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Mol Bio > Chapter 9 > Flashcards

Chapter 9 Flashcards

1
Q

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

A

Gene mutations

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2
Q

Alterations of a single or a few base pairs

A

Point mutations

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3
Q

Types of gene mutation

A

Silent mutation
Conservatove mutation
Non-conservative mutation
Framshift mutation

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4
Q

Substitution of one nucleotide with a different nucleotide

A

Silent

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5
Q

Without changing the amino acid sequence

A

Silent

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6
Q

Substitutions may change the amino acid sequence

A

Conservative

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7
Q

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

A

Conservative

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8
Q

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

A

Non conservative

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9
Q

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

A

Nonsense

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10
Q

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

A

Frameshift

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11
Q

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

A

Inherited mutation

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12
Q

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

A

Somatic mutation

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13
Q

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

A

Somatic mutation

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14
Q

Three Broad Approaches:

A
  1. Hybridization - based methods
    2 sequence ( polymerization) - based methods
  2. Enzymatic or chemical cleavage methods
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15
Q

more frequently used mutation screening

A

SINGLE-STRAND CONFORMATION POLYMORPHISMS (SECP)

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16
Q

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

A

SINGLE-STRAND CONFORMATION POLYMORPHISMS (SECP)

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17
Q

Steps in SSCP

A

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

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18
Q

SSCP DENATURATION OF DNA

A

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

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19
Q

SSCP DENATURATION IF EDTA

A

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

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20
Q

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

A

shape of the conformer

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21
Q

SSCP CAN BE RESOLVED in

A

polyacrylamide gel or by capillary electrophoresis
with temperature con tron

22
Q

SSCP band or peak patterns are detected by

A

silver stain, radioactivity , or fluorescent

23
Q

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

A

Reported to detect 35-100% of putative mutations.

24
Q

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

A

DENATURING GRADIENT GEL ELECTROPHORESIS (DEGE)

25
Q

stacking can affect denaturation of asDNA.

A

DENATURING GRADIENT GEL ELECTROPHORESIS (DEGE)

26
Q

DGGE ds DNA fragments________ bp

A

200-700

27
Q

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

A

urea and formamide

28
Q

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

A

Increases

29
Q

TWO gradient orientation used in D66P:

A

PERPENDICULAR DGGE
PARALLEL DGGE

30
Q

PERPENDICULAR DGGE

A

Horizontal

31
Q

Parallel DGGE

A

Parallel

32
Q

TwO methods that are similar in design to DGGE:

A

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

33
Q

for detecting known mutations than for screening

A

CONSTANT GRADIENT GEL ELECTROPHORESIS (CDGE)

34
Q

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

A

CONSTANT GRADIENT GEL ELECTROPHORESIS (CDGE)

35
Q

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

A

CONSTANT GRADIENT GEL ELECTROPHORESIS (CDGE)

36
Q

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

A

TEMPORAL TEMPERATURE GRADIENT GEL ELECTROPHORESIS
(IT6E)

37
Q

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

A

TEMPORAL TEMPERATURE GRADIENT GEL ELECTROPHORESIS
(TTGE)

38
Q

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

A

ALLELE - SPECIFIC OLIGOMER HIBRIDIZATON

39
Q

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

A

specific annealing temperatres and conditions (stringency),

40
Q

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

A

ASO

41
Q

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

A

Reverse dot blot

42
Q

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

A

factor V Leiden.

43
Q

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

A

MELT CURVE ANALYSIS

44
Q

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

A

Melt curve analysis

45
Q

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

A

etmidium bromide

46
Q

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

A

HIGH RESOLUTON MELI CURVE ANALYSIS (AR-MCA)

47
Q

method for detection of SNPS in DNA

A

Inversion probe assay

48
Q

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

A

INVERSION PROBE ASSAY

49
Q

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

A

HETERODUPLEX ANALYSIS

50
Q

Gel-based heteroduplex methods have been designed to

A

HN typing and hematological testing.

Mol Bio (14 decks)

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