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Lecture 5: Flashcards

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Biology 101 flashcards
1
Q

What kind of chromosomes are easy to see in FISH, with familiar down syndrome

A

Mitotic chromosomes (G2)

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2
Q

What kind of chromosomes are difficult to see with FISH, because the probes recognize ends of the chromosome in the domain–rather than at centromere

A

G1

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3
Q

In the Philadelphia Chromosome, probes are placed on either side of the…

A

break point

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4
Q

In the Philadelphia Chromosome, if the probes are on opposite sides of the centromere—what happens to the signal?

A

(G1) signals would not overlap

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5
Q

RNA folded up to 3D structure to have…

A

enzymatic activity

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6
Q

H-N bonds or H-O bonds are longer?

A

H-N

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7
Q

Longer RNA molecules can…

A

fold back and H bond with themselves

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8
Q

The earliest natural selection would have been for an RNA enzyme that can catalyze its own…

A

replication

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9
Q

RNA would ____ a cell to exist. It’s replication would only occur when ___ are available

A

not need, RNA nucleotides

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10
Q

Some naturally occurring lipids spontaneously
form….

A

double-membrane spheres if the lipid
concentrations are high enough

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11
Q

It has been proposed that the road to life began in…

A

pools of fresh water on volcanic islands that contained RNA nucleotides and lipids

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12
Q

Would provide enclosed spaces that the virus can dump its content into and replicate its RNA

A

Double membrane spheres

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13
Q

RNA splicing has proteins bound to it to make it more ___. Proteins largely but not entirely ___

A

efficient, replaced RNA

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14
Q

These RNA enzymes are thought to be ___ from before proteins were recruited

A

holdovers

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15
Q

What came along after proteins

A

DNA

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16
Q

DNA and RNA have how many phosphates?

A

3

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17
Q

Why can’t RNA form a B helix?

A

RNA cannot make a compact shape because O is too bulky on 2nd Carbon

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18
Q

ability to synthesize DNA using RNA as a template

A

Reverse Transcriptase

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19
Q

The bacterial chromosome, although in contact with cytoplasm, remains where?

A

in a domain

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20
Q

Supercoiling destabilizes what in the genome?

A

A/T rich

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21
Q

Stress as a result of negative supercoiling the DNA can cause ____ to come apart more easily

A

A/T rich regions

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22
Q

What regions in supercoiled DNA strand are A/T rich?

A

At origins of replication and at gene promotors (open complex formed easier)

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23
Q

What does not use supercoiling?

A

Eukaryotes

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24
Q

Can replicate themselves without replicating the genome

A

Transposable elements

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25
Q

Alu elements are long or short

A

short

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26
Q

E.coli F factor is an example of an..

A

invasion

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27
Q

What transposon cannot replicate? What can?

A

Simple, can= retro and replicative

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28
Q

Transposons can destroy a gene, causing an….

A

insertion mutation

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29
Q

What enzyme catalyzes excision and insertion in transposition

A

transposase

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30
Q

2 transposons of the same kind next to each other make up a…

A

Composite transposons

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31
Q

Recognizes IR’s and cuts and pastes

A

Transposase gene

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32
Q

Resolvase role in replicative transposition

A

Catalyzes recombination between 2 elements, causing co-integrant to form two separate structures (each with a copy of TE)

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33
Q

A cointegrant is made up of

A

plasmid and a bacterial chromosome

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34
Q

Transposons aid in the spread of…

A

antibiotic resistance genes

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35
Q

Most common transposition in humans

A

retro

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36
Q

Retrotransposition found in…

A

eukaryotes

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37
Q

What transposons are autonomous?

A

Eukaryotic and retro

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38
Q

Retrotransposition intermeditae

A

Reverse transcriptase

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39
Q

Retroelements use what in their transposition mechanism

A

RNA intermediates (RNA poly. 3)

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40
Q

The movement of retro-elements also requires two key enzymes…

A

Reverse transcriptase and integrase

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41
Q

Inserts double stranded DNA into genome

A

Integrase

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42
Q

Makes DNA copy of RNA and encodes for integrase

A

Reverse transcriptase

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43
Q

Transposons are ___ when they contain all the information necessary for transposition to occur

A

autonomous

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44
Q

Encode their own reverse transcriptase and their own integrase

A

Autonomous

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45
Q

Transposons are ___ when they lack a gene that is necessary for transposition to occur

A

nonautonomous

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46
Q

Majority of human transposons are…

A

autonomous

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47
Q

Have signal sequences to encode themselves but don’t encode for the proteins (reverse transcriptase or integrase)

A

autonomous

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48
Q

Alu elements are autonomous or non

A

non

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49
Q

Must abundant transposon

A

alu elements

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50
Q

Non-LTR retrotransposon or LTR retrotransposon are most abundant

A

Non LTR

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51
Q

Non-LTR retrotransposon have no…

A

repeats at the ends (ensure of how they replicate)

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52
Q

LTR retrotransposition are found? How long?

A

retroviruses, few hundred nucleotides long

53
Q

Like viral counterparts, they encoded viral related proteins that are needed for the transposition process

A

LTR retrotransposition

54
Q

Humans only have dead…

A

LTR retrotransposition

55
Q

The organization of retroelements can be

A

variable

56
Q

RNA viruses that make a DNA copy that integrates into the host’s genome

A

Retroviruses

57
Q

Humans dont have genuine ____ but they do have ___ that resemble ___

A

LTR transposons, ERVs, LTR transposons

58
Q

What makes up 1/3 of the human genome and are the most common retroelements in humans

A

LINE-1 and SINEs

59
Q

Length of LINE-1 vs SINEs

A

LINE-1: Up to 6 kb
SINEs: less than 500 bp

60
Q

Example of a SINE

A

Alu

61
Q

Present in more than 1,000,000 copies in the human genome

A

Alu

62
Q

Found in around 900,000 copies per genome

A

LINE-1

63
Q

Most successful: LINE-1 vs SINEs

A

LINE 1

64
Q

There are no LTRs in LINE-1 or SINE

A

LINE-1

65
Q

What family of retroelements doesn’t share any sequence similarities with viruses

A

Alu

66
Q

Alu family is derived from a…

A

single ancestral gene: 7SL RNA gene

67
Q

A part of a RNA-protein complex that transports proteins carrying a specific sequence to the ER (while still being synthesized)

A

7SL RNA gene

68
Q

A single retroelement can be copied into how many RNA transcripts in retrotransposition? What does this tell us?

A

many, they can accumulate rapidly in genome

69
Q

The original interpretation of retroelements is that they…

A

exist because they can

70
Q

Retroelements are similar to…

A

parasites

71
Q

They can proliferate within the host as long as they do not harm the host to the extend that they significantly disrupt survival

A

Parasites, selfish DNA theory

72
Q

slower dividing organisms= ___ TE

A

more

73
Q

Gene duplication involves ____, located where?

A

LINE-1 elements, Y chromosome or part of immune system

74
Q

LINE-1 elements help with ___

A

natural selection because of gene duplication

75
Q

Bacterial retroelements can carry

A

antibiotic resistance genes

76
Q

Retroelements may cause ___ through recombination

A

greater genetic variability

77
Q

Retroelements offer what?

A

evolutionary advantage

78
Q

A TE known as P element has expanded throughout the

A

fruit fly population worldwide, only strains found unless lab stocks were collected before 1950s

79
Q

TE can ___ enter the genome and ___

A

rapidly, proliferate

80
Q

Many transposons in humans are shut down and don’t multiply very often because…

A

cells recognize their repetitive nature

81
Q

TE can alter what in gene expression?

A

can donate promoters and enhancers that alter gene function

82
Q

Can spread from a TE and silence a nearby gene

A

Heterochromatin

83
Q

Heterochromatin: stable or unstable

A

unstable

84
Q

Can spread and contract influencing nearby genes differently in different people

A

heterochromatin

85
Q

If a transposable element loses its heterochromatin, this can cause…

A

expose DNA sequences that alter gene expression

86
Q

What can promote TE replication

A

radiation, stress

87
Q

Transposition: regulated or non-regulated

A

tightly regulated because it is usually harmful

88
Q

Eukaryotic cells were broken open and the DNA was seen in a bead on a string form known as….

A

nucleosomes

89
Q

The proteins in nucleosomes are called….

A

histones

90
Q

Histone proteins charge

A

basic, positively charged AA (Lysine and arginine)

91
Q

Histone proteins bind with the

A

negative charged phosphates on DNA backbone

92
Q

Have a globular domain and flexible charged amino terminus or tail

A

histones

93
Q

What makes up a nucleosome

A

8 histones + DNA

94
Q

What are the core histone types? How many make up an octamer?

A

H2A, H2B, H3, H4; two of each

95
Q

What is the linker histone? Binds what?

A

H1, linker DNA but not as tightly as core histones

96
Q

A nucleosome is composed of DNA wrapped around the octamer of __

A

histone proteins

97
Q

___ bp of DNA make ___ turns around the octamer

A

146, 1.65

98
Q

The nucleosome “beads on a string” structure ___ DNA legnth about ___

A

shortens, seven fold

99
Q

In real life, the DNA is ___ in relation to the histones

A

larger

100
Q

All beads on a string nucleosome images were obtained in conditions where a protein called ___ was missing from the chromatin

A

H1(get stretched out of bead)

101
Q

In conditions were a histone H1 is in the chromatin, a ___ chromatin fiber is seen: ___ nm in diameter. This is seen where?

A

thicker, 30 nm, in the cell

102
Q

In conditions where the 30 nm fiber is partially disrupted, you see a structure that looks like a….

A

zig zag

103
Q

30 nm fibers are organized into ___. Two proteins responsible for this are _____

A

loops, CTCF and SMC proteins

104
Q

The proteins (CTCF and SMC) in the loops are located at the

A

base

105
Q

In ___ the chromosomal DNA is even more highly compacted

A

metaphase

106
Q

DNA cannot go…

A

back and forth

107
Q

When not condensed in mitosis, where are chromosomes in the cell

A

take up territories

108
Q

The compaction level of ___ chromosomes is not completely uniform

A

interphase

109
Q

Heterochromatin vs. Euchromatin

A

Hetero:
- less condensed chromosome regions
- transcriptionally active
Euch:
- tighly compacted
- transcriptionally inactive

110
Q

Can be expressed with right transcription factors: hereo or euchromatin

A

euchromatin

111
Q

Repressive, not expressed: Hetero or euchromatin

A

hetero

112
Q

What type of chromatin is located in regions where 30 nm fiber forms radial loop domains

A

euchromatin

113
Q

What type of chromatin is located in radial loop domains, compacted even more

A

heterochromatin

114
Q

Two types of heterochromatin?

A

Constitutive vs faculative

115
Q

What type of heterochromatin: regions that are always heterochromatic

A

constitutive

116
Q

What type of heterochromatin: regions that interconvert between euchromatin and heterochromain

A

Facultative heterochromatin

117
Q

Examples of constitutive heterchromatin

A

around centromeres, telomeres, and TE

118
Q

Examples of facultative heterchromatin

A

cannot be expressed, Barr body (X inactive chromosomes)

119
Q

Facultative heterochromatin regulates…

A

gene expression

120
Q

Using ___, heterochromatin can be seen as dark staining regions in the ___ nucleus

A

electron microscopy, interphase

121
Q

Much of the heterochromain is localized….

A

to the periphery of nucleus and nucleolus

122
Q

Nuclear periphery moves around heterchromatin, helping to

A

maintain it

123
Q

Nuclear lamina helps to…

A

maintain heterochromatin

124
Q

A large proportion of heterochromatin associates with the ___ at the ___

A

nuclear lamina, at nuclear periphery

125
Q

Relationship between age and heterochromatin

A

as people age, less heterochromatin

126
Q

A mutation in the nuclear lamina comprises the maintenance of heterochromatin and causes pre-mature aging

A

Hutchinson-Gilford progeria

127
Q

What is defective in Hutchinson-Gilford progeria

A

Lamin A

128
Q

In Hutchinson-Gilford progeria, the person loses heterochromatin ___ faster

A

10x

Genetics (11 decks)

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