Week 1 Flashcards
During mitosis: Cohesin loads? Cohesin dissocaties from arms? Remainder of Cohesin dissocaties?
Loads: at DNA replication (S Phase) Dissociates from arms: Prophase Dissociates from centromere: Anaphase
What is the q arm and p arm?
the q arm is the long arm of the chromosome and the p arm is the short arm of the chromosome
Does sickle cell anemia display allelic heterogeneity?
no, sickle cell anemia is caused by one specific mutation only
Name this chromosomal abnormality: 45, X What sex is this person?What type of aneuploidy is this an example of?
Turner Syndrome Type: Monosomy Fact: 85% missing paternal X
What can’t MLPA identify?
Nothing bigger than one gene, nothing smaller than one exon. nothing other than deletions/duplications
what is a synonymous mutation? How damaging are these?
mutation of a nucleotide that does not alter the amino acid that is coded for. Most likely has no effect
define robertsonian translocations
a translocation between two acrocentric chromosomes by fusion at the centromere
Define polyploidy
more than two sets of the haploid normal of chromosome (>2n)
what are hairpin loops? how are they formed?
a secondary structure formed by RNA in which the presence of palindromic sequences allows RNA to fold on itslef
Define centromere in intelligent terms
The central constriction of the chromosome at metaphase. Repetitive alpaha-satellite DNA (171 bp repeats) embedded in large region of preicentric heterochromatin
why is RNA unstable
2’-OH
Name this chromosomal abnormality: clinical features include intellectual disability, characteristic facial appearance, weak muscle tone, increased risk of developing gastroesophageal reflux, celiacs, hypothyroidism, leukemia
Trisomy 21 or Downs syndrome
Name this chromosomal abnormality: 47, XX, +21
Trisomy 21 in a female, downs syndrome
Define Kinetichore in intelligent terms
large complex of proteins that bind to centromeric chromatin. This is where microtubules of the mitotic spindle attach
What are four reasons for nonpenetrance?
- Sex specific: a male cant get ovarian cancer even int BRCA1/2 is mutated 2. Later age onset: HD 3. Environmental triggers 4. influence by modifier genes or polymorphisms
what is a centromere?
The point of a chromosome that is attached to the mitotic spindle complex
Is trisomy inherited or sporadic?
Sporadic
During Meiosis I cohesin loads where?
Along arms of paired homologues
Are reciprocal translocation bad for the carrier? gametes?
carrier will have normal genomic content but may have abnormal content in gametes after meiosis
Define null allele
a non-functional allele. The other allele may still be functional (A_)
Define submetacentric
chromosome in which centromere is slightly above the middle
what is the role of the MUTYH gene
Base excision repair gene that excises guanine when it is inapproptiately paired with 8-oxo. Loss (bi-allelic LOF) has been correlated with increased colon polyps (MAP) and increased risk for colon cancer
what disease does OI stand for?
Osteogenesis imperfecta
describe non-Watson-crick pairing of RNA. What does this allow RNA to do?
RNA bases (A U G C) can pair with any combination of bases as long as one nucleotide acts as a hydrogen donor and the other a hydrogen acceptor . this allows RNA to form tertiary structures
Describe monozygotic twins, how do they appear on a pedigree?
Identical twins, have almost identical DNA, appear on a pedigree with a line between the two symbols
What genetic alterations can array-CGH identify
detects genetic gains and losses. CNV: deletions, duplications. Chromosome gains and losses
What five assumptions are made in Hardy-Weinberg Equilibrium?
No migration, random mating, no selection, no mutations, only two alleles involved
Alkylating agents preferentially modify which nitrogenous base?
guanine
Are chromosomes more condensed during prophase or metaphase?
During metaphase, condensin doesn’t begin to accumulate until prophase and is not released until telophase
in what direction is RNA synthesized
5’ to 3’
Define chromatid:
Entire linear molecule of DNA and associated proteins. This is what is visible under a microscope.
what are limitations to FISH?
limited by availability of probe and knowledge of target sequence.
Define translocations
2 pieces of chromosomal material exchanged between non-homologous chromosomes
What are the three steps (and their temps) of PCR
Denature DNA: 95DC Primer annealing: 68DC Elongation w/ Taq polymerase: 72DC
The supercoiling of chromatids has what effect on the transcription of genes?
stops the transcription of genes
What wont fish detect?
UPD, methylation
Define polymorphism
the condition of occurring in several different forms
main fxn of golgi apparatus
modification, packaging, and sorting of proteins and lipids
What is meant by the statement “chromosome structure is fluid”
the structure of a chromosome changes depending on the activity of cells
What is the fate of a soluble ER Protein
translated completely into the ER lumen and destined for lumen of an organelle (ER, Golgi, endosome, lysosome)
Which sex chromosome trisomies are characterized with having no significant phenotype other than the potential for mild learning disabilities?
47, XXX (triple X syndrome)47, XYY
What does this mean: 46, XX,t(5:6)(q11.2;q23)
a diploid female had a reciprocal translocation invovling chromosome 5 and 6. chromosome 5 was broken at q11.2 and chromosome 6 was broken at q23
When (MI, MII, or mitosis) is nondisjunction most common? Does it occur more frequently on the maternal or paternal side?
Meiosis I >90% maternal origin
Define Nucleosome:
DNA coiled around a core of 8 histones (octamer)
how can a father not have OI but offspring from 2 different marriages do?
Germline mosaicism. Father has some normal cells (he will appear phenotypically normal), but cells within his body (sperm) have the mutation.
Loss of function mutations can result in what (2) types of product
absent product: null allele Reduced product
in what direction are proteins synthesized?
N to C-terminal
what is a polysome?
an mRNA that is being simultaneously translated by multiple ribosomes
What are some issues with whole exome sequencing?
reads only short segments of DNA at a time, error prone (results have to be verified)
what is a compound heterozygote?
a condition in which two partially functioning alleles exist
In terms of chromosome condensation and visibility is a karyotype obtained during metaphase, anaphase or prometaphase preferred?
the less condensed the better/more visible the banding. Therefore prometaphase is preferred.
how are ROS created? what percent of respiratory chain productivity are they?
byproduct of mitochondrial activity, 2%
What is a nonsense mutation? how harmful?
a change in nucleotide that results in a premature stop codon. Almost always harmful.
recombination vs. translocaiton
recombination occurs between two homologous chromosomes and translocation occurs between non-homologous chromosomes
How is cohesin released between chromatids? In what direction?
Released stepwise from arms to centromere
Name this chromosomal abnormality: 47, XY, +13
Trisomy 13 in a male, AKA Patau Syndrome
What are the three classifications of tandem repeats from largest repeat unit to smallest repeat unit
largest repeat unit: satellite minisatellite microsatellite
How effective is the DNA repair mechanisms in our bodies?
99% effective, it corrects/catches 99% of replication errors
Describe telomeres: role, location, composition
Located at ends of the chromosome, composed of repeating TTAGGG, prevents chromosomal shortening during DNA replication
What equations (2) are used in hardy weinberg equilibrium?
- p^2+2pq+q^2=1 2. p+q=1 where p is the dominant allele, q is the recessive allele, and pq is heterozygous.
Proteins translated at free ribosomes are destined for (4)
cytosol, nucleus, mitochondria, peroxisome
What are the three types of chromosome abnormalities?
numerical, structure, moasicism
What is osteogenesis imperfecta (OI)? Inheritance? GOF or LOF?
clinically heterogeneous (varying degree of severity) characterized by brittle bones due to a lack of collagen. Autosomal dominant inheritance. LOF
on a pedigree, what does a circle with the number “2” inside refer to?
2 females in the sibship, a shortcut for writing families with numerous siblings
What is type 2 OI caused by? How severe?
A mutation in the alpha 1 chain (inappropriate AA, mutation of glycine) that renders the majority of procollagen abnormal. More severe than type I.
is sickle cell anemia caused by a LOF or GOF mutation?
GOF: gain of new cell shape However, the new shape results in a net loss of red blood cell function. This is an example of a GOF mutation that is recessive.
Mitochondrial disease inheritance represents which type of inheritance?
X-linked because only the mother passes on mitochondria
What are three categories/types of aneuploidy? How are they denoted?
Monosomy: (2n-1), 45 chromosomes, one is missing Trisomy: (2n+1), 47 chromosomes, one extra chromosome Tetrasomy: (2n+2), 48 chromosomes, two extra
Define Nondisjucntion, what is it a cause of?
A cause of aneuploidy, failure of homologous chromosomes (MI) or sister chromatids (MII or Mitosis) to separate properly
Describe this person: 45, XY, -21
A male with only one chromosome 21
what does this mean: g.82_83delTG
a sequence obtained from genomic DNA (as in during exome sequencing) shows a deletion of nucleotides T and G originally at positions 82 and 83
What is mismatch repair?
Corrects replication errors in which the wrong base pair was incorporated during replication.
What are four causes of structural chromosome abnormalities?
recombination between nonhomologous chromosomes, dsDNA breaks within chromatids, telomere instability, centromere pair separates in wrong plane during meiosis
CGH stands for
Comparative genomic hybridization
Name this chromosomal abnormality: clinical features include severe physical and intellectual abnormalities, cleft lip, extra fingers or toes, small/underdeveloped eyes, only 5-10% live past first year
Trisomy 13 AKA Patau syndrome
alpha-satellite: where is it found, role, length of repeat
found at centromere of all chromosomes, binding site for centromeric proteins of mitosis (kinetichore), 171bp repeats
What genetic alterations can FISH idnetify (6)
deletions, inversions, translocations, duplications, mosaicisms, marker chromosomes
How does a ribosome know whether or not to translate the attached mRNA at the ER or in the cytosol?
Determined by ER signal sequence on N-terminal of newly translated protein. ER signal sequence=moves to ER. no ER signal sequnence means the ribosome stays in the cytosol
How is Huntington’s Disease inherited? What are symptoms?
Autosomal dominant. personality change, memory loss, series of motor problems including involuntary movement of arms and legs.
Define mosaicism
two or more genetically distinct cell lines within a person
What is the major/primary protein component of chromatin?
Histones
Role of BLM gene (dsDNA damage)
makes helicase that maintains structure and integrity of DNA
what does this mean: c.187delAG
A sequence obtained from cDNA shows that a deletion of A and G at the 187th nucleotide occurred
What are 5 types of DNA damage repair?
Nucleotide excision repair, base excision repair, mismatch repair, dsDNA break repair, ssDNA break repair
What is a synonymous SNP? Nonsynonymous?
Synonymous: a change in nucleotide that does not change the amino acid Nonsynonymous: a change in nucleotide that does change the amino acid
main fxn of lysosomes
intracellular degradation
Describe telomeric minisatellites: overall length, length and identity of repeats, function, replenished by? when are they replenished?
10-15 kb of tandem hexanucleotide repeats (TTAGGG), prevent shortening of chromosome during replication and when the telomeres are gone apoptosis occurs, replenished by telomerase until birth and in cancer cells.
What genetic alterations will MLPA identify?
small duplicaitons/deletions of 1 exon, multiple exons, or the entire gene
what is the combinatorial mechanism?
explains how different genes are turned on in different cells. Suggests that each promoter contains a specific sequence for specific transcription factors to bind before transcription will start
This syndrome is caused by triplet repeat expansion in the 5’UTR of mRNA and results in the X chromosome literally breaking in half
Fragile X syndrome
What are 4 endogenous sources of DNA damage?
depurination, deamination, ROS, replication process itslelf
What is the major difference between Meiosis I and Meiosis II in terms of cohesin? (Metaphase)
Meiosis I: during Metaphase I cohesin releases from homologous chromosomes but not from centromere Meiosis II: During metaphase II cohesin at centromere is released
what is RNA splicing?
the removal of introns in pre-RNA to create mature RNA that is only composed of exons. this occurs in mRNA, tRNA and rRNA
What occurs if protein complex protecting telomeres is lost?
apoptosis occurs
what does this represent: 46,XY/47,XY,+21
A female with mosaicism. Normal/Abnormal. this is a girl with mosaicism where some of her cells have an additional chromosome 21
What are loss of function mutations? Normal inheritance pattern?
mutation that results in reduced or no protein function. Normally recessive exception is OI
How do proteins enter the mitochondria?
Proteins destined for mitochondria have N-terminal sequence that binds import receptors–>import receptor brings protein to mitochondrial translocator–> mitochondrial translocator unwinds and threads protein through outer and inner mitochondrial membrane
What determines the final destination of proteins?
Signal sequences located on either the C of N-termini of newly translated proteins
Telomerase is present during (2)
germs cells, and neoplastic tissue
where is mRNA made? Processed?
in the nucleus
What is unequal crossing over?
a condition where homologous chromosomes receive unequal amounts of chromosome during meiosis
beta-satellite: where, length of repeat
found near centromeres and variable regions of chromosome 1, 9, Y and acrocentrics. 68bp repeats
thymine dimers are repaired by which DNA repair system
NER
Duchenne muscular dystrophy is best identified by which technique in molecular genetics?
MLPA, DMD is generally caused by a duplication or deletion of an exon
What is the role of nuclear import receptors
Attach to proteins (TFs) that display nuclear localization signal seqeunces and transport them into nuclues via cytosolic fibrils of nuclear pore
What are the 5 acrocentric chromosomes
13, 14, 15, 21, 22
Define mosaicism
cells within same person have a different genetic makeup
Genetic variability is responsible for what two characteristics between individuals?
Diversity and individuality
What is nucleotide excision repair? what types of DNA damage does it repair?
NER: removes lengths of nucleotides in order to repair bulky, helix distorting damage. A common damage is thymine dimers caused by UV radiation
what is a missense mutation? How damaging are these?
a mutation of a nucleotide that alters the amino acid that is coded for. Could have no effect, small effect, or harmful effect…more data needed
how is Base excision repair being exploited in cancer therapeutics?
slowing down BER permits more disruption by chemotherapy’s induction of DNA damage
What does this mean: p.Phe134Leufs*51
refers to a protein where Phe at position 134 was changed to Leu…this frame shift created a stop codon 51 codons down.
Where are proteins always initially translated
The cytosol
proteins translated at ER-bound ribosomes are destined for (5)
ER, Golgi, endosomes, lysosomes, cell surface
What is base excision repair? What specific types of DNA damage will it repair?
repairs damage to single nitrogenous base. Ex: repairs purine loss, 8-oxo-guanine bases
Describe the process of whole exome sequencing
only sequences exons. Genomic DNA is fragmented–>fragments are bridge amplified (just another form of amplification)–>sequencing primers are added and sequenced using reversibly terminating nucleotides–>laser identifies the dNTP that was added to DNA strand
What is Swyer syndrome? what causes it?
Syndrome in which males (46, XY) develop external female sex characteristics. Caused by mutation in SRY TF on Y chromosome that in which the TF lacks a nuclear localization signal sequence
What is the relationship between centrosome, centromere, microtubules, and kinetichore
The kinetichore assembles at the centromere of chromosomes. The kinetichore is the attachment point of microtubules that originate from the centrosome at either pole of the cell during metaphase/anaphase
What is the percentage of genetic difference between individual humans?
0.3%. We are 99.6-99.9% identical
Describe Heterochromatin: packing? location? replicate late or early?
Condensed, located at centromeres, inactive loci and inactive X, late-replicating DNA.
what is clinical heterogeneity
diseases with very different phenotypes that are caused by mutations in the same gene
Describe the mitochondrial genome: Shape, copies/mitochondrion, genes, mutation rate, presence of introns/exons
Mitochondrial DNA is circular, each mitochondrion contains 5-10 copies of the circular DNA, 37 genes (rRNA, tRNA, 13 ox phos genes), high rate of mutations, no introns
Uniparental Disomy:
both chromosomes come from same parent
Aflotoxin B1 and tobacco polycyclic aromatic hydrocabons are examples of…
cancer causing agents
What is cDNA
double stranded DNA made from single stranded RNA using reverse transcriptase
Copy number variants/aberrations:
gain or loss of genetic material that can include the addition or absence of entire homologs of something much smaller
Main fxn of nuclues
contains genome, site of RNA and DNA synthesis
Achondroplasia: what is it? inheritance? GOF/LOF? MOA?
Dwarfism. Autosomal dominant. GOF. fibroblast growth receptor gene is mutated such that it is always turned on and always inhibiting bone growth.
What proteins are involved with mismatch repair, what are their 2 general role?
Two protein complexes: MLH1/PMS2; MSH2/MSH–>recognize mismatches and signal additional repair machinery
describe this person: 46, XX
A female with a normal number of chromosomes
what are the gates in which molecules enter or leave the nucleus
nuclear pores
What is a frame shift mutation? how harmful?
a change in nucleotide such that the reading frame for codons is shifted. Almost always harmful
Describe the range in severity of mosaicism
Phenotype may be mild depending on distribution of abnormal cells, and in general it is more mild the later mosaicism develops
How many bp in the human genome?
3x10^9 bp
What is non-penetrance
a mutation without a phenotype
Main fxn of ER
synthesis of most lipids; site of protein production and distribution to many organells
contrast becker muscular dystrophy with DMD
BMD is a milder form of DMD. Dystrophin gene is mutated in both. Dystrophin is absent in DMD and reduced/truncated in BMD
What is a cis-acting element
short stretch of DNA sequence that signals a specific protein to bind. Enhancer, silcencer and promoters all contain cis-acting elements
Duchenne muscular dystrophy: inheritance, how common, cause, gene involved
X-linked inheritance, most common X-linked disorder in man, caused by deletions (2/3), point mutations/insertions (1/3) in the dystrophin gene
How can triploidy occur (2)?
fertilization of ovum by two sperm or error in maternal meiosis II
What are some (4) types of structural abnormalities undergone by chromosomes?
Inversions, insertions, deletions, duplications
what is codon degeneracy?
one AA is coded for by multiple codons
What is the importance of the post-translational modifications of histones?
Histones can be modified to more tightly (gene silencing) or loosely (gene activation) associate with DNA
role of FANC genes (dsDNA damage)
locate dsDNA damage and triggers repair
The accumulation of condensin is triggered by what molecule?
CDK1, a M-phase promoting factor
Microsatellite DNA: length of repeats, locations, problems that arise due to these
Short tandem repeats (STRs) of 1-4 bp, occur in coding and noncoding regions throughout chromosomes, hotspots for mutation due to slippage during replication
What is formed when guanine is attacked by ROS? why is this bad?
8-oxoguanine is formed. this is as likely to pair with A as with C
Main fxn of Cytosol
contains metabolic pathways, ribosomes, cytoskeleton
What is type I OI caused by? How severe?
patients only have half the normal amount of alpha 1 chains to make collagen (null allele). The least severe type of OI
define aneuploidy
presence of abnormal number of chromosome in a cell (not exact multiple of n)
What is haploinsufficiency? What disease do we see it in?
A condition in which a person is missing one allele of a gene and the remaining allele is not sufficient to produce the normal wt condition. This is seen in osteogenesis imperfecta where a null allele weakens bones.
What is chorea?
involuntary movement of arms and legs, seen in HD
What is collagen I composed of?
Two alpha 1 and one alpha 2 chains that form a triple helix (procollagen)
At what point in the cell cycle does condensin release from the chromosome?
Condensin is released after anaphase and the chromosomes relax
What is unique about Turner Syndrome?
This is the only viable monosomy; an autosomal or 45, y mosonomy is not viable
where are ORF and UTR located?
These regions are on MATURE mRNA. The open reading frame is what is translated into protein and this is surrounded by a 5’ and 3’ untranslated region that is not translated
Name this chromosomal abnormality: 47, XXYWhat sex is this person?what type of aneuploidy?
Klinefelters syndrome, male, trisomy of sex chromosome
What does this mean: 45, XX, der(14;22)(q10;q10)
A female with 45 chromosomes due to a robertsonian translocation where the short arm of 14 and 22 stuck together to form a derivative chromosome (der(14;22)).becuase the translocation occurred at the centromere the location is q10;q10
How does heterochromatin and euchromatin appear after G-banding?
Heterochromatin: darkly stained Eurchromatin: lightly stained
Define chromosome morphology
Shapes and appearance of chromosome in condensed state
How can chromosomes be distinguished in a lab?
each chromosome has a distinct banding pattern that can be seen under a microscope after staining
what is a DNA silencer
a section of DNA (distance, location and orientation independent) that decreases transcription of a gene
If a protein lacks a signal sequence what is its fate?
remains in cytoplas
Role of condensin proteins
Cause ATP-dependent supercoiling of chromatids which is essential for chromosomal assembly and segregation. this also makes chromosomes visible under microscope
are there individuals that are homozygous for achondroplasia?
no. this state is lethal. would result in no bone growth.
what is more common, LOF or GOF mutations?
LOF is more common. GOF requires a very specific mutation in a specific location
Define acrocentric
chromosome in which centromere is near the tip
How many pairs of chromosomes are in the human genome? How many pairs of autosomes? Pairs of sex chromosomes?
23 pairs total (46 chromosomes)22 pairs of autosomes1 pair of sex chromosomes
main function of endosomes
sorting of endocytosed materials
Contrast role of cohesin vs. Condensin
Cohesin: Holds homologous chromosomes or sister chromatids together Condensin: Supercoils chromatids, essential for chormosomal assembly and segragation
what modification occur to produce mature mRNA
removal of introns, addition of 5’ CAP and 3’ poly A tail (these two are added after mRNA is synthesized
what is allelic heterogeneity
term used to describe the fact that multiple different mutations in the same allele can cause a single disorder
Describe MLPA
a genetic technique that uses multiple probes to hybridize to a single exon–> if all probes bind then they will ligate together–>each ligated probe is amplified with pcr–>fragment analysis (compared to a control) reveals if the probe was absent (deletion), present (normal), or in abundance (duplication)
Marker chromosome:
an abnormal chromosome that is distinctive in appearance but not fully identified
CNVs are responsible for ___% of variaiton in gene expression among individuals
17%
What are tandem repeats? in what region of DNA are they most commonly found?
pattern repeated one after another, directly adjacent. Most commonly found in noncoding regions of DNA
name this chromosomal abnormality: clinical features include small testes (with correlated testosterone decrease), gynocomastia (breast enlargement), reduced facial and body hair, infertility, micropenis
Klinefelters syndrome…
What type of errors are fixed by mismatch repair
replication errors caused by random mismatched nucleotides or microsatellites
What is the most common trisomy? what are other types (3)
Most common: Trisomy 16 (SAb) not viable, leads to loss of child. Other: Trisomy 21, 18, 13 (these are all viable)
When does condensin begin to accumulate during mitosis?
During prophase the chromosomes begin to condense
Define triploidy
3n, most common form of polyploidy, a condition in which an indiviual has 3 sets of the haploid number of chromosomes (69, XXX)
What does this mean: p. Gly796*
refers to a protein where codon 796 was changed from Gly to a stop codon.
What is the primary cause of genetic variability between individuals?
repeated elements
Cytoxan and platinum compounds are used to fight cancer, why?
Stops DNA replication preventing cancer cells from dividing
what is locus heterogenity
term used to describe the fact that mutations in different genes in the same pathway can cause the same disease
What are two ways that De Novo CNVs can arise?
homologous recombination errors, or replication errors
Dystrophin gene; role, chromosome location, size of protein
Role: protects STRIATED muscle membranes from damage, found on Xp21, 430 kDa protein
trinucleotide repeats are a type of…
microsatellites
What is a proband?
the person who is being studied on a pedigree. an arrow points to this individual on a pedigree
In what direction do ribosomes read mRNA
5’ to 3’
Minisatellite DNA: length of repeats, location?
variable number tandem repeats (VNTR) of 10-100bp, found at telomeres (ends of chromosomes)
CNVs play what role in humans?
play role in function of special senses, role in diseases such as cancer, autism, schizophrenia etc
What is the basic steps involved in performing a karyotype
cells are cultured–>colchicine is used to arrest cells in metaphase–>a hypotonic solution is added–> cells are dropped on slide and stained–>microscopic analysis
Why are histones important?
Needed for compaction of chromatin
For individuals with turner syndrome, what explains their skin folds at the base of their neck?
These individuals once suffered from cystic hygroma, a condition in which the thoracic duct could not drain and fluid accumulated in this region. Once the thoracic duct was able to drain the lymph drained, but the skin folds remained
what is FISH
a specific genetic test in which a fluorescently labeled probe is hybridized to DNA
What percent of all pregenencies and newborns are structural abnormalities seen?
0.9%
How do human populations break the rules of hardy-weinberg equilibrium? (4)
- consanguinity: inbreeding breaks concept of random mating 2. Genetic drift/founder effect: breaks rule of no migration 3. Biological fitness: those who are carrier of sickle cell (HbS) are resistant to malaria and therefore have improved fitness 4. Mutation rate: new mutations are occurin
Sanger sequencing can be used to identify which genetic alterations?
Small alterations in DNA: point mutations–>missense, splice site, nonsense, and silent mutations
what does MLPA stand for
Multiplex Ligation Probe Amplification (a technique in molecular genetics)
Triplet expansion in coding regions of mRNA tend to code for which AA?
glutamine
Define reciprocal translocaiton
an exchange of chromosomal material between two or more nonhomologous chromosomes
by what factor is a chromosome condensed due to condensin?
about 10,000x
What are SNPs
Single nucleotide polymorphisms: a change in a nucleotide that occurs in at least 1% of the population. The change does not necesarrily have to correlate with a change in phenotype
what is the role of miRNA
regulate amount of protein produced
Why do some cancer therapies inhibit ssDNA repair processes?
in some cases when dsDNA damage repair is lost (loss of BRCA1/2), if you remove a cells ability to repair ssDNA the cell will die. good to kill cancer cells
a developmental disorder caused by a deletion of genetic material from a specific region of chromosome 7, delayed speech, developmental delay, feeding issues, cocktail personality (very talkative and verbal), unique faces
williams Syndrome
What genetic alterations wont array-CHG detect?
balanced rearrangements, changes smaller than 20kb, UPD, methylations
What is a DNA enhancer
a section of DNA (distance, location and orientation independent) that increases transcription of a gene
what is a benefit of whole exome sequencing?
can be used to look at a number of related genes at the same time
Role of BRCA1/2 gene (dsDNA repair). initiated by (2)?
repair dsDNA breaks, initiated by FANC genes and ATM gene
What is the difference between SNPs and mutations?
SNPs are common in population and mutations are rare genetic events
What are the two type of chromatin
Euchromatin and Heterochromatin
Sanger sequencing is not effective in testing for…(2)
larger alterations, only looks at exons
Define cytogenic
inheritance in relation to structure and function of chromosomes
Name this chromosomal abnormality: clinical features include skin folds at base of neck, early loss of ovarian function, low hairline at base of neck, swelling of hands of feet (lymphedema), normal intelligence
Turner Syndrome
How do microsatellites disrupt replication/transcription machinery?
replication slippage, transcription machinery loses track, which can lead to insertions or deletions of repeat units
Describe G-banding of chromosomes
Trypsin is used to to partially digest histones, this relaxes the nucleosome coils, and a stain can bind naked DNA
What is the relevance of individuality in medicine (3)?
differences in disease susceptibility, response to therapeutics, and toxicity from therapeutics
What well known disease is caused by triplet expansion in a coding region of DNA?
Huntington’s Disease (polyglutamine expansion)
what is the role of tandem repeats in unequal crossing over?
crossing over sites are generally areas of tandemly repeated DNA. if the homologous chromosomes do not match up properly, due to tandem repeats, unequal crossing over can occur
Contrast a normal chromosome to a huntington’s chromosome
Normal: 10-30 CAG (Glutamine) repeats Huntington’s: triplet repeat expansion 36-121 CAG repeats
How are chromatids joined? what is the molecule?
Cohesin
What is the fate of a ER membrane protein
Destined to resid in the plasma membrane or in the membrane of an organelle (Golgi, endosome, lysosome, ER)
If type 2 OI is lethal, why doesn’t isnt the allele gone/phased out?
Germline mosaicism
What are copy number variations? what type of genetic alterations do they include?
CNV: variation in the number of copies of one or more sections of DNA. Includes deletions or duplications of genetic material
Why do triplet repeat expansion diseases exhibit anticipation?
triplet repeats tend to expand (replication errors), and it has been found that in some repeats the expansion leads to worsening disorders with unstable chromosomes
How common is turner syndrome?
1/2,500 briths
individuals with Xerederma pigmentosum are unable to perform what type of DNA repair?
NER
Role of ATM gene (dsDNA damage)
signals repair process
Define sister chromatids
DNA strands after replication but still joined
During meiosis II, where is cohesin found?
only between centromeres of sister chromatids
define sibship
group of offspring having same 2 parents
69, XXX is an example of…
triploidy
What is chromatin?
DNA/protein complex that makes up chromosomes
What is a specific disorder that array-CGH can identify?
Williams syndrome (a deletion in a region of chromosome 7)
Who is typically affected by X-linked disorders?
males
What is this?
Chromatin supercoiling around condensin
Name this chromosomal abnormality: 47, XY, +18
Trisomy 18 in a male
What is the fucntion of mitochondrial protein translocators?
unwind and thread proteins destined for the mitochondrial past outer and inner mitochondrial membrane
how does achondroplasia arise?
80-90% de novo mutations that are exclusively in paternal germline.
How can TFs exhibit dominant negative mutations?
if a mutation occurs where the DNA binding domain remains, but the activation/functional domain is removed
What is a copy # array-CGH
a comparative technique in molecular genetics where labeled patient DNA and control DNA compete to hybridize to a microarray slide.
on a pedigree, what does a square with the number 2 outside generally refer to?
refers to the age of the individual, in this case a 2 yr old male
How do numerical chromosomal abnormalities arise (2)?
errors in meiotic separation at metaphase, errors in fertilization
Deamination generally occurs in which n-base? what is the result
deamination of cytosine forms uracil
When is cohesin employed to hold chromatids together?
from S phase until metaphase/anaphase
Define metacentric
chromosome in which the centromere is roughly in the middle
What is the difference between ER and free ribosomes?
nothing, they are identical, their location depends on the mRNA they are translating
Mosaicism involves mitosis, meiosis, or both?
Mitosis
what is a trans-acting factor
protein factor that binds to the cis-acting factor (TFs)
Name this chromosomal abnormality: clinical features include abnormal ears that are rotated posteriorly, relatively large head with small features, unusual position of fingers with overlapping 2nd and 5th digits, only 5-10% will live past their first year of life
Trisomy 18
What are gain of function mutations? normal inheritance patter?
mutations that result in a unregulated function in the same pathway or a novel function in a different pathway. usually dominant inheritance.
Contrast chimericism and mosaicism
Chimericism: results when two eggs are fertilized by two different sperm and then the zygotes fuse. The person will have equal amounts of two different DNA sets Mosaicism: a normal zygote is formed (1 sperm, 1 egg) but a mutation arises somewhere along the road which results in cells having different DNA
Define: Heteroplasmy
A mitochondrial form of mosaicism where mitochondria within the same cell have different DNA
What is the clinical presentation of duchennes muscular dystrophy?
delayed motor development, weakness in striated muscles (skeletal, cardiac), pseudohypertrophy of the calf
What is role of the signal recognition particle (in regards to the ER membrane)
a SRP recognizes the ER signal sequence of newly translated proteins and directs ribosome to SRP receptor on the membrane of the ER. A protein translocator then threads the protein into ER lumen
Describe Euchromatin: what percent of genome? Packing? Transcription?
92% of genome, lightly packed, often under active transcription
What is the most common type of variation in the human genome? What percent of variation in gene expression is this responsible for?
SNPs (responsible for 83% of of variation in gene expression among individuals)
Define Consanguinity, how is it denoted on a pedigree
“with blood”, when a couple is related, denoted by two horizontal lines joining a couple in a pedigree
What are two type of exogenous DNA damage?
UV radiation, alkylating agents
Define anticipation
occurence of a genetic disease at an earlier age of onset or with an increasing severity in successive generations
A signal sequence with many hydrophobic residues is destined for…
import into the ER (Leu, Val, Gly, Ile, Phe)
how do structural chromosome abnormalities occur?
errors in crossing over
main function of peroxisomes
oxidation of toxic materials
What genetic alterations will cytogenic testing (karyotyping) identify (6)? Which will they not (3)?
Will: Anueploidy, translocations, inversions, deletions, duplications, mosaicisms Wont: methylation, uniparental disomy, any change smaller than 5Mb
what is “de novo”
new
A signal sequence with many positively charged residues is destined for the…
import into the nucleus (Lys, Arg)
what is a DNA promoter
a section of DNA that is located immediately upstream of transcription start site and acts as a switch that turns on/off transcription
Achondroplasia would best be diagnosed using which technique in molecular genetics?
Sangar sequencing (arises due to a point mutation)
What affect on meiosis can chromosomal structural abnormalities have?
can affect pairing (metaphase I) during meiosis depending on how big a piece is missing, added or inverted
What does this mean: p.Glu6Val
refers to a protein structure variant. glutamic acid of codon 6 was changed to valine
In what instances (2) will a female be affected by an X-linked disease?
- X-autosome translocation: this autosome will no longer be randomly inactivated because the autosome must be expressed 2. a case of 90:10 X-inactivation which is rare but possible.
What is a dominant negative mutation (LOF)? Ex?
heterozygous alleles, mutant allele produces a protein product that loses own function and interferes with the product of the normal allele. Ex: osteogenesis imperfect (type II)
Describe dizygotic twins, how do they appear on a pedigree?
fraternal twins, can have same sex or different sex, appear on a pedigree as a single branch without a horizontal line connecting them
what is a holoprotein
a protein with an attached prosthetic group
what is a prosthetic group. What prosthetic group does Hb and Mb contain?
something that attaches to a protein and is NOT a protein (heme)
Contrast hemoglobin and myoglobin. Composition? Funtion
Mb: a monomer, storage of oxygen (especially in skeletal muscle) Hb: a tetramer. transport of oxygen
What is the funciton of heme?
to reversibly bind oxygen
What is the composition of heme?
contains a porphyrin ring (with 4 nitrogen atoms) that bind an Fe2+ atom
Describe the proximal histidine of Mb and Hb
the proximal his of Mb and Hb subunits is sterically repelled by the porphyrin ring of heme. The iron center of heme binds to the proximal histidine and as a result the Fe is pulled above the plane of the ring. When oxygen binds Fe the iron is pulled back into place causing movement in the helix that contains the proximal His
How is CO naturally made in our bodies?
as a byproduct of heme biosynthesis.
Why is CO bad?
CO binds 300 fold more tightly to Mb or Hb than oxygen does
What is the normal amount of Hb bound to CO in our bodies?
~1.5%
What is our bodies defense against CO poisoning?
ligands that bind heme of Hb and Mb are forced to bind in a bent fashion. This is normal for O2 but not for CO
How many hemes are in Mb
one
How is the proximal His denoted (2 ways)
HIs 87 or His F8
What protein subunits comprise Hb?
A tetramer made of 2 alpha subunits and 2 beta subunits. known as a dimer of dimers (alpha-beta and alpha-beta)
What is the Kd of Hb? what does this mean?
3 mmHg. this is the concentration of oxygen to give half saturation of Mb. Kd=[Mb][O2]/[MbO2]
What are the two confirmational states of Hb? what are their oxygen affinities?
T state: low oxygen affinity R state: high oxygen affinity
Deoxy Hb prefers which state?
T state (low oxygen affinity)
Oxy Hb prefers which state?
R state (high oxygen affinity)
How many molecules of oxygen will Hb bind?
4
what is the likelihood of Hb being in the T state when no oxygen are bound?
10,000X more likely to be in T than R
What is the likelihood of Hb being in the T state when 1 oxygen is bound?
100X more likely to be in T than R
what is the likelihood of Hb being in the T state when 2 oxygens are bound?
50% will be in T and 50% will be in R
what is the likelihood of Hb being in the R state when 3 oxygens are bound?
100X more likely to be in R than T
what is the likelihood of Hb being in the R state when 4 oxygens are bound?
10,000X more likely to be in R than T
What is the basis for the confirmational changes seen in Hb when oxygen binds?
When oxygen binds to a iron atom of heme it moves back into the plane of the porphyrin ring and pulls the proximal histidine with it. this movement translates quaternary confirmational changes between subunits that chang oxygen affinity.
during confirmational changes of Hb, what subunits move/change interactions?
alpha1-beta1 and alpha2-beta2 subunits/dimers DO NOT move (interactions are too strong). a1a2, a1b2,a2b1 subunits do move/change interaction/change conformation. b1b2 interactions are too weak to change structure.
order the strengths of subunit interactions seen in Hb
a1b1=a2b2>a1a2>a1b2=a2b1>b1b2
What interactions stabilize the a1b2 interface of the T state (Hb)
His beta 146 and Lys alpha 40
what interaction stabilizes the a1a2 interface of the T state (Hb)?
HIs alpha 122 and Asp alpha 126
how does the Hb tetramer change as a whole from the T state to the R state
a 15 degree rotation of the ab dimers occurs from the T state to the R state with alpha subunits moving further apart and the B subunits moving closer together
What is an allosteic inhibitor?
binds a site other than the active site
Allosteric inhibitors of Hb stabilize which state?
T-state (decrease Hb affinity for oxygen, more oxygen is unloaded)
What affect does a decrease in pH have on Hb binding of oxygen
favors the T (deoxy) state, more oxygen is unloaded
what affect does a increase in 2,3-BPG have on Hb binding of oxygen
an increase in BPG (as seen with an increase in altitude) favors the T (deoxy) state and more oxygen is unloaded
what are three allosteric effectors of Hb?
pH, 2,3-BPG, CO2
what affect does a increase in pCO2 have on Hb binding of oxygen
an increase in CO2 favors the T (deoxy) state whcih causes more oxygen o be unloaded
What is the Bohr effect
the effect of pH on the oxygen affinity of Hb
What explains the acid bohr effect?
the T (deoxy) state has a greater affinity for protons than the R state (certain AA residues mainly His have greater affinities for H due to specific interactions present in the T state)
in addition to O2, Hb also transports what?
proton and CO2
Hb is in what state in the lungs? tissues?
Lungs: R (oxy) state Tissues: T (deoxy) state
Where does 2,3-BPG come from
derived from 1,3-BPG one of the few metabolic pathways (glycolysis) remaining in a mature erythrocyte
what is an erythrocyte
mature RBC
What is the shorterm physiological adjustment to high altitudes?
substantial increase in intra-erythrocyte concentration of BPG
where does BPG bind Hb?
in a cleft between two beta subunits that has an abundance of positive charges to neutralize the negative BPG
why is is problematic that stored blood decreases in BPG concentration?
as BPG drops, Hb holds onto its oxygens more tightly, this wont help patients who need RBCs to deliver oxygen
what is the function of inosine
inosine is used to replenish BPG in stored blood becuase it can be taken up by RBCs (BPG cant pass the membrane), and converted to BPG
How does Hb transport CO2? does this favor T or R state
the N-termini of both alpha and beta subunits are carbamoylated (essentially a carboxylic acid is added to N-termini), this stabillizes the T state over the R state
what percent of CO2 is transported by Hb?
20%
alpha2 beta2 is what type of Hb? seen in?
HbA. see in adults (normal Hb)
HbA2 is seen in?
this is a minor adult form of Hb
HbF is seen in? Role?
this is fetal Hb. has i higher affinifty for Oxygen and ensures the fetus is supplied oxygen (alpha2 gamma2)
what chromosome are alpha-globin sequences found?
chromosome 16
what chromosome are beta-globin sequences found?
chromosome 11
myoglobin folding most closely resembles the folding of which subunit of Hb?
beta
what is an alpha thalassemia?
a lack of the alpha subunit of Hb which decreases total Hb
what is a beta thalassemia?
a lack of the beta subunit of Hb which decreases total Hb
describe thalassemia in heterozygous individuals?
the affected subunit (alpha or beta) is present in significantly lower levels than normal (>50%,
how do we compensate for thalassemias?
our bodies will express fetal or embryonic subunits in an upregulated form to help compensate
how many copies of the alpha-globin gene do we have? What type of mutation alter these?
4 copies, 2 copies on each chromosome 16. Deletions!
If 1 out of the 4 alpha globin copies is muated, what are the effects
silent carrier, asymptomatic
if 2 of the 4 alpha globin gene copies is mutated, what are the effects?
alpha-thalassemia trait; reduced mean cell volume, mild anemia
if 3 of the 4 alpha-globin gene copies is mutated, what are the effects?
Hemoglobin H disease; detectable levels of Beta tetramers (dont work well), moderate anemia, not lethal
if all copies of the alpha-globin gene are mutated, what are the effects?
Hemoglobin barts; no oxygen carrying capacity; neonatal (newborn) death (gamma chain tetramers that done function)
Beta thalassemia: how many mutations lead to it. Types of mutations?
-over 100 different mutations. promoter mutations, splice site mutatoins, missense mutations (result in a decrease in beta subunits, of varying degrees)
What is clinical heterogeneiy
a disease with varying degrees of severity
what are some symptoms of major beta-thalassemia?
Cooley’s Anemia: transfusion-dependent, infants are pale and listless (unenergetic), enarged spleen, liver and hear, deformed bones
Heinz body hemolytic anemias: cause of disease, effect
caused by severeal different point mutations that do not alter beta subunit number but make the subunit unstable. and degrade Hb
what casues sickle cell anemia (HbSS)
a single point mutation (on chromosome 11) that causes an amino acid change from glutamate (charged) to valine (nonpolar) at position 6 of the beta subunit
Hemoglobin C: what is it casued by. what are the effects?
a change in the same amino acid that causes sickle cell but this time it is a Glu6Lys (negative charged AA to positive charged AA). Results in premature lysis of RBCs
HbSC, HbSS, HbCC
HbSC; one allele has C mutation, the other allele has S mutation; often milder than HbSS HbSS: traditional sickle cell, both alleles have S mutation HbCC: both alleles have C mutaion, mild anemia due to moderate reduction in red blood cell lifespan
Describe glycosylation of Hb
glucose in blood can bind to exposed amino groups and form glycosylated proteins. This can be used as a diagnostic for diabetes (HbA1c) and does not impact function of Hb
What is the role of dystrophin?
a protein that connects the cytoskeleton of muscle fibers to the extracellular matrix
