Biology 1001A Lecture Notes - Lecture 14: National Center For Biotechnology Information

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emeraldcattle11

7 May 2018

School

Western University

Department

Biology

Course

Biology 1001A

Professor

Beth Mac Dougall- Shackleton

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Question 1 of 3

1.0 Points

The program BLAST allows you to compare your query sequence with more than 100,000,000

sequence deposited in the databases at NCBI.

Which of the following statements about BLAST is correct?

A. It can only be used to compare highly similar sequences.

B. It can detect similarity between gene sequences but not protein sequences.

C. A query sequence of under 500 nucleotides is too short to result in a specific match.

D. It starts by looking for small regions of high similarity between sequences.

Question 2 of 3

1.0 Points

Which of the following statements about the E-value of a BLAST report is correct?

A. It is a probability that two sequences are similar simply by chance.

B. Two sequence with low similarity usually have a low E-value.

C. The higher the E-value the greater the chance of homology.

D. It coveys how strong the alignment is between two sequences.

Question 3 of 3

1.0 Points

Which of the following character strings contains the most information?

The word: TOMORROW

The protein sequence: MLSAGPVK

A. The protein because the same amino acid can be coded by more than one codon.

B. The protein because each amino acid is actually a triplet of base pairs.

C. The word because there are more character options at each position.

D. The word because it actually has meaning.

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Document Summary

The program blast allows you to compare your query sequence with more than 100,000,000 sequence deposited in the databases at ncbi. Which of the following statements about blast is correct: it can only be used to compare highly similar sequences. It can detect similarity between gene sequences but not protein sequences. C. a query sequence of under 500 nucleotides is too short to result in a specific match. D. it starts by looking for small regions of high similarity between sequences. It is a probability that two sequences are similar simply by chance. Two sequence with low similarity usually have a low e-value. C. the higher the e-value the greater the chance of homology. D. it coveys how strong the alignment is between two sequences. The protein because the same amino acid can be coded by more than one codon. The protein because each amino acid is actually a triplet of base pairs.

Related Questions

What is the percent sequence identity between hemoglobin (2HHB) and myoglobin (1A6M)?

	A.	93%
	B.	39.46%
	C.	25.17%
	D.	4.08%

QUESTION 2

Which of the following statements is consistent with the sequence similarity parameter?

	A.	The abundance of amino acids with similar properties that are arranged in the same order is equal to the abundance of identical amino acids.
	B.	These parameters are not related and cannot be compared.
	C.	The abundance of amino acids with similar properties that are arranged in the same order is less than the abundance of identical amino acids.
	D.	The abundance of amino acids with similar properties that are arranged in the same order is higher than the abundance of identical amino acids.

QUESTION 3

Which of the following statements is consistent with the similarity parameter and visualization of the aligned structures?

	A.	Hemoglobin and myoglobin do not have similar structures.
	B.	Hemoglobin and myoglobin have only moderately similar structures, as indicated by the large abundance of gray chains.
	C.	Hemoglobin and myoglobin have very similar structures.
	D.	Hemoglobin and myoglobin are perfectly aligned at every amino acid.

QUESTION 4

Hemoglobin (2HHB) is ___ amino acids shorter than myoglobin; the sequence alignment considers only ___ amino acids, and alignment results show that hemoglobin is missing a contiguous strand of ___ amino acids.

	A.	10; 141; 6
	B.	10; 141; 5
	C.	10; 147; 6
	D.	10; 147; 5

QUESTION 5

Which of the following statements best describes the evolutionary relationship between hemoglobin and myoglobin?

	A.	The low sequence identity indicates that hemoglobin and myoglobin are not related, as tertiary structure cannot be used to study protein evolution.
	B.	Both the high sequence identity and structural similarity suggest that hemoglobin and myoglobin are related.
	C.	The difference in sequence identity and similarity values suggests that hemoglobin and myoglobin are related.
	D.	The high structural similarity suggests that hemoglobin and myoglobin are related, while the low sequence identity suggests that the genes for each protein have diverged through mutation and deletion of several amino acids.

QUESTION 6

The comparison of sequences and tertiary structures in this exercise indicates that:

	A.	only similar amino acid sequences can provide the same tertiary structure.
	B.	different amino acid sequences can provide very similar tertiary structures.

QUESTION 7

The structures of deoxyhemoglobin and oxyhemoglobin are derived from the same source, have the same exact amino acid sequence and length, and differ only in the presence of noncovalently bound oxygen.

	A.	True
	B.	False

QUESTION 8

When using the Sequencing and Structure Alignment tool, the degree of the structural similarity is shown by the superimposition of the backbones. Accordingly, which of the following statement best describes the comparison of deoxyhemoglobin and oxyhemoglobin?

	A.	Only slight differences in the backbone traces occur throughout the aligned proteins.
	B.	The only differences in the backbone traces occur near the oxygen-binding sites.
	C.	The backbone traces of the proteins are drastically different.
	D.	The backbone traces of the proteins are identical.

QUESTION 9

The alignment of 2HHB and 1HHO shows that the binding of oxygen results in _______ in the protein.

	A.	minor conformational changes at sites proximal and distal to the oxygen-binding site
	B.	no conformational change
	C.	drastic conformational changes
	D.	minor conformational changes only within the oxygen-binding site

QUESTION 10

The alignment of 2HHB and 1HHO shows that the conformation of the Fe-heme group _____ upon oxygen binding.

	A.	changes
	B.	does not change

Question #1: Which of the following is true?a)A cladogram does not show relationships between organisms, but it does show how much evolutionary time has passed.b)A phylogram shows relationships between organisms, as well as how much evolutionary time has passed.c)A cladogram shows relationships between organisms, as well as how much evolutionary time has passed.Question #2: The term ÂindelÂ refers to:a)ÂInsertions and deletionsÂ when comparing sequences; one cannot determine whether extra nucleotides were inserted in one sequence or deleted in anotherb)ÂIndeliverableÂ Â refers to entering a sequence in the ClustalW2 website that is not recognized.Question #3: Which is an example of FASTA format?a)Name: ATCCGTAb)>Name ATCCGTAc)ATCCGTAQuestion #4: Which is NOT true about the ExPASy website?a)All of these are true.b)During our lab, we will access it via the BLAST website.c)You can find information about your geneÂs role in biological processes.d)It gives you links to many other websites with information on your gene.Question #5: Once you click on the Accession number in your BLAST results, what kind of information will you NOT find?a)DNA sequenceb)Amino acid sequencec)Person(s) who published the datad)All of the above can be found.

cyansheep824

QUESTION 1

A mutation caused by exposure to gamma rays is called a spontaneous mutation

	a.	True
	b.	False
	c.	Sometimes, depending on the type of base change
	d.	Gamma rays do not cause mutations

QUESTION 2

A recessive mutation affecting an essential biochemical pathway can be detected________

	a.	when the organism is heterozygous for that mutation.
	b.	when the organism is homozygous for that mutation.
	c.	in either homozygous or heterozygous conditions.
	d.	only by sequencing (recessive mutations never show a phenotype).

QUESTION 3

During DNA replication, the newly synthesized chain grows by adding

	a.	nitrogenous bases
	b.	the sugar-phosphate backbone
	c.	nucleosides
	d.	dNTPs

QUESTION 4

During replication, the DNA strand 5â- AAGTCTAGCCTAG -3â will serve as a template for the polymerization of:

	a.	5â- CTAGGCTAGACTT -3â
	b.	5â - TTCAGATCGGATC -3â
	c.	5â - GATCCGATCTGAA -3â
	d.	3â - AAGTCTAGCCTAG -5â

QUESTIOn 5

Given the following DNA sequences, select which statement(s) is(are) correct.

Sequence 1:

5â-TGGACGCTAA-3â

3â-ACCTGCGATT-5â

Sequence 2:

5â-AATCGCAGGT-3â

3â-TTAGCGTCCA-5â

Sequence 3:

5â-ACCTGCGATT-3â

3â-TGGACGCTAA-5â

	a.	Sequences 1 and 2 are the same
	b.	Sequences 1 and 3 are the same
	c.	Sequences 2 and 3 are the same
	d.	Sequences 1, 2 and 3 are all different

QUESTION 6

Repetitive sequences in the genome are hotspots for:

	a.	Deamination
	b.	Depurination
	c.	Thymine dimer formation
	d.	Replication errors

QUESTION 7

Select which statement(s) about the Ames test is(are) correct

	a.	it has been designed to understand mutation repair systems in Salmonella typhimurium
	b.	it uses mammalian liver extract
	c.	it allows to study whether chemical compounds or their enzymatic breakdown products are mutagenic
	d.	it is based on whether a chemical compound causes reversion mutations from his+ to his-
	e.	two of the above are correct
	f.	three of the above are correct

QUESTION 8

Select which statement(s) is(are) correct.

	a.	All DNA strands have a direction, and it is specified by the carbons in the sugar backbone.
	b.	All DNA strands have a direction, and it is specified by hydrogen bonds between nucleotides.
	c.	In order to form proper base pairs in a double stranded DNA molecule, the two strands must run in opposite directions.
	d.	A and C are correct.
	e.	B and C are correct.

QUESTION 9

Studies of gene mutation frequencies have shown that:

	a.	mutations are rare, and genomes are generally stable.
	b.	mutation frequencies differ among organisms and also between genes, suggesting certain genes are more susceptible to mutation.
	c.	mutation frequencies are consistent between organisms, and each region of DNA is equally susceptible to random mutations.
	d.	Both A and B are correct.
	e.	Both A and C are correct.

QUESTION 10

The compound 5-bromodeoxyuridine (BrdU) is a derivative of uracil, and if BrdU becomes incorporated during DNA replication, it pairs with adenine. This compound is best classified as which type of mutagen?

	a.	base analog
	b.	base inducer
	c.	intercalating agent
	d.	oxidative agent
	e.	alkylating agent

QUESTION 11

The rate of mutation of the fruit fly is higher than the rate of mutation of Algae

True

False

QUESTION 12

Thymine dimers are most commonly caused by which of the following?

	a.	X-rays
	b.	Alkylating agents
	c.	U.V. irradiation
	d.	DNA intercalating agents

QUESTION 13

What chemical group is found in the 3â end of a DNA strand?

	a.	an alcohol
	b.	a hydroxyl
	c.	a methyl
	d.	a phosphate

QUESTION 14

What chemical group is found in the 5â end of a DNA strand?

	a.	an alcohol
	b.	a hydroxyl
	c.	a methyl
	d.	a phosphate

QUESTION 15

Which is the correct order of molecules binding to DNA during DNA replication?

	a.	Helicase, SSB, primase, DNA pol III, DNA pol I, ligase
	b.	SSB, DNA pol I, ligase, helicase, DNA pol I, primase
	c.	primase, helicase, DNA pol III, ligase, DNA pol I, SSB
	d.	SSB, helicase, primase, DNA pol III, DNA pol I, ligase

QUESTION 16

Which statement(s) is(are) correct about strand slippage?

	a.	It can cause disorders such as Huntingon disease.
	b.	It is a process that causes mutations altering the number of DNA repeats.
	c.	It is a process that incorporates nucleotide base analogs and trinucleotide repeats.
	d.	a and b are correct.
	e.	b and c are correct.
	f.	a, b and c are correct.

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Biology 1001A Lecture Notes - Lecture 14: National Center For Biotechnology Information

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