Sollars - Combined Flashcards
(187 cards)
1
Q
What can be said on the distribution of mitochondrial genomes?
A
2 - 10 copiesCytoplasmic segregationHeteroplasmy (uneven distribution)
2
Q
What pathology is common in mitochondrial DNA disease?
A
Liver pathology
3
Q
For MtDNA disease, what is the effect of Heteroplasmic vs Homoplasmic?
A
Heteroplasmic is rare, and strong (multisystem, death)Homoplasmic is more common, and weaker (associated w/disease)
4
Q
Why would someone being treated for HIV-1 or Hepatitis B be affected by Mitochondrial DNA Depletion?
A
gamma-Pol resembles HIV polymerase (which we attack)
5
Q
What do MtDNA diseases in the exonuclease domain deal with?
A
Proofreading—fidelity
6
Q
What do MtDNA diseases in the polymerase domain deal with?
A
Efficiency
7
Q
What is the role of y-Pol (gamma)?
A
Replicates MtDNA
8
Q
What can occur when checks in the cell cycle to not properly occur to ensure fidelity of genome?
A
Cancer
9
Q
What is faster, prokaryotic or eukaryotic DNA replication?
A
Prokaryotic (50 bp/s vs 1000 bp/s)
10
Q
If you see a DNA Pol + Greek symbol, what are you dealing with?What about a Roman numeral?
A
Eukaryote = GreekProkaryote = Roman
11
Q
What enzyme acts on the unrprotected end of linear chromosomes? What other problems can occur
A
ExonucleaseChromosomal fusion events
12
Q
Cellular Senescence
A
Phenomenon which normal cells cease to divide, possibly triggered by gradual loss of telomere
13
Q
Cellular Crisis
A
When Cellular Senescence does not occur, and cells continue to divide–can lead to mutation events and cancer
14
Q
Telomerase
A
Enzyme to replicate end of chromosomes
15
Q
When will a cell enter Senescence?
A
When it reaches Telomere Associated Repeats (TAR)
16
Q
What is the mechanism for Telomere building?
A
After removal of original RNA primer, will have stretch of ssDNA1. Telomerase contains RNA template matching telomeric repeat element2. ssDNA above is extended farther3. Primase synthesized RNA primer4. 3’ ends of primer accepts DNA polymerase5. RNA primer removed from 5’ end
17
Q
Fragile Sites
A
Non-staining gaps, observed in characteristic sites on several chromosomes.
18
Q
How are fragile sites inherited?
A
Mendelian codominant fashion
19
Q
When would chromosomes be visible in the classic fashion?
A
After S-Phase
20
Q
What is the purpose of the centromere?
A
Attachment of chromosomes to cytoskeleton
21
Q
What 3 things do you need for chromosomes?
A
CentromereTelomereOrigin of Replication
22
Q
What are three morphological classifictions of chromosomes?
A
MetacentricSubmetacentricAcrocentric
23
Q
Satellite DNA
A
Any fraction of the DNA that differs sufficiently in its base composition from that of the majority of the DNA fragments to separate as one or more bands distinct from the bands containing the majority of the DNA during centrifugation
24
Q
When does each chromosome have an identical nucleoprotein copy joined by a centromere (sister)?
A
After S-phase and DNA replication
25
Replication of Origin
Nucleotide sequence at which DNA synthesis begins
26
Type of Chromosome w/a centrally placed centromere =Type of Chromosome that appears J-shaped at anaphase because the centromere is nearer one end than the other = Type of Chromosome with a nearly terminal centromere =
MetacentricSubmetacentricAcrocentric
27
Complex of nucelic acids (DNA/RNA) and proteins (histones/nonhistones) comprising eukaryotic chromosomes
Chromatin
28
What type of chromatin is highly condensed and shows no evidence of active gene expression? What type contains transcriptionally active DNA and is extended?
HeterochromatinEuchromatin
29
How many chromosomes does a haploid cell contain?
23
30
What is the structure of mitochondrial chromosomes?
Circular
31
What is the difference between Unique Sequence DNA and Repetitive DNA?
Unique = single copy per haploid genome, low conservation, protein coding, intronic, intergenic Repetitive DNA = Repeated sequences, >50% of genome
32
Satellite DNA
Any fraction of the DNA that differs substantially in base comp (either A+T rich, or G+C rich); forms bands
33
Short Interspersed Nucleotime Elements (SINES)and Long Interspersed Nucleotide Elements (LINES)
SINES: Alu repeatsLINES: L1 (Line-1)Both are Dispersed Repetitive DNA
34
What are major differences between mitochondrial DNA and Nuclear Genome?
Mitochondrial genome is 10,000x smaller; each cell contains thousands of copies; is highly conserved for coding; and displays maternal inheritance Nuclear genome is much larger but only contains two copies and displays traditional maternal/paternal inheritance
35
What is the most common cell used for chromosome preparation?
Circulating Lymphocytes
36
What cell cycle would you stop the cell at in order to best study the chromosomes?
Metaphase
37
Define each number for the following gene:10p23
10(chromosome) p(arm) 2(region) 3(band) Hint: Remeber C.A.R.B
38
What type of study is treatment with trypsin following by staining with Wright's (Giemsa)?What is characteristic of this study?
G-bandingCharacteristic, and reproducible patterns of light and dark bands
39
What type of study features fluorescent dye binding to A-T rich regions preferentially?
Q-banding
40
What technique freezes cells earlier in their cycle, and is useful in detecting subtl structural abnormalities?
High-resolution banding (prophase or metaphase banding)
41
What is the difference between R and G bands?
R = early replication, light bands, genes are mostly concentrated hereG = A-T rich dark bands, few expressed genes, rich in L1 sequences
42
What type of band is light, G-C rich, contains expressed genes, and is rich in Alu?
R-band
43
What type of band is A-T rich, has few expressed genes, and is rich in L1 repeated sequences?
G-bands
44
Fluorescent in situ Hybridization (FISH) Commonly used for what?
Analysis method to us a labeled, chromosome specific DNA segment to hybridized with metaphase, prophase, or interphase chromosomes and visualize under a fluorescent microscope Conformation of Down's syndrome
45
Spectral Karyotyping (SKY)
Using multiple fluorescent probes specific for each chromosome to generate specific colors along most of its length. Greatly incrased accuracy and efficiency of detecting abnormalities.
46
Comparative Genomic Hybridization (CGH)
DNA from test source is labeled with a green gluoropore and control normal DNA is labeled with red fluorophores. Two mixed, hybridized to normal chromosomes. Deletions or additions will alter the green:red ratio.Widely used in cancer genetics.
47
Individualized Medicine
Treating patient based upon biochemistry and genetic factors. "Tailored" medicine
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Pharmacogenomics
Study of the role of inherited and acquired genetic variation in drug response
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Cytogenetics
Study of chromosome structure and identification of microscopically visible abnormalities. Examination of the ordered array of chromosome or karyotype
50
Molecular Genetics
Study of structure and function of genes, includes gene mapping and recombinant DNA based tech
51
Biochemical Genetics
How genetic defects disrupt normal metabolism/cell control--need this to design treatment
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Population Genetics
Study of how allele frequencies present in a population.
53
Clinical Genetics
Diagnosis/detection of inherited disorders; treatment/management; risk assessment; genetic counseling; and pharmacogenomics
54
Pharmacogenomics
Study of the role of inherited ad acquired genetics variation in drug response
55
Law of Segregation (1st Law)
Each individual possesses two genes for a particular characteristic. Only one of these genes is transmitted to the offspring
56
Which law deals with unaffected carriers of disease?
Law of Segregation
57
Monohybrid cross
Mating cross designed to produce an individual that has parent contributions that are different for one trait
58
What is the ratio of progreny in the F2 generation?
3:1
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What are characteristics that appear in the F2 generation?
Recessive
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Dominant
Forms of gene that fully manifest their effects on a trait when present in the heterozygous state
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Recessive
Forms of a gene whose effects on a trait are masked by dominant allelles
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Codominance
Alleles are codominant if each is expressing independently of the presence of the otherEx: A/B alleles in blood typing
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Genotype vs Phenotype
Genotype: Genetic (allelic) composition of individual (Xx, etc)Phenotype: Observable physical, biochemical, etc feature (color, height, etc)
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Law of Independent Assortment (2nd Law)
Members of different pairs of factors assort independently. or..Members of different pairs of alleles are assorted independently into gametes during gametogenesis, and that subsequent pairing of male and femail gametes is random.
65
What is the molecular basis for the law of Independent Assortment?
Genes are present on independent chromosomes, and chromosomes undergo recombination along their length fairly frequently
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Epistasis
when one gene masks the expression of another Ex. Blue eyes
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Linkage
greater association in inheritance of two or more nonallelic genes than is to be expected from independent assortment
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Genomic Imprinting
– degree of which a gene expresses itself depends upon parent transmitting
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Mitochondrial Inheritance
inheritance of a trait encoded in the mitochondrial genome
70
Germline Mosaicism
when an individual is composed of two or more cell lines in their germ cell population, where these cell lines are of different genetic or chromosomal constitutionex. Seen in schizophrenia
71
Single Gene Defect
Stem from polymorphism or mutations in one gene; easy to recognize modes of inheritanceExamples: Cystic fibrosis, sickle cell, Marfan
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Chromosome Disorder
Defect is due not to a single mistake in genetic blueprint, but to an excess or deficiency of genes contained in whole chromosome or chromosome segmentsEx: Down's, Patau
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Multifactorial Inheritance
Most common defect, can include environmental and genetic factors. These can recur in families, but do not show any particular pedigree pattern
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What can be useful in determining if disorder is inherited?
Comprehensive family historyMedical literatureTwin studies/segregation analysis
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Congenital
Present at birth,ex. Congenital AIDS
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Familial
Trait or disorder tends to cluster in families
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Sporadic
Indicates no evidence for vertical transmission or familial clustering exists
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Inherited vs Genetic
Inherited - vertical transmission (e.g. father to daught) of the diseaseGenetic - a gene or chromosome is involved in the susceptibility to or cause of the disease
79
Types of repair involving excision and replacement
MismatchNucleotide excisionBase exchange
80
What does Mismatch Repair preserve?
Fidelity
81
When does Mismatch repair occur?How is the correct strand recognized?What can result when it's broken?
Repairs errors after replicationDNA methylation makes the correct strandHNPCC (Lynch Syndrome) can result when broken
82
What does Nucleotide Excision Repair fix? What can a defect in Excinuclease result it?
Repairs damage resulting from large distortions in the DNA double helix. Defect in excinuclease can result in Xeroderma Pigmentosum
83
What can UV light do to DNA?What repair system corrects this?
Can cause pyrimidine dimers--adjacent thymines dimerize. Nucleotide Excision Repair fixes this.
84
What does DNA contain thymine, not uracil?
Cytosine can spontaneously convert to Uracil, and you would have C-G, A-U. Would throw off repair systems with no way to dope the scope.
85
What creats an abasic site in DNA, and much slower in ribonucleotides and RNA?
Depurination
86
How does Ricin work?
Depurination of RNA
87
Base-Excision RepairWhat comes through and fixes the last step?
Repairs altered bases resulting from spontaneous changes and environmental stress (deamination, depurination)Produces an apyrimdinic site that needs to be repaired (gap in the chain)Deoxyribose Phosphate Lyase removes the base free phosphate, and DNA Polymerase and DNA Ligase fill in the gap
88
What is the most common single base mutation in human cancer?What can remove the incorrect methyl markers?
C to T or G to ABase Excision Repair
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Direct Repair
Specific enzymes are dedicated to repairing specific DNA damage; following use will be "inactive" and degraded.
90
Double Stranded Break RepairCause? NHEJ?HR?Experimental Use?
Cause: High energy radiation and oxidative free radicalsNHEJ = Nonhomologous end-joining (NHEJ) repair; uses different DNA strand to repair; more error prone!HR = Homologous Recombination (HR); BRCA1/BRCA2; may signal breast cancer risk if abnormal BRCAUse: CRISPR
91
DNA Recombination
Rearrangement or exhange of genetic information b/t two DNA molecules of b/t two different parts of the same DNA molecule
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Legitimate DNA RecombinationWhat type of junction is formed?When is it most commonly seen?
Fidelity is preserved, event occurs at aligned points on genetic map, no information is lost, regions of high homologyHolliday JunctionMeiosis
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illegitimate Recombination
Fidelity is not preserved; recombination occurs between segments not aligned on the map. Ex: Unequal Crossing Over
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Viral Integration
Example of illegitimate DNA recombination; some are site specific, others not. HIV is not site specific
95
Movement of Transposons
Example of illegitimate DNA recombination, over 1-million Alu sequences through genome, some disruptions can cause disease if transposon is inserted where it would disrupt another gene
96
What are the three rules of DNA Replication?
1. DNA Replication is semiconservative2. Replication begins at an Orgin, proceeds bidirectionally 3. DNA synthesis proceeds in a 5' - 3' direction and is semi continuous
97
What does each daughter cell duplex consist of?
One parental strand and one newly synthesized strand
98
Where are origins usually found--why?
Around A-T base pairs due to weaker hydrogen bonding compared to G-C (2 vs 3)
99
Which end are deoxynucleotides added to growing chains?
3' end
100
What initiates strands during DNA synthesis?
RNA primers
101
Synthesis of the leading strand is ______?Synthesis of the lagging strand is ______?
Continuous Discontinuous
102
What are the three steps of initiation?
1. DNA-A binds origin of replication2. Helicase dissociates helix3. ssDNA binding proteins keep DNA from reannealing
103
What does elongation require?What enzyme grows leading strand?What is the orientation compared to the parent strand?
RNA primersDNA Polymerase III; works in 5'-3' direction; beginning at the 3' end of each RNA primerComplimentary and antiparallel to the parent template
104
How is the lagging strand synthesized in DNA synthesis?
Small Okazaki Fragments
105
What initiates Okazaki Fragments?What completes them?
RNA Primer Synthesis by PrimaseCompleted by DNA Polymerase III, made in a 5' - 3' direction
106
What molecule class alleviates supercoiling strain via nicks and repairing nicks?
Topoisomerases
107
When does proofreading occur?What does it ensure?
ElongationEnsures fidelity
108
If DNA Polymerase mismatches a nucleotide--how does proofreading occur?
3'-5' Exonuclease activity to excise the mismatched nucleotide;occurs bia enzyme backing up
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DNA Polymerase I
Removes RNA primersSpecial 5'-3' Exonuclease ActivityProofreadingDNA Repair
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DNA Polymerase II
DNA repair
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DNA Polymerase III
Latches on, stays onSynthesizes most DNA during leading and lagging strandsProofreading
112
DNA Polymerase IV, V
DNA Repair
113
What three methods is genetic fidelity preserved?
1. Geometry - Active site of DNA Polymerase; must have 3 rings... tautomerization causes problems2. Proofreading; 3'-5' Exonuclease Activity3. Mismatch Repair and DNA Methylation - Parent strand methylated, copied not. Helps identify correction version to repair.
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What does proofreading's 3'-5' Exonuclease activity preserve?
Fidelity
115
Why is the parent strand methylated and copied not?
Helps identify correct version to repair
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What is the 1st rule of DNA replication?
DNA replication is semiconservative; each parental strand is used as a template for the synthesis of a new complementary strand
117
What does the first rule state a daughter cell will receive?
One of the two identical DNA molecules
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What does each daughter duplex consist of?
One parental strand, and one newly synthesized strand
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What is conservative replication?
Both templates go on to the same cell
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Where are origins of replication found and why?
Sites rich in A-T, due to weaker hydrogen bonding (2vs3) than G-C pairing
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What direction do replication forks move from the origin of replication?
Bidirectional
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What is the 2nd law of DNA replication?
Replication begins at an origin, and proceeds bidirectionally
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What is the 3rd rule of DNA replication?
DNA synthesis proceeds in a 5'-3' direction, and is semi-discontinuous
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Where are new deoxynucleotides added to the growing chain?
3' end
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What initiates each new DNA strand during replication?
RNA primer
126
How is synthesis of the leading vs lagging strand?
Leading = continuousLagging = discontinuous
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AAA+ ATPases
DnaA binds to the origin of replication and disassociates the helical strands; energy of ATP cleavage is used to produce conformational change in DnaA, which forces the strands apart
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DNA Ligase
Creates phosphodiester bonds by using the energy of ATP cleavage, to seal "nicks" in the DNA strand
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DNA Polymerase
"Workhorse" enzyme; responsible for strand elongation, require ssDNA template AND RNA primer
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Helicase
Cause disassociation of the two strands of the double helix, unwinding the structure using energy released from ATP cleavage
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Nucleases
Sever phosphodiester bonds of the DNA backbones; two types--exo/endo nuclease
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Primase
Responsible for synthesizing short stretches of RNA complementary to the template DNA strand that serve as primer
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TopoisomeraseWhat additional functions do they contain?What is difference in Type I and Type II
Adjusts supercoiling of DNA double helices, both alleviating stress and introducing negative supercoiling. Endonuclease and Ligase (cut and seal) Type I = cleave one strand of double helixType II = cleave both strands of double helix
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What occurs at Initiation?
1. DnaA binds the origin of replication2. Helicase breaks double helix3. ssDNA binding proteins maintain disassociation
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Elongation is accompanied by what function to ensure proper base pairing?
Proofreading
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What molecule is instrumental in alleviating supercoiling strain?
Topoisomerases
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What initiates the Okazaki fragment?
Synthesis of an RNA primer by primase
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What powers DNA synthesis?
dNTP to dNMP (2 Pi)
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What is DNA gyrase?
Type II Topoisomerase
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Topoisomerase II Poisons
Stabilize covalent DNA topoisomerase II complex
141
Catalytic Inhibitors
Topoisomerase II inhibitors (w/out stabilizing covalent complex)
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When does proofreading occur and what does it ensure?
Elongation, fidelity
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What enzyme excises the mismatched pair in proofreading?
3'-5' Exonuclease
144
When does termination occur?
When replication forks join up
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What is the central dogma?
DNA - Transcription - RNA - Translation - Protein
146
What is the general structure of DNA?
Polynucleotide sequence joined through 3'-5' phosphodiester bonds. Polar primary structure, strands run antiparallel, exterior is hydrophilic, interior hydrophobic, helix has major and minor grooves
147
What is often found at the 5' and 3' ends of DNA?
5' - Phosphate 3' - Hydroxyl
148
What is the role of Actomycin D?
Anticancer drug which intercalates b/t the planar bases of DNA
149
What are Chargaff's Rules?
A=T, G=C, Purines = Pyrimidines (A+G=T+C)
150
What is a major exception to Chargaff's Rules?
Base composition in an organism can be affected by environment, age, and/or nutrition
151
What are the hydrogen bonding rules in DNA? What does this result in?
A-T = 2G-C = 3Sequences rich in A-T pairings will be weaker than those rich in G-C pairings
152
What is the most common form of DNA?What is Z-DNA? A-DNA?
B-DNALeft handed double helix rich in G-CA-Form made by dehydrating B-DNA, found in RNA hybrids or RNA-RNA double strands
153
What has an impact on viscosity and UV-absorption? What is this called, and how is it used?
Denaturation Hyperchromic Effect, used as standard to measure purity of DNA in preparations
154
Is melting point uniform for strands of DNA?
No, elevation/depression depends on differences in A/T , G/C rich regions (2 vs 3 hydrogen bonds)
155
What is Chromatin?
Complex of nucleic acids (DNA/RNA) and proteins (histones/nonhistones) comprising eukaryotic chromosomes
156
What is the role of histones in DNA secondary structure?What is their electrochemical makeup?What is the role of Histone H1?
DNA wraps around histone complexes to form nucleosomesLarge amounts of basic amino acids (H, K, R) leading to a positive charge which attracts negatively charged DNAHistone H1 associated with linker DNA b/t nucleosomes, induces positive supercoiling in the linker region
157
What are the two types of Chromatin?
Euchromatin - loosely packed, transcriptionally activeHeterochromatin - tightly packed, transcriptionally inactive
158
What occurs when the axis of the DNA helix is coiled on itself?What types of this are there?What must cells do as a result?
SupercoilingPositive - Winds in same direction as helixNegative - Winds in opposite direction as helixCells must actively maintain an unwound state necessary to facilitate access to DNA
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What class of molecules relax supercoiling stress?What type of supercoiling to they maintain? How?
TopoisomerasesMaintain Negative Supercoiling by breaking DNA then resealing the breaks
160
What does Ciprofloxacin target?
Bacteria topoisomerase
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What does doxorubicin target?
Human type II topoisomerase inhibitor
162
What drives the differences in packaging in viruses, bacteria, and higher organisms?
Genome size. In humans, DNA is organized in chromosomes; in mitochondira and backteria they are circular (which are also loosely termed chromosomes)
163
CentromereWhat is different about metaphase?
Region to which spindle traction fibers attach during mitosis/meiosis. Joining point for two replicated chromatids During metaphase, centromere is narrower than distal regions, termed primary chromosomal constriction
164
Telomere
Repeated DN sequence w/specialized proteins found and ends of eukaryotic chromosomes; chromosomes lose 100 nucleotides from ends per cell division (can be repaired by some cells)
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Origin of Replication
Nucleotide sequence at which DNA syntheis begins, multiple sites in humansBacteria only have one due to circular chromosome
166
Rett Syndrome
X-linked genetic disorder observed in females; 99% of cases are mutations--lack of reproductive function. Cause: Defect in methyl-CpG-binding protein 2, involved in chromatin formation---DNA packaging error
167
What is Royal Jelly an example of?
Epigenetics--also a deviation from Chargaff's rules
168
DNA MethylationWhere does it usually occur? What is the usual result?
Acts to sterically inhibit interaction with DNA molecules and further serve as a binding site for proteins Usually occurs in the promoter regionUsually silences genes--but may also activate
169
DNA Methyltransferases (DNMTs)
Catalyze DNA methylation using S-adenosyl methionine (SAMe) as donor
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Ten-Eleven Translocation (TET) Enzymes
Remove methylation
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Thymine-DNA Glycolase (TDG)
Removes thymine moieties from G/T mismatches by hydrolyzing the carbon-nitrogen bond
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What modification is occuring in Histone Modification?How does it occur?What is the result?What major enzymes cause this to occur?
AcetylationTransfer of acetyl group from Acetyl Co-A to E-amino group of lysinePartial neutralization of the (+) charge on histon, decreasing affinity to DNAHAT (+ acetyl)HDAC (- acetyl)
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HATs / HDACs
Histone Acetylransferases (HATs) - add acetyl to histoneHistone Deacetylase (HDACs) - remove acetyl from histone
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How are hypomethylating agents used?What does it do?
Treatment of some medically fit patients with adverse features of AMLBlocks DNA Methyltransferae (Inhibits DNA methylation)
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HDAC Inhibitors?
Used in some individuals with lymphoid malignancies, such as multiple myeloma and Sezary Syndrome
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What is the basic formula for a nucleotide?
Nitrogeneous Base (information) + Pentose (structure) + Phosphate (energy)
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What are the purines? What are the pyrimidines?What is the general structure of each?
Purines: Adenine (A), Guanine (G)Pyrimidines: Cytosine (C), Thymine (T), Uracil (U) Purines are two rings, Pyrimidines are single ringHint:Purines are Always GiganticPyrimidines are Certainly Usually Tiny
178
What is the major weakness of the bond structure of all nitrogeneous bases?
Tautomerism alters the hydrogen bonding side of the molecule
179
What is the structural difference of Ribose (RNA) and Deoxyribose (DNA)?
Ribose has an additional hydroxyl group at pos. 2 of the pentose ring
180
What is the formula for a nucleoside?What is the predominant form of nucleosides?
Purine base + ribose sugarAnti (syn = minor)
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What is the general structure for a nucleotide?How are these used to store energy, what is an exampe?
Nucleoside + Phosphate GroupThe high E bonds of the phosphate groups; example is Adenosine Triphosphate (ATP)
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How do nucleotides function as energy sources in the cell?
Phosphate groups give method to carry energy in bonds
183
How are do nucleotides function as building blocks in the cell?
Nucleotides can bind to glucose, or similar molecules to donate in various reactions; can also serve as methyl donor in certain pathways
184
How are do nucleotides function as Regulatory Signal in the cell?
Substances like Cyclic AMP (CAMP) can act as second messengers mediated the response from certain hormones
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How are do nucleotides function as Coenzymes in the cell?
Give energy and participate in oxidation-reducation reactions; can carry acyl groups (fatty acids) in metabolism
186
What is the structure and role of 5-Fluorouracil?
Anti Cancer Agent; nitrogeneous base analogue which causes DNA to break
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What is the structure and role of AZT?What is one known side-effect?
Anti HIV drug, activated by polymerase which transcribes viral genome Mitochondrial issues .. remember where bacteria came from bro
