Lect 1 Functions/Dysfunction of Genomic Regulation Flashcards by Austin Collison

The nucleus comprises _% of the total volume of Hepatocytes

What is its role in the cell?

Cell regulation, Proliferation, and DNA transcription

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What is the Central Dogma?

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

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

Reverse Transcribed (Reverse Transcriptase)

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Name the Purine Bases

Name the Pyrimidine Bases

Adenine, Guanine, Hypoxanthine, Xanthine
Cytosine, Uracil, Thymine

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2 Big features about DNA

The bases are connected via _ bonds

A has _ bonds to T

G has _ bonds to C

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

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

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Nucleosomes are made up of what?

DNA and Histone Octamer

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

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

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

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What are the basic unit of chromosome packing?

Proteins that bind to DNA made up to two classes

Nucleosomes

Histone Proteins and Non-Histone Chromosomal Proteins (TFs)

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

Protein + DNA = _

8 histone proteins (Histone Octamer)

Chromatin

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Euchromatin is the _ portion of the genome

What color does it stain?

Active

Light

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Heterochromatin is _ chromatin that contains very few active genes

What color does it stain?

Where is it highly concentrated?

What is the Position Effect?

Very condensed, inactive chromatin

Dark

Telomeres and Centromeres

Activity of a gene depends on relative position on chromosome

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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?

1953

1966

February, 2001

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

1.5%

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Alternative RNA Splicing

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

Begin with GT and end with AG

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Histone Deacetylation causes what?

Active Repression of Gene Expression

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Histone Acetylation causes what?

Active Promotion of Gene Expression

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Histone Proteins Undergo Post-Translational Modification (PTM)

Types of PTMs on Histone Tails include: _

Methylation

Acetylation

Phosphorylation

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Methyl groups are added to the which DNA bases?

Which enzymes are used?

DNA Methylation will repress what?

Cytosine and Adenine

Methyl Transferase enzymes

Gene Transcription when at a Gene Promoter

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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 _

Important Component of Cancer Development
Transcriptional silencing
- Can be inherited by daughter cells following cell division

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

DNA polymerase requires what to begin processing?

5’ to 3’ Direction

A primer with a free 3’ -OH to begin

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DNA Replication is _

The replication fork leads to _

Semi-Conservative (Daughter and Parent Strand)

Bi-Directional DNA Replication

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

Continuous synthesis of leading strand

Okazaki Fragments

Nomenclature of Bases

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

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

DNA Helicase function?

Unwinds DNA by binding and hydrolyzing ATP

Single Stranded DNA Binding Protein (SSBP) function?

* Binds to ssDNA & straightens region of chain * Help stabilize unwound DNA * Prevent hairpin formation

Topoisomerase function? What is it called in Bacteria? Why would this be targetted?

Relieves overwound supercoils DNA Gyrase Drugs targeting Topoisomerase are used as anti-cancer agents

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

Blocks cell cycle Generate single and double stranded breaks Harms integrity of genome Leads to apoptosis and cancer cell death

**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?

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

DNA Ligase function

Seal nicks of DNA between Okazaki fragments

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?

Pyrimidine Dimers Non-Ioninzing Radiation

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?

Ionizing Radiation

**Spontaneous DNA Damage** What does depurination mean? What does deamination mean?

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)

Possible Outcomes of Spontaneous DNA Damage

DNA Replication Ensues or Base Deletion/Substitution

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

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

**DNA Damage Caused by Chemical Agents** What are Cross-Linking agents? What are Alkylating Agents? What are Intercalating Agents?

* Nitrogen Mustard, Cisplatin, Mitomycin C, Carmustine * Dimethyl Sulfate (DMS), Methyl Methanesulfonate (MMS) * Thalidomide

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

Pyrimidine Dimer Photolyase + Light

Base Excision Repair is used for what type of damage?

* Single base mismatches and nondistorting alterations (Depurination)

Nucleotide Excision Repair is used for what type of damage? What condition can occur with deficiency in this repair mechanism?

* Chemical adducts distorting DNA (Pyrimidine Dimers, BPDE-guanine adducts, cisplatin adducts) * Xeroderma Pigmentosum

Xeroderma Pigmentosusm is caused by what? What are the consequences of this malfunction and what happens at the DNA level?

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

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?

* Mismatched base in daughter strand * MutS and MutL * Hereditary Nonpolyposis Colorectal Cancer (HNPCC) * Autosomal Dominant Manner

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

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

Double Strand Break Repair (Recombination Repair) What is Nonhomologous End Joining? What is Homologous Recombination?

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

Breast Cancer can occur due to mutations in what genes? What repair mechanism is associated with these mutations?

BRCA1 and BRCA2 are tumor suppressor genes Homologous recombination repair

Transcription Coupled Repair is used for what type of damage? What disorder is associated with this mechanism?

Initiated when RNA polymerase stalls at a lesion in the DNA template strand during transcription Cockayne's Syndrome

Cockayne's Syndrome is caused by what? What are the consequences? What type of inheritance is it?

* 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

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

* Phosphorylation * Acetylation * Methylation * Ubiquitination * SUMOylation

What is Epigenetics?

* 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

Epigenetic Mechanisms are affected by these factors and processes:

Development (in utero, childhood) Environmental chemicals Drugs/Pharmaceuticals Aging Diet

HDAC inhibitors are used as \_

Anticancer Agents

CpG Islands vs CpG Sites and Methylation

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

Significance of Methylation of CpG Islands?

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

Ubiquitin attaches where on proteins?

Attached to lysine residues on target proteins