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BIO 140 > Module 3 > Flashcards

Module 3 Flashcards

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1
Q

Paved the way for genomics
Evaluate genetic variation within and among individuals, species, and higher order taxonomic groups

A

DNA Marker Technologies

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2
Q

For genetic variation to be useful to geneticists, they
must be:

A
  1. heritable
  2. discernible to the researcher
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3
Q

Genomic sources:

A

Nuclear genes and Plastid (Mitochondrial) genes

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4
Q
  • Usually come in pairs in diploid organisms
  • May occur as different alleles in heterozygotes
A

Nuclear Genes

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5
Q
  • Maternally inherited
  • Usually more variable than nuclear genes due to rapid mutation
  • Result from a lack of repair mechanisms during replication
  • Haploid
A

Plastid genes (i.e. Mitochondrial genes)

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6
Q

Differentiate type I and II markers

A

Type I - markers associated with genes of known function
Type II - associated with anonymous genomic segments

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7
Q

DNA Marker Technologies are dependent on:

A

*Gel electrophoresis
*Polymerase chain reaction (PCR) – for nucleic acids

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8
Q

*Separates nucleic acids or proteins on the basis of their rate of movement through a gel in an electrical field
*Makes use of either agarose or acrylamide gel matrix

A

Gel Electrophoresis

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9
Q

*Amplifies EXPONENTIALLY specific segments of DNA or RNA
*Pioneered by Kary Mullis
*Follows principle of DNA replication

A

Polymerase Chain Reaction (PCR)

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10
Q

3 Stages of PCR

A

Denaturation, Annealing, Extension

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11
Q

Stage wherein
- Makes the dsDNA single stranded
- Helicase absent; expose it to elevated temperatures to unwind

What is the temp?

A

Denaturation; 95 celsius

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12
Q
  • Form H-bonds at specific sites where they are complimentary
  • At 95 C no more H-bonds can form; lowering temperature to ___ in order for
    free nucleotides to bind
A

Annealing; ~50 celsius

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13
Q

T or F: In Annealing, 72 C is the temperature where DNA polymerase optimally functions

A

F, In extension 72 C is the temperature where DNA polymerase optimally functions

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14
Q
  • mRNAs found in cells can also be amplified
  • Makes use of reverse transcriptase enzyme
  • Produces ds copy DNA; From an RNA template, it produces a copy DNA
A

Reverse Transcriptase Polymerase Chain Reaction (RT PCR)

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15
Q

How to identify the mRNA and what is this trait’s function?

A

poly-A tail which protects the 3’ end of mRNA
Serves as primer binding site

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16
Q

Steps in RT PCR:

A
  1. Lyse cells and purify mRNA
  2. Hybridize with Poly(T) primer
  3. Make DNA copy with reverse transcriptase -> RNA-DNA complex
  4. Treat with alkali to degrade RNA -> makes ssDNA
  5. Hairpin loop will serve as a primer to amplify another round -> dsDNA
17
Q

Name the following DNA tools and Techniques:

  1. RFLP
  2. RAPD
  3. AFLP
  4. SSCP
  5. DNA S
A
  1. Restriction Fragment Length Polymorphisms (RFLP)
  2. Randomly Amplified Polymorphic DNA (RAPD)
  3. Amplified Fragment Length Polymorphism (AFLP)
  4. Single-stranded Conformational Polymorphism (SSCP) Analysis
  5. DNA Sequencing
18
Q

a. Look for variation in the sequence at the restriction site only
b. Type 1 marker - target is known

A

RFLP (Restriction Fragment Length Polymorphisms)

19
Q

Makes use of radioactively labeled DNA probes
Developed by E.M. Southern
Not all fragments are visualized

A

Southern Blot Analaysis

20
Q

Steps in Southern Blotting

A
  1. Restriction enzyme cuts the genome
  2. Run through electrophoresis
  3. Make a sandwich with a nitrocellulose filter, gel, sponge
  4. Transfer the bands to the nitrocellulose plate
  5. Submerge nitrocellulose filter containing probes
  6. Radio/fluoro enabled, shows band with probe attachment
21
Q

Blotting targeting mRNA

A

Northern Blotting

22
Q

Blotting targeting proteins

A

Western Blotting

23
Q

Makes use of PCR
Type 2 marker - Target regions are unknown
Primers are short (10-20 nt)

A

RAPD (Randomly Amplified Polymorphic DNA)

24
Q

Causes of variation in RAPDs

A
  • Base substitutions at the primer binding sites
  • INDEL between two RAPD primers
25
Q

Type of marker used in AFLP (Amplified Fragment Length Polymorphism)

A

Type 2

26
Q

Determines variations between DNA sequences

Makes use of ds PCR products

Type I marker used

PCR products are denatured and run on a gel matrix

A

Single-stranded conformational polymorphism (SSCP) analysis

27
Q

Ultimate profiling method of variation

A

DNA sequencing

28
Q

2 Methods of DNA sequencing

A

Maxam-Gilbert Method –enzyme cleavage

Sanger Method –chain termination

29
Q

Steps in _________:

  1. Hydroshearing, Sonication, and enzymatic shearing
  2. Fragment Sequencing
  3. Fragment assembly of overlap
A

Shotgun Genome Sequencing

30
Q

Enzymes with different amino acid
sequences but similar catalytic activity

A

Isozymes

31
Q

Isozymes coded by different alleles of the same locus

A

Allozymes

32
Q

DNA and RNA markers (4)

A

SNPs (Single Nucleotide Polymorphisms)
Indels (Insertions and Deletions)
STS (Sequence Tagged Sites)
VNTRs (Variable Number Tandem Repeats)

33
Q

Most abundant type of genetic variation in humans

Different alleles exist in single base pair positions in genomic DNA

There is variability pair n the nucleotide present in the defined site in the DNA

A

SNPs (Single Nucleotide Polymorphisms)

34
Q

Insertions or deletions of DNA in particular locations of a chromosome

Could be 10 bp to 1-5 kbp for transposable elements

A

Indel polymorphisms

35
Q

Short DNA sequence that only occurs once and its location is known

Type I marker used

Rely on some degree of sequence knowledge

A

Sequence-Tagged Sites (STS)

36
Q

Consists of multiple copies of tandemly arranged simple sequence repeats
(SSRs)

Mini and micro satellites

A

VNTRs (Variable Number Tandem Repeat)

37
Q

11-16 bp repeated up to 1000 times

Scattered across the genome

A

Minisatellites

38
Q

also known as short tandem
repeats (STR)

1-6 bp long repeated several times
for a total length of 100-200 bp

A

Microsatellites

BIO 140 (8 decks)

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