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Genetics BSC-315 > Exam 3 > Flashcards

Exam 3 Flashcards

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1
Q

Chromosomes have a versatile, modular structure for packaging DNA that supports flexibility of

A

form and function

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2
Q

__ is the generic term for any complex of DNA and protein found in a nucleus of a cell

A

chromatin

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3
Q

__ are the separate pieces of chromatin that behave as a unit during cell division

A

chromosomes

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4
Q

Chromatin is 1/3 __, 1/3 __, and 1/3 __

A

DNA, histones, nonhistone proteins

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5
Q

DNA interaction with __ and __ proteins produces sufficient level of compaction to fit into a cell nucleus

A

histones; nonhistone proteins

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6
Q

What are histones?

A

proteins that interact directly with DNA

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7
Q

How do histones interact with DNA?

A

histones neutralize DNA in the first level of compaction

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8
Q

The core histone complex makes up the

A

nucleosome

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9
Q

What are the five types of histones?

A

H1, H2A, H2B, H3, and H4

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10
Q

Of the five types of histones, which ones are core histones?

A

H2A, H2B, H3, and H4

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11
Q

160 base pairs of DNA wraps twice around a

A

nucleosome core

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12
Q

40 base pairs of linker DNA connect

A

adjacent nucleosomes

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13
Q

Which histone associates with linker DNA as it enters and leaves the nucleosome core?

A

H1

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14
Q

Diameter of DNA helix is

A

20 A

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15
Q

Diameter of nucleosome core is

A

100 A

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16
Q

Histones make up __ of all chromatin protein by weight

A

half

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17
Q

There are about 200-200,000 molecules of each kind of __ protein in chromatin

A

nonhistone

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18
Q

What are the functions of nonhistone proteins?

A
  • structural role: chromosome scaffold
  • chromosome replication: e.g. DNA polymerases
  • chromosome segregation: e.g. kinetochore proteins
  • transcription: largest group
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19
Q

The __ is the fundamental unit of chromosomal packaging

A

nucleosome

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20
Q

When DNA wraps twice around nucleosome core octamer, what does that result in?

A

a 7-fold compaction of DNA

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21
Q

How does spacing and structure of nucleosomes affect genetic function?

A
  • determines whether DNA between nucleosomes is accessible for proteins to initiate transcription, replication, and further compaction
  • arrangement along chromatin is highly defined and transmitted from parent to daughter cells during DNA replication
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22
Q

DNA must be condensed __ 7-fold

A

more than

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23
Q

What does the nucleosome do?

A

condenses naked DNA 7-fold to a 100 A fiber

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24
Q

What does supercoiling do?

A

causes additional 6-fold compaction of DNA, achieving a 40-50-fold condensation relative to naked DNA

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25
Q

What does the radical loop-scaffold do?

A

through progressive compaction of 300 A fiber, condenses DNA to rod-like mitotic chromosome that is 10,000 times more compact than naked DNA

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26
Q

100 A fiber is compacted into 300 A fiber by

A

supercoiling

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27
Q

What does the radical loop-scaffold model for higher levels of compaction state?

A
  • several nonhistone proteins (NHPs) bind to chromatin every 60-100 kb and tether the 300 A fiber into structural loops
  • other NHPs gather several loops together into daisy like rosettes
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28
Q

What is heterochromatin?

A

chromatin that is highly condensed, and usually inactive transcriptionally. Genes near heterochromatin have reduced expression or are “silenced”

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29
Q

When heterochromatin is constitutive what does that mean?

A

chromatin is condensed in all cells (e.g. most of the Y chromosome and all pericentromeric)

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30
Q

When heterochromatin is facultative what does that mean?

A

chromatin is condensed in only some cells and relaxed in other cells (e.g. position effect variegation, X chromosome in female mammals)

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31
Q

What is euchromatin and what is found in it?

A

relaxed chromatin that is usually transcriptionally active; housekeeping genes are found in this region (e.g. proteins that maintain cell function and are always expressed)

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32
Q

Transcription is controlled by

A

chromatin structure and nucleosome position

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33
Q

The more compacted DNA is,

A

the less transcription takes place

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34
Q

What are the three major mechanisms that can regulate chromatin patterns?

A
  • histone modifications
  • remodeling complexes
  • histone variants
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35
Q

What are histone modifications?

A

the addition of methyl or acetyl groups

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36
Q

What do remodeling complexes do and how do they do it?

A

remodeling complexes can alter nucleosome patterns; they do it by

  • changing accessibility of promoter sequences
    • remove or reposition promoter-blocking nucleosomes
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37
Q

What can histone variants do?

A

they can cause different nucleosomal structures (e.g. CENP-A at centromeres)

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38
Q

Promoters of transcribed genes are located in

A

nucleosome free regions

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39
Q

Promoters of non-transcribed genes are wrapped in

A

nucleosomes

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40
Q

Origins of replication are also

A

devoid of nucleosomes

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41
Q

When transcription is required, promoters are exposed by

A

removing or repositioning nucleosomes

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42
Q

In histone modification and chromatin remodeling, the histone tails can undergo __ __ with chemical groups

A

covalent modification

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43
Q

In histone modification and chromatin remodeling, enzymes can add

A

chemical groups (methyl groups, phosphate groups, ubiquitin, etc.)

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44
Q

In histone modification and chromatin remodeling, modified tails can alter __ and bind __ __ __

A

nucleosomes; chromatin modifier proteins

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45
Q

In histone modification and chromatin remodeling, what does acetylation of lysines do?

A
  • prevents close packing of nucleosomes
  • favors expression of genes in euchromatin
  • de-acetylation results in reduced transcription
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46
Q

In histone modification and chromatin remodeling, what does methylation of lysines and arginines do?

A
  • can either close or open chromatin, depending on specific amino acid modified
    • ex: adding methyl group to H3 lysine 9 favors heterochromatin formation
  • de-methylation reverses
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47
Q

What is the rate of DNA synthesis in human cells?

A

about 50 nt/sec

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48
Q

Most mammalian cells have about __ origins

A

10,000

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49
Q

The human genome has about __ base pairs

A

3.2 billion (avg 70 million per chromosome)

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50
Q

It would take __ hours to replicate the human genome if there was only one origin of replication

A

800

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51
Q

T or F? Many origins are active at the same time

A

T

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52
Q

Nucleosomes are __ and __ during DNA replication

A

disassembled; reformed

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53
Q

DNA is packaged in nucleosomes within __ of synthesis

A

minutes

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54
Q

Chromatin fiber unwinds __ to synthesis

A

prior

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55
Q

Synthesis of histones (in cytoplasm) and transport into nucleus is tightly correlated with

A

synthesis of DNA

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56
Q

Newly synthesized DNA associates with

A

new histones

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57
Q

In very early embryo, both __ __ are active

A

X chromosomes

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58
Q

In humans, random X-inactivation occurs about __ __ after fertilization

A

2 weeks

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59
Q

Some cells have __ X inactivated, other cells have __ X inactivated

A

maternal; paternal

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60
Q

All cell descendants have the same

A

inactive X

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61
Q

Adult female calico cates are __ at X-linked genes

A

mosaic

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62
Q

In female calico cats heterozygous for X linked mutation:

A
  • some cells have wild-type allele inactivated

- some cells have mutant allele inactivated

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63
Q

What is an example of facultative heterochromatin?

A
  • dosage compensation in mammals so that X-linked genes in XX and XY individuals are expressed at same level
  • random inactivation of all except one X chromosome in XX
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64
Q

What are Barr bodies?

A

darkly stained heterochromatin masses observed in somatic cells at interphase

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65
Q

An XX person has how many Barr bodies?

A

one

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66
Q

An XXX person has how many Barr bodies?

A

two

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67
Q

An XXY person has how many Barr bodies?

A

one

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68
Q

Chromosomes support the __, __, __, and __ of genetic info

A

packaging, replication, segregation, expression

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69
Q

What are chromosomal abnormalities characterized by a change in the number of chromosomes?

A
  • aberrant euploidy

- aneuploidy

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70
Q

What are chromosomal abnormalities characterized by a change in the structure of chromosomes?

A
  • deletion
  • duplication
  • translocation
  • inversion
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71
Q

Chromosomes have distinct “banding patterns” from staining that can be used as

A

physical markers for locations of genes

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72
Q

On a chromosome, the short arm is called the __ arm

A

p

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73
Q

On a chromosome, the long arm is called the __ arm

A

q

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74
Q

What are the types of chromosomal rearrangements?

A
  • deletion
  • duplication
  • inversion
  • translocation
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75
Q

What is deletion?

A

the loss of a segment of a chromosome

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76
Q

What is duplication?

A

the gain of a segment of a chromosome

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77
Q

What is inversion?

A

the reversal of a region of a chromosome

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78
Q

What is translocation?

A

the movement of a segment of a chromosome among chromosomes

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79
Q

What is ploidy?

A

the basic number of chromosomes sets

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80
Q

What is euploidy?

A

the normal number of chromosomes within a cell for a species

-for ex., the euploid number of chromosomes in a human somatic cell is 46

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81
Q

What does haploid (n) mean? and what is an example of a type of cell that is haploid?

A

one chromosome set; this is the normal state for some cell type/organisms
-ex: human germ cells

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82
Q

What does diploid (2n) mean? and what is an example of a type of cell that is diploid?

A

two of the same chromosome set; this is the normal state for many organisms
-ex: human somatic cells

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83
Q

What does polyploid (>2n) mean?

A

more than two sets of chromosomes

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84
Q

What is transposition?

A

a type of sequence rearrangement with a significant genomic impact

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85
Q

What are transposable elements?

A

small segments of DNA that move from one position of DNA to another

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86
Q

Who discovered transposable elements?

A

Barbara McClintock with her study of mottling of corn color

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87
Q

What do retrotransposons do?

A

transpose (move their DNA) via reverse transcription of an RNA intermediate

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88
Q

What do transposons (a.k.a DNA transposons) do?

A

move their DNA directly without an RNA intermediate

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89
Q

What is a common mechanism retrotransposons use?

A

transcription by RNA polymerase into an RNA that encodes a reverse transcriptase-like enzyme.

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90
Q

The transcriptase-like enzyme can

A

copy RNA into a single strand of cDNA and then use that single DNA strand as a template for producing double stranded cDNA

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91
Q

Some retrotransposons have a __ __ at the 3’ end of the RNA-like DNA strand, which is similar to mRNA molecules

A

poly-A

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92
Q

What are the retrotransposons in humans?

A
  • LINES (long interspersed elements

- SINES (short interspersed elements)

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93
Q

What is the hallmark of DNA transposons?

A

that their ends are inverted repeats (mirror images) of each other
-these repeats are 10-200 bp long

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94
Q

DNA between the transposon’s inverted repeats commonly contains a gene encoding __, a protein that catalyzes transposition through its recognition of those repeats

A

transposase

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95
Q

What is the DNA transposon mechanism?

A
  1. excision of the transposon from its original genomic position
  2. integration into a new location
  3. the double-stranded break at the transposon’s excision site is either
    - repaired accurately
    - the transposon will be lost from the original genomic site after transposition
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96
Q

__% of the human genome consists of transposable elements

A

44%

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97
Q

Approximately 90% of the transposable elements in the human genome are

A

retrotransposons

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98
Q

Of the 90% of the transposable elements in the human genome that are retrotransposons, 20% are __ and 13% are __

A

LINES; SINES

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99
Q

__% of the human genome consists of DNA transposons

A

3

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100
Q

Most of the transposable elements in the human genome are __ and cannot __

A

defective; move anymore

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101
Q

Insertion of a transposable element near or within a gene can affect __ and change __

A

expression; phenotype

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102
Q

Retrotransposon insertion mutations have been shown to cause about 100 know human diseases, including,

A

forms of hemophilia A, hemophilia B, cystic fibrosis, and muscular dystrophy

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103
Q

What is aneuploidy?

A

the loss or gain of one or more chromosomes

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104
Q

What are aneuploids?

A

individuals whose chromosome number is not an exact multiple of the haploid number (n) for that species

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105
Q

__ for any autosome is generally lethal

A

monosomy

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106
Q

__ for most autosomes is usually lethal, with a few exceptions

A

trisomy

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107
Q

Most organisms tolerate aneuploidy for

A

sex chromosomes

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108
Q

What are monosomic individuals?

A

individuals that lack one chromosome from the normal haploid number (2n-1)

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109
Q

What are trisomic individuals?

A

individuals that have one chromosome in addition to the normal diploid number (2n+1)

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110
Q

What are tetrasomic individuals?

A

organisms with four copies of a particular chromosome (2n+2)

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111
Q

How does aneuploidy occur?

A

chromosomal nondisjunction in meiosis

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112
Q

What is chromosomal nondisjunction in meiosis?

A

a process by which chromosomes or chromatids fail to separate during meiosis that results in gametes with an abnormal number of chromosomes

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113
Q

Chromosomal nondisjunction in meiosis usually results in the addition of loss of a __ chromosome

A

single

-resulting organism will have either 45 (one less) or 47 (one more) chromosome in its cells

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114
Q

T or F? Nondisjunction can occur during meiosis I or meiosis II

A

T

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115
Q

What happens in nondisjunction during meiosis I?

A

homologous pairs fail to separate during anaphase

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116
Q

What happens in nondisjunction during meiosis II?

A

sister chromatids fail to separate during anaphase

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117
Q

What are syntenic blocks?

A

colored segments that contain at least two genes whose order is conserved in the mouse genome

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118
Q

The human genome has about __ genes

A

25,000

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119
Q

The part of the genome corresponding to exons is the

A

exome

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120
Q

Most of a genome is non-coding DNA, what is it made of?

A
  • exome (expressed regions) = about 2%
  • introns
  • centromeres, telomeres, transposable elements
  • simple repeating sequences
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121
Q

What are gene-rich regions?

A 
chromosomal regions that have many more genes than expected from average gene density over entire genome
-ex in humans: class III region of major histocompatibility complex (60 genes within 700 kb region)
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122
Q

What are gene deserts?

A

regions of >1 Mb that have no identifiable genes

-3% of human genomes is comprised of gene deserts

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123
Q

T or F? Biological significance of gene-rich regions and gene deserts is not known

A

T

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124
Q

Exons often encode __ __

A

protein domains (sequence of amino acids that fold into functional units)

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125
Q

Shuffling, addition, and deletion of domain regions can produce new __ in cells and organisms

A

functions

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126
Q

Reorganization of domain provides raw material for

A

evolution

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127
Q

After exon shuffling, protein products have novel

A

domain architectures

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128
Q

Gene families can evolve by __ followed by __

A

duplication; divergence

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129
Q

What are gene families?

A

groups of genes that are closely related in sequence and function
-ex: hemoglobin genes (alpha and beta globes), immunoglobins (antibodies)

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130
Q

Changes in number and arrangement of exons can alter

A

functions

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131
Q

Duplication and divergence of genes can create genes with both __ and __ functions

A

new; old

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132
Q

Rearrangements and duplications create many possibilities for

A

novel functions

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133
Q

Virtually all knowledge of gene structure, expression, and regulation came from studies of

A

bacteria and bacteriophages

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134
Q

The advent of recombinant DNA technology depended on understanding of

A

bacterial genes, chromosomes, and restriction enzymes

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135
Q

All bacteria are __, which lack a defined nuclear membrane

A

prokaryotes

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136
Q

All bacteria lack

A

membrane-bound organelles

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137
Q

Most bacteria have a cell wall made of __ that surrounds the cell membrane

A

carbohydrate and peptide polymers

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138
Q

Bacteria have a single

A

chromosome

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139
Q

Bacteria divide __

A

rapidly (1 hour in minimal medium, 20 min. in high nutrient conditions)

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140
Q

__ is the most studied and best understood bacterial species

A

E.coli

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141
Q

E.coli inhabits the intestines of

A

warm-blooded animals

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142
Q

E.coli can grow in

A

complete absence of oxygen or in air

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143
Q

E.coli are phototrophic, meaning

A

they can grow in minimal media

  • single carbon and energy source (e.g. glucose)
  • inorganic salts
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144
Q

The E.coli genome is tightly packed with

A

genes

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145
Q

Describe the genome of the K12 strain of E.coli that was sequenced

A
  • 4.6 Mb
  • about 90% of genome encodes protein
  • 4288 genes, but function known for only 60%
  • on average, 1 gene per kb
  • no introns
  • very little repetitive DNA
  • small intergenic regions
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146
Q

Individual E.coli strains contain a subset of the E.coli __

A

pangenome

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147
Q

What is the core genome of E.coli?

A

about 1000 genes that are found in all strains

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148
Q

What is the pangenome of E.coli?

A

the core genome plus all genes that are found in some strains but not others (about 15,000 genes)

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149
Q

The typical bacterial genome is composed of one circular __

A

chromosome

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150
Q

In bacteria, the DNA molecule condenses by

A

supercoiling and looping

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151
Q

Each bacterium replicates and then divides by __ __ into two daughter cells

A

binary fission

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152
Q

__ __ elements dot the genomes of many types of bacteria

A

insertion sequences (IS)

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153
Q

What are insertion sequences and what do they do in bacteria?

A

small transposable elements

  • inverted repeats (IRs) at ends
  • carry transposase gene, which initiates transposition by recognizing IRs
  • can move to other locations in genome
  • can disrupt genes by insertion into coding regions (cause of many spontaneous mutations)
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154
Q

Tn elements in bacteria are __ __ __

A

composite transposable elements

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155
Q

Tn elements contain

A

transposase gene and genes conferring resistance to antibiotics or toxic metals

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156
Q

What are plasmids?

A

smaller circles of DNA that carry genes beneficial to the host cell

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157
Q

Plasmids don’t carry genes essential to the host, but may

A

benefit the host under certain conditions

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158
Q

What are some examples of genes that are beneficial to the host

A
  • genes that protect host against toxic chemicals (e.g. mercury) and metabolize environmental pollutants (e.g. toluene, petroleum products)
  • pathogenic genes (e.g. toxins produced by S. dysenteriae)
  • genes encoding resistance to antibiotics
  • multiple antibiotic resistance often due to composite IS/Tn elements on a plasmid
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159
Q

Movement of antibiotic resistance genes TO the plasmid was facilitated by

A

transposons

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160
Q

Multiple antibiotic resistance genes can be transposed from the plasmid as a

A

unit

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161
Q

Bacteria must be grown and studied in

A

cultures

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162
Q

What are some examples of mutant variation in bacteria?

A

-altered colony morphology
>large or small; shiny or dull; round or irregular
-resistance to bactericides
>antibiotics, bacteriophages (e.g. MRSA!)
-Auxotrophs: unable to reproduce in minimal media
-defective in using complex chemicals from the env
>ex: breaking down lactose into glucose and galactose
-defective in proteins essential for growth
>conditional lethal mutations, e.g. temp-sensitive (ts)

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163
Q

Rapid bacterial multiplication allows for detection of

A

very rare genetic events

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164
Q

What does effectively haploid mean?

A

straightforward relationship b/w mutation and phenotypic variation

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165
Q

What happens in selection?

A

est conditions in which only the desired mutant will grow

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166
Q

What happens in a genetic screening?

A

examine each colony for a particular phenotype using a technique called replica plating

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167
Q

Genomic analysis has revealed widespread occurrence of __ __ __ in many bacterial species

A

gene transfer mechanisms

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168
Q

Gene transfer is an important mechanism for __ __ __ __ __ and to development of pathogenic strains of bacteria

A

rapid adaptation to environmental changes

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169
Q

Describe lateral (or horizontal) gene transfer

A

traits are introduced from unrelated individuals or from different species

170
Q

Describe vertical gene transfer

A
  • occurs in sexually reproducing organisms

- traits are transferred from parent to offspring

171
Q

In the three mechanisms for gene transfer in bacteria,

A
  • donor bacterium provides the DNA that is transferred

- recipient bacterium receives the DNA, which can result in altered phenotype

172
Q

In conjugation, the F plasmid contains genes for

A

synthesizing connections between donor and recipient cells

173
Q

What is conjugation?

A

direct transfer of DNA from donor cell to connected recipient cell

174
Q

Donors for conjugation are __

A

F+ (carry a special F plasmid)

175
Q

Recipients for conjugation are __

A

F- (don’t carry an F plasmid)

176
Q

F plasmid has three

A

IS elements

177
Q

__ __ __ cells are formed when an F plasmid integrates into the bacterial chromosome through recombination between IS elements

A

high frequency recombinant (Hfr)

178
Q

20-30 different Hfr strains can be generated that differ in the __ and __ of the integrated F plasmids

A

location; orientation

179
Q

Integrated F plasmid replicates with __ during cell division

A

chromosome

180
Q

Her strains retain all __ __ __ and can be a donor for conjugation with an F- strain

A

F plasmid functions

181
Q

Transfer of DNA starts in the F plasmid at the

A

origin of transfer

182
Q

Chromosomal genes located next to F plasmid sequences are transferred to the

A

recipient

183
Q

Transferred chromosomal DNA recombines into __ __ in recipient

A

homologous DNA

184
Q

Usually conjugation terminates before

A

entire chromosome transfers

185
Q

How are F’ plasmids created?

A
  • an Hfr plasmid comes out of a bacterial chromosome

- a few chromosomal genes will be removed with it, generating an F’ episome (plasmid)

186
Q

What are merodiploids?

A

partial diploids in which two gene copies are identical

187
Q

What are merodiploids useful for?

A

complementation testing

188
Q

To select for Trp+ transformants, plate on minimal media with

A

histidine and no tryptophan

189
Q

To select for His+ transformants, plate on minimal media with

A

tryptophan and no histidine

190
Q

To screen for His+ Trp+ co-transformants, test Trp+ individual
transformants and His+ individual transformants for growth on
minimal media with

A

neither tryptophan nor histidine

191
Q

What are the questions that represent the challenges of gene regulation?

A
  • what should be expressed?
  • when should a gene be expressed?
  • where should a given gene be expressed?
  • how much of a protein is needed, so what level of expression is needed?
192
Q

RNA polymerase participates in all three phases of

A

transcription

193
Q

During initiation, what is present?

A

core RNA polymerase plus sigma (σ) factor

194
Q

During elongation, what is present?

A

core RNA polymerase without σ factor

195
Q

Most promoters are __ to the transcription start point

A

upstream

196
Q

RNA polymerase makes strong contacts at __ and __

A

-10, -35

197
Q

Core RNA has four subunits, what are they?

A 
two alpha (α), one beta
(β), one beta prime (β')
198
Q

What happens during initiation?

A

DNA is unwound and polymerization begins

199
Q

Elongation continues until

A

RNA polymerase recognizes termination signal

200
Q

What are the two kinds of transcription termination in bacteria?

A

Rho-dependent and Rho-independent

201
Q

Describe Rho-dependent termination

A

Rho protein binds to RNA polymerase and removes it from RNA

202
Q

Describe Rho-independent termination

A

20 nt sequence in RNA forms stem-loop

203
Q

What are examples of transcriptional control of gene expression?

A
  • binding of RNA polymerase to promoter
  • Shift from initiation to elongation
  • Release of mRNA at termination
204
Q

Binding of RNA polymerase to promoter is the most critical step in

A

regulation of most prokaryotic genes

205
Q

What are some examples of post transcriptional control of gene expression?

A
  • stability of mRNA
  • efficiency of translation initiation
  • stability of polypeptide
206
Q

Regulation of transcription requires __ that __

A

regulatory proteins; modify ability of RNA polymerase to recognize and bind promoter

207
Q

Proteins bind to __ to regulate transcription

A

DNA

208
Q

Gene regulation changes with __ context

A

environmental

209
Q

Positive regulation __ transcription

A

enhances

210
Q

Positive regulatory proteins help __ transcription

A

activate

211
Q

Negative regulation __ transcription

A

inhibits

212
Q

Negative regulatory proteins help __ transcription

A

block

213
Q

Utilization of lactose by E.coli provides a __ __ of gene regulation

A

model system

214
Q

What are the two enzymes required for lactose utilization?

A

permease and β-Galactosidase

215
Q

What does permease do in lactose utilization?

A

transports lactose into cell

216
Q

What does β-Galactosidase do in lactose utilization?

A

splits lactose into glucose and galactose

217
Q

In the absence of lactose, both permease and β-Galactosidase are present at __ __ levels

A

very low

218
Q

Cells prefer to use __ as an energy source

A

glucose

219
Q

In a medium with both lactose and glucose, bacteria will choose __ first, until it’s gone

A

glucose

220
Q

Lactose is the __ of the genes encoding permease and β-Galactosidase

A

inducer

221
Q

What is induction?

A

stimulation of synthesis of a specific protein

222
Q

What is an inducer?

A

molecule responsible for induction

223
Q

What are the advantages of using lactose utilization by E.coli as a model for understanding gene regulation?

A
  • Lac- mutants survive and can be maintained on media with glucose and so lac genes are not essential for survival (you can keep your mutants alive)
  • simple says for lac expression
  • lactose induces a 1000-fold increase in β-Galactosidase activity
  • lots of progeny
224
Q

What does the operon theory state?

A

one signal can simultaneously regular expression of several clustered genes

225
Q

Jacques Monod and Francois Jacob hypothesized that lac genes are transcribed together as a single mRNA (polycistronic) from a single

A

promoter

226
Q

What are the three structural genes of the lactose operon?

A

lacZ, lacY, and lacA

227
Q

What is a promoter?

A

site to which RNA polymerase binds

228
Q

What does the cis-acting operator site do?

A

controls transcription initiation

229
Q

What does the trans-acting repressor do?

A

binds to the operator (encoded by lacI gene)

230
Q

What does an inducer do?

A

prevents repressor from binding to operator

231
Q

What is the lac-operon?

A

a cluster of genes transcribed simultaneously (lacZ, lacY, lacA)

232
Q

Describe lac-operon induction when lactose is present

A
  1. inducer binds repressor
  2. repressor changes shape and cannot bind to operator
  3. RNA polymerase binds to the promoter and initiates transcription of the polycistronic lac mRNA
233
Q

Repression of lac gene expression occurs in the __ of lactose

A

absence

234
Q

Lac repressor is a __ regulatory element

A

negative

235
Q

lacZ encodes

A

β-Galactosidase

236
Q

lacY encodes

A

permease

237
Q

lacA encodes

A

transacetylase

238
Q

lacA is not necessary for

A

lactose catabolism

239
Q

lacZ and lacY mutations led to new phenotype, what is it?

A

inability to utilize lactose

240
Q

If cells grow in lactose medium, the mutations

A

complement

241
Q

If cells do not grow in lactose medium, mutations

A

fail to complement and are in the same region

242
Q

What is characteristic of lacZ-?

A
  • inability to produce β-Galactosidase

- no induction of β-Galactosidase activity by lactose inducer

243
Q

What is characteristic of lacY-?

A
  • inability to produce permease

- no induction of permease activity by lactose inducer

244
Q

What is characteristic of lacI-?

A

constitutive expression of β-Gal and permease

245
Q

__ __ express the enzymes in the absence and presence of inducer

A

constitutive mutants

246
Q

Why must lac I be a repressor?

A

cells require lac I protein to prevent expression of lac Z and lac Y in absence of an inducer

247
Q

The PaJaMo experiment provided evidence that lacI encodes a

A

repressor

248
Q

Jacob and Monod proposed that lacI encodes a repressor that binds to an operator site near the __ promoter

A

lac

249
Q

What does the binding of an inducer to a repressor do?

A

changes the shape of the repressor so that it can no longer bind to DNA

250
Q

When there is no inducer present, the repressor is able to

A

bind to DNA

251
Q

Repressor is an allosteric protein, meaning that

A

it undergoes reversible changes in conformation when bound to another molecule

252
Q

lacI- mutants have a __ __ that cannot bind to operator

A

mutant repressor

253
Q

lacI(s) mutants have a __ that binds to operator but can’t bind to the inducer

A

superrepressor

254
Q

In lacI(s) mutants, lac genes are __ in the absence and the presence of inducer

A

repressed

255
Q

lacO(c) mutants have a mutant operator that can’t bind the __

A

repressor

256
Q

In lacO(c) mutants, lac genes are __ in the absence and the presence of inducer

A

expressed

257
Q

What are the 2 ways to get constitutive expression?

A
  1. mutation in lacI (lacI-) that prevents the repressor from binding the operator whether lactose is present or not
  2. Mutation in operator DNA sequence (lacO(c)) the prevents repressor from recognizing and binding
258
Q

How can you distinguish between the two ways to get constitutive expression?

A

using the cis/trans test with merodiploids

259
Q

Describe trans-acting elements

A

can diffuse through the cytoplasm and act at target DNA sites on any DNA molecule in the cell

260
Q

Describe cis-acting elements

A

can only influence expression of adjacent genes on the same DNA molecule (operator, promoter, etc)

261
Q

Cis DNA elements need to be on same chromosome as

A

genes they regulate

262
Q

Trans elements are proteins produced on one molecule that can interact with

A

DNA on either molecule

263
Q

If lacI(s) is cis-acting, then lacZ+ chromosome will be

A

inducible

264
Q

If lacI(s) is trans-acting, then lacZ+ will be

A

non-inducible

265
Q

lacI(s) protein acts in

A

trans

266
Q

lacO(c) acts in

A

cis

267
Q

The lacO(c) mutation affects expression of genes only on

A

the DNA that it is located on

268
Q

Why does the O+ operator have no effect in the lacO(c) mutation?

A

because it is adjacent to a mutant lacZ on the plasmid and can’t impact the lacZ+ on chromosome

269
Q

Initiation of transcription under control of regulatory genes whose protein products bind to DNA near promoter alter

A

RNA polymerase

270
Q

What is the biochemical evidence for lac repressor binding to lacO?

A
  • lac repressor has two separate domains
  • lac repressor has a helix-turn-helix (HTH) motif
  • most DNA-binding regulatory proteins are oligomeric (one domain), with two to four subunits
271
Q

Mutated DNA sequences in many different lacI- mutants are clustered in the __ __ domain of lac repressor

A

DNA-binding

272
Q

Mutated sequences in many different lacI(S) mutants are clustered in the __ __ domain of the lac repressor

A

inducer-binding

273
Q

A protein with an HTH (helix-turn-helix) motif has two __ __ separated by a turn in the protein

A

α-helical regions

274
Q

The HTH motif fits into the major groove of

A

DNA

275
Q

One of the α-helical regions of a protein with an HTH motif has amino acids that ‘recognize’ a specific

A

DNA sequence

276
Q

HTH motifs are found in many __ __ proteins

A

DNA-binding

277
Q

lac repressor tetramer binds to __ sites

A

two

278
Q

lac repressor is a tetramer, with each subunit containing a DNA-binding __ __

A

HTH motif

279
Q

Two repressor subunits of lac repressor bind to

A

O1

280
Q

Two repressor subunits of lac repressor bind to either __ or __

A

O2 or O3

281
Q

The binding of the repressor subunits of lac repressor to O1, O2, and O3 causes the formation of a loop that leads to

A

highly efficient repression

282
Q

When lac repressor is bound to lac operator, functional binding of RNA polymerase to the promoter is

A

blocked

283
Q

Many negative regulators (e.g. lac repressor) prevent transcription initiation by blocking

A

the functional binding of RNA polymerase

284
Q

Many positive regulators (e.g. CRP-cAMP) establish contact with RNA polymerase that

A

enhances transcription initiation

285
Q

The lac operon of E.coli is regulated by both __ and __

A

lactose; glucose

286
Q

When both glucose and lactose are present, only __ is utilized

A

glucose

287
Q

Lactose induces __ __ __, but only in the absence of glucose, even if lactose is present

A

lac mRNA expression

288
Q

Positive regulation increases transcription of lacZ, lacY, and lacA only when

A

lactose is present and glucose is absent

289
Q

Lactose prevents repressor from binding to

A

lacO

290
Q

lac repressor is a __ regulator of lac transcription

A

negative

291
Q

lac mRNA expression cannot be induced if

A

glucose is present

292
Q

Glucose controls the levels of

A

cAMP

293
Q

cAMP binds to __ __ __

A

cAMP receptor protein (CRP)

294
Q

CRP-cAMP is a __ regulator of lac transcription, but ONLY in absence of glucose

A

positive

295
Q

Describe catabolite repression

A

overall effect of glucose is to prevent lac gene expression by limiting availability of cAMP

296
Q

CRP-binding sites have a two-fold __ __

A

rotational symmetry

297
Q

CPR protein binds as a

A

dimer

298
Q

CRP-binding site consists of two recognition sequences, one for each

A

subunit of the CRP dimer

299
Q

CRP-cAMP complex makes direct contact with

A

RNA polymerase

300
Q

Without interaction with CRP-cAMP, RNA polymerase can bind to the promoter but is less likely to __ __ __ __ __

A

unwind DNA and initiate transcription

301
Q

What is a reporter gene?

A

protein-encodind gene whose expression in the cell is quantifiable by sensitive and reliable techniques

302
Q

How do you measure gene expression?

A
  • fuse coding region of lacZ to cis-acting regulatory regions from other genes
  • conditions that induce expression of gene of interest will generate β-gal
303
Q

How do you control gene expression?

A
  • fuse the lac regulatory sequences to the coding region of a foreign gene
  • inducible expression of the foreign gene controlled by IPTG
304
Q

lacZ fusion is used to perform genetic studies of the regulatory region of

A

gene X

305
Q

Conditions that regular expression of the test regions from gene X will alter the levels of

A

β-galactosidase

306
Q

Specific regulatory sites can be identified by constructing and testing mutations in the test regions of

A

gene X

307
Q

Expression of gene X is under the control of the

A

lac regulatory system

308
Q

Expression of human growth hormone in E.coli is controlled by

A

lac control region

309
Q

How do eukaryotes use complex sets of interactions?

A
  • regulated interactions of large networks of genes
  • each gene has multiple points of regulation
  • turning on and off genes in right place ad time
310
Q

What are the themes of gene regulation in eukaryotes?

A
  • environmental adaptation, growth, and division in prokaryotes
  • maintenance of homeostasis in multicellular eukaryotes
    • genes are turned on and off in right place and time
    • differentiation and precise positioning of tissues and organs during embryonic development
311
Q

Eukaryotic genomes are __ than prokaryotic genomes

A

larger

312
Q

Compared to prokaryotes, eukaryotes have additional

A

levels of complexity for controlling gene expression

313
Q

__ __ in eukaryotes makes DNA unavailable to transcription machinery

A

chromatin structure

314
Q

Additional __ __ events occur in eukaryotes

A

RNA processing

315
Q

In eukaryotes, transcription takes place in __ and translation takes place in __

A

the nucleus; the cytoplasm

316
Q

Both eukaryotes and prokaryotes utilize DNA binding proteins for

A

transcriptional regulation

317
Q

There are multiple steps where production of the final gene product can be regulated in

A

eukaryotes

318
Q

Eukaryotes can regulate these steps to control __ __ in different tissues

A

cell differentiation

319
Q

What does RNA polymerase I do?

A

transcribes genes that are the major RNA components of ribosomes (rRNAs)

320
Q

What does RNA polymerase II do?

A

transcribes genes that encode all proteins

321
Q

What does RNA polymerase III do?

A

transcribes genes that encode the tRNAs and certain other small RNA molecules

322
Q

RNA pol II catalyzes synthesis of the __ __, which is complementary to the template strand of the gene

A

primary transcript

323
Q

Most RNA pol II transcripts undergo further processing to generate __ __

A

mature mRNA

324
Q

What does RNA splicing do?

A

removes introns

325
Q

What does addition of 5’ GTP cap do?

A

protects RNA from degradation

326
Q

What are the further processes that RNA pol II transcripts must undergo to generate mature mRNA?

A
  • RNA splicing
  • addition of 5’ GTP cap
  • cleavage of 3’ end by ribonuclease, and addition of 3’ polyA tail (poly-A polymerase)
327
Q

Promoters are usually adjacent to

A

the protein-coding gene

328
Q

Promoters include the transcription initiation site and often have

A

about 7 base pair TATA box

329
Q

Binding of RNA pol II allows __ __ of transcription

A

basal level

330
Q

Describe enhancers

A

can be distant (10,000s of bps) from gene, or even within gene introns or reversed in orientation

331
Q

Binding of proteins can augment or repress __ __

A

basal transcription

332
Q

Trans-acting factors interact with cis-acting elements to control rates of

A

transcription initiation

333
Q

How do the direct effects of transcription factors come about?

A
  • through binding to DNA
  • basal factors
  • activators and repressors
334
Q

How does the indirect effect of transcription factors come about?

A

through protein-protein interactions

335
Q

Basal transcription factors assist the binding of RNA pol II to

A

promoters

336
Q

What are the key components of the basal factor complex?

A
  • TATA box-binding protein (TBP)
    • binds to TATA box
    • first of several proteins to assemble at promoter
  • TBP-associated factors (TAFs)
    • bind to TBP assembled at TATA box
337
Q

Basal factors bind to promoters of all __ __ __

A

protein-encoding genes

338
Q

What is the ordered pathway of assembly at promoter?

A
  1. TBP binds to TATA box: produces “bend” in DNA of TATA box
  2. TAFs bind to TBP
  3. RNA pol II binds to TAFs
339
Q

RNA pol II associates with basal complex and initiates

A

basal level of transcription

340
Q

Activators are transcription factors that bind to

A

enhancers

341
Q

What is the significance of activators?

A

binding of different activators to enhancers is responsible for much of the variation in levels of transcription of different genes in different cell types

342
Q

How do activators increase levels of transcription?

A

by interacting directly or indirectly with basal factors at the promoter

343
Q

Binding of activators to enhancers increases

A

transcriptional levels

344
Q

Low level transcription occurs when only __ __ are bound to promoter

A

basal factors

345
Q

When basal factors AND activators are bound to DNA, rate of transcription __

A

increases

346
Q

What are the two functional domains of activator proteins?

A
  1. sequence-specific DNA binding domain (bind enhancer)

2. transcription-activator domain (which binds other trans-factors)

347
Q

__ __ leads to physical interaction of distant DNA regions

A

DNA looping

348
Q

What are the mechanisms of activator effects of transcription?

A
  • stimulate recruitment of basal factors and RNA pol II to promoters
  • recruit coactivators to open chromatin structure
349
Q

What are the effects of activators on transcriptions?

A
  • stimulate recruitment of basal factors and RNA pol II
  • stimulate activity of basal factors
  • facilitate changes in chromatin structure
350
Q

What do the DNA-binding domains of activator proteins do?

A

interact with major groove of DNA

-certain amino acids have high-affinity binding to specific nucleotide sequence

351
Q

What are the three best-characterizes motifs?

A
  1. helix-loop-helix (HLH)
  2. helix-turn-helix (HTH)
  3. zinc finger
352
Q

__ __ __ are activators, but only in the presence of specific hormones

A

steroid hormone receptors

353
Q

Steroid hormones don’t bind directly to DNA but are __ of steroid hormone receptors

A

coactivators

354
Q

In the absence of hormone, steroid hormone receptors can’t bind to DNA and can’t

A

activate transcription

355
Q

In the presence of hormone, steroid hormone receptors bind to enhancers for specific genes and activate

A

expression

356
Q

T or F? Not all transcription factors activate gene expression

A

T

357
Q

When a repressor binds to the same enhancer sequence as the activator, what effect does it have on the basal transcription level?

A

no effect

358
Q

Describe quenchers

A

bind to the activator but do not bind to DNA; the repressor blocks the activator from functioning

359
Q

Some repressors eliminate virtually all basal transcription from a promoter by blocking

A

promoter access

360
Q

In humans, about __ genes or __% of genes encode transcriptional regulatory proteins

A

2000; 10%

361
Q

Each regulatory protein can act on __ genes

A

many

362
Q

Each regulatory protein can have __ of enhancers

A

dozens

363
Q

The same transcription factors can be an activator or a repressor depending on

A
  • the cell that it’s in

- which cis-regulatory element it binds to

364
Q

Regulatory proteins have vast complexity for precise control of

A

gene expression

365
Q

What are the two methods that cells use to regulate transcription?

A
  • binding of transcription factors to enhancers

- DNA methylation

366
Q

What does binding transcription factors to enhancers do?

A

modulates the spatial and temporal expression of many genes that are expressed only in particular tissues at specific times during development

367
Q

Describe methylation

A

(a biochemical modification of DNA itself)
-a methyl (CH3) group is added to the 5th carbon of the cytosine base in a 5’ CpG 3’ dinucleotide pair on one strand of the double helix

368
Q

DNA methylation is important for controlling expression of

A

“housekeeping genes”

369
Q

DNA methylation also regulates some

A

cell-type specific genes

370
Q

Why can DNA methylation alter gene expression heritability without changing the base sequence of DNA

A

because methylation affects transcription levels, and methylation patterns are copied during DNA replication (this is called the epigenetic phenomenon)

371
Q

Methylation is key to epigenetic in mammals and is called

A

genomic imprinting

372
Q

What organisms have no DNA methylation?

A

C. elegans and yeast

373
Q

What organisms have very little DNA methylation?

A

other invertebrates and lower euks

374
Q

DNA methylation at CpG islands __ gene expression

A

silences

375
Q

DNA methylation usually __ the transcription of eukaryotic genes

A

inhibits

376
Q

DNA methylation usually inhibits the transcription of eukaryotic genes particularly when it occurs in the vicinity of the

A

promoter

377
Q

In vertebrates and plants, CpG islands occur near many

A

promoters of genes

378
Q

CpG islands are commonly __ in length and contain a high number of __

A

1000 to 2000 bp; CpG sites

379
Q

DNA methylation is thought to play an important role in the silencing of tissue-specific genes to prevent

A

them from being expressed in the wrong tissue

380
Q

Nucleosomes can make promoters __

A

inaccessible

381
Q

What are epigenetic changes?

A

changes in chromatin structure that are inherited from one generation to the next

  • DNA sequence is not altered
  • but particular cells with altered chromatin will have altered gene expression, which can be inherited from one cell generation to the next
382
Q

Chromatin reduces binding to basal factors and RNA pol II to

A

very low levels

383
Q

Nucleosomes can be __ or __ by chromatin remodeling complexes

A

repositioned or removed

384
Q

After remodeling, DNA at promoters and enhancers becomes __ __ to transcription factors

A

more accessible

385
Q

Transcription is active near __ CpG islands

A

unmethylated

386
Q

CpG islands are regions with a high concentration of

A

CpG dinucleotides

387
Q

Near genes, CpG islands are usually unmethylated because

A

an activator binds and blocks access by DNMTs

-the chromatin is open and transcription is activated

388
Q

DNA methylation at CpG islands __ gene expression

A

silences

389
Q

In the absence of activators, the CpG islands become

A

methylated

390
Q

Methyl-CpG-binding proteins (MeCPs) binds and close the

A

chromatin structure

391
Q

Gene expression repression is often long-term because

A

the methylation pattern is maintained through numerous cell divisions

392
Q

Long-term repression through DNA methylation is called

A

silencing

393
Q

DNA methylation is an __ __ because it can heritably alter gene expression without changing DNA sequence

A

epigenetic phenomenon

394
Q

Cytosine methylation pattern is copied during

A

DNA replication

395
Q

DNA methylation patterns are copies during DNA replication by

A

a special DNMT present at the replication fork

-this DNMT recognizes semi-methylated DNA (on the parent strand) and methylates the newly synthesized strand

396
Q

Sex-specific DNA methylation is responsible for

A

genomic imprinting

397
Q

What is the Mendelian rule?

A

parental origin of allele does not affect F1 phenotype (usually!)

398
Q

Describe genomic imprinting

A

expression of a gene depends on whether it was inherited from the mother or father
-epigenetic effect (no change in DNA sequence)

399
Q

__ __ __ is transcriptionally silenced if it was transmitted from the father and the maternally inherited allele is expressed

A

paternally imprinted gene

400
Q

__ __ __ is transcriptionally silenced if it was transmitted from the mother and the paternally inherited allele is expressed

A

maternally imprinted gene

401
Q

imprinted =

A

silenced

402
Q

Clinical geneticists realized that genomic imprinting existed long before molecular biology techniques made it possible to confirm its existence, how?

A

pedigree analysis of rare diseases

  • the patterns were clear in certain rare cases where the condition was caused by a deletion that removed the imprinted gene
  • the inheritance of the deletion and the disease could be followed in karyotypes
403
Q

When examining a pedigree chart of an imprinted gene, the sex of the parent carrying a mutant allele determines offspring __, not sex of the offspring!

A

phenotype

404
Q

If there is a deletion of a paternally imprinted autosomal gene.. fathers can pass the deletion to their sons and daughters and they will not be affected because

A

the child’s wild-type maternal allele would be expressed

405
Q

The genomic imprint is ___ during mitosis

A

maintained

406
Q

Patterns of DNA methylation must be __ during meiosis before being passed on to the next generation

A

reset

407
Q

Imprinting is

A

sex-specific

408
Q

Methylation is removed in

A

germ-line cells

409
Q

Imprinting occurs in the __ __ and is accompanied by heavy __

A

germ line; methylation

410
Q

Epigenetic imprints are erased during __ __ __ and reset by __ __ __

A

germ-line development; sex-specific patterns

411
Q

Complementary base pairing between a small RNA and mRNA can prevent

A

gene expression

412
Q

What are the 3 classes of small regulatory RNAs that have been identified

A
  1. micro-RNAs (miRNAs)
  2. small interfering RNAs (siRNAs)
  3. Piwi-interacting RNAs (piRNAs)
413
Q

Each small RNA class leads to the production of

A

single-stranded RNAs of slightly different lengths

414
Q

Each small RNA class is in the range of __ nucleotides

A

21-30

415
Q

What are the targets of miRNAs?

A

mRNAs

416
Q

What are the effects of miRNAs?

A

-block mRNA translocation/ destabilize mRNAs

417
Q

What are the targets of siRNAs?

A

mRNAs

418
Q

What are the effects of siRNAs?

A

block translation/ destabilize mRNAs

419
Q

In order to prevent gene expression, small RNAs work with proteins in the __ family

A

Argonaute

-form ribonucleoprotein complexes

420
Q

The small RNA in each ribonucleoprotein complex guides the complex to

A

particular nucleic acid

  • this nucleic acid target will have perfect or partial complementarity with the small RNA
  • the mRNA will not be expressed in most cases
  • this is a type of post transcriptional RNA modulation

Genetics BSC-315 (3 decks)

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