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MCM Exam 2-RH > Functions & Dysfunctions of Genetic Regulation > Flashcards

Functions & Dysfunctions of Genetic Regulation Flashcards

1
Q

Central Dogma of Genetics

A

DNA–> RNA–>protein (via transcription, translation)

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2
Q

Structure of DNA

A

double helix, sugar/phosphate backbone w bases (AGCT); antiparallel strands

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3
Q

Euchromatin

A

protein involved w DNA Packaging, ubiquitous within DNA, almost always activated

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4
Q

Heterochromatin

A

condensed DNA, found mainly in centromeres and at the edges, very little gene expression

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5
Q

methylation on packaging

A

adding a methyl group

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6
Q

base pairing

A

A and T have 2 double bonds, G and C have 3 (stronger); 142 h-bonds b/w DNA and histone octamer

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7
Q

DNA packaging

A

DNA wraps around a histone w condensed chromosomes that prevent mutations and protect against damage

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8
Q

Structure of histone

A

Proteins made up of a lot of AA but specifically many Lysine and Arginine (basic, positively charged) that attract the negatively (from phosphate groups) charged DNA

Mnemonic: Lysine Arginine Histone

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9
Q

Human genome project

A

Began in late 90’s early 2000’s and took a very long time to finish and it was only 90% done; cost a billion dollars whereas now it takes about 24 hours and $1000

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10
Q

Personalized medicine

A

Uses each patient’s individual DNA to hybridize information

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11
Q

Binding proteins to DNA

A

1) Histones

2) non-histone binding

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12
Q

Nucleosomes

A

Basic unit of chromosome packing (includes histone and non-histone portion); 8 histone proteins (histone octamer)

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13
Q

Chromatin

A

Protein + DNA

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14
Q

Position effect

A

Gene activity is based on location on the chromosome

If a previously actively expressed gene is moved near the heterochromatin (centromere or telomere)—> becomes silenced

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15
Q

Alternative RNA splicing

A

Exons/introns can be cut differently on the RNA to produce different gene combos (avg: 2 different ways/ genes)

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16
Q

Histone Deacetylation (HDAC)

A

HDAC activity represses gene activity by removing acetyl group and resestablishing normal DNA-histone interaction

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17
Q

Histone Acetyl Transferase (HAT)

A

Add an acetyl group to histone (N-terminal lysine) which reduces DNA interaction because the positive charge is removed;promotes gene expression as its not as tightly wound

Ex: estrogen (steroid hormone) promotes gene expression

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18
Q

DNA Methylation

A

Adding methyl group to DNA (cytosine and adenine) by specific methyl transferase enzymes

Change activity but not DNA sequence (ex: will repress gene expression when its at a gene promoter)

Key processes affected: genomic imprinting, xchromosome inactivation, repression of transposable elements, aging, carcinogenesis

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19
Q

Hypermethylation

A

**important in Cancer Development

Gene promotes will lead to silencing/target

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20
Q

Hypomethylation

A

Too little methylation—> inactivate chromosome and loss of imprinting abilities

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21
Q

DNA Replication

A

DNA polymerase (DNA-dependent) synthesizes new DNA from 5’-3’; NEEDS free 3’ OH

New chain is assembled based on the template of the old chain (needs to be separated and then double are made)
Requires dATP, dGTP, dCTP, dTTP

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22
Q

Replication fork

A

Origin & direction of expansion

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23
Q

Semi-discontinuous

A

HAS to go from 5’—3’ but not both sides can be the correct way sooo one side is leading and one is lagging

Lagging strand goes from 3’-5’ of ORIGINAl but is made 5’-3’ in Okazaki fragments

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24
Q

Helicase

A

Unzips & unwinds helix by using ATP to bind and conformationally change

25
Topoisomerase
Uncoils the tangled coils by breaking phosphodiester bonds Target for anticancer drugs because they block the cell cycle and generate breakage which harms the entire genome—> apoptosis and cell death
26
Single stranded binding proteins
Sit on the single strand of the DNA helix to keep it open and expose the bases and prevent formation of hair puns, stabilizes the DNA
27
DNA Ligase
Glues back together the pieces of Okazaki fragments
28
DNA polymerase
Adds DNA to replicating DNA
29
Nucleoside analogues inhibitors
These lack the 3’ OH group and act as drugs that can inhibit DNA replication (anticancer); need to be converted to dNTPs before they can actually inhibit Ex: ara-c, acyclovir, azidothymidine
30
Spontaneous damage
Depurination, Deamination
31
Depurination
Essentially: removal of purine (adenine or guanine) Due to cutting off n-glycosidic bond
32
Deamination
Amino group of either base is hydrolyzed and adenine turns to hypoxathine, guanine turns to xanthine and cytosine turns to uracil
33
Ionizing Radiation
ex: xrays | Change base damages, directly break strands, DNA-protein cross links
34
Non-ionizing radiation
Ex: UV light Add a covalent bond between adjacent pyrimidine bases—> toxic, mutagenic and carcinogenic photoproducts
35
Metabolic activation
Ex: (Benzo(a)pyrene and aflatoxin B1) Activated by hepatic cytochrome P450 and eventually forms a bulky adduct w exocyclic amino which prevent replication and gene expression
36
Agents that direct modify DNA
Ex: crosslinking agents, alkylation agents and intercalating agents
37
Crosslinking agents
cross links between DNA bases either in the same strand or complementary strands Ex: nitrogen mustard, crisp Latin, carmustine, mitt ya in C (anticancer)
38
Alkylating agents
methylated base changes and changing phosphodiester into phosphtriesters Ex: DMS and MMS Products include: 7-methylguanine, 3-methyladenine
39
Intercalating agents
Come in between stacked bases of DNA double helix—> unwinding and separating base pairs Ex: ethidium bromide, thalidomide and aanthracycline antibiotics
40
Thymine modifications
In CpG sites/islands (cytosine-phosphate-guanine) and it replaces a T w a G—> stably silences the genes so it’s useful for cancer cells
41
Direct repair mechanism
Repairs cyclobutane pyrimidine dimers by using DNA photolyase which binds to the dimer, absorbs the light and then breaks the bond (photoreactivation)
42
Direct Repair Mechanism
Of O6-methylgaunine Uses methylguanine methyltransferase to move methyl from guanine to the cysteine and removes damage
43
Base excision repair (BER)
Repairs single base mismatches and small alterations Uses: DNA glycosylases (they can flip out th base) Recognize wrong base, DNA Glycosylase comes in and hydrolyzes the N-glycosidic link to remove the altered base, recognized by AP endonuclease —> cuts the phosphodiester bond, AP Lyase removes it; DNA Polymerase B and DNA ligase replace it and glue it back together
44
Nucleotide excision repair (NER)
Repairs chemicals that alter or distort normal change Ex: fixes UV light induced pyrimidine dimers, BPDE from chemical agent mutation, cisplatin additions Distortion is detected, unwind double strand,nick in either side of the damage, nucleotides (29 for humans, 13 in E.coli) are removed DNA polymerase e (DNA polymerase I in Ecoli fill in the gap using the undamaged side as the template and then glued together using ligase Clinical: xeroderma pigmentosum
45
Mismatch excision repair
When a wrong nucleotide is inserted—> wrong base pairing= wrong number of hydrogen bonds=deformity Binds to DNA at deformation and and distinguish between parent and daughter to identify daughter cell; endonuclease comes in to cut the daughter strand and helicase/exonuclase removes a segment of DNA that has the mismatch, polymerase fills the gap, ligase seals the nick Deficiencies: increase susceptibility to hereditary non-polyposis colorectal cancers
46
Recombination repair
Due to ionizing radiation or anti cancer agents—> breaking of double strand or inner strand cross linking Homologous/Nonhomologous
47
Nonhomologous end joining recombination repair
Nonhomologous end joining: ends are joined together by DNA ligase which fixes the break in double strand but leaves a few bases out; preferred method w translocation or deletions
48
Homologous repair
Homologous recombination: when the DNA breaks after replication but before division —> helices are close together Broken ends have 3’ overhang, single stranded region invades good copy and pairs it w the complementary strand, DNA polymerase begins filling in the gaps and then they’re glued back to the 5’ ends
49
Transcription-coupled repair
RNA polymerase stalls during transcription (In eurkaryotes: ERCC-6 and ERCC-8 recognize it and bring in other enzymes to help fix) Defective ERCC-6 and ERCC-8–> Cockayne syndrome =growth defects
50
Translesion synthesis
Uses DNA polymerase n and some weird shape to fix thymine dimers or apurini AP sites
51
Xeroderma pigmentosum
Skin is extremely sensitive to light and are more sensitive to direct sunlight and are prone to developing melanomas and sarcomas because UV light usually makes dimers which can be fixed in normal people w NER but these have defects in XP proteins in the NER
52
Hereditary nonpolyposis colorectal cancer
Mutations in MER complex—> no good copy and then the MER complex cant fix the tumors
53
Cockayne Syndrome
Rare autosomal recessive congenital disorder Biochem: mutations in the ERCC6 and ERCC8 in TCR of DNA Developmental and neurological delay, photosensitivty, premature aging, hearing loss, eye abnormalities
54
BRCA mutations and breast cancer
BRCA1 and BRCA2 (breast cancer susceptibility genes)—> tumor suppressor genes Mutations= bigger risk of women developing cancer Mutations= increased risk of breast cancer for men’s BRCA1=increase risk of cervical, uterine, pancreatic and colon cancer in women, and pancreatic testitcular and prostate in men BRCA2=risk of melanoma, pancreatic stomach, gall bladder, bile duct cancer=women
55
Methylation of CpG islands
Stable silence of genes | Occurs at 5 of the pyrimidine ring of Cytosine (within CpG sites)—> 5-methylcytosine
56
UPS Protein Degradation Pathway
Sustains homeostasis | Oxidative stress, cellular differentiation, varying nutrient supply, elevating/reducing temperature, stress
57
Ubiquitin
Small amino acid that is in all cells and sticks to the lysine residues on the target proteins; attach to each other to form chains which are targeted for destruction
58
SUMOylation Cycle
Sumo exists as a precursor w two glycines that will chop off the XX part Resevouir of modification—> active from that gets integrated into various substrates
59
SUMO/Ubiquitin
NF4 will stick ubiquitin onto proteins and has some SUMO interacting motifs to bind sumos

MCM Exam 2-RH (9 decks)

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