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GENETICS > Genetic Exam 2 > Flashcards

Genetic Exam 2 Flashcards

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1
Q

The normal chromosome complement of a cell in mitotic metaphase: Human male:

A

22 pairs of autosomes + X + Y

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2
Q

The normal chromosome complement of a cell in mitotic metaphase: Human female:

A

22 pairs of autosomes + 2 Xs

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3
Q

What are sex chromosomes

A

Chromosomes that specific es sex (X and Y in humans)

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4
Q

What are autosomes chromosomes?

A

All other non-sex chromosomes

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5
Q

What is the human Karyotype? (4x)

A
  1. Represents the chromosome complement
  2. Produced as a metaphase spread
  3. Trad method: Giemsa staining
  4. Mod method: chromosome painting
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6
Q

What is Giemsa staining

A

Dyes like Giemsa (and others) stain smaller segments of the chromosomes

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7
Q

When using Giemsa staining what regions stain darker

A

G-bands, gene poor, heterochromatin

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8
Q

When using Giemsa staining what regions stain lighter

A

R-bands, gene rich, euchromatin

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9
Q

Are banding pattern specific to each chromosome when using Giemsa staining

A

Yes

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10
Q

What is a major different between Chromosome painting and Giemsa staining

A

Chromosome painting color each chromosome a different color while Giemsa staining results black or white staining on all chromosomes

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11
Q

What is Chromosome painting

A

Makes DNA probes specific to each chromosome which are then labeled with fluorescence

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12
Q

Which technique is this?

Make DNA probes specific to each chromosome
Label DNA probes with fluorescence
Hybridize the probe to the metaphase spread (squash)
Wash off unbound probes
Examine the slide on fluorescent microscope

A

Chromosome painting

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13
Q

What does 9q34 refers to?

A

Chromosome 9, long arm, band 34

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14
Q

What does Xp28 refer to?

A

Chromosome X, short arm, band 28

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15
Q

Bands and inter bands are assigned with numbers

A

True

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16
Q

How do we ensure genes on the X chromosome are expressed at similar levels in both sexes?

A

Unequal dosage in different sexes by increasing the activity of genes in the Chromosome X for males or reducing the activity of genes in X chromosomes for females

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17
Q

How do mammals compensate for dosages of X linked genes

A

X chromosomes inactivation in females

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18
Q

How do Drosophila compensate for dosage of X chromosomes

A

Increase transcription activity on X chromosomes in males

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19
Q

How does C elegans compensate for dosage of X chromosomes

A

Decrease transcription activity in both X chromosomes in females

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20
Q

What are complex traits?

A

Affected by the alleles of 2+ genes (genetic factors) as well as by environmental factors

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21
Q

What are 3 categories of complex traits

A

Continuous traits (quantitative traits)
Categorical traits
Threshold traits

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22
Q

What are categorical traits

A

The phenotype corresponds to any one of a number of discrete categories

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23
Q

What is an example of Categorical traits

A

The number of puppies in a litter; flower colors; animal fur colors

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24
Q

What are threshold traits

A

A few phenotypic classes, determined by multiple genes & the environment. When a threshold is reached, it shows one phenotype; otherwise, it shows another phenotype

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25
Q

What is an example of threshold traits?

A

Adult onset diabetes

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26
Q

Flower color is an example of what complex trait

A

Categorical traits

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27
Q

Animal fur color is an example of what complex trait

A

Categorical traits

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28
Q

Adult onset diabetes is an example of what complex trait

A

Threshold

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29
Q

Heights and weights is an example of what complex traits

A

Continuous traits

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30
Q

Blood pressure in humans is an example of what complex trait

A

Continuous traits

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31
Q

A large variance means what

A

The distribution is spread out

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32
Q

A small variance means what

A

The distribution is clustered around the mean

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33
Q

What is normal distribution

A

When the data are symmetrical, the distribution can be approximated by a smooth, bell shaped curve

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34
Q

A feature of normal distribution is that one standard dev is ______%, two standard dev is ______%, three standard dev is ______%

A

68%, 95%, 99.7%

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35
Q

What are causes of variation (4x)

A
  1. Genotypic variation
  2. Environment variation
  3. Variation due to genotype-by-environment interaction
  4. Variation due to genotype-by-environment association
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36
Q

What is Genotypic variance?

A

Differences in genotype that cause phenotypic variance

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37
Q

What is Environmental variation?

A

differences in the environment that cause phenotypic variance

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38
Q

What assumptions are made for the Segregation of 3 genes affecting a quantitative trait

A

Each Uppercase allele adds one unit to the phenotype
Each lowercase has no effect

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39
Q

What is the results of the segregation of three genes affecting a quantitative trait?

A

7 phenotypic categories, mean = 3, variance 1.5

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40
Q

The distribution of phenotypes as determined by 3 genes or 30 genes are not alike (T/F)

A

False

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41
Q

In the absence of environmental variation, the distribution of phenotypes alone provides what information?

A

Limited info about the # of genes involved and no info on dominance relations

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42
Q

If genotype and environment separately and independently affect phenotype, how can you calculate phenotype variance?

A

variance(p) = variance(g) + variance (e)

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43
Q

If genotype and environment do not act separately and independently they are what variance

A

G-E Interactions or G-E Associations

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44
Q

What are G-E interactions?

A

Environmental effects on phenotype differ according to genotype

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45
Q

What are G-E associations?

A

Different genotypes are not distributed at random in all possible environments (certain genotypes are preferred with certain environments)

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46
Q

What is an example of G-E associations?

A

Framers feed their cows in proportion to their milk production levels

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47
Q

What is an example of G-E interactions?

A

Strain A is superior when environmental quality is low, but strain B is superior when environmental quality is high

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48
Q

What are 3 methods to identify genes affecting complex traits?

A
  1. Linkage analysis in mapping QTLs
  2. GWAS
  3. Candidates genes for complex traits
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49
Q

What is Quantitative trait Loci mapping?

A

Identifying QTL through linked genetic markers

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50
Q

What is Quantitative trait Loci?

A

A gene that affects a complex trait

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51
Q

Can QTLs be identified in pedigrees?

A

No

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52
Q

Common alleles affecting complex traits account for a small fraction of total heritability (T/F)

A

True

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53
Q

How many GWAS were identified for Chron’s disease?

A

71

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54
Q

How many % does 71 loci account for phenotypic variation in Chron’s disease

A

23%

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55
Q

What are candidate genes

A

Genes we suspect could contribute to a complex trait that we test the function of

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56
Q

What are some examples of candidate genes?

A

SLC6A4 is an candidate gene for depression that encode a serotonin transporter

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57
Q

What is serotonin?

A

A neurotransmitter that influences anxiety and depression

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58
Q

What is the function of Serotonin transporter SLC6A4

A

Transport serotonin from neurons that make it to neurons that receive it; also recycles serotonin (uptake)

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59
Q

The target of antidepressant drugs are

A

SLC6A4 which will inhibit uptake

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60
Q

S form is

A

the short allele

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61
Q

L form is

A

the long allele

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62
Q

How do S and L forms differ

A

in # of tandem repeats in the promoter region

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63
Q

L/L genotype does what

A

cells make more mRNA and in turn more SLC6A4 protein

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64
Q

S/L and S/S genotypes do what

A

have a higher risk of depression

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65
Q

What is the G-E interaction for depression?

A

Among Ecstasy users (environment factor) depression scores highest in S/S genotype which means ecstasy results in the biggest difference in S/S genotype

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66
Q

What is euploid

A

possessing a normal complement of chromosomes

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67
Q

What is aneuploid

A

possessing an abnormal number of one chromosome (or region of chromosome)

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68
Q

What is monosomy

A

Only possess one copy of chromosome

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69
Q

What is trisomy

A

Possess 3 copies of chromosome

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70
Q

What is polyploid

A

contains extra complete set(s) of chromosomes (triploid, tetraploid, etc)

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71
Q

In human pregnancies, which type of aneuploid is most common

A

monosomy

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72
Q

In humans which type of aneuploid is most harmful

A

monosomy

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73
Q

Down syndrome is what type of aneuploid

A

Trisomy 21

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74
Q

How common is Down syndrome

A

1 in 750 live births

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75
Q

What is the most common cause of Down syndrome?

A

nondisjunction during meiosis

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76
Q

What is the least common cause of Down syndrome?

A

chromosomal translocations

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77
Q

What are some symptoms of Down syndrome?

A

intellect disability
physical abnormality (heart defect)
characteristic facial appearance

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78
Q

Occurrence of Down syndrome _________ as women ag

A

increases

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79
Q

What are some examples of environmental effects on nondisjunction?

A

Bisphenol A (BPA), alcohol, smoking, pollutants, oral contraceptives

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80
Q

Why are sex chromosome abnormalities more common than trisomy 21

A

Dosage compensation ensures extra X chromosomes are inactivated and Y chromosomes only contain a small # of genes

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81
Q

47 XXY

A

Klinefelter syndrome: male, tall, sterile, mild impairment

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82
Q

45X

A

Turner syndrome: female, short, no sexual maturation

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83
Q

47 XXX

A

female, mostly normal, mild impairment (more frequent)

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84
Q

47 XYY

A

male, mostly normal

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85
Q

What is chromosomal deletion

A

a segment of a chromosome is missing

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86
Q

The bigger the deletion, the more harmful (T/F)

A

True

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87
Q

How can chromosomal deletion occur

A
  1. chromosomal breakage and reunion
  2. ectopic recombination between direct repeats
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88
Q

What are direct repeats?

A

two repeated blocks that have the same orientation

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89
Q

What is a chromosomal duplication

A

a chromosome has a region that’s duplicated (present twice)

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90
Q

What is tandem duplication

A

the segment is duplicated and is in the same orientation immediately adjacent to another

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91
Q

Unequal crossing over between duplication results in

A

even more tandem copies

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92
Q

Human red-green color genes are __________ thus pairings can happen

A

highly similar (96%)

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93
Q

What results in color blindness

A

the unequal crossover in red-green chromosome

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94
Q

What is chromosomal inversion

A

a chromosome in which linear order of a group of genes is reversed

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95
Q

What results in chromosomal inversion

A

ectopic recombination between inverted repeats

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96
Q

What are inverted repeats

A

two repeats that are in reversed order (opposite to direct repeats)

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97
Q

What are translocations

A

interchange of parts between nonhomologous chromosomes

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98
Q

What is reciprocal

A

two reciprocally interchanged parts

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99
Q

What is heterozygous translocation?

A

one pair interchanged, one pair normal

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100
Q

What is homozygous translocation?

A

both pairs interchanged

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101
Q

What is Robertsonian translocation

A

a special type of nonreciprocal translocation where 2 nonhomologous acrocentric chromosomes fuse their short arms resulting in 1 chromosome with a centromere

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102
Q

___ % of down syndrome results from Robersonian translocation

A

3

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103
Q

Segregation of Robertsonian translocation ratio

A

1/4 (adjacent 1) 1/4 (adjacent 2) 2/4 (alternate)

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104
Q

Polyploidy is not common in higher plants (T/F)

A

False

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105
Q

What is polyploidy

A

Containing multiple complete sets of chromosomes

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106
Q

How many flowering plants are polyploidy

A

30-80%

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107
Q

What are some examples of plant polyploidy

A

corn, wheat, cotton

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108
Q

What is the effect of triploid on plants

A

trouble with meiosis and used to produce seedless crops

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109
Q

What type of polyploidy does seedless watermelon have

A

cross between diploid and tetraploid results in triploid seed

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110
Q

What is monoploid

A

the basic set of chromosomes that’s multipled in a polyploid species

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111
Q

What is haploid

A

the set of chromosomes present in the gamete

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112
Q

How common is sexual polyploidization

A

1-40% frequency, under genetic control

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113
Q

What is sexual polylploidization

A

The increase in chromosome number takes place in meiosis through the formation of unreduced gametes

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114
Q

What is asexual polyploidization

A

The increase in chromosome number takes place in mitosis through the doubling of the complement of chromosomes

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115
Q

What is autopolyploidy

A

all chromosomes derive from a single diploid species

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116
Q

What is allopolyploidy

A

sets of chromosomes derive from 2 or more different ancestral species

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117
Q

What is Plasmid

A

nonessential bacterial DNA thats not part of the genome

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118
Q

Can plasmids replicate independent of genome replication

A

Yes

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119
Q

How are plasmids passed on

A

passed on to progeny

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120
Q

What is the shape of plasmid

A

circular or linear

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121
Q

How many copies of number do plasmids have

A

high copy number (50) or low copy number (1-2)

A few kb to a few hundred kb

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122
Q

What is F plasmid

A
  1. F factor (fertility)
  2. Can be transferred from F+ to F- during conjugation
  3. Conjugative plasmid
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123
Q

What is conjugation

A

the joining of 2 bacterial cells in the genetic transfer process

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124
Q

Transfer of F plasmid between cells begins as

A

a single strand

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125
Q

What is the results of F+ x F- mating

A

Transfer is replicative, Donor remains F+ and recipient becomes F+

Only plasmid DNA is transferred

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126
Q

What are some useful bacteria; mutants

A
  1. Antibiotic resistant mutants
  2. Nutritional mutants
  3. Carbon-source mutant
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127
Q

What are some examples of antibiotic mutants

A

Streptomycin-resistant (Str-r) and Streptomycin sensitive (Str-s)

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128
Q

What are some examples nutritional mutants

A

Prototroph: wild type cells (grow in minimal medium)
Auxotroph: unable to synthesize essential nutrient

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129
Q

What are carbon source mutants

A

cannot utilize a particular source of carbon or energy

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130
Q

What is an example of carbon source mutant

A

Lac-mutants cant grow on media that only have lactose as carbon source

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131
Q

What is selective medium

A

Medium that allows the growth of only one type of cell

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132
Q

What is nonselective medium

A

Medium that allows all types to grow

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133
Q

How do I isolate mutants that do NOT grow on selective media?

A

Minimal media + penicillin (kills dividing cells)

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134
Q

What is replica plating

A
  1. Transfer process: Use sterile velvet to pick up bacteria and then transfer onto replica plate
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135
Q

What is DNA-mediated transformation

A

Recipient cells acquire genes from free DNA molecules in the medium

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136
Q

In nature (soil), free DNA can be from lysis of donor cells (T/F)

A

True

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137
Q

What are the two steps of DNA-mediated transformation

A
  1. Taking up the DNA
  2. Homologous recomb with recipient DNA
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138
Q

Are all species capable of transformation

A

No

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139
Q

If two genes a and b are widely separated, chances of them being co-
transformed are

A

low

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140
Q

If they are close, they often present on _________ then
their co-transformation rate is __________

A

If they are close, they often present on a single donor fragment, then
their co-transformation rate is close to the frequency of single-gene
transformation

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141
Q

The farther apart two genes are, the less likely they will be co-
transformed (T/F)

A

True

142
Q

How is Hfr plasmid is formed

A

The integration of F into bacterial chromosome by reciprocal recomb

143
Q

How much of F DNA make up the bacterial chromosome

A

2%

144
Q

Result of Hfr x F- Mating

A
  1. Donor remains Hfr
  2. Recipient does not become F+ because they did not gain the whole F+ dna. Some recipients will become recomb where transferred fragment gets integrated
145
Q

How long does it take for the whole genome to get transfered

A

100 minutes

146
Q

Do cells usually separate after 100 minutes during transferring of DNA

A

No

147
Q

What is Time of Entry mapping

A

based on the order of transfer of genes you can determine the sequence as the further away a gene is, the longer it takes for that gene to get transferred

148
Q

What is transduction

A

DNA fragment transfer from one cell to another by a phage particle containing the bacterial DNA

149
Q

Where is the DNA contained on a T2 phage particle

A

Head

150
Q

What is generalized transduction

A

In generalized transduction, the phage can carry any part of the DNA and transfer to another

151
Q

What are the types of mutations

A

By tissue of origin, by function, by molecular nature.

152
Q

What are origin mutation

A

Spontaneous, induced ( presence of known mutagen ),

153
Q

What are cell type mutations

A

Somatic ( non reproductive cells) & germline ( reproductive cells)

154
Q

Which type of cell type mutation is transmitted to the next generation

A

Germ line mutation

155
Q

What is nucleotide (nt) substitutions

A

A nt pair is replaced with another pair

156
Q

What is transitions

A

T→ C or C → T (pyrimidine to pyrimidine)

A → G or G → A ( purine → purine )

157
Q

Phages carries a _________ piece of any part of the bacterial genome during ____________

A

small piece, lytic cycle

158
Q

Phages when infecting other bacterium cells, can _______

A

transduce the new host genome through recomb

158
Q

What do phages do to bacterial cells

A

lyses (break the bacterial genome)

159
Q

Roughly how many phage particles contain bacterial DNA

A

1 in 10^6

160
Q

How can generalized transduction be used in mapping

A

Using Cotransduction, the farther 2 markers are, the less likely they will be contransduced

161
Q

What is Cotransduction

A

2 markers getting transduced into one bacterium

162
Q

____% E coli phage capable of lytic cycle and ____% undergoes lysogeny

A

75% and 25%

163
Q

What is lysogeny

A

When a phage infects a host but doesn’t destroy the host

164
Q

What is lytic cycle

A

When a phage infects a host and destroy the host

165
Q

Phage DNA is integrated into the bacterial genome during

A

lysogeny

166
Q

Once integrated, the phage is now a _______

A

prophage

167
Q

After the phage integrates into bacterium, the bacterium is called

A

a lysogen

168
Q

For lysogeny, phage will cut themselves out of the bacterium to move to another host, which is called

A

excision

169
Q

Excision is ____% accurate

A

99.9%

170
Q

What happens when there is an error during excision

A

Specialized transduction

171
Q

What is specialized transduction

A

DNA excised from bacterium genome may carry a small piece from host, adjacent from the integration site

172
Q

When a specialized transduction occurs the new host will

A

May gain a small piece of the previous host

173
Q

Is the gene from specialized transduction random

A

No, only genes nearby the integration site

174
Q

What is C-value paradox

A

the noncorrelation between complexity of organisms and genome size

175
Q

What is an example of C value paradox

A

Salamanders having 30x genome than humans

176
Q

E Coli genomic DNA is ____________ um long, while cell is _ um long

A

1500 and 2

177
Q

The largest human chromosome is ___mm long

A

82

178
Q

How does the DNA achieve compactness?

A

Supercoiling

179
Q

Relaxed DNA molecule has _ base pair per helical turn

A

10

180
Q

What is relaxed DNA

A

no twisting other than helical twisting

181
Q

What is supercoiling of DNA

A

the segments of double stranded DNA are twisted around one another

182
Q

Underwinding the helix creates

A

bubbles and supercoils

183
Q

Bubble of unpaired bases compensates for

A

underwinding

184
Q

Underwound DNA can also compensate by forming

A

negative supercoils

185
Q

What is Topoisomerase I

A

relaxes supercoiled DNA to remove helical constraints that can otherwise hinder DNA replication and transcription (+/- linking #) doesn’t require ATP

186
Q

What is Topoisomerase II

A

Topoisomerase II is an enzyme that is able to break and rejoin double-strand DNA molecules (+/- 2 linking #) requires ATP/NADH

187
Q

What is Topoisomerase also known as

A

Gyrase (super unwound -2) or reverser Gyrase (super wound +2 )

188
Q

What is topoisomerase

A

breaking one or both strands, changing the bp number per turn and rejoining the broken strands

189
Q

Bacterial genome structure (3x)

A
  1. DNA is compacted due to supercoiling
  2. Also due to protein that wrap, bend, or compact the molecule
  3. DNA is a condensed unit called nucleoid
190
Q

What is a nucleoid

A

a set of looped domains (supercoiled DNA attached to a protein core)

191
Q

What is chromatin

A

DNA associated with numerous proteins in a stable and ordered aggregate

192
Q

What is Histone

A

the major class of proteins that associate with DNA

193
Q

What are Eukaryotic genome structure

A
  1. Chromatin
  2. Histone
194
Q

How many amino acids are in Histone

A

100-200

195
Q

What are some characteristics of histones (4x)

A
  1. rich in lysine and arginine (+ charged)
  2. attracted to negatively charged phosphate groups in DNA backbone
  3. H1, H2A, H2B, H3 and H4
  4. Sequences highly similar among different organisms
196
Q

Chromatin shows a _______ structure under electron microscope

A

bead-like

197
Q

Nucleosomes

A

the bead-like unit in chromatin

198
Q

The average length of DNA fragment _________ per nucleosome

A

~200bp

199
Q

The average length of core DNA ___ per core particle

A

~145 bp

200
Q

Histone Tails (amino ends) are subject to modifications (5x)

A
  1. Acetylation
  2. Methylation
  3. Phosphorylation
  4. Certain mods are associated with double strand break during recomb and DNA repair
  5. Other mods regulate gene activity (transcription levels)
201
Q

The internal structure of nucleosomes contain

A

H2A, H2B, H3, H4 (2 each)

202
Q

Chromosome condensation during cell division (early prophase)

A
  1. form loops
203
Q

Chromosome condensation during cell division (late prophase)

A
  1. shortens
204
Q

Chromosome condensation during cell division (metaphase)

A
  1. Compresses laterally
205
Q

Proteins that help with condensation:

A
  1. Cohesions
  2. Condensins
  3. Topoisomerase II
206
Q

Nucleosomes further from _______

A

coils

207
Q

The eukaryotic genome contains:
______%: unique sequences
______%: high repetitive sequences (__________ per repeat, as many as 10^5 copies)
______% middle repetitive sequences (______ copies)

A

30-75%: unique sequences
5-45%: high repetitive sequences (5-300 per repeat, as many as 10^5 copies)
1-30% middle repetitive sequences (10-1000 copies)

208
Q

How many unique sequences do viruses and prokaryotes have

A

almost all unique sequences

209
Q

How many unique sequences do sea urchins have

A

40%

210
Q

How many unique sequences do humans have

A

over 50%

211
Q

How many unique sequences do drosophila have

A

70%

212
Q

Highly repetitive sequences are what sizes and also called what

A

mostly are fairly short (aka satellite sequences)

213
Q

Where are highly repetitive sequences located in

A

heterochromatin

214
Q

Where is heterochromatin

A
  1. adjacent to centromeres and near chromosome arms ie telomere
  2. are interspersed with euchromatin and contains a small # of genes
215
Q

Which contains more genes Euchromatin or Heterochromatin

A

Euchromatin

216
Q

Euchromatins are where in relation to a chromosome

A

In between the Heterochromatin

217
Q

What are middle repetitive sequences

A

Contains genes coding for groups of genes (rRNA, tRNA, histones, etc)
Contain transposable elements (TEs)

218
Q

What are transposable elements

A

contains terminal repeats that, allow transposase to bind or allow themselves to be recognized and ligated to target insertion sites

DNA sequences that move from one location on the genome to another

219
Q

What is transposase

A

an enzyme that carries out the transposition

220
Q

In the human genome, how many TEs are not able to transpose

A

50%

221
Q

TEs always own active transposase

A

False

221
Q

TEs may encode their own transposase

A

True

221
Q

What types of repeats may TEs have

A

terminal direct repeats, inverted repeats, or no terminal repeats

222
Q

What are direct repeats

A

sequences that have the same 5’ to 3’ polarity and are in the same DNA strand

223
Q

What are inverted repeats

A

sequences that are opposite DNA strands in order to preserve the same 5’ to 3’ polarity

224
Q

What are non-long terminal repeats

A

Have no terminal repeats, include LINE and SINE and are most abundant ones in mammalian genomes

225
Q

What is LINE

A

long interspersed nuclear element

226
Q

What is SINE

A

short interspersed nuclear element

227
Q

Human genome contains a significant amount of TEs

A

True

228
Q

What are centromeres

A

a narrow constriction along the chromosome

229
Q

What is a central component of kinetochore

A

centromeres

230
Q

What is kinetochore

A

where spindle fibers bind to pull DNA apart during cell division

231
Q

What are holocentric chromosomes

A

Centromeric sequences spread throughout the chromosome

232
Q

What is an example of holocentric chromosome

A

C elegans

233
Q

What is the most common centromeres

A

Localized centrosomes

234
Q

Centromeres in yeast are big and complex

A

False (small and simple)

235
Q

What are the lengths of centromeres in other eukaryotes

A

hundreds of kb in size

236
Q

What are telomeres

A

a special DNA protein structure at the end of chromosome

237
Q

What becomes shorter with each round of DNA replication without telomerase

A

telomeres

238
Q

What do telomerase do

A

adds tandem repeats to the end of the chromosome thus preventing it from shortening

239
Q

The simple sequences in telomeres in human

A

5’ TTAGGG 3’

240
Q

The simple sequence in telomeres in Tetrahymena

A

5’ TTGGGG 3’

241
Q

What is Hayflick’s limit

A

in most cells, telomerase are limited so telomere length limits # of cell divisions

242
Q

Telomere length is restored as fast as it was shortened

A

False

243
Q

How many divisions can human progenitor cells go for

A

about 70

244
Q

What is the difference between embryonic stem cells and cancer cells vs progenitor cells

A

Embryonic stem cells and cancer cells have high telomerase activity

245
Q

What are the 4 stages of DNA replication

A
  1. Initiation
  2. Elongation
  3. Termination
  4. Fidelity
246
Q

What are the key features of DNA replication (5x)

A
  1. Semi conservative replication
  2. Proceeds in 5’ to 3’ direction
  3. Catalyzed by DNA polymerases
  4. Requires free deoxynucleoside triphosphate (dNTP)
  5. Requires free 3’OH group on stand being synthesized
247
Q

What is the semiconservative model of replication

A

One strand is used as template to make new complementary strand

248
Q

How is free dNTP used as a substrate

A
  1. dNTP is added to growing chain
  2. O-P bond forms between phosphate group and 3’ OH
  3. pyrophosphate is released
  4. dNTP (A T G C) is selected according to base pairs
249
Q

Can new dNTP be added to 5’ end

A

No

250
Q

What is initiation

A
  1. starts with RNA primer which is the elongated by adding deoxyribonucleotides to its 3’ end
251
Q

What is elongation

A
  1. Chain grows from 5’ to 3’
  2. requires DNA polymerase
  3. Continuous on leading strand
  4. Discontinuous on lagging strand
252
Q

What is Fidelity

A
  1. Errors occur 10^-5 where there is a mismatch in base pairs per round of replication (ie 6000 mismatches per cell cycle in humans)
  2. Polymerase has proofreading ability
253
Q

Are there different mechanisms in prokaryotes and eukaryotes for termination

A

Yes

254
Q

What type of replication does E coli have

A

theta replication

255
Q

Wat kind of replication does F plasmid, phage, and etc have

A

rolling circle replication

256
Q

What is theta replication

A

Replication occurs on a continuous DNA, is bidirectional w/ 2 replication forks

257
Q

What is rolling circle replication

A

Starts with a single-strand cleavage that produces a 3’ end and 5’ end and results in linear tandem repeats of parental sequences

258
Q

What occurs in late stages of replication od dsDNA phages with circular DNA

A

Rolling circle replication

259
Q

Replication between F plasmid and Hfr conjugation and recipient E coli is

A

Rolling circle replication

260
Q

What are the key enzymes/proteins involved in DNA replication (5x)

A
  1. Gyrase
  2. RNA primer
  3. DNA ligase
  4. Helicase
  5. SSB protein
261
Q

What is Helicase

A

an enzyme that uses ATP to unwind the DNA

262
Q

What is SSB proteins (Single strand DNA binding)

A

binds to and stabilizes the single-strand DNA

263
Q

What is Gyrase

A

a type of Topoisomerase II: releases torsional stress caused by unwinding

264
Q

Primase

A

a special RNA polymerase that synthesizes the RNA primer

265
Q

Polymerase

A

add new nucleotides to daughter molecule

266
Q
A
267
Q

Transcription

A

The synthesis of an RNA molecule from corresponding DNA segment

268
Q

Promoter

A

The region where RNA polymerase and other transcription factors binds to initiate transcription (20-200nt)

269
Q

Translation

A

Info transfer from the mRNA to amino acid sequences and the chemical run that link the amino acids to polypeptide chain

270
Q

Transcript

A

The RNA product of transcription

271
Q

Ribosome

A

Particles in the cytoplasm where translation takes place

272
Q

rRNA

A

ribosomal RNA, component of the ribosome

273
Q

mRNA

A

Messenger RNA, template for translation

274
Q

tRNA

A

Transfer RNA, the RNA that recognizes the codon in the mRNA and transfers the corresponding amino acid during translation

275
Q

Polypeptide

A

A string of amino acids connected by peptide bond

276
Q

Protein

A

One or more polypeptide chains folded into a higher order structure

277
Q

TSS

A

Transcription start site

278
Q

In Ecoli, genes and proteins are

A

Colinear

279
Q

If genes and proteins are colinear a mutation earlier in the gene results in

A

Amino acids positions earlier in protein sequence

280
Q

One strand of DNA is used as template to make

A

RNA

281
Q

Usually only one DNA strand is transcribed for a particular gene

A

True

282
Q

Transcription in prokaryotes- Initiation
Need:

A

The RNA polymerase + promoter sequence

283
Q

Promoter sequence in E. coli starts at what sequences

A

-35 and -10

284
Q

Consensus sequence

A

Sequence of nucleotides determined by the majority rule from the actual sequences

285
Q

What does Polymerase does

A
  1. Unwind DNA
  2. Bind to unwound DNA
  3. Adding nucleotide to the growing rNA chain (require free OH group)
286
Q

RNA polymerase

A

Synthesizes RNA

287
Q

DNA polymerase

A

DNA replication

288
Q

Transcription in prokaryotes- Termination
Intrinsic termination

A

By a terminator sequence in DNA

289
Q

Transcription in eukaryotes- Polymerases

RNA Pol I, Pol II, Pol III

A

Pol I: rRNA production
Pol II: mRNA (12 subunit holoenzyme)
Pol III: tRNA and 5S rRNA

290
Q

Transcription in eukaryotes- Promoters
TATA box

A

25-30 not upstream of the transcription start site

291
Q

Transcription in eukaryotes – Transcription factors (TFs)

A
  1. DNA binding proteins that regulate the initiation of transcription
  2. 26 general TFs interact with Pol III complex
  3. Enhancers and silencers
292
Q

DNA binding proteins that regulate the initiation of transcription

A
  1. General transcription factors (required for transcription)
  2. Tissue specific transcription factors (regulate gene expression in a tissue-specific and timing-specific manner)
293
Q

Enhancers and silencers

A

DNA fragment bound by TFs that are often located far upstream or even downstream of TSS to regulate transcription levels

294
Q

Transcription in eukaryotes - Initiation (2 steps)

A
  1. TATA box binding protein binds and bends promoter DNA
  2. Other transcription factors start to bind, unwind and stabilize DNA
295
Q

Transcription in eukaryotes - Elongation

A

Only one DNA strand is transcribed (template strand)

296
Q

Base pairing specificity comes from:

A
  1. weak hydrogen bond between bases
  2. structural changes near the active site of PolII that promote the electron transfer during polymerization
297
Q

Transcription in eukaryotes - termination (3x)

A
  1. No specific terminator sequence known
  2. End of transcript established by RNA processing
  3. One round does not have to finish to start another round of transcription
298
Q

Primary transcript:

A

The RNA molecule produced from transcription from DNA template

299
Q

Prokaryotes RNA processing

A

Primary transcript = mRNA

300
Q

Eukaryotes RNA processing

A

Primary transcript (processing—>) mRNA

301
Q

RNA processing – 5’ capping

A
  1. Adding a 5’ modified guanosine (a cap)
  2. For mRNA to bind to ribosome for protein translation
302
Q

RNA processing – 3’ polyadenylation

A
  1. Adding a poly-A tail at 3’ end
  2. Determines mRNA stability
303
Q

RNA processing - splicing

A
  1. Introns
  2. Exons
  3. Splicing
304
Q

Introns

A

The segments in primary transcript that are not used in protein translation and need tp be excised

305
Q

Exons

A

The segments that will form the mRNA sequence

306
Q

Splicing

A

Cutting out the introns and connecting exons

307
Q

RNA processing: Capping machinery

A

Is recruited early, when length of pre-mRNA is only 20-40 nucleotides

308
Q

RNA processing: splicing machinery

A

Is recruited to each intron as the intron is being transcribed

309
Q

RNA processing: Polyadenylation
Introns

A

Are not necessarily spliced in the same order in which they are transcribed

310
Q

RNA processing: Polyadenylation
Splicing

A

Recruits proteins to the exon junction that function later to facilitate export of the mRNA

311
Q

RNA processing: Polyadenylation

A

Is recruited when transcription is terminated

312
Q

RNA processing: Polyadenylation at what step

A

Terminatio

313
Q

RNA processing: Capping and splicing machinery at what step

A

Transcription initiation and elongation

314
Q

RNA processing: Release and export at what step

A

Release and export

315
Q

RNA processing: Release and export what occurs

A
  1. 5’ cap is in place
  2. All introns are remove prior to the release of the mRNA
  3. Exon are marked with export proteins and first round proteins to detect premature termination condones
  4. Poly A tail has been added to 3’ end
316
Q

Protein synthesis - ribosomes

A

Protein + RNA complex that synthesizes polypeptide chain using mRNA as template

317
Q

ribosomes size (E coli and Eukaryotes)

A

Small and large subunits
1. E. coli 30S subunits and 50S subunits
2. Eukaryotes 40S subunit and 60S subunits

318
Q

Protein synthesis - tRNA

A

an RNA molecule that recognizes each triplet codon on the mRNA and transfer a specific amino acid to the growing peptide chain

319
Q

Aminoacyl-tRNA synthetases

A

enzymes that catalyzes the attachment of each amino acid to its corresponding tRNA molecule

320
Q

Protein synthesis- Prokaryotes

A

Transcription and translation: simultaneous and colocalized
Polycistronic mRNA: common

321
Q

Protein synthesis- Eukaryotes

A

Transcription and translation: separate (nucleus and cytoplasm)
Polycistronic mRNA: rare or nonexistent

322
Q

Does nt substitutions always result in a change in protein sequence?

A

No

323
Q

Synonymous mutations/ silent mutations

A

No change in protein sequence

324
Q

Nonsynonymous mutations/ missense mutations

A

A change in amino acid

325
Q

SOS repair found where

A

In E. coli and other bacteria

326
Q

SOS repair alway active?

A

No, induced by DNA damage

327
Q

SOS repair

A

Bypass system that allow DNA replication to happen across pyramiding diners or DNA distortions and maintains the integrity of the genome but produced error prone DNA

328
Q

Template-directed gap repair results in

A

Error free repair

329
Q

Double-strand gap repair

A

Non-homologous end joining: error-prone joining of ends

330
Q

DNA damage bypass

A

The damaged region is skipped over during replication, minimizing harmful effect

331
Q

Photoreactivation

A

UV-induced pyrimidine dimers can be reversed by enzymes that breaks the bond joining the two Ts using the energy of light

332
Q

Proofreading Function of DNA polymerase

A

3’ to 5’ exonuclease activity
Cleaves the unpaired nucleotide and gives a 2nd chance to get it right

333
Q

Okazaki fragments

A

Lagging strands

334
Q

Joining precursor fragments (4 steps)

A
  1. Junction of 2 fragments with RNA primer present
  2. DNA polymerase 1 degrades primer and synthesizes DNA complement to template
  3. DNA ligase, seals the resulting nick
  4. Intact double helical molecule
335
Q

Where is the termination replication site

A

opposition to replication origin

336
Q

How long is the termination replication sequence?

A

23bp repeats

337
Q

What is a termination replication site

A

bind to a protein that inhibits helicase activity

338
Q

Replication in eukaryotes

A
  1. multiple origins of replication on each chromosome
  2. Replication proceeds bidirectionally
339
Q

Does RNA primers have to be removed and replaced with nucleotides

A

Yes

340
Q

How are RNA primers removed

A
  1. DNA polymerase delta elongates DNA strand from upstream
  2. RNA primer for previous lagging strand fragments is encountered
  3. Singe stranded DNA binding protein, RPA, flips out RNA and a bit of DNA
  4. RPA recruits specific endonucleases to cleave the flipped piece out
341
Q

How are RNA primers replaced

A

Excised primer RNA and SNA are broken down by exonucleases and Polymerase delta continues until newly synthesized DNA replaces primer and then ligase together

342
Q

The importance of Telomerase in replication

A

Degradation of RNA results in 2 daughter chromosomes with terminal deletions
Telomerase adds repeat sequences to the end of chromosomes to prevent degradation

343
Q

Sanger sequencing

A
  1. DNA replication-based sequencing tech
  2. Uses dideoxy terminators that are fluorescently tagged
  3. Still in use for routine small fragments
344
Q

Next generation sequencing (NGS)

A
  1. Highly throughput
  2. Synthesis based
  3. Short reads (< a few hundred bp)
  4. Tens of millions of short reads assembled
345
Q

Mechanism of Next Gen sequencing

A
  1. Prepare genomic DNA samples
  2. Attach DNA to surface
  3. Bridge amplification
  4. Fragments become double stranded
  5. Denaturation leaves single strand
  6. Complete amplification
346
Q

Contig Assembly

A

fragments from NGS sequencing are then assembled into the full genome

347
Q

H1 are ______ histone

A

linker

348
Q

Transverison

A

T –> A, T–> G, C–> A, C–> G (pyrimidine –> purine)
A –> T, A –> C, G –> T, G –> C (purine –> pyrumidine)

349
Q
A

GENETICS (2 decks)

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