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MCM Exam 2 > Lect 1 Functions/Dysfunction of Genomic Regulation > Flashcards

Lect 1 Functions/Dysfunction of Genomic Regulation Flashcards

1
Q

The nucleus comprises _% of the total volume of Hepatocytes

What is its role in the cell?

A

6%

Cell regulation, Proliferation, and DNA transcription

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2
Q

What is the Central Dogma?

RNA can be _ into DNA and RNA viruses use this enzyme

A

DNA (Replication w/ Mitosis) –> RNA –> Protein

Reverse Transcribed (Reverse Transcriptase)

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3
Q

Name the Purine Bases

Name the Pyrimidine Bases

A
  • Adenine, Guanine, Hypoxanthine, Xanthine
  • Cytosine, Uracil, Thymine
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4
Q

2 Big features about DNA

The bases are connected via _ bonds

A has _ bonds to T

G has _ bonds to C

A

Double Stranded and Anti-Parallel

Hydrogen Bonds

A has 2 H-Bonds with T

G has 3 H-Bonds with C

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5
Q

Mitotic chromosomes are condensed 500x when compared to interphase chromosomes, Why?

A

To prevent physical damage to DNA as chromosomes separate and pass on to daughter cells

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6
Q

Nucleosomes are made up of what?

A

DNA and Histone Octamer

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7
Q

Approximately 20% of histone protein AA residues are what? Why those two?

What is the target of post translational modications in histone proteins?

A
  • Lysine (Lys, K) or Arginine (Arg, R)
    • Lots of (+++) charge attracted to negatively charged DNA backbone
  • Lysine residues
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8
Q

What are the basic unit of chromosome packing?

Proteins that bind to DNA made up to two classes

A

Nucleosomes

Histone Proteins and Non-Histone Chromosomal Proteins (TFs)

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9
Q

Each nucleosome core particle consist of a complex of how many proteins?

Protein + DNA = _

A

8 histone proteins (Histone Octamer)

Chromatin

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10
Q

Euchromatin is the _ portion of the genome

What color does it stain?

A

Active

Light

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11
Q

Heterochromatin is _ chromatin that contains very few active genes

What color does it stain?

Where is it highly concentrated?

What is the Position Effect?

A

Very condensed, inactive chromatin

Dark

Telomeres and Centromeres

Activity of a gene depends on relative position on chromosome

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12
Q

DNA History

Watson and Crick described the helical structure of DNA when?

The genetic code was determined when?

Sequence of human genome was announced when?

A

1953

1966

February, 2001

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13
Q

_% of the human DNA sequence in exons and responsible for protein coding

A

1.5%

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14
Q

Alternative RNA Splicing

99% of all Introns begin with _ and end with _

A

Begin with GT and end with AG

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15
Q

Histone Deacetylation causes what?

A

Active Repression of Gene Expression

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16
Q

Histone Acetylation causes what?

A

Active Promotion of Gene Expression

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17
Q

Histone Proteins Undergo Post-Translational Modification (PTM)

Types of PTMs on Histone Tails include: _

A

Methylation

Acetylation

Phosphorylation

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18
Q

Methyl groups are added to the which DNA bases?

Which enzymes are used?

DNA Methylation will repress what?

A

Cytosine and Adenine

Methyl Transferase enzymes

Gene Transcription when at a Gene Promoter

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19
Q

Hyper- and Hypo-DNA-Methylation in Cancer

What is the significance of alterations in DNA Methylation?

Gene Promoter CpG Islands acquire abnormal hypermethylation which leads to _

A
  • Important Component of Cancer Development
  • Transcriptional silencing
    • Can be inherited by daughter cells following cell division
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20
Q

DNA-dependent DNA polymerase synthesizes new DNA from _ to _ direction

DNA polymerase requires what to begin processing?

A

5’ to 3’ Direction

A primer with a free 3’ -OH to begin

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21
Q

DNA Replication is _

The replication fork leads to _

A

Semi-Conservative (Daughter and Parent Strand)

Bi-Directional DNA Replication

22
Q

DNA Replication is Semi-Discontinuous with _ synthesis of the Leading Strand and _ formed with Discontinuous synthesis of the lagging strand

A

Continuous synthesis of leading strand

Okazaki Fragments

23
Q

Nomenclature of Bases

Building block of DNA is a deoxyribonucleotide which is composed of _

A

2-deoxyribose with a base attached at the 1’ position and phosphate attached at the 5’ position

24
Q

DNA Helicase function?

A

Unwinds DNA by binding and hydrolyzing ATP

25
Q

Single Stranded DNA Binding Protein (SSBP) function?

A
  • Binds to ssDNA & straightens region of chain
    • Help stabilize unwound DNA
    • Prevent hairpin formation
26
Q

Topoisomerase function?

What is it called in Bacteria?

Why would this be targetted?

A

Relieves overwound supercoils

DNA Gyrase

Drugs targeting Topoisomerase are used as anti-cancer agents

27
Q

What cellular consequences occur by using Topoisomerase Inhibitors as Anti-Cancer Agents?

A

Blocks cell cycle

Generate single and double stranded breaks

Harms integrity of genome

Leads to apoptosis and cancer cell death

28
Q

Nucleoside Analog Inhibitors of DNA Synthesis

DNA synthesis involves forming 3’ to 5’ phosphodiester bonds, nucleoside analogues lacking 3’ -OH group act as drugs inhibiting what process?

What nucleosides need to be converted to dNTPs before they can act as inhibitors of DNA polymerase?

A

DNA replication

Arabinosylcytosine (ara-C, cytarabine); Acylguanosine (acyclovir); azidothymidine (AZT)

29
Q

DNA Ligase function

A

Seal nicks of DNA between Okazaki fragments

30
Q

What is the term for UV radiation (sun) producing covalent linkages between two adjacent T-T or C-T?

What is another name for this radiation?

A

Pyrimidine Dimers

Non-Ioninzing Radiation

31
Q

DNA damage can also occur from exposure to reactive forms of O2 in the cell or chemicals in the environment. What is this radiation called?

A

Ionizing Radiation

32
Q

Spontaneous DNA Damage

What does depurination mean?

What does deamination mean?

A

Purine base (adenine/guanine) removed from nucleotide

Amino group of purine/pyrimidine is base is hydrolyzed (C –> U, A –> H, G –> X, 100 bases/day)

33
Q

Possible Outcomes of Spontaneous DNA Damage

A

DNA Replication Ensues or Base Deletion/Substitution

34
Q

Methylated Cytosine Residues in CpG Sites/Islands are problematic and causes what?

A

Methylation of CpG islands staby silences genes (Cancer/DNA Repair Genes)

35
Q

DNA Damage Caused by Chemical Agents

What are Cross-Linking agents?

What are Alkylating Agents?

What are Intercalating Agents?

A
  • Nitrogen Mustard, Cisplatin, Mitomycin C, Carmustine
  • Dimethyl Sulfate (DMS), Methyl Methanesulfonate (MMS)
  • Thalidomide
36
Q

Direct Repair (Enzymatic Repair) is used for what type of damage?

What enzyme is used?

A

Pyrimidine Dimer

Photolyase + Light

37
Q

Base Excision Repair is used for what type of damage?

A
  • Single base mismatches and nondistorting alterations (Depurination)
38
Q

Nucleotide Excision Repair is used for what type of damage?

What condition can occur with deficiency in this repair mechanism?

A
  • Chemical adducts distorting DNA (Pyrimidine Dimers, BPDE-guanine adducts, cisplatin adducts)
  • Xeroderma Pigmentosum
39
Q

Xeroderma Pigmentosusm is caused by what?

What are the consequences of this malfunction and what happens at the DNA level?

A

Defects in proteins of NER Complex

Skin extremely sensitive to direct sunlight, prone to developing melanomas and squamos cell carcinomas

UV radiation causes thymine dimers to form

40
Q

Mismatch Excision Repair used for what type of damage?

What two proteins are used in the MER Complex?

What disorder is associated with MER deficiency? How is it inherited?

A
  • Mismatched base in daughter strand
  • MutS and MutL
  • Hereditary Nonpolyposis Colorectal Cancer (HNPCC)
    • Autosomal Dominant Manner
41
Q

Hereditary Nonpolyposis Colorectal Cancers (HNPCC) is caused by what?

A

Inherited mutations in one of the alleles of genes in the MER complex –> increased susceptibility to HNPCC

Acquired mutation in remaining good copy of gene –> MER system non functional –> tumor development

42
Q

Double Strand Break Repair (Recombination Repair)

What is Nonhomologous End Joining?

What is Homologous Recombination?

A
  • Nonhomologous End Joining:
    • Rejoins ends by DNA ligation (one or more nucleotides lost)
  • Homolgous Recombination
    • Damaged duplex repair using information on undamaged homologous duplex
43
Q

Breast Cancer can occur due to mutations in what genes?

What repair mechanism is associated with these mutations?

A

BRCA1 and BRCA2 are tumor suppressor genes

Homologous recombination repair

44
Q

Transcription Coupled Repair is used for what type of damage?

What disorder is associated with this mechanism?

A

Initiated when RNA polymerase stalls at a lesion in the DNA template strand during transcription

Cockayne’s Syndrome

45
Q

Cockayne’s Syndrome is caused by what?

What are the consequences?

What type of inheritance is it?

A
  • Defect in Transcription Coupled Repair (TCR)
    • RNA polymerase permanently stalled at sites of damage in important genes
  • Growth retardation, skeletal abnormalities, sensitivity to sunlight
  • Autosomal Recessive Congetial Disorder
46
Q

Post Translational Modifications (PTMs) (P-A-M-U-S)

A
  • Phosphorylation
  • Acetylation
  • Methylation
  • Ubiquitination
  • SUMOylation
47
Q

What is Epigenetics?

A
  • Mechanism for regulating gene activity indenpendent of DNA sequence determining which genes are turned on or off:
    • In a particular cell type
    • In different disease states
    • In response to physiological stimulus
48
Q

Epigenetic Mechanisms are affected by these factors and processes:

A

Development (in utero, childhood)

Environmental chemicals

Drugs/Pharmaceuticals

Aging

Diet

49
Q

HDAC inhibitors are used as _

A

Anticancer Agents

50
Q

CpG Islands vs CpG Sites and Methylation

A

Methylation of CpG Islands (Promoter/Regulator Regions) is more significant than Methylation of CpG Sites (Random Sites)

70% of promoters contain CpG islands proximal to start of transcription

51
Q

Significance of Methylation of CpG Islands?

A

Multiple methylated CpG sites in CpG islands of promoters stably silences genes

52
Q

Ubiquitin attaches where on proteins?

A

Attached to lysine residues on target proteins

MCM Exam 2 (14 decks)

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