthologs Section:6.1 2 are homologous molecules that are found in a given species but possess different biological functions. Ans:Paralogs Section:6.1 amplification of well-preserved samples allows the determination of nucleotide sequences from extinct organisms. Ans:PCR Section:Introduction 6.5 4 Two molecules are said to be if they have been derived from a common ancestor Ans:homologous Section:6.1 5 In the Blosum-62 substitution matrix,a large score corresponds to substitution that occurs only rarely. Ans:negative Section:6.2
Chapter 6 Exploring Evolution and Bioinformatics 2 6 ____________ The process by which different evolutionary paths end up at a similar structure or mechanism. Ans: e Section: 6.3 7 ____________ Used to present a graphical depiction of how sequences are related in evolutionary terms. Ans: h Section: 6.4 8 ____________ Technique used prior to sequencing to demonstrate the evolutionary relationships between Neanderthals and Homo Sapiens. Ans: j Section: 6.5 9 ____________ An example of a conservative amino acid change. Ans: b Section: 6.2 10 In some sequence alignments it is necessary to include a ____________. Ans: g Section: 6.2 Fill in the Blank Questions 1 __________________ are homologous molecules that are found in different species and have similar or identical functions. Ans: Orthologs Section: 6.1 2 __________________ are homologous molecules that are found in a given species but possess different biological functions. Ans: Paralogs Section: 6.1 3 ________________ amplification of well-preserved samples allows the determination of nucleotide sequences from extinct organisms. Ans: PCR Section: Introduction & 6.5 4 Two molecules are said to be _________________ if they have been derived from a common ancestor. Ans: homologous Section: 6.1 5 In the Blosum-62 substitution matrix, a large ________________ score corresponds to substitution that occurs only rarely. Ans: negative Section: 6.2
Chapter 6 Exploring Evolution and Bioinformatics w 6 Analysis of substitution matrices indicates that cysteine(C)and residues tend to be conserved more than other amino acid residues. Ans:tryptophan (W)Section:6.2 7 The process by which very different evolutionary pathways lead to a protein with similar function is referred to as evolution. Ans:convergent Section:6.3 8 Repeated motifs,or domains,can be detected in proteins by aligning sequences with Ans:themselves Section:6.3 9 A conservative substitution of a lysine(K)residue would be replacement with a/an residue. Ans:arginine(R)Section:6.2 10 Comparison of three-dimensional structures indicated that heat shock protein 70 is a paralog of despite only 15.6%sequence identity. Ans:actin Section:6.3 Multiple Choice Questions 1 Protein sequence comparisons can provide estimates of A) protein function. D All of the above B) protein shape. E) b and c only C) pathways of evolutionary descent. Ans:E Section:Introduction 2 The definition of a homolog is A) molecules related by sequence similarity. B) two molecules derived from a common ancestral protein. C) molecules with similar domains. D) All of the above. E) None of the above. Ans:B Section:6.1 3 Paralogs differ in A)detailed biochemical functions. D) All of the above. B) ancestral evolution. E) None of the above. C)ornithology. Ans:A Section:6.1 4 An example of a conservative substitution would be A)Ala to Trp D) All of the above B)Gly to Ser. E) None of the above. C)Asp to Glu. Ans:C Section:6.2
Chapter 6 Exploring Evolution and Bioinformatics 3 6 Analysis of substitution matrices indicates that cysteine (C) and __________________ residues tend to be conserved more than other amino acid residues. Ans: tryptophan (W) Section: 6.2 7 The process by which very different evolutionary pathways lead to a protein with similar function is referred to as _________________ evolution. Ans: convergent Section: 6.3 8 Repeated motifs, or domains, can be detected in proteins by aligning sequences with __________________. Ans: themselves Section: 6.3 9 A conservative substitution of a lysine (K) residue would be replacement with a/an ____________ residue. Ans: arginine (R) Section: 6.2 10 Comparison of three-dimensional structures indicated that heat shock protein 70 is a paralog of ____________, despite only 15.6% sequence identity. Ans: actin Section: 6.3 Multiple Choice Questions 1 Protein sequence comparisons can provide estimates of A) protein function. D) All of the above B) protein shape. E) b and c only C) pathways of evolutionary descent. Ans: E Section: Introduction 2 The definition of a homolog is A) molecules related by sequence similarity. B) two molecules derived from a common ancestral protein. C) molecules with similar domains. D) All of the above. E) None of the above. Ans: B Section: 6.1 3 Paralogs differ in A) detailed biochemical functions. D) All of the above. B) ancestral evolution. E) None of the above. C) ornithology. Ans: A Section: 6.1 4 An example of a conservative substitution would be A) Ala to Trp. D) All of the above. B) Gly to Ser. E) None of the above. C) Asp to Glu. Ans: C Section: 6.2
Chapter 6 Exploring Evolution and Bioinformatics 4 5 An open reading frame is necessary to compare A) DNA promoter sequences. B) alignments of potential protein coding regions. c) cDNA alignments. D All of the above. E) None of the above Ans:B Section:6.2 6 Based on their three-dimensional structures,actin and Hsp-70 are considered A)homologs D)All of the above. B) orthologs E) None of the above. C) paralogs. Ans:C Section:6.3 7 What percentage of proteins contain two or more similar domains? A)10%B)36%C)8%D)All of the above.E)None of the above. Ans:A Section:6.3 8 An example of proteins that evolved similar mechanisms by convergent evolution is A)DNA polymerase and elastase. D) b and c B) chymotrypsin and subtilisin. E) None of the above C) neuramidase and glycolase. Ans:B Section:6.3 9 Which of the following sequences would retain the base-pairing necessary to form a hairpin loop?The original sequence is UUGCUCAGUAAGAGCAA. A) UAGCUCAGUAAGAGCUA D) All of the above. B) UACCUCAGAGAGCUA E) None of the above. C)UUGUUUCAGAGAGCAA Ans:A Section:6.3 10 Evolutionary trees provide relative scales of divergence.How can these be reconciled with real times? A)by comparing the amount of sequence divergence B)by comparing proteins from convergent evolution C) by using fossil records when possible D)All of the above. E)None of the above. Ans:C Section:6.4 11 Which of the following molecules is the most stable? A)mRNA D) IRNA B)hemoglobin E) mitochondrial DNA C)carbohydrates Ans:E Section:6.5
Chapter 6 Exploring Evolution and Bioinformatics 4 5 An open reading frame is necessary to compare A) DNA promoter sequences. B) alignments of potential protein coding regions. C) cDNA alignments. D) All of the above. E) None of the above. Ans: B Section: 6.2 6 Based on their three-dimensional structures, actin and Hsp-70 are considered A) homologs. D) All of the above. B) orthologs. E) None of the above. C) paralogs. Ans: C Section: 6.3 7 What percentage of proteins contain two or more similar domains? A) 10% B) 36% C) 8% D) All of the above. E) None of the above. Ans: A Section: 6.3 8 An example of proteins that evolved similar mechanisms by convergent evolution is A) DNA polymerase and elastase. D) b and c B) chymotrypsin and subtilisin. E) None of the above C) neuramidase and glycolase. Ans: B Section: 6.3 9 Which of the following sequences would retain the base-pairing necessary to form a hairpin loop? The original sequence is UUGCUCAGUAAGAGCAA. A) UAGCUCAGUAAGAGCUA D) All of the above. B) UACCUCAGAGAGCUA E) None of the above. C) UUGUUUCAGAGAGCAA Ans: A Section: 6.3 10 Evolutionary trees provide relative scales of divergence. How can these be reconciled with real times? A) by comparing the amount of sequence divergence B) by comparing proteins from convergent evolution C) by using fossil records when possible D) All of the above. E) None of the above. Ans: C Section: 6.4 11 Which of the following molecules is the most stable? A) mRNA D) rRNA B) hemoglobin E) mitochondrial DNA C) carbohydrates Ans: E Section: 6.5
Chapter 6 Exploring Evolution and Bioinformatics 12 An example of paralogs would include A) hemoglobin and myoglobin. D) All of the above. B) actin and keratin. E) None of the above. c) DNA polymerase and trypsin. Ans:A Section:6.1 13 In a combinatorial study of RNA described in the text,what functional feature was of interest? A) ATP binding D) All of the above. B) loop formation E) None of the above. C)replication ability Ans:A Section:6.5 14 A population of molecules in which it is easy to study evolutionary processes using combinatorial chemistry. A)proteins D) All of the above. B) nucleotides E) None of the above. C)lipids Ans:B Section:6.5 15 If a cys-cys disulfide bond is required in a structure,this would be an appropriate amino acid substitution for cys. A)arg B)his C)lys D)All of the above. E)None of the above Ans:E Section:previous chapters Short-Answer Questions 1 Why are protein comparisons of three-dimensional shape more revealing than primary sequences? Ans:The amino acid sequence can provide clues to a protein's function and its relationship to other proteins.However,the shape can provide more information about the arrangement of the amino acids in space.This information is critical to understanding protein function Comparison of structure can reveal other relationships that may not be apparent from the sequence alone. Section:Introduction 2 How does one determine if two homolog proteins are paralogs or orthologs? Ans:From functional studies,paralogs have similar sequences,but differ in function. Orthologs have similar or identical functions. Section:6.1 3 Why is it more effective to compare protein sequences,rather than DNA sequences,in evolutionary studies? Ans:More effective statistical comparisons can be made using amino acids as there are 20 amino acids versus 4 bases.Furthermore,base alterations may result in meaningless silent mutations. Section:6.2
Chapter 6 Exploring Evolution and Bioinformatics 5 12 An example of paralogs would include A) hemoglobin and myoglobin. D) All of the above. B) actin and keratin. E) None of the above. C) DNA polymerase and trypsin. Ans: A Section: 6.1 13 In a combinatorial study of RNA described in the text, what functional feature was of interest? A) ATP binding D) All of the above. B) loop formation E) None of the above. C) replication ability Ans: A Section: 6.5 14 A population of molecules in which it is easy to study evolutionary processes using combinatorial chemistry. A) proteins D) All of the above. B) nucleotides E) None of the above. C) lipids Ans: B Section: 6.5 15 If a cys-cys disulfide bond is required in a structure, this would be an appropriate amino acid substitution for cys. A) arg B) his C) lys D) All of the above. E) None of the above. Ans: E Section: previous chapters Short-Answer Questions 1 Why are protein comparisons of three-dimensional shape more revealing than primary sequences? Ans: The amino acid sequence can provide clues to a protein’s function and its relationship to other proteins. However, the shape can provide more information about the arrangement of the amino acids in space. This information is critical to understanding protein function. Comparison of structure can reveal other relationships that may not be apparent from the sequence alone. Section: Introduction 2 How does one determine if two homolog proteins are paralogs or orthologs? Ans: From functional studies, paralogs have similar sequences, but differ in function. Orthologs have similar or identical functions. Section: 6.1 3 Why is it more effective to compare protein sequences, rather than DNA sequences, in evolutionary studies? Ans: More effective statistical comparisons can be made using amino acids as there are 20 amino acids versus 4 bases. Furthermore, base alterations may result in meaningless silent mutations. Section: 6.2