Deck 6: Exploring Evolution and Bioinformatics

Question 1

The process by which very different evolutionary pathways lead totwo proteins with similar functions is referred to as _________________ evolution.

Answer 1

convergent

Question 2

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

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

Answer 2

B

Question 3

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

Answer 3

PCR

Question 4

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

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

Question 5

Homologs that exist in the same species are called _____.

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

Question 6

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

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

Question 7

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

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 8

An amino acid substitution to another of similar size and charge is called a _____ substitution.

A) replicative
B) conservative
C) convergent
D) homologous
E) orthologous

Question 9

___________________ can be detected in proteins by attempting to align a given sequence with itself, internally.

Question 10

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

Question 11

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

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

Question 12

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

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

Question 13

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

Question 14

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

Question 15

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

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 16

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

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

Question 17

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

Question 18

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

Question 19

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

Question 20

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

Question 21

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

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

Question 22

Define the terms homologs, paralogs, and orthologs.

Question 23

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

Question 24

What does an open reading frame encode?

A) DNA promoter sequences
B) potential protein coding regions
C) DNA terminator sequences
D) origins of replication
E) All of the answers are correct.

Question 25

Which of the following molecules is the most stable?

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

Question 26

A BLAST search provides

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.

Question 27

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

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 28

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

Question 29

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

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

Question 30

Homologs are two molecules

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 31

What is a substitution matrix?

Question 32

) An example of a conservative substitution would be

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

Question 33

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

Question 34

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?

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 35

How are sequence alignments made?

Question 36

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

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

Question 37

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

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

Question 38

Protein sequence comparisons can provide estimates of

A) protein function.
B) protein shape.
C) pathways of evolutionary descent.
D) All of the answers are correct.
E) protein shape and pathways of evolutionary descent.

Question 39

How are three-dimensional structures useful in evolutionary comparisons?

Question 40

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

Question 41

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

Question 42

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

Question 43

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

Question 44

In addition to examining the base sequence, what other features of RNA are useful in determining evolutionary patterns?

Question 45

If using protein structure is a better method to determine evolutionary relationships, why is most analysis done using DNA sequences?

Question 46

What evidence exists for a duplication event that led to the $\alpha$ and $\beta$ -hemoglobin?

Question 47

What are the three criteria necessary for evolution to occur?

Question 48

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