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Test Bank Biochemistry, Seventh Edition 7th Edition by Jeremy M. Berg ,‎ John L. Tymoczko,‎ Lubert Stryer

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.

1. a) BLAST
2. b) glutamine to asparagine
3. c) orthologs
4. d) alignment
5. e) convergent evolution
6. f) paralogs
7. g) gap
8. h) evolutionary tree
9. i) sequence templates
10. j) combinatorial chemistry
11. k) glycine to tryptophan
12. l) conservative

1.	____________ Homologs that perform similar or identical functions.
	Ans:	c
	Section: 6.1

2.	____________ Homologs from the same organism that perform different functions.
	Ans:	f
	Section: 6.1

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: 6.3

5.	____________ A database search procedure used to find homologous sequences in proteins.
	Ans:	a
	Section: 6.2

6.	____________ The processes 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.	____________ is a technique that produces large populations of molecules and selects for a biochemical property.
	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

11.	__________________ are homologous molecules that are found in different species and have similar or identical functions.
	Ans: Orthologs Section: 6.1

12.	__________________ are homologous molecules that are found in a given species but possess different biological functions.
	Ans: Paralogs Section: 6.1

13.	________________ amplification of well-preserved samples allows the determination of nucleotide sequences from extinct organisms.
	Ans: PCR Section: Introduction and 6.5

14.	Two molecules are said to be _________________ if they have been derived from a common ancestor.
	Ans: homologous Section: 6.1

15.	In the Blosum-62 substitution matrix, a large ________________ score corresponds to substitution that occurs only rarely.
	Ans: negative Section: 6.2

16.	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

17.	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

18.	___________________ can be detected in proteins by attempting to align a given sequence with itself, internally.
	Ans: Repeated motifs or Domains Section: 6.3

19.	Evolutionary trees are constructed with the assumption that the number of sequence differences is related to the time since the two sequences ________________________.
	Ans: diverged Section: 6.4

20.	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

21.	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

22.	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

23.	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

24.	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

25.	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

26.	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

27.	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

28.	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

29.	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

30.	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

31.	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

32.	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

33.	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

34.	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

35.	A BLAST search provides the following information.
	A) three-dimensional motifs B) a list of sequence alignments C) an estimate that an alignment occurred by chance D) All of the above. E) b and c only
	Ans: E Section: 6.2

Short-Answer Questions

36.	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

37.	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

38.	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

39.	How are sequence alignments made?
	Ans:	Two sequences are aligned and the best matches determined for all possible juxtapositions. In some cases, gaps are introduced to maximize the number of possible matches. Statistical formulas are used to determine the best fit according to defined parameters.
	Section: 6.2

40.	What is a substitution matrix?
	Ans:	A substitution matrix is deduced from aligned sequences, and scores correlate to how often an amino acid is substituted.
	Section: 6.2

41.	What is the difference between a simple scoring system for alignment and the Blosum-62 matrix?
	Ans:	The Blosum-62 allows an examination of substitutions that considers mutations that are conservative. Thus, conservative substitutions can be considered in the scoring used to determine the significance of the change in the alignment and allow more significant conclusions about evolutionary relationships.
	Section: 6.2

42.	How are three-dimensional structures useful in evolutionary comparisons?
	Ans:	The structural details can be correlated with specific functions. Enough of the structure must be maintained to retain the function, thus sequence changes occur that do not disrupt the structure. It is difficult to determine which amino acids are critical to the structure without evaluation of the three-dimensional structure. Thus, comparisons of proteins with similar structures reveal more critical information than sequence alignments.
	Section: 6.3

43.	If a protein contains a repetitive region, what might be assumed, and what should be done next to test the hypothesis?
	Ans:	Similar sequences imply a gene duplication event, which may indicate that that region of the protein has an important functional or structural role. The next steps would be to determine if the region of repetition is statistically significant and to examine the three-dimensional structure of the region.
	Section: 6.5

44.	In addition to examining the base sequence, what other features of RNA are useful in determining evolutionary patterns?
	Ans:	Changes to bases that retain the ability to form base-pairs with partner bases in other sections of the sequence imply that the base-pair is important. These conservative changes will retain the three-dimensional shape of the RNA molecule.
	Section: 6.3

45.	What evidence exists for a duplication event that led to the a and b-hemoglobin?
	Ans:	Lamprey is a fish that diverged from bony fish long ago. It has hemoglobin that contains a single type of subunit.
	Section: 6.4

46.	What are some of the inherent difficulties of using DNA from ancient samples?
	Ans:	Contamination of the DNA source is a major problem. In addition, old samples are often too degraded to be of real utility.
	Section: 6.5

47.	What are the processes by which evolution occurs?
	Ans:	There are three distinct steps: 1) Generation of a diverse population, 2) selection of members based on some criteria, and 3) reproduction of the selected members.
	Section: 6.5

48.	If using protein structure is a better method to determine evolutionary relationships, why is most analysis done using DNA sequences?
	Ans:	Relatively few protein structures have been determined. It is faster, easier, and cheaper to determine DNA sequences.
	Section: Entire Chapter

49.	Briefly describe the ATP – RNA binding experiment that showed that a structure had evolved that was capable of specific binding to ATP.
	Ans:	RNA sequences, synthesized by combinatorial chemistry, were selected for the ability to bind ATP using ATP affinity columns. The ATP-binding RNA molecules are released from the column and replicated, a process that occurs several times. The final RNA products with significant ATP-binding ability are isolated and characterized.
	Section: 6.5

50.	In an evolutionary tree, what is the relationship between the length of the branch connecting each pair and the sequence differences?
	Ans:	The length of the branch connecting each pair of proteins is proportional to the number of amino acid differences between sequences.
	Section: 6.4