Chapter 9

Question 1

Deletions, insertions, inversions, translocations, and other changes that can affect one base pair to hundreds or thousands of base pairs

Answer 1

Gene mutations

Question 2

Alterations of a single or a few base pairs

Answer 2

Point mutations

Question 3

Types of gene mutation

Answer 3

Silent mutation
Conservatove mutation
Non-conservative mutation
Framshift mutation

Question 4

Substitution of one nucleotide with a different nucleotide

Answer 4

Silent

Question 5

Without changing the amino acid sequence

Answer 5

Silent

Question 6

Substitutions may change the amino acid sequence

Answer 6

Conservative

Question 7

But the replacement and the original amino acid have similar biochemical properties, e.g., leucine for valine, change will not affect protein function significantly

Answer 7

Conservative

Question 8

Substitution of a biochemically different amino acid, e.g., proline for glutamine, which changes the biochemical nature of the protein

Answer 8

Non conservative

Question 9

Terminates proteins prematurely when a nucleotide substitution produces a stop codon instead of an amino-acid

Answer 9

Nonsense

Question 10

Insertion or deletion of more or efewer than three nucleotides throwing the triplet code out of frame

Answer 10

Frameshift

Question 11

Detected from the most convenient and noninvasive specimen material, such as blood or buccal cells

Answer 11

Inherited mutation

Question 12

Often more challenging to find because cells harboring mutations may be only a small fraction of the total specimen that consists of mostly normal cells

Answer 12

Somatic mutation

Question 13

Under these circumstances, detection procedures must identify a single mutated gene from among thousands of normal genes

Answer 13

Somatic mutation

Question 14

Three Broad Approaches:

Answer 14

1. Hybridization - based methods
   2 sequence ( polymerization) - based methods
2. Enzymatic or chemical cleavage methods

Question 15

more frequently used mutation screening

Answer 15

SINGLE-STRAND CONFORMATION POLYMORPHISMS (SECP)

Question 16

is determined by the migration of the single-stranded
conformers in polyacrylamide gels under precisely controlled denaturing and temperature conditions.

Answer 16

SINGLE-STRAND CONFORMATION POLYMORPHISMS (SECP)

Question 17

Steps in SSCP

Answer 17

short,double-stranded PCR produts➡️Dilute
long ➡️Denatured followed by rapid cooling

Question 18

SSCP DENATURATION OF DNA

Answer 18

10-10 mM NaH, 80% formamide for 5 mins at 95°c

Question 19

SSCP DENATURATION IF EDTA

Answer 19

0.004 mM EDIA 10% formamide for 5 mins
at 55°- 60°C

Question 20

the _____________________ depends on the complementary
nucleotides available for hydrogen bonding and folding

Answer 20

shape of the conformer

Question 21

SSCP CAN BE RESOLVED in

Answer 21

polyacrylamide gel or by capillary electrophoresis
with temperature con tron

Question 22

SSCP band or peak patterns are detected by

Answer 22

silver stain, radioactivity , or fluorescent

Question 23

SSCP CAN BE Reported to detect ___________% of putative mutations.

Answer 23

Reported to detect 35-100% of putative mutations.

Question 24

exploits differences in denaturation between a normal &
mutated DNA molecure caused by even one nucleotide
difference in a sequence

Answer 24

DENATURING GRADIENT GEL ELECTROPHORESIS (DEGE)

Question 25

stacking can affect denaturation of asDNA.

Answer 25

DENATURING GRADIENT GEL ELECTROPHORESIS (DEGE)

Question 26

DGGE ds DNA fragments________ bp

Answer 26

200-700

Question 27

DGGE fragments are separated on polyacrylamide gels containing a gradient of concentrations

Answer 27

urea and formamide

Question 28

As the dsDNA fragments moves through the gel, the denaturing conditions _____________, sequences reach their denaturing point, and the complementary strands begin to denature.

Answer 28

Increases

Question 29

TWO gradient orientation used in D66P:

Answer 29

PERPENDICULAR DGGE PARALLEL DGGE

Question 30

PERPENDICULAR DGGE

Answer 30

Horizontal

Question 31

Parallel DGGE

Answer 31

Parallel

Question 32

TwO methods that are similar in design to DGGE:

Answer 32

CONSTANT GRADIENT GEL ELECTROPHORESIS (CDGE) TEMPORAL TEMPERATURE GRADIENT GEL ELECTROPHORESIS (IT6E)

Question 33

for detecting known mutations than for screening

Answer 33

CONSTANT GRADIENT GEL ELECTROPHORESIS (CDGE)

Question 34

Requires the initial determination of optimal denaturant concentration for a particular gene mutation

Answer 34

CONSTANT GRADIENT GEL ELECTROPHORESIS (CDGE)

Question 35

ascertained by perpendicular DEGE or by using computer programs designed to predict the melting characteristics of a nuleotide sequence for a range of temperature and denaturing concentrations

Answer 35

CONSTANT GRADIENT GEL ELECTROPHORESIS (CDGE)

Question 36

similar 10 CDGF (difference is temperature) In that specific concentrations of formamide and urea are used to denature DNA dupiexes

Answer 36

TEMPORAL TEMPERATURE GRADIENT GEL ELECTROPHORESIS (IT6E)

Question 37

differences in denaturation unlike DG, are resolved by slowly raising the temperature of the gel during migration

Answer 37

TEMPORAL TEMPERATURE GRADIENT GEL ELECTROPHORESIS (TTGE)

Question 38

utilizes the differences in melting temperatures of short sequences of -20 bases with one or two mismatches and those with no mismatches.

Answer 38

ALLELE - SPECIFIC OLIGOMER HIBRIDIZATON

Question 39

a single- stranded probe will not bind to a near complementacy target sequence with one or two mismatched bases, whereas a probe perfectly complementary to the target sequence will bind

Answer 39

specific annealing temperatres and conditions (stringency),

Question 40

a DOT BLOT method, similar to vouthern bior using immobilized targer and jabered probe in solution-

Answer 40

ASO

Question 41

AsO can also be carried out as a _____________ to capture probe methoas developed for infectious disease testing.

Answer 41

Reverse dot blot

Question 42

ASO method has been proposed for detection of fre quently occuring mutations such as

Answer 42

factor V Leiden.

Question 43

exploits tne sequence- and stacking - directed denaturation characteriStes of DNA duprexes.

Answer 43

MELT CURVE ANALYSIS

Question 44

very useful as a post amplification step of RT-PCR.

Answer 44

Melt curve analysis

Question 45

PR amplicons generated in the presence of a DNA- specific fluorescent due such as

Answer 45

etmidium bromide

Question 46

uses fluorescent resonance energy transfer (FRET) propes that hybridize next to ong another across the sequence position being anargned.

Answer 46

HIGH RESOLUTON MELI CURVE ANALYSIS (AR-MCA)

Question 47

method for detection of SNPS in DNA

Answer 47

Inversion probe assay

Question 48

the probe hybridizes to the targer sequence, the two ends flanking the potential SP being tested

Answer 48

INVERSION PROBE ASSAY

Question 49

formed when a single strands that are not complementary hybridize to ano another

Answer 49

HETERODUPLEX ANALYSIS

Question 50

Gel-based heteroduplex methods have been designed to

Answer 50

HN typing and hematological testing.