Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Bodies, Tissues and fluids > repetitive DNA > Flashcards

repetitive DNA Flashcards

1
Q

see PowerPoint for

A

the human genome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what two things are repetitive DNA composed of

A

tandem repeats

interspersed repeats

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what are tandem repeats composed of

A

Satellites

Minisatellites

Microsatellites – STR’s (short tandem repeats), SSRs (simple sequence repeats)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what are interspersed repeats composed of

A

LINES

SINES

LTRs

Transposons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what is nearly half of the human genome derived from

A

transposable elements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what are transposable elements

A

abundant in gene sequences and are also present in a significant portion of mature mRNAs, mostly in their untranslated regions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

transposable elements are fundamental components of what

A

most eukaryotic genomes, with important contributions to their size, structure and variation. They occur as families with a variable copy number and they are (or were) able to transpose from one locus to another.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what are Class I elements also called

A

retroelements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what can Class I elements be divided into

A

LTR retrotransposons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what are LTR retrotransposons

A

flanked by long terminal repeats (LTRs) sharing an over-all organization similar to retroviruses and non-LTR retrotransposons, which terminate at one end with a poly(A) tract and have structural features of long and short interspersed nuclear elements (LINEs and SINEs, respectively).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what 2 things have LTR retrotransposons been further classified as

A

gypsy/Ty3-like

copia/Ty1-like

elements based on the order of their encoded proteins, that include a reverse transcriptase (RT) and integrase (IN).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what are Class II elements also called

A

(DNA) transposons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

how are DNA transposons characterised

A

by terminal inverted repeats (TIRs)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

how are DNA transposons grouped

A

into superfamilies on the basis of the target site duplication, the presence or not of the DDE triad (acidic amino acid motif), the sequence similarities at the DNA and protein levels (e.g. Tc1/mariner, hAT, Mutator-like, CACTA).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Most DNA transposons are organised in families of what two things

A

autonomous and non autonomous elements, characterized by their ability to respond to the same transposase.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

satellite DNA

A

α (alphoid) 171bp, centromeres

β (Sau3A) 68bp, certain centromeres

Sat 1 25-48bp most centromeres

Sat 2 & 3 5bp all chromosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

mini satellite DNA

A

Telomeric >6bp all telomeres

Hypervariable 9-64 many near telomeres

18
Q

micro-satellite DNA

A

SSRs <10bp (or <6bp), dispersed

19
Q

who discovered Hypervariable minisatellite DNA

A

Alec Jeffreys

20
Q

what are Hypervariable minisatellite DNA

A

repetitive sequences within the DNA.

21
Q

what varies between individuals of the mini satellite regions

A

Composition and length

22
Q

what may be within these mini satellite regions

A

interspersed polymorphic restriction sites

23
Q

what happens when you treat the DNA with endonucleases

A

cleaves the DNA into fragments to create a pattern that is unique to each individual.

24
Q

how can the patterns of restriction fragments be viewed

A

Using the Southern blotting technique

This results in a barcode-like pattern which is unique to the individual. This became known as DNA fingerprinting.

25
Q

advances to DNA fingerprinting

A

provides a simple pattern with high discriminatory power.

However, requires a large amount of sample material for the analyses, which is a disadvantage in criminal applications. In addition, inter-laboratory standardisation has been difficult to achieve and its relatively slow and expensive and difficult.

PCR of STR loci has overcome these difficulties and has greatly enhanced the role of DNA profiling in forensic science.

26
Q

where are STRs found

A

dispersed throughout the whole genome and can be found in large numbers, even in the gene introns.

27
Q

what are the most common STRs

A

Dinucleotide polymorphisms but they are strongly affected by strand slippage during amplification, producing artefactual stutter bands

28
Q

what STR repeats are less prone to slipping

A

Tetra- and pentanucleotide repeats so more suitable for forensic analysis

29
Q

STR methods

A

can be easily standardised and are suitable for multiplexing. Amplicon (PCR product) length measurement is automated; its cheap, quick, accurate and easy.

30
Q

what are STRs, SSRs or micro satellites defined as

A

tandemly repeated tracts of DNA composed of 1–6 base pair long motifs.

The number of repeats in a tract is usually less than ten and if it is higher then repeat length polymorphism is often observed. In rare cases, the repeat number may reach hundreds and even thousands.

31
Q

all SSRs together occupy how much of the human genome

A

3%

32
Q

• At each STR locus there are two alleles and an individual will be either

A
  • Homozygous – e.g. AGAT repeated 8 times, AGAT repeated 8 times, reported as 8,8 genotype
  • Heterozygous – e.g. AGAT repeated 8 times, AGAT repeated 5 times, reported as 5,8 genotype
33
Q

simple sequence repeats

A
  • The genomic distribution of the SSRs of different motif lengths and sequences is strongly biased. With the exception of monomeric motifs, the classes of repeated dimers, tetramers and hexamers, which show nearly equal density in the genome, are 3–4 times more abundant than those of trimers and pentamers.
  • When the occurrence of SSRs in different functional genome regions is considered, it turns out that most of them show much higher density in non-coding regions.
  • Exceptions to the rule are trimers and hexamers which are nearly two times more prevalent in exons compared to introns and intergenic regions
34
Q

microsatellites

A
  • In the human (and mouse) genome, microsatellite density is nearly twofold higher near the ends of chromosome arms.
  • Microsatellites are also frequently found in the proximity of interspersed repetitive elements such as short interspersed repeats (SINEs) and long interspersed elements (LINEs).
35
Q

SGM+ is now being replaced with what

A

DNA-17

36
Q

what is Amelogenin

A

not an STR

its a length polymorphism and used in sex determination

37
Q

appearance of PCR products

A

• PCR products are small in size and products from different loci overlap – hence the need for a fluorescent label.

38
Q

the more alleles at each locus…

A

the better discrimination providing allele frequencies are approximately equal.

39
Q

point to note

A

not all STRs are simple motifs that perfectly repeat a tetra nucleotide motif

40
Q

see pp for

A

image of replication slippage

41
Q

see pp for

A

basic gene structure and expression

Bodies, Tissues and fluids (16 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions