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Molecules to Medicine > Unit 1 > Flashcards

Unit 1 Flashcards

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Organic Chemistry 101 flashcards
1
Q

Gibbs Free Energy under non-standard conditions

A

ΔG=ΔG0’+RTln([products]/[reactants]

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2
Q

Gas Constant

A

R is the gas constant:1.987 cal/mol ºK.

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3
Q

Gibbs Free Energy related to equilibrium constant

A

ΔG0’ = -RT log K’eq cal/mol

or possibly ln

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4
Q

Gibbs Free energy of redox reaction

A

ΔG’o = -nF ΔE’o

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5
Q

Faraday Constant

A

96,500 joules/volt mol

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6
Q

Difference between DNA and RNA nucleotides

A

DNA is missing a -OH on the 2’ ribose carbon

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7
Q

Nucleotide

A
  • nucleotide: base-sugar-phosphate
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8
Q

Nucleoside

A

nucleoside: base-sugar (e.g.: deoxyadenosine)

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9
Q

Base

A

A/T/C/G/U

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10
Q

Solubility of Nucleotides

A

pyrimidines > purines; nucleotides > nucleosides > bases

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11
Q

Gout and Lesch-Nyhan Disease

A

buildup of purines in our tissues. Purines are the least soluble = tissues that have these buildups have gross cellular defects

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12
Q

AZT and DDI

A

Act as chain terminators (mimics nucleotide but doesn’t have 3’ OH. DDI (dideoxyinosine) can be used to inhibit HIV reverse transcriptase activity) AZT=Azidothymidine

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13
Q

Avery, Cloud, and Mccarty

A

discovered that DNA is the important information carrier in our cells (live/dead virulent/nonvirulent experiments with mice)

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14
Q

Chargaff’s Rule

A

Base pairing!

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15
Q

Handedness of Helices in DNA

A

Right!

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16
Q

Base pairs per turn of helix

A

10

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17
Q

Nitrosamine

A

Converted to nitrous acid, a deaminating agent that causes mutations, found in cigarette smoke

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18
Q

Puromycin function

A

an antibiotic that mimics the 3’ acceptor end of a tRNA that has an amino acid. It binds in the ribosome as it is translating & covalently attaches to a growing polypeptide chain –> terminates chain, prevents completion of translation.

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19
Q

Cisplatin

A

Base alkylating agent (cancer)

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20
Q

Actinomycin D and doxorubicin

A

a naturally occurring antibiotic that has also been used as a chemotherapy. “Intercalates”
into DNA (inserts a ring structure that can stack with DNA bases) and alters the double-helical structure.
Interferes with DNA replication and transcription

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21
Q

Etoposide and Camptothecin

A

chemotherapeutics that target topoisomerases that relax DNA supercoiling
(super-twisting of the double-helix). Topoisomerases are necessary during DNA replication to avoid
supercoiling as the double helix is opened up to copy the strands. Topoisomerases must break the DNA
backbone to “relax” supercoiled DNA. Drugs that interfere with this process usually leave DNA breaks that
cannot be repaired

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22
Q

Change-causing mutations

A
  • Uncorrected replication errors
  • Depurination
  • Deamination
  • Alkylation
  • Pyrimidine Dimers
  • Reactive Oxidative Species
  • Base adducts
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23
Q

Depurination

A

Purine (A/G) is removed, leaving only sugar phosphate backbone (unstable)

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24
Q

Deamination

A

Amine group is removed from cC to form a U, which will then be base paired with A/T

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25
Q

Alkylation

A

Addition of a methyl group to the sixth oxygen on guanine–> O6-methylguanine

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26
Q

Pyrimidine Dimers

A

Thymine-thymine double bonds

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27
Q

Base adducts

A

BPDE addition to guanosine results in base matching with A by DNA pol

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28
Q

Direct Reversal of DNA Damage

A

1) repair of nick caused by DNA ligase in phosphodiester backbone
2) Removal of methyl from 6-O-methyl guanosine by MGMT

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29
Q

Mismatch Repair (MMR)

A

MutS and Mut L (prokaryotes) or MSH/MLH (Eukaryotes) scan strands and bind when they find an error. Then helicase unwinds, endonuclease cleaves, oligonucleotide is excised, polymerase refills, ligase seals.
New strand is ID’d in Eukaryotes by increased number of nicks.

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30
Q

Base Excision Repair (BER)

A

*For mutations that are do not cause structural changes in DNA and are not targeted by Nucleotide excision Repair (ex. C–> U or methylation)
Depends on glycosylase, which cuts the wrong base away from the phosphosugar backbone. The abasic site is then removed by 2 endonucleases (3’ and 5’ cuts), refilled by DNA Pol, and sealed by ligase.

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31
Q

Nucleotide Excision Repair (NER)

A

*Corrects issues that distort DNA structure and block polymerase function (ex. thymine dimers and BPDE base adducts)
Distorted DNA is recognized by protein complex that binds. Helicase unwinds (part of TFIIH complex) and endonucleases cut either sides of ~30 bp oligonucleotide. Pol fills in gap, ligase sease.

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32
Q

Diseases caused by mutation in NER genes

A

xeroderma pigmentosum, cockayne syndrome, tricothiodystrophy

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33
Q

Repair pathway for big mutations that cannot be fixed by NER

A

Trans-lesion synthesis

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34
Q

Protein Kinases important for DNA damage checkpoint

A

ATM and ATR

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35
Q

Mismatch repair defect associated disease

A

hereditary non-polyposis colorectal cancer

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36
Q

DNA Polymerase I

A

helps correct & repair DNA. Replaces the RNA primer with DNA: has 5’-3’ exonuclease activity to remove RNA, then 5’-3’ polymerase activity to fill in the gap.

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37
Q

DNA Polymerase III

A

MAJOR REPLICATIVE ENZYME – has a sliding clamp that keeps it attached to DNA over long distances

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38
Q

RNA Polymerase I

A

Makes ribosomal RNA= is the busiest of the all the pols – makes over 90% of the RNA in our cells

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39
Q

RNA Pol II

A

mRNA, snRNA, miRNA, lncRNA
- has unique C-terminal domain (CTD) on large subunit
o This binds to proteins that help regulate elongation & processing of the mRNA transcript

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40
Q

RNA Pol III

A

tRNA

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41
Q

E Coli Polymerase

A

1 type of polymerase for everything

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42
Q

alpha-amantin

A

a toxin found in mushrooms. Binds to RNA pol II at the site of the bridge helix. Prevents translocation, elongation of the growing mRNA chain –> kills you

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43
Q

rifampicin

A

Antibiotic: binds bacterial RNA polymerase and blocks the RNA exit channel

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44
Q

Components of RNA Pol II initiation complex

A

TFIIA, TFIIB, TFIID (TATA-binding protein), TFIIE (also has helicase activity and ATPase), TFIIH(also participates in NER, acts as helicase.
CDK7 (Part of TFIIH) phosphorylates CTD on RNA Pol II during promoter clearance

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45
Q

TATA binding protein function

A

TBP binds in minor groove and directs assembly of initiation complex

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46
Q

5’ Capping Steps

A

1) remove triphosphate on 5’ end with triphosphatase
2) Transfer GTP to the chain backwards (5’-5’) with guanylyltransferase
3) Methylate GTP with guanylyl-7-methyl transferase

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47
Q

Purposes of 5’ cap

A

1) removes 5’ triphosphate
2) makes 5’ end resistant to exonucleases
3) Helps with splicing and processing with cap-binding complex
4) Translation factor eIF4E recognizes cap and transports mRNA to ribosomes
5) degradation of 5’ cap is a sign for mRNA degradation

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48
Q

Conserved sequences in introns

A

5’ GU……..A……………AG 3’

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49
Q

Genetic Disorders caused by Splicing

A

Marfan’s syndrome - mutations in fibrillin transcript. They are tall and prone to aneurysms
Abnormal splicing of CD44 gene promotes tumor metastasis

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50
Q

Binding sites of snRNA’s in splicing

A

1) u1snRNA==>5’ GU
2) u2 snRNA ==> Branch point A
3) u2AF snRNA ==> 3’ AG

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51
Q

Termination Codons

A

UAG, UGA, UAA

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52
Q

poly A site consensus sequence

A

AAUAAA

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53
Q

Poly-A tail formation

A

1) new mRNA is cleaved at the Poly-A consensus sequence

2) Poly-A tail is added and capped with PAB (poly-A-binding protein)

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54
Q

Poly-A tail functions

A

1) Protection from degradation
2) export from nucleus
* cancer cells often have shorter polyA tails to avoid detection

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55
Q

Overexpression of EIF4E

A

Leads to malignant transformation

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56
Q

Treatment of Spinal Muscular Atrophy

A

Rescue of SMN1 mutations by altering splice sites

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57
Q

alpha-Thallasemia

A

Several types of anemias. Can be caused by mutation of AAUAAA or mutation of gene in beta-gobin promoter
-Mutations also often disrupt alpha helix structure

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58
Q

Hemophilia-B-Leyden

A

X-linked disorder that involves clotting
Mutation in Promoter IX gene
Androgen receptor can bind nearby and promote translation, so before puberty they only make 1% of factor IX and after puberty they make 60% of normal factor IX

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59
Q

Fragile X syndrome

A

CGG repeats in the FMR1 gene, leading to increased methylation of the cytosine (CpG) and increased gene silencing

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60
Q

Targets for drugs attacking DNA metabolism

A
  • Synthesis of precursors (dNTP)
  • Intercalation (getting in the middle)
  • Covalently binding bps
  • Topoisomerases
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61
Q

Craniosynostosis

A

Defect of homeodomain protein that binds too tightly to MSX2 gene, leading to premature closure of skull
Gain of fxn

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62
Q

Androgen Insensitivity Syndrome

A

Mutation of DNA-binding region or ligand (androgen) domain of androgen binding protein, a zinc finger DNA binding protein. Secondary sex characteristics are not developed and person may be infertile

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63
Q

Waardenburg Syndrome Type II

A

Mutation in a gene for a transcription factor that plays a role in development of melanocytes. Characterized by deafness and pigmentation anomolies

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64
Q

TF’s that form heterodimers (combinatorial control)

A

zinc finger, bZIP, bHLH

65
Q

Possible modifications of histone lysine residues

A

acetylation, ubiquination, phosphorylation, methylation

66
Q

Rubinstein-Taybi Syndrome

A

Mutation in gene coding for CBP protein (a HAT)

results in mental retardation, craniofacial abnormalities,

67
Q

Leukemia

A

Gain of function fusion proteins –> sometimes transcriptional factors will fuse with HDAC or HAT, altering the activity of the regulators

68
Q

Tamoxifen

A

Breast cancer drug that works by binding to estrogen receptor and recruiting co-repressors

69
Q

Examples of nuclear entry protein regulation

A

NF-KappaB is sequestered in cytoplasm by IKappaB

Ca2+/Calcineurin regulate entry of NF-AT into nucleus (immune response and heart effects)

70
Q

Examples of regulation of amount of activator/repressor

A

Levels of beta-catenin in a cell is regulated by APC, which is often mutated in familial adenomatous polyposis (colon cancer
MDM2 binds p53 protein and leads to its degradation. (p53 is a VERY important tumor supressor. “guardian of the genome”

71
Q

Example of inhibition of DNA binding activity of a sequence specific binding protein

A

Id proteins bind to HLH proteins as a heterodimer, but prevent binding to DNA because they lack a DNA binding domain

72
Q

Example of protein modification that alters activity of a sequence specific binding protein

A

CREB (phosphorylated by G protein activates a HAT (CBP) which recruits RNA Pol II

73
Q

High Energy Bonds

A

ATP is an example of a phosphoanhydride bond.

Acetyl coA contains high energy thioester bonds (C-S)

There are 3 types of high energy phosphate bonds:

  1. Phosphoanhydride (ATP)
  2. Phosphocreatine (P-N)
  3. Phosphoenolpyruate bonds (C-O-P)
74
Q

Rapamycin

A

dephosphorylates 4eBP, which then goes to bind and inactivate eIF4E

75
Q

function of eIF4E

A

Initiates eukaryotic translation. Binds 5’ cap, recruits other IF’s and small subunit. Small subunit then scans down until it finds AUG

76
Q

Bacterial Initiation

A

EF1 and EF3 bind small subunit, which binds the shine delgarno sequence, placing the AUG in the P site
eF2 brings over a special formylmethionine. Then GTP hydrolysis causes release of IF’s and binding of the large subunit

77
Q

Polycistronic bacterial genes

A

Bacterial genes may contain many AUG sites, and any with a Shine Delgarno sequence will be translated. These genes often exist in operons.

78
Q

Factors that drive regulation of Translation

A

Varying the activities of elongation or initiation factors
mRNA structure and sequence
Binding of proteins to the mRNA
Action of small molecules (such as antibiotics)

79
Q

mTOR

A

A central player in many processes, regulates translation

ex. Induces phosphorylation of e1F4E-binding proteins

80
Q

Regulation of eIF4e

A

eIF4e is inhibited by eIF4e-bp. eIF4e is turned off when it’s phosphorylated (via mTOR)
Stress and Rapamycin–> dephosphorylation of 4eBP

81
Q

Regulation of eIF2alpha

A

Phosphorylation inhibits it, which prevents binding of initiator tRNA from being delivered to the ribosome
Phosphorylated by: Interferon (produced when cell is infected by virus), other cell stressors

82
Q

IRES-driven translation

A

*In some cases, viruses cleave eIF4G, shutting down cap dependent initiation and only allowing IRES-driven translation

83
Q

a) Hemoglobin wayne mutation

b) Hemoglobin constant spring mutation

A

1) 3’ frameshift mutation

2) Sense mutation

84
Q

mRNA editing example

A

apoB is edited by cytosine deamination (C–> U), creating a stop codon and a truncated protein in the intestine, so the protein is differentially expressed in the liver and intestines

85
Q

Kozak Sequence

A

RNA sequence upstream of an AUG that modulates the likelihood that the small subunit will bind on a given AUG site

86
Q

Antibiotics that target the ribosome

A

Streptomycin, Erythromycin, Tetracycline, Chloramphenicol

87
Q

Translational regulation of intercellular Iron levels

A
  1. Transferrin binds iron extracellularly
  2. TR (transferrin receptor) transports transferrin-Fe compound into cell
  3. Ferritin – sequesters excess Fe
  4. Iron Response Element (IRE) – sequence in transferrin receptor mRNA that binds to IRE-BP
  5. Iron Response Binding Protein (IRE-BP) – bind Fe & regulate expression of ferritin & TFR

Basically = during times of low iron, IRE-BP is free to bind to IRE on mRNA that encodes for transferrin receptor; prevents degradation of mRNA & translation occurs. More Fe gets into cell. During high iron, IRE-BP is bound to iron, and mRNA gets degraded.

88
Q

Amino Acid H-bond donor mnemonic

A

THYNQ WRKS (Thymine, histidine, tyrosine, asparagine, glutamine, tryptophan, arginine, lysine, serine)

89
Q

Amino Acid H-bond acceptor mnemonic

A

Y STD? GQ : Tyrosine, serine, threonine, aspartate, glycine, glutamine

90
Q

Essential Amino acid mnemonic

A

WHR FVT MILK (Tryptophan, histidine, arginine, phenylalanine, valine, threonine, methionine, isoleucine leucine, lysine)

91
Q

Hydroxyproline

A

-Important in collagen formation
-Vitamin C is necessary for enzyme to work
Disease failure–> scurvy

92
Q

Gamma-Carboxy Glutamate

A

-Occurs in clotting factor proteins
-Enzyme requires vitamin K (Vitamin K deficiency causes clotting disorders)
Warfarin is a blood thinner that inhibits this enzyme

93
Q

Glycosylation

A

O-linked: Serine/Threonine
N-Linked: Asparagine
O-linked is basis of ABO blood typing
Disorders of gylcosylation lead to congenital disorder of glycosylation –>hypotonia, psychomotor retardation, seizures

94
Q

Acetylation and methylation

A

Lysine and Arginine make histones extremely positive and are targets for acetylation and methylation
-this leads to histone modification and is a target for cancer drugs (ex. vorinostat targets a HDAC)

95
Q

Reversible phosphorylation

A

-Ser/Thr/Tyr
-catalyzed by kinase/phosphatase and useful in signal transduction
Ex. Gleevec is a leukemia treatment
In lukemia, bcr-abl is a mutated kinase that is permanently on, Gleevec targets the kinase domain and turns off oncogenic effects

96
Q

Ubiquination

A
  • protein marked with other protein, multi-ubiquitin chain marks protein for degradation
  • in multiple myeloma, proteasomes are overactive. Ubiquitination of proteasomes can inhibit cancer activity
97
Q

sickle cell anemia mutation

A

missense mutation involving one amino acid change (glutamate–>valine)
(**Note, there are also normal healthy differences in people that don’t affect function called polymorphisms)

98
Q

Proteases

A

digest peptide bonds of any protein (ex. Trypsin in digestion)
* many proteins are activated by cleavage (insulin, trypsin, some transcription factors, blood clotting cascade involves protein cleavage)

99
Q

Peptidases/ specific proteases

A

HIV protease-cleaves a specific protein that is needed for HIV to reproduce (inhibited by crixivan)
Angiotensin II formed by cleavage by ACE (inhibited by captopril)

100
Q

Alpha helix

A

Carbonyl-O binds with i+4 N-H group (both in backbone)
usually right handed
side chains flare out to the outside
Residues 1 and 8 stack
- Each turn is 3.6 residues and 5.4 Angstroms
Fits well into major groove of DNA

101
Q

Leucine Zipper Domain

A

2 alpha helices with 7 residue turns, and a Leucine or isoleucine every 7 positions

102
Q

Helix stabilizers and breakers

A

Breakers: Proline and glycine
Stabilizers: Alanine and Leucine
Mostly alpha helixes: Structural fibrous proteins (keratin, myosin) and globular proteins (hemoglobin/myoglobin)

103
Q

Beta Sheets

A

ex. fibroin silk, spider webs, immunoglobulin, pepsin, HIV protease
- Also H-bond between 1 and 4 residue
- 180 turn spans 4 acids and usually has a glycine in position 3 or a proline in 2 (~6% of prolines are cis)

104
Q

Amino Acids that promote beta sheets

A

Trp, Ile, Val

105
Q

Amino acids common in beta turns

A

Gly and Pro

106
Q

Circular dichroism analysis

A

Measures absorption difference of L and R circularly polarized light. the curve depends on the secondary structure (chain conformation)

107
Q

Main classes of tertiary proteins

A

Fibrous: typically insoluble, made of a single secondary structure
Globular: typically water soluble, or lipid soluble (membrane proteins)

108
Q

Dissociation constant for protein binding (Kd)

A

** Opposite of equilibrium
kd=[P][L]/[PL]
Kd==> when 50% of ligand is bound to a protein

109
Q

Logic behind embedding heme group in myoglobin/hemoglobin

A 
Myoglobin needs to bind oxygen to deliver to tissues, but protein chains have no affinity for oxygen. 
Some transition metals can bind oxygen, but if just floating in fluid, they would generate free radicals. 
Free heme (an organometallic compound) can bind oxygen, but free heme would be oxidized from Fe2+ to Fe3+ and would no longer be able to bind oxygen. 
SO --> heme + 4 globular protein subunits = hemoglobin 
heme+1 globular protein subunit= myoglobin
110
Q

Binding of Heme to myoglobin

A

Iron in Heme is coordinated with a Histidine residue from the myoglobin protein

111
Q

Mxn of CO poisoning

A

CO can also bind the O2 binding site in Heme and it binds WAY better than O2
-A protein pocket decreases the affinity for CO, but it still binds much more strongly

112
Q

Why is Myoglobin not a good O2 transporter?

A

Myoglobin has great affinity for oxygen in lungs, but the affinity is too high in tissues –> would not release the oxygen.

113
Q

Why is hemoglobin a good O2 transporter

A

Sigmoid binding curve due to positive cooperativity (first binding increases binding affinity at other sites)
-4 hemoglobin subunits (2 alpha, 2beta) all interact
Oxygen binding triggers a switch from T (tense, lower O2 affinity) to R (relaxed, higher O2 affinity) state.

114
Q

Bohr Effect

A

blood in lung has higher pH than blood in metabolic tissues. O2 binds well in higher pH conditions and releases well in lower pH conditions. Thus, the pH conditions of the various tissues encourage binding/release of O2 –> increases transfer efficiency

115
Q

Methods of protein denaturation

A

Heat, pH, chemicals (urea, guanidium (dissolves polar), detergent, organic solvent)

116
Q

Ribonuclease refolding experiment

A

Proteins, even after being denatured, can refold & regain activity completely –> thus, the folding of a protein relies only on the primary structure. The environment provided by the cell is not always required.
When you denature, you disrupt tertiary and quaternary structures

117
Q

Hsp70/Hsp40

A

Protein folding chaperones

  • induced at higher temperatures
  • bind to hydrophobic regions of proteins & prevent them from aggregating
  • can help with transport (unfolded) across cell membranes
118
Q

Chaperonin

A
  • GroEl/GroES complex in E. coli
  • Form a complex together with ATP binding that encourages folding of a protein (alternatively hydrophobic/hydrophilic environments)
  • 7 subunit rings
119
Q

Protein disulfide isomerase

A
  • Helps with protein folding

- gets rid of improper disulfide bonds and reforms them correctly

120
Q

Peptide Prolyl isomerase

A

Turns Proline from trans–> cis for incorporation in beta turns
* cyclophilin is a PPI that activates calcineurin (stimulates immune response)
cyclophilin is inhibited by cyclosporin (immunosupressant)

121
Q

CF protein misfolding

A

defects in cystic fibrosis transmembrane conductance regulator (CFTR)
most common mutation is the deletion of F508
F508 deletion causes protein misfolding

122
Q

Prion disease misfolding

A 
prion protein (PrP) changes from alpha-helices to mostly beta-pleated sheets --> insoluble, aggregate --> become deadly PrpC-healthy
PrpSc--> prion disease
123
Q

Alzheimer’s misfolding

A

plaque made up of the b-amyloid (Ab42) and the tangle made up of cytoskeletal protein tau

124
Q

Parkinson’s misfolding

A

Lewy bodies (protein accumulation)

125
Q

amyloidosis

A

accumulation in areas other than the brain. Includes heart, lung, kidney

126
Q

Gel filtration chromatography

A

separates by size; small proteins go slower, getting stuck in little bead traps

127
Q

Ion exchange chromatography

A

separates by charge. Cation exchange resin is negatively charged –> binds cations. Negatively charged proteins go faster

128
Q

Affinity Chromatography

A

resins have immobilized ligands; separates based on affinity

129
Q

SDS Page (polyacrylimide gel)

A

Gel electrophoresis bind with SDS, so they have uniform size. Proteins migrate through polyacrylamide gel and the smaller ones move faster

130
Q

Mass Spec

A

Determines mass of a protein

131
Q

Edman degradation

A

determines the sequence of a protein, one aa at a time, from the N-terminus end

132
Q

Western blot

A

immunological studies of proteins. Take a protein, run it through gel. Blot it onto a PVDF membrane. Treat with an antibody, wash, then detect if the antibody bound through another molecule that will bind to the antibody, typically with something attached that you can visualize.

133
Q

RNA interference

A

An endogenous gene silencing mechanism, present in virtually all
eukaryotic cells, by which short double-stranded RNA molecules induce translational inhibition
and/or degradation of mRNAs containing partially complementary sequences.

134
Q

Gene knockdown

A

An experimental technique used to reduce gene expression using sequencespecific
oligonucleotides, typically by RNA interference (RNAi) or antisense mechanisms.

135
Q

RNA-induced silencing complex

A

The catalytic effector complex of RNA interference
(RNAi)-mediated gene silencing. The RISC is a multiprotein complex that incorporates one
strand of a small interfering RNA (siRNA) or microRNA.

136
Q

siRNA

A

endogenous siRNA’s act as transcriptional repressors (heterochromatin formation), mRNA clevage, mobile element silencing

137
Q

Argonaute

A

** RISC component
A family of proteins that bind to small RNAs and that are conserved in all
domains of life. They mediate target recognition via base‐pairing interactions between their
bound small RNA and complementary coding or non‐coding RNAs.
-Has endonuclease activity in miRNA decay of mRNA (but not all have slicer activity)

138
Q

pi RNAs

A

Mobile element (transposon) silencing and regulation of transcription
Small RNAs that are associated with the PIWI protein
complex and that emanated from transposon-like elements
-Primarily related to germ-line regulation and gametogenesis

139
Q

Guide strand of mature siRNA or miRNA

A 
In mature, duplex small interfering RNAs (siRNAs) and microRNAs (miRNAs),
the strand with intrinsic sequence characteristics that favour its association with the RNAinduced
silencing complex (RISC). It is usually turned into the active siRNA or miRNA.
140
Q

Passenger strand of mature siRNA or miRNA

A

: In mature, duplex small interfering RNAs (siRNAs) and microRNAs
(miRNAs), the strand with less preference for RNA-induced silencing complex (RISC) loading. It
is usually quickly degraded or can turn into a miRNA

141
Q

Aptamers

A

Oligonucleotides (DNA or RNA) selected to bind with high affinity to defined
structures.

142
Q

Enhancer RNA (eRNA)

A

a class of lnc RNA that is implicated in enhancer function

143
Q

RNA-mediated Transcriptional Gene Silencing (TGS)

A

Typically uses repressive chromatin remodeling

144
Q

RNA-directed DNA Methylation (RdDM)

A

a plant TGS pathway characterized by the

involvement of two specialized RNA polymerases, Pol IV and Pol V.

145
Q

miRNA

A

~21 nt’s
pretty specifically act through translational repression of mRNAs and mRNA degradation. There are also limited cases of translational activation.
Perfect match–> degradation
Imperfect match–>repression

146
Q

miRNA targeting

A
  • miRNA binds with 3’UTR of mRNA and guides effector complex to target
  • can also target 5’ UTR or coding region- binding region affects function
  • miRNA’s can be sequestered by lnc RNA’s and crcular RNA’s
147
Q

Dicer

A

– The ribonuclease of the RNase III family that cleaves miRNA precursor
(pre-miRNA) and double-stranded RNA molecules into 21–25-nucleotidelong
double-stranded RNA with a two-base overhang on the 3’-ends

148
Q

Restriction point in cell cycle

A

Point in G1 where the cell decides whether it will replicate based on cell size, hormones, etc.

149
Q

Main goal of somatic cell cycle (besides creating another cell)

A

is to ensure exact duplication of the genome in S phase followed by exact of division of the genome in M phase to produce identical daughter cells.

150
Q

Fluctuating CDK activities

A
  • M- high CDK prevents building Pre-Replication Complex
  • G1- low CDK allows building of Pre-RC
  • S- high CDK activates replication and prevents any more Pre-RC building
151
Q

Retinablastoma Protein

A

Rb (Retinoblastoma protein) is an inhibitor of
the cell cycle. When cells divide, the Rb inhibition must be removed. Rb is inhibited by CDK phosphorylation resulting in an “inhibitor of an inhibitor”, that is a double negative, which is a positive: Rb - X CDK - = +. Rb is known tumor
suppressor in that loss of Rb results in tumors in retinoblastoma and also in other cancers (e.g. small cell lung cancer).

152
Q

Two families of CDK inhibitors

A

Cip/kip and ink4 – all are encoded by CDKN gene.
Cip/kip are non-specific
ink4 is specific to certain CDK’s
*one ink4 enzyme is a tumor suressor

153
Q

MCM DNA

A

an important protein in the pre-rc

154
Q

Pre-RC activation proteins

A

a S-CDK and DDK result in MCM DNA activation and loading of other initiation complex proteins

155
Q

DNA Replication and Damage Checkpoint proteins

A

p53 and Chk2 inhibit CDK cyclin2 complexes
Li-fraumeni syndrome–> mutation in p53 or Chk2 leads to high susceptibility to cancer
ATM and ATR are also important kinases
-mutations are like li fraumeni but with neurological symptoms

156
Q

BRCA1/2

A

BRCA1/2 regulate the ATM/ATR phosphate pathway. Mutations lead to high likelihood of breast or ovarian cancer
BRCA1 and 53BP1 are pivotal regulators directing cell towards HR or NHEJ, respectively, and BRCA1 is pivotal for proper HR function

157
Q

5 sources of DS DNA breaks

A
  1. Endogenous (immune system rearrangements [critical for Igs, T Cells], single strand breaks during DNA replication, meiosis)
    a. VDJ recombination – needed for Ig rearrangements
    b. DNA replication
    c. Successful meiosis
  2. Exogenous
    a. Ionizing radiation [cosmic rays and soils]
    b. Medical imaging and treatments
158
Q

Major considerations in ID-ing next-gen sequencing variant

A

1) Read depth/coverage
2) Error Rate
3) contiguity- short read sequences won’t associate haplotypes, long reads will.

Molecules to Medicine (5 decks)

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