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MCM-COM 2018 > Function/dysfunction- Gene Reg > Flashcards

Function/dysfunction- Gene Reg Flashcards

1
Q

What is the nucleus’s role in the cell

A

Cell regulation, proliferation, and DNA transcription

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2
Q

What is the central dogma of genetics

A

DNA —(transcription)—>RNA —(translation) —> Protein

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3
Q

What is the exclusive carrier of information from DNA to Protein ?

A

mRNA

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4
Q

T/F

RNA can be reverse transcribed into DNA

A

True

*reverse transcriptase relates to RNA Virus (HIV)

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5
Q

How many bonds are between A-T and C-G in double stranded DNA

A

AT is double (hydrogen) bond

GC is triple (hydrogen) bond

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6
Q

Why are mitotic chromosomes condensed 500 times more than interphase chromosomes

A

To prevent physical damage to the DNA as chromosomes are separated and passed to daughter cells

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7
Q

What bonds are between DNA and the histone octamers in each nucleosome

A

Hydrogen bonds

  • hydrophobic interactions
  • salt linkages
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8
Q

T/F

DNA is wound around histone Proteins

A

True

20% of histone protein amino acid residues are lysine or arginine

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9
Q

What is a nucleosome

A

Basic unit of chromosome packing:

- has 8 histone proteins 
- histone octamer = protein which DNA is wound around
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10
Q

Protein + DNA =

A

Chromatin

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11
Q

Euchromatin vs Heterochromatin

A

Euchromatin

  • lightly packed
  • undergoes transcription
  • most active portion of genome

Heterochromatin

  • very condensed
  • stains darkly
  • genetically inactive
  • high concentrated at centromeres and telomeres
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12
Q

What is the position effect?

A

Activity of a gene depends on relative position on chromosome

  • is actively expressed gene is relocated near Heterochromatin it will be silenced
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13
Q

T/F

Copy number variations are detected by comparative genome hybridization and are the basis for our differences as humans

A

True

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14
Q

What is RNAi

A

RNA interference

  • miRNA inhibit gene expression or translation
    • this happens by a miRNA precursor folds on itself and a Dicer enzyme cuts dsRNA into short segments. one strand is degraded and the single strand left is miRNA. The miRNA associates with a protein complex that prevents gene expression by degrading or blocking target mRNA
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15
Q

What are Long terminal repeats?

A
  • identical sequences of DNA repeated
  • found at retrotransposons (proviral DNA) ends
  • formed by reverse transcription of retroviral RNA
  • used by viruses to insert their genetic material into the host genome
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16
Q

What base pairs are found at intron/exon border?

A

GT is at beginning

AG is at end

  • intron is spliced out info
  • exon is the info kept
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17
Q

What gives gene diversity

A

Alternative RNA splicing

*exons and introns

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18
Q

What does HDAC and HAT do?

A

Histone Deacetylase actively represses gene expression

  • keeps chromatin condensed
  • have corepressor proteins

Histone acetyl transferase promotes gene expression

  • allows chromatin to open and be transcribed
  • has coactivator proteins

*both bind to promoter region

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19
Q

T/F

histone protein tails are the target of numerous Post-translational modifications

A

True

PTM’s occur at the n-terminus

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20
Q

What is DNA methylation ?

A

PTM

  • methyl group added to DNA (cytosine and adenine) by methyl transferase enzymes
  • represses gene transcription at gene promoter
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21
Q

What happens when CpG islands are hypermethylated

A

Transcriptional silencing which can be passed down to daughter cells

  • can cause cancer if it is in DNA repair gene
  • causes 5-methyl cytosine to become thymine
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22
Q

What does hypomethylation cause

A

Chromosomal instability and loss of imprinting

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23
Q

Which direction is new DNA synthesized

A

5’—>3’

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24
Q

DNA polymerase requires a primer with a _______ to begin processing

A

With a free 3’ -OH group

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25
Q

What unwinds DNA to begin DNA replication

**uses ATP

A

DNA helicase

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26
Q

What binds to exposed DNA to help stabilize unwound DNA and prevents hairpin formation in DNA replication

A

single-stranded DNA-binding protein (SSBP)

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27
Q

What does DNA polymerase do ?

A

Replicate DNA in 5’—>3’ direction, makes RNA-DNA primer, fills in gaps

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28
Q

What does endonuclease do in DNA replication

A

Remove RNA primers

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29
Q

What relieves supercoiling during DNA replication by breaking phosphodiester bond? And is the target for many pharm drugs for anti-cancer agents?

A

DNA topoisomerase

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30
Q

Topoisomerase inhibitors

A

1- irinotecan used in colorectal cancer
2- etoposisde

They block the cell cycle, generate breaks, lead to apoptosis and cancel cell death

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31
Q

T/F

DNA polymerase can proofread

A

True

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32
Q

What does UV radiation do to cause DNA Damage

A

Produces a covalent linkage between adjacent pyrimidines (T-T or C-T)
**pyrimidine dimers

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33
Q

Spontaneous DNA damage

A

Depurination- 5000 purine lost a day by hydrolysis
**leaves free OH end on remaining sugar phosphate

Deamination- C to U change 100 times a day (any base pair change)

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34
Q

Benzo(a)pyrene turns to BPDE (an epoxide) means what **in well done-grilled meats

A

Pro carcinogen turns in a known carcinogen

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35
Q

Examples of cross linking agents (DNA Damage by chemicals)

A

Nitrogen mustard
Cisplatin
Mitomycin C
Carmustine

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36
Q

Examples of alkylating agents ( DNA Damage by chemicals)

A 
Dimethyl sulfate (DMS)
Methyl methanesulfonate (MMS)
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37
Q

Example of intercalating agent (DNA damage by chemicals)

A

Thalidomide

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38
Q

What repair mechanism fixes pyrimidine dimers and methylguanine

A

Direct Repair (enzymatic repair)

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39
Q

What repair mechanism fixes single base mismatches

A

Base excision repair (BER)

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40
Q

What repair mechanism is associated with xeroderma pigmentosum

A

Nucleotide excision repair (NER)

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41
Q

What repair mechanism is associated with hereditary nonpolyposis colorectal cancer (HNPCC)

A

Mismatch excision repair (MER)

*fixes mismatched bases in daughter strand

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42
Q

What repair mechanism is associated with BRCA breast cancer

A

Recombination repair

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43
Q

What repair mechanism is associated with cockayne syndrome ?

A

Transcription coupled repair (TCR)

  • RNA polymerase is permanently stalled at sites of damage in important genes
  • causes growth retardation, skeletal abnormalities, and sunlight sensitivity
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44
Q

HDAC remove acetyl groups from the _____ on core histone and nonhiston proteins

A

Lysines

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45
Q

2 HDAC inhibitors

A

Vorinostat and entinostat

-anticonvulsives and anti cancer drugs

46
Q

Embryonic stem cells vs adult stem cells

A

embryonic are pluripotent (capable of becoming any cell type)

Adult are undifferentiated cells that generate cells types in the tissues in which they reside (ex. Hematopoietic stem cells will produce blood cells only)

46
Q

Stem cells differentiate into specialized cells in stages. These stages involve multiple facets that combine to produce epigenetic markers in the cells’s DNA that restrict DNA expression and thus the type of cell that the stem cell can become. Can this DNA expression be passed on to daughter cells?

A

Yes, through cell division

47
Q

DNA Structure:

Where are the nucleotides linked in DNA?

A

The 3’ OH group is connected to 5’ phosphate group by a phosphodiester bond.

*every DNA strand has a phosphate residue at the 5’ terminus and a free hydroxyl group at the 3’ terminus

48
Q

In no dividing stages of the cell cycle (G1, G0, G2, S) the transcriptionally active chromatin is called _____; the inactive chromatin is called ______; and in the M phase of the cell cycle chromatin becomes _____

A
  1. Euchromatin
  2. Heterochromatin
  3. Mitotic Chromosomes which are condensed 500 times more than interphase chromosomes to prevent physical damage to the DNA as they are separated and passed to daughter cells
49
Q

T/F

The 2’ C of ribose in RNA has an OH group while DNA does not

A

True

50
Q

Imprinting is an _____ process that involves the methylation and histone modification of egg or sperm cells during their formation while the genetic sequence is unchanged. Imprinting is duplicated in all somatic cells

A

Epigenetic

51
Q

If Uniparental disomy occurs in imprinted genes (silenced genes) then essentially the child was passed on only 1 gene and it does not function therefore diseases occur such as

A

Prader-WIllie or Angelmans

52
Q

What is the presence of more than one type of mitochondrial DNA (some normal some mutant) within a cell or organism. Symptoms do not occur until adulthood bc the cell must divide enough times before sufficient amount are present to cause problems

A

Heteroplasmy

53
Q

What is topoisomerase in bacteria called

A

DNA gyrase

54
Q

What does single-stranded DNA binding protein do in DNA replication?

A

Binds to the ss-DNA that has been separated to prevent them from reannealing

55
Q

What does DNA ligase do in DNA replication

A

Seals nicks between Okazaki fragments

56
Q

What does FLAP endonuclease 1 (FEN1) do in DNA replication ?

A

Removes RNA primers

57
Q

What bonds does Helicase disrupt when it unwinds DNA at the replication fork ?

A

Hydrogen bonds between complementary nucleotides

58
Q

What are telomeres and how are they shortened? What prevents shortening?

A

Telomeres cap DNA and are made of repeats of non-coding DNA. They are shortened after the removal of the last RNA primer from the 5’. Shortening limits the number of times cells can divide bc loss of telomeres triggers apoptosis.
Telomerase (reverse transcriptase) prevents shortening. Only in germ line and stem cells, not in somatic cells.

59
Q

T/F

DNA synthesis involves the formation of 3’—>5’ phosphodiester bonds

A

True

60
Q

_____- lack the 3’ -OH group and can act as a drug that inhibits DNA replication

A

Nucleoside analogues

Ex:
Acyclovir 
Ara-C
Cytarabine 
AZT
61
Q

Nucleoside analogues need to be converted to _______ before they can inhibit DNA polymerase

A

dNTPS

62
Q

Ara-C is a nucleoside analogue that contains the sugar arabinose and is converted by cells into ara-CTP. Hoe does Ara-CTP inhibits DNA synthesis ?

A

Ara-CTP is a potent competitive inhibitor of DNA polymerase

*used to treat leukemia

63
Q

The nucleoside analogue AZT is used to treat what? How does it do this?

A

Used in HIV therapy.

-the drug is taken up by HIV-infected cells and is activated by viral reverse transcriptase. Because the AZT lacks a 3’OH group it stops viral DNA synthesis

64
Q

What nucleoside analogue is used to treat herpes? How does it do this?

A

Acyclovir

  • thymidine kinase catalyzes 1 phosphorylation
  • the host’s enzyme converts the monophosphate into a triphosphate
  • it lacks a 3’ OH group and therefore stops DNA synthesis during replication
65
Q

Physical vs chemical agents that damage or mutate DNA

A

Physical agents

  • ex: ionizing radiation and nonionizing radiation
  • displace electrons from atoms
  • sources of IR is x-rays and CT scans

Chemical agents

  • react with functional groups on DNA
  • intercalate between DNA bases
66
Q

What is the term for a chemical agent that causes permanent damage to DNA

A

Mutagen

*most mutagens are carcinogens

67
Q

Transition vs a transversion point mutation

A

Transition is a purine substituted as a purine and vice verse

Transversion is a purine substituted as a pyridimidine and vice versa

68
Q

Two examples of spontaneous damage to DNA.

A
  1. Depurination
    - purine base is removed via hydrolysis of N-glycosidic bond between base and deoxyribose
    - results in a apurinic or abasic site in the DNA strand with free OH end
  2. Deamination
    - amino group of purine or pyrimidine base is hydrolyze such that adenine is converted to hypoxanthine and guanine is converted to xanthine and cytosine is converted to uracil.
69
Q

Ionizing radiation is radiation-induced DNA damage. What changes are made to DNA as a result ?

A
  • 40-60 chemically distinct base damages
  • direct strand breaks
  • DNA-protein cross-links
70
Q

Nonionzing radiation (UV light) is a type of radiation -induced DNA damage. What changes are made to DNA as a result?

A

-damages DNA by promoting the formation of a covalent linkage between adjacent pyrimidine bases which results in 2 major photoproducts that are toxic, mutagenic, and carcinogenic

71
Q

What are the two types of major photoproducts that are toxic, mutagenic, and carcinogenic created by non-ionizing radiation damage of DNA?

A
  1. Pyrimidine cyclobutane dimers (more common)
  2. 6-4 covalent linkage of 2 pyrimidines
    - the mutations are present in the P53 gene from UV exposure and are associated with basal and squamous cell carcinomas
72
Q

What are the two groups that broadly classify chemical agents that cause DNA damage ?

A
  1. Agents that require metabolic activation
    - ex: benzo(a)pyrene, aflatoxin B1
  2. Agents that act directly to modify DNA
    - ex: cross linking agents, alkylating agents, and intercalating agents
73
Q

What does Benzo(a)pyrene do to damage DNA?

A
  • chemical agent present in many combustion products (cig smoke, exhaust, charred meat)
  • makes a bulky adduct with guanine and PREVENTS REPLICATION AND GENE EXPRESSION
  • also inhibits P53
74
Q

What does a cross-linking agent do to damage DNA?

A
  • chemical agent
  • forms cross-links between bases in same DNA strand or between complementary DNA

Ex: nitrogen mustard, cisplatin, carmustine

*well known chemo drugs

75
Q

What do alkylating agents do to damage DNA?

A
  • chemical agent
  • induce methylated base changes and alkylation of phosphodiesters into phosphotriesters

Ex: DMS, MMS

76
Q

What do intercalating agents do to damage DNA?

A
  • chemical agent
  • insert between stacked bases of the DNA double helix which causes some unwinding of the helix and separation of base pairs

Ex: ethidium bromide, anthracyline antibiotics

77
Q

DNA repair mechanism: Direct repair (enzymatic repair) repairs what

A
  • pyrimidine dimers
  • O6 methylguanine

Uses DNA photolyase and methyguanine methyltransferase

78
Q

DNA repair mechanism: base excision repair (BER) fixes what

A

Single base mismatches, and nondistoring alterations such as depurination

79
Q

DNA repair mechanism: nucleotide excision repair (NER) fixes what

A

Chemical adducts that distort DNA (pyrimidine dimers, and adducts)

*related to xeroderma pigmentosum

80
Q

DNA repair mechanism: mismatch excision repair (MER) fixes what

A

Mismatched base in daughter strand

*related to hereditary nonpolyposis colorectal cancer (HNPCC)

81
Q

DNA repair mechanism: recombination repair (nonhomologous end joining and homologous recombination) fix what?

A

Double-strand breaks, interstrand cross-linking

*related to BRCA 1/2 breast cancer

BRCA 1 and BRCA 2 genes encode proteins that facilitate homologous recombination

82
Q

DNA repair mechanism: transcription-coupled repair (TCR) fixes what?

A

Type of NER that is initiated when Stalled RNA polymerase during transcription occurs (not replication)

*related to cockayne syndrome

83
Q

DNA repair mechanism: transversion synthesis (bypass synthesis) fixes what?

A

Unrepaired thymine dimers or apurini AP sites

84
Q

Individuals with xeroderma pigmentosum have a defet in proteins of the ______ complex

A

NER complex (XP proteins)

  • the NER complex recognizes distortions in DNA and marks them for removal
  • DNA ligase fills in the removed gaps
85
Q

Individuals with defective proteins in the ____ complex have increased susceptibility to hereditary nonpolyposis colorectal cancers

A

MER complex (MSH2 or MLH1)

  • mutation of one allele causes increased susceptibility
  • mutation in both promotes tumor development
  • MER complex binds to deformed DNA from mismatched bases
  • endonuclease cuts the strand, exonuclease removes strand, polymerase fills the gap, ligase seals the nick
86
Q

Defects in the genes encoding ____ and ____ lead to cockayne syndrome.

A

ERCC-6 and ERCC-8 which are TCR proteins

87
Q

How do xeroderma pigmentosum and cockayne syndrome differ in manifestation?

A

Patients with cockayne syndrome do not exhibit pigmentary skin changes. Xeroderma patients have changes in skin pigment

88
Q

What disease is characterized by skin that is extremely sensitive to sunlight and prone to developing melanomas and squamous cell carcinomas due to ineffective XP proteins of the NER complex?

A

Xeroderma pigmentosum

-XP proteins help the NER complex fix cyclobutane thymine dimers in DNA caused by UV light

89
Q

XP proteins help the NER complex fix _______ in DNA caused by UV light

A

Cyclobutane thymine dimers.

*defect leads to xeroderma pigmentosum

90
Q

What rare autsomal recessive, congenital disorder that is characterized by developmental and neurological delay, photosesitivity, hearing loss, eye abnormalities, and progeria (premature aging) that is caused by mutant ERCC6 and ERCC8 genes that fail to repair DNA via TCR

A

Cockayne syndrome types A and B.

  • A from ERCC6
  • B from ERCC8- 70% of most cases
91
Q

Mutations of the tumor suppressor genes BRCA 1 and BRCA 2 cause a 5-fold increase in developing ____ in women. Mutations in men also cause the same disease

A

Breast cancer

Mutations of BRCA 1 also associated with cervical, uterine, pancreatic, colon, testicular and prostate cancer

Mutations of BRCA 2 is also associated with increased risk of melanoma, pancreatic, stomach, gallbladder, and bile duct cancer in women

92
Q

Post-translational covalent modification of: methylation

A
  • transfer of one or more methyl groups from S-adenosine-L-methionine to lysine or arginine residues of histone proteins
  • catalyzes by HMTs (histone methytransferases)
  • mediates heterochromatin formation and participates in regulating gene expression of euchromatic sites
  • REPRESSES GENE TRANCRIPTION
  • CHANGES DNA ACTIVITY WITHOUT CHANGING SEQUENCE
93
Q

Post-translational covalent modification of: SUMOylation

A

— major regulatory of protein function

  • covalent attachment of a memeber of the SUMO (small ubiquitin like modifier) family to lysine residues in target proteins
  • analogous to ubiquitination but involves addition of SUMOs
94
Q

Post-translational covalent modification of: ubiquitination

A
  • the addition of ubiquitin to a substrate protein
  • can mark proteins for degradation, alter cellular location, affect activity, and promote/prevent protein interactions

*most often noted for the the proteasome pathway for protein destruction

95
Q

Post-translational covalent modification of: histone acetylation/deacetylation

A
  • enzymatic addition of acetyl group to histone lysines (COCH3) from acetyl Coenzyme A
  • HATs are the enzyme that transfers acetyl group. (Histone acetyltransferases)
  • HDACs are the opposite of HATs and inhibit HAT function
  • acetylation = gene expression
  • deactyletion = repressed gene expression

*involved in the regulation of transcription, gene silencing, cell cycle progression, apoptosis, DNA replication….

96
Q

Post-translational covalent modification of: phosphorylation

A

-amino acid residues Serine and threonine are phosphorylated but protein kinases

97
Q

What is Chargraffs rule

A

In DNA the number of Adenines = thymine and guanines = cytosines

98
Q

Base pairing in DNA (between AT and CG) can be disrupted by what two things

A

Heat or alkaline pH

99
Q

Noncovalent mechanisms that give DNA structure its stability

A

Hydrophobic interactions, van der walls forces, base stacking

100
Q

DNA double helix is present mostly in what form

A

B form

*other forms are A and Z

101
Q

What is a nucleosome

A

*SHOWS HOW DNA IS PACKED

It is DNA wrapped around pairs of four histones (8 TOTAL) by hydrogen bonds. (Hydrophobic interactions and salt linkages aid stability)

  • nucleosomes are further packed into chromatin
  • rememeber 20% of histone is lysine or arginine
102
Q

____ is the protein around which DNA is wound

A

Histone Octamer

103
Q

PTM (post-translational modification) of histones by methylation, acetylation, and phosphorylation, impact gene expression by altering ______

A

Chromatin structure

104
Q

Fanconi anemia groups A-G is caused by what defect

A

Defect in DNA interstrand cross-link repair

*causes congenital abnormalities, leukemia, and genome instability

105
Q

Ataxia telangiectasia is caused by what defect

A

Defect in the ATM protein

  • ATM protein is a protein kinase activated by double-strand breaks
  • there no breaks are fixed

*causes leukemia, lymphoma, gamma ray sensitivity, and genome instability

106
Q

Thymine dimers are corrected by what

A

Direct repair

-photolyase fixes thymine dimer

107
Q

In Mismatch Exicision repair: _____ binds while _____ scans for the nick and triggers degradation of the nicked strand

A

MutS binds

MutL scans

108
Q

What is a mechanism for regulating gene activity independent of DNA sequence that determines which genes are turned on or off by using PTMs

A

Epigenetics

109
Q

What factors affect epigenetics

A 
Development 
Environment 
Drugs
Aging 
Diet

MCM-COM 2018 (14 decks)

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