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MCM Final > Genetics > Flashcards

Genetics Flashcards

1
Q

Silent mutations are:

A

Different codon but the same, intended AA

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2
Q

Missense mutation

A

Intended AA changed; results may vary

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3
Q

Nonsense mutation

A

Intended AA changed to a stop codon

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4
Q

Frameshift mutation

A

1 or more nucleotide added/removed

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5
Q

What 3 things happen to convert pre-mRNA to mature mRNA?

A

Splicing, poly A tail, and 5’ cap

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6
Q

How does mRNA processing differ in prokaryotes?

A

They don’t have RNA processing

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7
Q

AZT is a chain ____________. How does it work?

A

Terminator

It does not have a 3’ hydroxyl so when it gets incorporated it will not allow another base to add onto it

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8
Q

Ara-C is what type of inhibitor

A

It’s a competitive inhibitor for DNA polymerase

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9
Q

Xeroderma Pigmentosum individuals are sensitive to ________

A

Sunlight

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10
Q

Xeroderma pigmentosum individuals are prone to developing what 2 things?

A

Melanomas and squamous cell carcinomas

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11
Q

Xeroderma pigmentosum is caused by a defect in _________________ which causes the accumulation of _____________ in their DNA

A

Nucleotide excision repair

Thymine dimers

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12
Q

What are the main 3 symptoms of cockayne syndrome

A

Developmental and neurological delay
Sensitivity to sun
Progeria

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13
Q

Cockayne syndrome has a defect in what repair pathway

A

Transcription coupled repair

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14
Q

Why is reverse transcriptase special?

A

It was previously thought that DNA –> RNA and there was no back track

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15
Q

GC base pairs have __ h bonds while AT only have __

A

3, 2

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16
Q

Histones are ________ that form _____ h bonds with DNA to form a ___________

A

Octamers, 142, nucleosome

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17
Q

Histones _________ highly conserved among species

A

Are

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18
Q

Approximately _____ % of histones primary structure are made up of positively charged AA ( ________ & __________)

A

20, Lys, Arg

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19
Q

The two classes of DNA binding proteins are histones and ____________

A

Transcription factors

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20
Q

Protein + DNA = ____________

A

Chromatin

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21
Q

_______chromatin is the active form of DNA and is transcriptionally _________.

A

Eu, active

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22
Q

Approximately __% of the genome is euchromatin

A

92

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23
Q

Transcriptionally inactive DNA is called ______________

A

Heterochromatin

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24
Q

What is the position effect?

A

The activity of a gene depends on it’s position in the chromosome. Actively expressed genes will be silenced if relocated near heterochromatin

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25
Q

In 1953, Watson and Crick describe _________________________

A

Double helical structure of DNA

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26
Q

In 1966, the ______ _________ was discovered

A

Genetic code (codon table)

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27
Q

The human genome project made ___ cop(ies)y of the genome and cost around ________

A

1 copy of the 23 chromosomes

1B

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28
Q

miRNA is important because it can ___________

A

Interfere with the translation of proteins by binding to complimentary strands

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29
Q

miRNA is made by enzymes called ________

A

Dicers

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30
Q

________ ____ _________ gives out exons the ability to recombine into different mature proteins

A

Alternative RNA splicing

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31
Q

Introns begin with _ _ and end with _ _

A

GT, AG

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32
Q

There are approximately ___ splice alternatives for each gene

A

2

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33
Q

When a histone is __________ it is transcriptionally inactive

A

Deacetylated

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34
Q

_____________ histones are transcriptionally active.

A

Acetylated

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35
Q

Acetyl groups are added to histones by _________ and removed by ___________

A 
Histone acetyl transferase (HAT)
Histone deacetylase (HDAC)
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36
Q

Binding of a ligand to PXR causes it to become _________. How is this done?

A

Active
When a ligand binds to PXR there is a conformational change which causes the corepressor to come off the PXR/RXR complex and the coactivator binds and transcription begins

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37
Q

What are the big histone post-translational modifications (5) that we mentioned?

A

Methylation, acetylation, phosphorylation, ubiquitinylation, SUMOylation

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38
Q

Methyl groups are directed added to what nitrogenous bases

A

C and A

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39
Q

Directly methylated DNA has what effect

A

Repression

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40
Q

DNA is read __ to __ but is synthesized __ to __

A

3–>5, 5–>3

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41
Q

What protein unwinds DNA into ssDNA?

A

DNA helicase

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42
Q

What keeps the ssDNA from coiling on itself?

A

Single-stranded DNA binding protein

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43
Q

UV radiation most often causes what? How are they repaired?

A

Thymine dimers, NER

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44
Q

What are the two types of spontaneous DNA damage?

A

Depurination, guanine/adenine are completely removed from the 1’ site of the sugar

Deamination, cytosine loses an amine group and becomes uracil

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45
Q

Spontaneous DNA damage results in

A

Depends on whether the correct or incorrect strand is used as the template during repair

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46
Q

Methylation of CpG islands can potentially _______ genes that are essential for the __________ process

A

Silence, repair

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47
Q

When 5-methyl cytosine is deaminated it forms ________. This accounts for 1/3 of all point mutations associated with inherited human disease.

A

Thymine

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48
Q

________ found in well done meats can be converted from a __________________ to a __________________ by out metabolism

A

Benzopyrene, pro-carcinogen, carcinogen

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49
Q

Hereditary nonpolyposis colorectal cancers are caused by what repair mechanism

A

Mismatch excision repair

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50
Q

BRCA1/2 breast cancer is associated with a defect in what repair mechanism

A

Recombination repair

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51
Q

Fanconi anemia is associated with

A

DNA interstran cross-link repair

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52
Q

Incorrect bases in base excision repair are recognized by what enzymes

A

DNA glycosylases

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53
Q

Errors in DNA bases are removed by __________ during base excision repair. The __________ bond is cut by AP endonucleases and _________ removes the deoxyribose phosphate

A

DNA glycosylase, phosphodiester, AP lyase

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54
Q

After a base has been excised (base excision repair) the correct base is added by _________________ and _______________ seals the DNA again

A

DNA polymerase beta, DNA ligase

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55
Q

Familial colorectal cancer assumes the pattern of being ________ __________

A

Autosomal dominant

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56
Q

What enzyme is permanently stalled at sites of damage in Cockayne syndrome?

A

RNA polymerase

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57
Q

Some new drugs have shown promise in cancer, Alzheimer’s, and RA, they don’t allow histones to be transcriptionally active by inhibiting what enzyme?

A

HAT

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58
Q

HDAC inhibitors have shown promise in anti-convulsives and anti-cancer. What do they do? What kinds of genes would these be important in?

A

They do not allow histones to be deacetylated

Especially important in repair mechanisms as to prevent cancers

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59
Q

____________ is a drug that inhibits bacterial RNA synthesis but also increases the amount of CytP450 expressed in the liver cells. What is the effect of this upregulation?

A

Rifampicin, other drugs are metabolized more quickly causing faster clearance

60
Q

What are the symptoms of rifampicin use?

A

Red color to urine, sweat, and tears (blood, sweat, and tears)

61
Q

Rifampicin interacts with what 2 categories of drugs the most?

A

Contraceptives and anticoagulants

62
Q

What are the 5 main epigenetic mechanisms?

A 
Developmental stage
Environmental chemicals
Drugs
Aging
Diet
63
Q

The most active AA in ubiquitin is _______

A

Lysine, Lys, or K

64
Q

What portion of ubiquitin is connected to lysine residues?

A

GG (2 aspartates)

65
Q

Where does transcription occur in Eukaryotes?

A

Nucleus

66
Q

Where does translation occur in eukaryotes?

A

Depends on whether the protein is going to be in the cytosol (made on free ribosomes) or secreted/incorporated in a membrane (RER)

67
Q

Proteins are synthesized from __ terminus to ___ terminus

A

N, C

68
Q

The mRNA strand is like the __________ strand but ___ is replaced with ____

A

Coding, T, U

69
Q

_ _ _ is the start codon in eukaryotes. _______ is the start codon in prokaryotes

A

AUG, met

Fmet

69
Q

Sickle cell anemia arises when ___ is incorrectly inserted instead of _____

A

Val, Glu

70
Q

Sickle cell anemia results from an error in what subunit?

A

HBB (human beta globin)

71
Q

Duchenne MD results from large _________ and ___________ deletions to ___________

A

In-frame, out-of-frame, the dystrophin gene

72
Q

Muscle is replaced with what in Duchenne MD? What is elevated?

A

Fat and fibroid, elevated CK

73
Q

______________ deletions cause a milder form of Duchenne MD, which is called __________ MD

A

In-frame, Becker

74
Q

tRNA must be activated with ________ which is catalyzed by ____________________

A

ATP, aminoacyl-tRNA synthetase

75
Q

The prokaryotic ribosome is made of two units _______ and ______ giving it a total sediment coefficient of ______

A

30, 50, and 70

76
Q

The eukaryotic ribosome is made of a ______ subunit, a _______ subunit, and a total of ____________

A

40, 60, 80

77
Q

The three sites in the ribosome are:

A

The acceptor site, the peptidyl site, and the empty/exit site

78
Q

What is required for eukaryotic initiation of translation?

A

5’ cap, polyA tail, Kozak sequence, and ATP dependent mRNA

79
Q

What is the shine delgarno sequence?

A

The prokaryotic signal (AGGAGG) to begin initiation

80
Q

The pre-initiator complex has 3 main events

A
  1. GTP-bound-initiator-tRNA attaches to small subunit
  2. IF in pro and eIF in euk attach to the small subunit
  3. The large subunit meets with this complex, GTP is cleaved from IF-GTP complex, and translation begins
81
Q

Streptomycin binds to the ______ subunit of ___________. What does this prevent?

A

30s (16s rRNA), prokaryotes, prevents assembly of the initiation complex

82
Q

What are the energy requirements for adding an AA to a chain?

A

1 ATP to activate the tRNA
2 GTP, one on the elongation factor and one to translocate the tRNA in the ribosome
2 GTP for each protein (1 for association of complete ribosome and 1 for the dissociation of the ribosome)

83
Q

What transfers AA to the incoming AA (still attached to original tRNA)?

A

Peptidyl transferase

84
Q

What is the MoA of tetracycline?

A

Binds to the 30s subunit and prevents entry of tRNA to ribosome

85
Q

What is the MoA of chloramphenicol?

A

It inhibits both pro and mito peptidyl transferase

86
Q

Clindamycin and erythromycin bind to what?

A

The 50s subunit and block translocation of the ribosome

87
Q

Erythromycin is commonly used to treat what?

A

Pertussis or whooping cough

88
Q

Cycloheximide inhibits _________

A

Peptidyl transferase in euk

89
Q

Diphtheria toxin inactivates _______________ which interferes with _________________

A

GTP bound eEF-2, ribosomal translocation

90
Q

Shiga toxin and ricin both bind to ___________ which does what?

A

The 60s subunit, which blocks entry of aminoacyl-tRNA

91
Q

Tetracycline is analogous to what?

A

Shiga toxin and Ricin. Tetracycline blocks entry of tRNA by binding to the large subunit in pro, while Shiga and Ricin bind to the large subunit in euk and also block tRNA entry

92
Q

Chloramphenicol is analogous to what?

A

Cycloheximide, they both block peptidyl transferases

93
Q

Diphtheria toxin is analogous to what?

A

Clindamycin and erythromycin because they all block ribosomal translocation

94
Q

What does puromycin do?

A

It is a premature chain terminator in translation. It is resistant to hydrolysis so it blocks ribosomal action

95
Q

What happens when a release factor is loaded?

A

tRNA dissociates, polypeptide chain is freed, ribosome complexes dissociate, and mRNA is released

96
Q

What is the signal for proteins destined for the cytoplasm?

A

None

97
Q

What is the signal for proteins destined for the nucleus?

A

KKKRK

98
Q

What is the signal for proteins destined for the membranes?

A

N-terminal a polar region (stop-transfer sequence)

99
Q

What is the signal for mitochondrial proteins? What does it allow?

A

N terminal hydrophobic alpha helix, allows interaction with chaperone proteins

100
Q

Where do proteins get glycosylated?

A

In the ER as they are synthesized

101
Q

How long is the ER targeting signal peptide?

A

15-60 AA and has 1 or 2 basic AA and a hydrophobic sequence of 10-15 AA

102
Q

What causes I-cell disease?

A

Lysosomal proteins are not tagged with mannose 6p so they are found in high levels in the plasma

103
Q

Protein folding is done by what major class? What is the name of the barrel shaped protein? What do chaperonins require?

A

Chaperones, chaperonins, ATP

104
Q

Alzheimer’s is due to _________ of __________ ___________ protein

A

Misfolding, amyloid precursor

105
Q

Supplementation of __________ has been shown to help with Alzheimer’s

A

Lysine

106
Q

Creutzfeldt-Jakob aka ____________ is due to _______________

A

Mad cow disease or Kuru, prions

107
Q

The most common glycosylation site is

A

N-linked on the -NH of Asn

108
Q

What are the two types of glycosylation sites and what amino acids do they affect?

A 
O linked (Ser and Thr)
N linked (Asn)
109
Q

Over glycosylation can be done to what body part in what condition?

A

Eye lens, diabetes

110
Q

Parkinson’s results from ______________________ which aggregate to form __________. This reduces the availability of ____________

A

Mutated alpha-synuclein aggregates, Lewy bodies, dopamine

111
Q

Huntington disease is a mutation in the ________ gene. What does this cause?

A

Huntingtin, this causes repetition of CAG triplet and the over-incorporation of Gln. This forms aggregates

112
Q

_________ are segments of DNA in a chromosome

A

Genes

113
Q

Location that a gene occupies

A

Locus or loci

114
Q

Chromatid

A

One of the two identical copies of a chromosome

115
Q

Centromere

A

Connects identical sister chromatids

116
Q

___________ region at the end of a chromosome for stability

A

Telomere

117
Q

__________ is a condition in which cells from a patient have different genotypes or karyotypes

A

Mosaicism

118
Q

Down syndrome has a trisomy at chromosome __

A

21

119
Q

Klinefelter syndrome has what two mosaicisms

A

Some 46XY; some 47XXY

120
Q

Turner syndrome has what mosaicism:

A

46XX; some 45XO

121
Q

__________ is called X-inactivation and happens _____________

A

Lyonization, randomly

122
Q

_______________ is the failure of one or more pairs of homologous chromosomes to separate normally during division

A

Non-disjunction

123
Q

There are 3 types of non-disjunction. What are they?

A

1 in meiosis I
1 in meiosis II
1 in mitosis early in embryology

124
Q

____________ is the cells with abnormal chromosome number

A

Aneuploid

125
Q

Are methylated genes up or down regulated? Can this be inherited?

A

Down, yes

126
Q

How is genetic information used?

A
  1. pedigree analysis
  2. Gene defect
  3. Molecular diagnosis
  4. Personalized medicine
  5. Population genetics
127
Q

____________ is the first diagnosed person in the pedigree

A

Proband

128
Q

What is a feature of autosomal dominant in a pedigree?

A

Affected children have an affected parent

Does not prefer one sex over the other

129
Q

What is a feature of autosomal recessive pedigrees?

A

Affected individuals have normal parents

Increased occurrence in consanguineous mating

130
Q

Why are females protected from x-linked recessive?

A

Lyonization of X chromosome

131
Q

What is penetrance? What is one example of a disease with less than 100% penetrance?

A

The percentage of individuals with a disease genotype that don’t show the disease phenotype
Retinoblastoma

132
Q

Traits in which variation is thought to be caused by the combined effect of genes are called _______________

A

Polygenic

133
Q

When environmental factors cause variation in a trait it is said to be ____________

A

Multifactorial

134
Q

What is locus heterogeneity?

A

When a single disorder is caused by mutations at different chromosomal loci

135
Q

Each nucleosome core particle is a complex of ____ histone proteins

A

8

136
Q

Cytosine can be spontaneously delaminated to what base?

A

Uracil

137
Q

Intercalating agents such as thalidomide cause what to happen?

A

They insert in between nitrogenous bases and cause frame shifts during DNA replication

138
Q

________________ repair defects cause BRCA1/2 breast cancer

A

Recombination

139
Q

Ataxia telangiectasia (AT) causes leukemia, lymphoma, gamma ray sensitivity, and genome instability. What repair pathway is affected? What kind of damage activates it?

A

ATM protein, a protein kinase activated by dsDNA breaks

140
Q

What are the two types of dsDNA repair? How do they work?

A
  1. Non-homologous end joining - after an accidental double break the protruding pieces are clipped to where both sides are flush and then pushed together (you lose whatever nucleotides were present in the “overhang”)
  2. Homologous recombination - again dsDNA break happens but this time, a sister chromatid is used as a template to repair and replace the the nucleotides
141
Q

What protein is affected in Cockayne syndrome?

A

RNA polymerase is permanently stalled at sites of damage

142
Q

HDAC inhibitors stop the removal of acetyl groups from histones, which allows the genes to remain transcriptionally active, what are 2 HDAC inhibitors?

A

Vorinostat and Entinostat

143
Q

How do sickle cell RBCs differ from WT RBCs?

A

Sickle cell RBCs lost their disc shape so they are not able to fold and bend to get through capillaries and have a poor oxygen carrying capacity

144
Q

What initiator do prokaryotes use? Eukaryotes? What initiating factor do they use?

A

Pro- n-formyl-methionine
Euk - methionine
Pro - IF
Euk - eIF

145
Q

Hypophosphatemia follows which inheritance pattern? What does this cause? How do you treat it?

A

X-linked dominant
Low P in blood due to deficient reabsorption in kidneys, softening of bones due to poor absorption of Ca in intestines, vit D metabolism problems
Treated with oral phosphate and vitamin D

MCM Final (10 decks)

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