Unit 2 Flashcards
What joins the ends of DNA together in cloning?
T4 DNA ligase
What gel is used to separate small and large bases of DNA?
Agarose - large
Acrylamide - small
What is the order of vector size?
Plasmids, bacteriophage lambda, cosmoids, BACs, YACs
What is a cosmoid?
It’s a bacteriophage that takes out every gene besides DNA replication and packaging so we can fit out own DNA into it. The other essential genes we have the bacteria producing.
What is one major disadvantage of YACs?
Yeast cells undergo a lot of homologous recombination.
What is multi-plex PCR?
Using a sample and a bunch if different primers to amplify more than one gene of interest; need to know how to separate them though (usually by size)
What is the purpose of microarrays?
To view the expression level of a cell and what genes are being expressed.
What is the mutation that causes fragile X?
CGG repeats in the first exon (FMR1) of the FRAXA gene
Can pre-mutation carrier males for fragile X give the full mutation to his children?
No, sperm carrying full mutation is selected against.
What are the gender specific risks for pre-mutation fragile X carriers?
Male - developing ataxia later in life
Female - developing premature ovarian failure
What method is used to detect fragile X pre-mutation genome?
Southern Blot - uses EcoR1 and Eag1 which will only cut unmethylated DNA.
PCR cannot replicate the CGG repeats.
What is Thalassemia?
Alpha or beta globin genes aren’t being produced. Homotetramers are formed by the other leading to inclusion bodies and red blood cell death.
What is the order of produced hemoglobin in development?
Epsilon/zeta, gamma, beta. Alpha produced constantly
What causes sickle cell disease?
A point mutation that switches GAG(G) to GTG(G) or AAG(G).
What restriction site does sickle cell get rid of?
Mnl1
What causes many cases of alpha thalassemia?
Unequal crossover between regions of homology
What is Hb Constant Spring?
UAA to CAA in stop codon that results in 31+ amino acids extra. Unstable alpha globin. Beta globin homotetramers form.
Cystic fibrosis is a defect in what?
A chloride channel
What is the time span of embryogenesis?
From fertilization to 8 weeks
What’s the difference between Carnegie stages and postovulatory age?
Carnegie is described based on physical appearance while postovulatory age is based on time since last ovulation.
What is the morula?
A 16 cell embryo, is compact and forms 3 days after fertilization
What is the zona pellucida?
Extra membrane of an egg cell that persists until the blastocyst gets to the uterine wall
What are trophoblasts?
The edge cells in a blastocyst
What do the inner mast cells differentiate into?
Epiblast - will become the embryo
Hypoblast - will become supportive tissue
What is the process of gastrulation?
Forming an endo, meso and ecto derm from the epiblast
What are contiguous gene syndromes?
They’re syndromes that relate phenotypic abnormalities due to unrelated genes being deleted together
What is spina bifida?
Failure to close the neural tube
What is Williams syndrome?
Deletion if a section of a chromosome that includes the elastin gene as well as other things. Low IQ, excellent music skills, ect.
What is velocardiofacial syndrome?
2nd most common syndrome, cleft palate and conotruncal heart defects characteristics. Small deletion (micro deletion)
What is a homologous gene?
A gene that is similar in structure and evolutionary origin to a gene in another species
What is genome equivalence? How does it relate to differential gene expression?
Every somatic cell has the same genes. However, their expression levels are different depending on the cell
What is the induction system?
Cells release factors that when they reach competent cells, or responders, they react accordingly.
What is pax6?
A competence factor in eye development. Heterozygous loss of pax6 results in aniridia.
What are morphogens?
Concentration dependent signaling molecule.
What is an example of a signaling pathway?
Growth factor beta and hedgehog
What is heterotaxy?
Also called situs ambiguus, when half of the organs are correct symmetry and the rest is inverted, can cause vascular problems
What is Kartsgener’s syndrome and what is it’s significance?
Bronchiectasis, infertility and 50% situs inversus. Showed that cilia beating controlled left-right orientation.
What are the common diseases of the mitochondria?
Neuropathies, encephalopathies and myopathies
How many mitochondria must be mutated in a cell for it to show a mutated phenotype?
85%
Can Eco R I cut methylated DNA?
Yes, Eag I cannot
What is the MOI for fragile X?
X-linked Dominant with 80% male penetrance and 30% female penetrance
What determines the probability of expansion in fragile X syndrome?
The number of CGG repeats and whether they are interrupted by an AGG
Hydrops Fatalis is what?
A type of Thalessemia where both alpha hemoglobin genes on both chromosomes are deleted, it’s abbreviated (–/–)
What is alpha Thal Train?
There are two types Thal 1 where one chromosome has both alpha gene deletions, and Thal 2 where each chromosome has 1 alpha gene deletion.
What is organ primordia?
organs in their earliest recognizable form of development
What is the postovulatory age?
It’s the time since last ovulation (right before pregnancy) and is used to determine the developmental stage of the fetus
What are embryonic cells called during cleavage?
Blastomeres
What is Axenfeld-Rieger syndrome?
Primarily and eye disorder but has other defects. Inherited via autosomal dominant.
What is holoprosencephaly?
Caused by a multifactorial way. Most commonly a malformation of the forebrain. Can be caused by maternal diabetes, trisomy 13, 18.
What mutated genes have been associated with holoprosencephaly?
Hedgehog signaling pathways
What is thalidomide and what was the problem with it?
It was a drug used to help morning sickness but ended up causing phocomelia (shortness of limbs)
What is the most sensitive period for inducing birth defects?
Weeks 3-8 during embryogenesis
What is a septal defect?
A hole in the heart
What is truncus arteriosus and what is it associated with?
The outflow tract fails to separate and there is only one valve out of the heart. It is a common symptom in 22q11.2 deletion syndrome.
What is Teralogy of Fallot?
Four heart defects: Ventricular septal defect Pulmonary stenosis Overriding aorta Ventricular hypertrophy
What is nuchal translucency?
During ultrasound, there is a layer of fluid between skin and muscle. Thicker layers are characteristic of Down syndrome.
What is cfpDNA?
Cell free placental DNA, exists in the mothers blood, can be collected and sequenced. Screening test
What is amniocentesis?
Taking placenta with a needle through the abdomen to test for genetic defects. Usually done after 13-14 weeks.
What does elevated levels of AFP indicate?
Alphafetoprotein elevation indicates neural tube defects
What is the acetylcholinesterase test?
If AChE is abnormal it will confirm NTD
What is chorionic villus sampling?
CVS is done between 10-12 weeks (earlier can cause limb defects) and takes chorionic cells to test. No AFP test can be done
What is the pKa of D and E?
4
What is the pKa of H?
6.5
What is the pKa of C?
8.5
What is the pKa of K?
10
What is the pKa of R?
12
What is the pKa of the amino and carboxy end?
8 and 4
What are the two mutations of p53 and what do they affect?
The DNA contact site which affects it’s activity and the beta sandwich site which affects it’s stability
What are two methods to treat mutated p53?
Replace the missing side chain with an inorganic molecule to make the protein stable and to stop the degradation of p53 in the hopes some won’t be mutated and help the cell deal with the problem
What causes cystic fibrosis?
The delta 508 mutation makes it really difficult to fold so there is a small amount of protein that is actually present
What is the proposed mechanism of IAPP and what is odd about it?
They interact with the B cell membranes and form pores that open them and kill them. Mature fibers actually protect by taking the soluble aggregates out of the membrane
What are the different cancer types and where are they found?
Sarcoma - bone, cartilage, fat, muscle
Carcinoma - epitheloid tissues
Leukemia - bone marrow
Lymphoma - lymph nodes and spleen
What is CML?
Chronic myelogenous leukemia. Translocation of 9;22 and involves a kinase that is put under a new promoter so it is always active. Treated with gleevec
What is APL?
Acute promyelocytic leukemia. Translocation of 15;17. Uses FISH to detect and diagnose
What is knudson’s two hit hypothesis?
There needs to be two mutations in a cell to cause retinoblastoma. Sporadic is usually unilateral while inherited is usually bilateral
What is Li Fraumeni?
An inherited mutation of p53 which makes you susceptible for many types of cancer
What are breakage syndromes?
Chromosome instability (breakages or forks) and defects in DNA repair genes. Fragile X is NOT in this classification.
What is Hereditary Nonpolyposis Colon Cancer?
2-4% hereditary colon cancer but results in 90% lifetime risk of males who inherit a mutation and 70% of females. Mutation of mismatch repair genes
What way can you detect DNA repair defects?
Microsatellite fingerprinting. If there is a DNA repair defect, the amount of replications can be different and noted on a gel
How can figuring out the cause of cancer help?
It can help determine which treatment will be the most effective.
What does modular mean?
That two domains act independently
What is the wobble hypothesis?
The third base of an anticodon doesn’t need to fulfill base pairing specificity
What is the Shine-Dalgarno sequence?
A sequence upstream of the start codon that binds the ribosome
In X linked recessive cases, what is special about the number of affected males?
They are q
