bioinformatics platings

Question 1

If you want to examine the threedimensional structure of a protein, you will
look into which database?

Answer 1

PDBe

Question 2

This is the process of identifying locations of genes, all the protein coding regions, and the regulatory sequences in a genome

Answer 2

Genome annotation

Question 3

In a sequence alignment, a dot between
matched bases indicates

Answer 3

non-identical bases

Question 4

In pairwise sequence alignments, gaps are more often seen in Local alignments than in global alignments.

Answer 4

False

Question 5

When you get a BLAST result for a DNA
sequence, the Graphic Summary refers to

Answer 5

red bars specifying sequences found in the database that aligns to your sequence

Question 6

You have sequenced five PCR products of DNA samples of Escherichia coli you have isolated from clinical specimens. You want to determine in which nucleotide bases the five DNA sequences vary, which tool will
be most helpful to you?

Answer 6

MUSCLE

Question 7

If you want to compare the amino acid
sequence of your protein with those that are stored in the databases, which tool will you use?

Answer 7

BLASTp

Question 8

When you search GenBank for the DNA
sequence of gene X, you will find a link
called FASTA. This refers to

Answer 8

a nucleic acid or protein sequence
represented by single-letter codes

Question 9

Sequence alignment helps scientists to

Answer 9

• trace out evolutionary relationships
• infer the functions of newly
  synthesized genes
• predict new members of gene
  families

Question 10

Which of the following is a nucleotide
sequence database?

Answer 10

EMBL

Question 11

It is a diagram representing evolutionary relationships among organisms

Answer 11

Phylogenetic tree

Question 12

This is a unique identifier given to a DNA or protein sequence record to allow tracking of different versions of that sequence and the associated sequence overtime in a single
data repository

Answer 12

Accession number

Question 13

If you are studying a set of all RNA
molecules in a mouse, you are dealing with

Answer 13

Transcriptomics

Question 14

The alignment procedure that tries to align regions with high level of matches without considering the alignment of the rest of the sequences.

Answer 14

Local alignment

Question 15

An example of global sequence alignment

Answer 15

ADLGAVFALCDRYFQ
I I I I I I I I I I I
ADLGRTQN-CDRYYQ

Question 16

How many primers are needed for a successful PCR of a gene that is common among different species?

Answer 16

Two

Question 17

Which of the following may result in no band or faint band in agarose gel electrophoresis?

Answer 17

-The annealing temperature is too high
(Low Ta causes non-specific binding of
primers to target, forming non-specific
bands)

Question 18

Which is true about the reverse primer?

Answer 18

-It is the complement of the 3-prime end of the sense DNA template

Question 19

What is the effect of homology between the three-prime ends of the forward and reverse
primer?

Answer 19

Formation of primer dimer

Question 20

The primers used in polymerase chain
reaction are

Answer 20

Single-stranded DNA oligonucleotide

Question 21

If the primer sequence is TCG, which
section of the DNA will it anneal to?

Answer 21

AGC

Question 22

How many primers are needed for a
successful PCR of a gene when the only
information available is the protein amino amino sequence?

Answer 22

more than four

Question 23

How many primers are needed for a
successful PCR of a known sequence of a gene?

Answer 23

two
(You only need one forward and one reverse
primer.)

Question 24

What would be the expected effect on a PCR reaction if the primers used were slightly shorter and more variable than the intended oligonucleotide sequences?

Answer 24

The reaction would yield a mixture of nonspecific products.

Question 25

What type of PCR primers are designed
when the only information available is the protein amino acid sequence?

Answer 25

Degenerate primers

Question 26

Primer annealing means

Answer 26

The binding of the primer to the template DNA

Question 27

If the melting temperature of a pair of
primers is calculated as 62 C, at what
annealing temperature would you set your PCR cycling?

Answer 27

-57 C
(The annealing temperature should be 5 C
lower than the Ta)

Question 28

Which of the following is the LEAST factor to consider when optimizing a new primer
pair?

Answer 28

Denaturation temperature
(Must be optimized.)

Question 29

What is the function of a primer?

Answer 29

-to identify the particular region of the DNA to be copied by PCR

Question 30

Which double-stranded DNA molecule has the highest melting temperature

Answer 30

An oligonucleotide with a large number of repeating C-G-C codons