Cytogenetics

Section

Question	Answer
histones	package and order DNA into structural units called nucleosomes; chief protein components of chromatin; associated with inactive genes
nucleosome	segment of DNA wound around a histone protein core; "beads on a string"
non-histone proteins	proteins which remain after the histones have been removed; trascription factors
condensin	large protein complexes that play a role in chromosome assembly and segregation (eukaryotes); holds sister chromatids together (napkin ring)
What does condensin cause to occur in chromatid?	ATP-dependent supercoiling
CDK-1	triggers accumulation of condensins, also known as M phase promoting factor
cohesion	protein that regulates the separation of sister chromatids during cell division
synaptoneamal complex	protein basket that forms b/t two pairs of sister chromatids (homologous chromosomes); mediates chromosome pairing, syanpsis, crossing-over; stabilizes homologous pairs
chiasmata	the point where two homologous non-sister chromatids exchange genetic material during chromosomal crossover during meiosis
cis elements	transcription start sites, include promoters, binding sites for TFs, silencers and enhancers; located on the strand of DNA it is acting on
separase	protease which triggers dissociation of cohesin at anaphase by proteolytically cleaving cohesin subunit (necessary for sister-chromatid separation), irreversible entry into anaphase
anaphase-promoting complex (APC)	marks target cell cycle proteins for degradation; unable to perform its role until the spindle checkpoint has been cleared
securin	inhibits the protein separase until the APC come in and destroys securin
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Question	Answer
Mitosis, Prophase I	sister chromatids held by cohesin, condensins accumulate, gene transcription ceases, mitotic spindle assembles (microtub. grow from polar centrosomes)
Mitosis, Prometaphase I	starts with breakdown of nuclear envelope; mitotic spindles contact chromosomes at kinetochores located at centromere
Mitosis, Metaphase II	chromosomes aligned, still joined by cohesins at centromeres
Mitosis, Anaphase II	sudden release of cohesins. microtubules pull chromatids to opposite poles
Mitosis, Telophase II	nuclear envelopes reassemble around daughter nuclei, condensins released and gene transcription resumes
Cytokinesis	cytoplasm divided, begins while daughter nuclei forming
Meiosis, Prophase I	sister chromatids held together by cohesins, homologous pairs held together by chiasmata and DNA recombo, protein basket stabilizes homologous pairs
Meiosis, Metaphase I	crossovers resolve, protein basket dissolves, cohesins release from arms but not from centromere
Meiosis, Anaphase I	recombined sister chromatids still joined, move to the same pole
Meiosis II division	no additional DNA replication, minimal interphase
Meiosis, Metaphase II	cohesins at centromere dissolve
Meiosis, Anaphase II	sister chromatids pulled to opposite poles (like mitosis), haploid cells result
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Question	Answer
heterochromatin	condensed DNA, low activity
euchromatin	transcribing/translating DNA segments, high activity
centrosome	central constriction of the chromosome at metaphase; composed of repetitive alpha-satellite DNA or 0.5-1.5 Mb; embedded in large region of pericentric heterochromatin
kinetochore	large complex of proteins that bind to centromeric chromatin; microtubles of mitotic spindle attach here
telomeres	located at the ends of the chromosomes; composed of repeated 6 bp motif (TTAGGG); protected however telomere repeats are lost in each cell cycle
telomerase	adds repeats, lost bits of DNA allowing the cell to divide unbounded, (caution: same unbounded growth is a crucial step in enabling cancerous growth)
3 types of chromosome morphology/position	metacentric (towards the middle), submetacentric (off center), acrocentric (towards the tip)
acrocentric chromosomes	13, 14, 15, 21, 22; these are unique and susceptible to a type of abnormality in children
FISH (Fluorescence in situ hybridization)	rapid, objective, high efficiency of hybridization and detection; combines cytogenetics w/ molecular genetic technology; based on the ability of a segment of SS-DNA (probe) to anneal to its complementary target sequence
What can FISH be used to study?	metaphase and interphase cells; advanced knowledge of gene sequence required; limits? need to know sequence of interest/need to develop probe
Comparative Genomic Hybridization (CGH)	fluorescence hybridization to normal metaphase chromosomes; studying copy number changes (variants) in DNA, cancer studies, chromosomal abnormalities, neuromuscular disease, mental retardation; total chromosome paint should hyrbridize 1:1 unless an area of DNA in sample has too few or too many copies
What can CGH detect?	copy number changes in dna-->DNA losses of 5-10 Mb and DNA duplications <1 Mb; amplified dna must exceed 2 Mb to be detected
array CGH	fluorescence hybridization to several thousand probes on a glass slide
What can array CGH detect?	copy number changes of 5-10 kB; high-resolution CGH detects structural variations at 200 bp; primary screeing for people with dysmorphic syndromes, MR/DD, autism spectrum, multiple anomalies; breakpoints in unbalanced chromosomal rearrangements
polyploidy	any multiple of the haploid number of chromosomes where n=23, so 46, 69; caused by the fertilization of the same egg by 2 or more sperm, errors in Meiosis II
triploidy	69XXX or 69XXYmost common example of polyploidy, 3n; occurs in 1% of conceptions, 10-20% of all chromosomally abnormal SAbs
What is the cause of triploidy?	fertilization by two sperm or error in maternal meiosis II
nondisjunction	lack of crossing-over/recombination; problem in development is usually maternally related, Meiosis I is timeframe of common mishap
aneuploidy	chromosome number which is not an exact multiple of the haploid number, n; absence or addition of a sex chromosome, Down syndrome; caused by non-disjunction; more than 90% from maternal origin, Meiosis I mistakes are most common (lack of recombination)
Types of aneuploidy?	monosomy (2n-1=45), trisomy (2n+1=47), and tetrasomy (2n+2=48)
trisomies	associated with autosomal chromosomes, errors in meiosis I, chromosomes 13 (early death),18 (early death), 21 (smallest/mildest phenotype) are smaller dna molecules w/ large sections of heterochromatin, allow pregnancies to come to term; Trisomy 16 most common but leads to SAb
monosomies	associated w/ sex chromosomes, autosomal monosomies don't occur in liveborn infants, more genetic information tolerated better than insufficient info
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Question	Answer
diandric	46 chromosomes from the father, SAb likely, much larger placenta (maternal sets have longer gestational survival, fetuses look more human-like)
translocation	interchromosomal (1/500 - 1/1000 in population)
reciprocal translocation	exchange of chromosomal material between two or more nonhomologous chromosomes; common de novo rearrangement, occur randomly; no disruption of coding regions or change in phenotype (balanced reciprocal translocations); associated w/ increased paternal age, no phenotype predictions, potentially passed to offspring
Robertsonian translocation	most commone type of structural abnormality; a translocation between two acrocentric chromosomes (13, 14, 15, 21, 22) by fusion at the centromere with loss of their short arms to form a single abnormal chromosome; carries risk of serious congenital anomaly
chromosomes for phenotipically normal RT?	14, 21 and 45
most common tranlocation?	14q and 21q-->one normal 14, 2 normal 21 chromosomes, and the RT chromosome of 14 and 21
inversions	requires two breaks in a chromosome; a piece of the chromosome is flipped upside down in one region
pericentric inversion	(0.12-0.7%) break points of the exchange are on either side of the centromere
paracentric inversion	(0.1-0.5%)breakpoints of the exchange are within the same arm; next to rather than surrounding the centromere
deletions	loss of part of a chromosome resulting in partial monosomy; 2 kinds: terminal (from the end) and interstitial (from the middle portion of the chromosome) small to >1kb (~1 million/genome)
insertions	material added from another chromosome; small to >1kb (~1 million/genome)
duplications	duplicated material from same chromosome
silent mutations	mutation that involves the change of only a single base in the DNA sequence that does not result in an AA change; may affect genomic interactions
missense mutation	a single base change that results in a change in AA; sometimes caused by abnormal phenotypes, others cause AA polymorphisms w/ no clinical consequence
nonsense mutation	a single base change that changes an AA to a stop codon; result in premature truncation of the protein product, considered deleterious
frameshift mutation	always considered deleterious, insertion or deletion of bases in anything other than multiples of 3 disrupts the reading frame
splice site mutation	alters the recognition sequence needed for accurate splicing of introns; may result in the abnormal removal of the intron
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Question	Answer
chromosomal mosaicism	results from two or more genetically distinct cell lines; can be for whole chromosomes, chromosomal segments or genes; post-conception problem
somatic mosaicism	variation among the different body cells; normal finding in a person but frequently masked; occurs via mitotic disjunction or through loss of an existing trisomy during mitosis
germline mosaicism	variation limited to the gametes without overt expression in other cells
confined placental mosaicism	mosaicism in the extraembryonic tissues but not in the embryo
chorionic villus sampling	samples chorionic ectoderm and mesoderm
amniocentesis	samples the amniotic mesoderm, amniotic ectoderm, and fetal ectoderm
cordocentesis	samples the fetal mesoderm (blood)
single nucleotide polymorphisms (SNPs)	>1% of chromosomes (~10 million/genome) most common type of repeated genetic element, associated w/ population diversity, noted in untranslated 5' to 3' regions, within introns and in the extragenic reigons of DNA; >90% of genes contain at least one SNP; responsible for variation in gene expression among people; ex: cytochrome P450 (CYP) genes have SNP variants which differ by race and ethnicity
tandem repeats	may produce sequence variations most commonly found in noncoding regions, composed of a repeat unit that is repeated many times in the region
3 classes of tandem repeats?	satellite DNA, minisatellite DNA, and microsatellite DNA
copy number variants	form of structural variation; copy number changes greater than 500bp and less than 5 Mb; detected by array CGH; there are at least 3600 per genome and account for 10% of genes; responsible for our sense of smell
satellite DNA	found near the centromere, 100 kb to several Mb in length, FISH used to identify individual chromosomes, ex: alpha-satellite dna has 171 bp tandem repeats, may serve as binding site for mitotic centromeric proteins; ex: beta-satellite has variable regions of 1, 9, Y and acrocentric chromosomes, 68 bp, adjacent to centromeres
minisatellite DNA	20-50 copies of 6-100 bp repeats (~150,000/genome) shorter than satellite, found in hypervariable sequences or at telomeres; sequence similarity increases the likelihood of recombination at these sites; ex: telomeeix minisatellites made of hexanucleotide tandem repeats (TTAGGG); used in fingerprinting and forensics
microsatellites	1-6 bp repeats of <200 bp in length (>1 million, ~3% of genome) small regions of short tandem repeats (STRs) of 1-4 nucleotides that occur throughout the entire genome, dinucleotide repeats are most common=hotspots for mutation b/c replication machinery is apt to slip/stutter here and affect reading frame, >1 million per genome
DNA microarray	set of analyses that provide rapid substantial info about DNA, RNA and protein level; analysis of thousands of nucleic acid hybridization experiments using microelectronic fabrication, miniaturization and integration with bioinformatics, used in cancer and transplantation medicine, dna probes synthesized directly onto a chip in known order
imprinting	normal inactivation of genes by CpG methylation based solely on the parental origin of the gene-->expression of single allele is the normal state, gene that is not expressed or silent is imprinted (parent-of-origin effect)
histone acetyltransferase (HAT)	acetylation which relaxes chromatin structure, increased gene transcription
histone deacetylase (HDAC)	deacetylation which condenses chromatin structure, decreases gene transcription
histone methyltransferase (HMT)	methylation which has a variable effect on transcription depending on gene
UPD (uniparental disomy)	occurs when both copies of the same chromosomal region are inherited from the same parent; maternal=ovarian teratoma, paternal=hydatidiform mole of placenta (no fetus)
RNA binding protein (FMRP)	product of FMR1; involved in dendritic transport, translational regulation; influences synaptic plasticity (how we learn things) and neurobehavioral development
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Question	Answer
8-oxoguanine	one of the most common DNA lesions resulting from ROS; can result in a mismatched pairing with ADENINE resulting in G to T and C to A substitutions in the genome
how to correct thymine dimer (cyclobutane ring) caused by UV irradiation?	nucleotide excision repair
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