Cell Quiz Review - Dr Magranndrmagrann.com/MLT/ChemPPT Flashcards Unit 5.docx · Web viewChem PPT Flashcards, Unit 5 31 Reproductive hormones of hypothalamic-pituitary-gonadal axis

Chem PPT Flashcards, Unit 5

Reproductive hormones of hypothalamic-pituitary-gonadal axis are:

Gonadotropin-releasing hormone (GnRH),Luteinizing hormone (LH),Follicle-stimulating hormone (FSH),Sex steroids synthesized by: Ovaries, Testes,Adrenal glands

The function of the testes is to: synthesize the sperm and androgens.Sertoli cells are found in the: seminiferous tubules of the testesSertoli cells have a crucial role in sperm maturation and secretion of ___ which is:

inhibin, a glycoprotein that inhibits the pituitary secretion of FSH.

The principal androgen in the human male is ___ which is required for sexual differentiation, spermatogenesis and promotion and maintenance of sexual maturity at puberty

testosterone

GnRH is synthesized in the ___ and is transported to the anterior pituitary gland, where it stimulates the release of both ___ and ___.

Hypothalamus, LH and FSH

In adult men, GnRH, LH and FSH are secreted in pulsatile patterns with higher concentrations found in the ___ and lower concentrations in ___.

Early morningLate evening

LH acts are Leydig cells to stimulate the conversion of ___ to ___.

cholesterol to pregnenolone

FSH acts on ___ and ___ and is central to the initiation (in puberty) and maintenance (in adulthood) of the spermatogenesis.

Sertoli cells and spermatocytes

Sex steroids and inhibin provide ___ feedback control of LH and FSH secretion, respectively.

negative

LH secretion is inhibited by ___ and by its metabolites, estradiol (E2) and dihydrotestosterone (DHT).

testosterone

What are androgens also known as? Androgenic hormone or testoidWhat are androgens? Any any natural or synthetic compound, usually

a steroid hormone, that stimulates or controls the development and maintenance of male characteristics

Androgens also control or stimulate the activity of the accessory male sex organs and development of male secondary sex characteristics.

True

What are the original anabolic steroids and the precursor of all estrogens?

Androgens

What are some types of androgens? TestosteroneDihydrotestosteroneAndrostenedioneDehydroepiandrosterone

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AndrostenediolAndrosterone

What is DHT? DihydrotestosteroneWhat is DHEA? DehydroepiandrosteroneWhat is the principal androgenic steroid hormone?

Testosterone

Where is testosterone produced? In the Leydig cells of the testes in response to stimulation by LH of the anterior pituitary gland

To a lesser extent, testosterone is also produced by the ovaries in females.

true

Small amounts of testosterone are also secreted by the ________ glands.

Adrenal

What is the principal male sex hormone and an anabolic steroid?

Testosterone

Why is testosterone important in male development?

It plays a key role in the development of male reproductive tissues, such as the testis and prostate.It promotes secondary sexual characteristics, such as increased muscle, bone mass, and the growth of body hair.

Testosterone is essential for health and well-being as well as the prevention of osteoporosis.

True

On average, in adult males, testosterone levels are about __ to __ times greater than in adult females.

7 to 8

Daily production of testosterone is about ___ times higher than females because of higher metabolic consumption.

20

Which androgen is a metabolite of testosterone, and a more potent androgen than testosterone in that it binds more strongly to androgen receptors?

Dihydrotestosterone

DHT is the essential androgen responsible for formation of primary sex characteristics in males during embryogenesis, for development of most male secondary sex characters at puberty, and for adult male sexual function.

True

Where is DHT produced? In the skin and and reproductive tissue.What does DHT contribute to later in life? Male balding, prostate growth, and sebaceous

gland activityWhat is androstenedione? An androgenic steroid produced by the testes,

adrenal cortex, and ovaries.Androstenedione is the parent structure of _____, they are converted metabolically to testosterone and other androgens.

Estrone

The use of androstenedione as an athletic or True

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bodybuilding supplement is banned by the International Olympic Committee, as well as other sporting organizations.Where is the steroid hormone DHEA produced? In the adrenal cortex from cholesterolDHEA is the primary precursor of ______ _______.

Natural estrogen

What is DHEA also called? Dehydroisoansdrosterone or dehydroandrosterone

What is the steroid metabolite thought to act as the main regulator of gonadotropin secretion?

Androstenediol

What is a chemical byproduct created during the breakdown of androgens, or derived from progesterone, that also exerts minor masculinising effects, but with one-seventh the intensity of testosterone?

Androsterone

What are the male reproductive abnormalities? Hypogonadotropic hypogonadismHypergonadotropic hypogonadismDefects in androgen actionErectile dysfunctionGynecomastia

What occurs when defects in the hypothalamus or pituitary prevent normal gonodal stimulation and isassociated with decreased testosterone and gonadotropin concentrations?

Hypogonadotropic hypogonadism

Factors include for hypogonadotropic hypogonadism

congenital or acquired panhypopituitarismhypothalamic syndromesGnRH deficiencyhyperproteinemiamalnutrition or anorexiaiatrogenic causes

What is the most common form of hypogonadotropic hypogonadism?

Kallmann syndrome

What is Kallmann syndrome? -Results from a deficiency of GnRH in the hypothalamus during embryonic development.-It is characterized by hypogonadism and anosmia (loss of sense of smell) in male or female patients.-It is a congenital defect with several genetic causes that result in gonadotropic deficiency

What is a primary gonodal disorder (primary testicular failure) characterized by increased concentrations of LH and FSH and decreased concentrations of testosterone?

Hypergonadotropic hypogonadism

Causes of Hypergonadotropic hypogonadism: -acquired causes (irrigation, castration, mumps orchitis, or cytotoxic drugs)

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-chromosome defects such as Klinefelter syndrome-defective androgen synthesis (20α-hydroxylase deficiency)-testicular agenesis; seminiferous tubular disease-aging is associated with gonadal failure causing decreased testosterone secretion

Which disorder arises from mutations in the androgen receptor (AR) gene?

Androgen Insensitivity Syndrome (AIS)

Testicular feminization is an old term for what syndrome?

Androgen Insensitivity Syndrome (AIS)

Androgen Insensitivity Syndrome (AIS) individuals with a male karyotype (46, XY) with female external genitalia and intra-abdominal testes.

True or FalsePatients with Androgen Insensitivity Syndrome (AIS) have circulating testosterone less than or equal to that of a healthy male.

False

Greater than or equal to

True or FalsePatients with Androgen Insensitivity Syndrome have LH concentrations that are typically increased.

True

A male medical issue previously called impotence is now referred to as?

Erectile Dysfunction

Erectile Dysfunction is defined as? the persistent inability to develop or maintain a penile erection that is sufficient for intercourse and ejaculation in 50% or more of attempts

Some causes of Erectile Dysfunction include: vascular disease diabetes mellitushypertension uremianeurologic disease hypogonadism, hyperthyroidism hypothyroidismneoplasms drugs

A benign growth of glandular breast tissue in men is referred to as?

Gynecomastia

Gynecomastia is associated with an increase or decrease of what hormone ratio?

Associated with an increase in the estrogen/androgen ratio

Why is transient gynecomastia is found in 60% to 90% of all newborns?

because of high estrogen concentrations that cross the placenta

When does the second peak of gynecomastia occur in the male? Why?

second peak occurs during puberty in 50% to 70% of healthy boys which may be due to low serum testosterone, low DHT, or high estrogen/androgen ratio

The last peak of gynecomastia occurs in what population and why?

last peak is found in the adult population most frequently among men aged 50 to 80 years, which may be due to testicular failure or

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increase body fat resulting in increased peripheral aromatization of testosterone to estradiol (E2).

What is the function of the ovaries? To produce ova and secrete the sex hormones progesterone and estrogen

What is the primary female sex hormone and is responsible for development and regulation of the female reproductive system and secondary sex characteristics?

Estrogen

What do estrogen and progesterone participate in the regulation of?

1) Menstrual cycle2) Breast and uterine growth

Maintenance of pregnancyWhat else does estrogen have an effect on? Calcium homeostasis and is therefore beneficial

to bone massWhich plasma proteins concentrations are increased by estrogen?

1) SHBG2) Corticosteroid binding globulin

Thyroxine binding globulinWhich estrogen is the primary form of estrogen in the body during menopause?

Estrone (E1)

Which estrogen is the predominant estrogen during reproductive years both in terms of absolute serum levels as wel as in terms of estrogenic activity?

Estradiol (E2)

Estradiol (E2) is the strongest with a potency of approximately how many times that of estriol?

80 times

What is the most important estrogen in non-pregnant females who are between the menarche and menopause stages of life?

Estradiol (E2)

What is the predominant circulating estrogen in terms of serum levels during pregnancy?

Estriol (E3)

What is the most abundant of all estrogens but also the weakest?

Estriol (E3)

What estrogen is produced only during pregnancy?

Estetrol (E4)

Where are estrogens primarily secreted? 1) Ovarian follicles2) Corpus luteum

Placenta (during pregnancy)Where are minute quantities of estrogens secreted?

1) Adrenal glandsTestes (In men)

What hormones are produced by healthy human ovaries?

1) Estrogens2) Progestogens

AndrogensWhat is the main source of estrogens in pregnant women?

Placenta

What is the main source of estrogens in non-pregnant women?

Ovaries

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What is the major estrogen secreted by the ovaries?

E2

What is the major product secreted by the placenta?

E3

What is E3 formed from in the placenta? Plasma dehydroepiandrosterone sulfate (DHEAS)

What is the predominant hormone during late pregnancy?

E3

What hormone is an endogenous steroid and progestogen sex hormone involved in the menstrual cycle, pregnancy and embryogenesis?

Progesterone (P4)

What is the major progestogen in the body? ProgesteroneWhat is progesterone a metabolic intermediate in the production of?

Other endogenous steroid including sex hormones and corticosteroids

Progesterone plays an important role in the function of what part of the body?

The brain, functioning as a neurosteroid

Progesterone is important in what part of pregnancy?

Preparing the uterus for implantation of the blastocyst and in maintaining pregnancy

In non-pregnant women, from where is progesterone mainly secreted?

Corpus luteum

During pregnancy, what becomes the major source of progesterone?

Placenta

What are minor sources of progesterone? 1) Adrenal cortexTestes (in men)

The median age of menarche in the united states is ___?

12.43 years

Adrenarche precedes puberty by a __(few years/few months)?

few years

During the normal menstrual cycle, a closely coordinated interplay of feedback occurs. What 3 organs and/or glands play a role for theses effects to occur.

hypothalamus, anterior pituitary glandand the ovaries

What hormone changes lead to functional and structural changes in the ovaries, uterus, cervix and vagina?

Cyclic hormone

A menstrual cycle consists of what 3 phases? follicular phase, ovulationand luteal phase

What are the 5 major hormones that influence the control and effects of the normal menstrual cycle?

GnRH, FSH, LH, Estradioland Progesterone

This is an individual who is genetically female but whose phenotype characteristics are to varying degrees, male.

female pseudohermaphroditism

The most common cause of congenital adrenal hyperplasia (CAH) is the deficiency of what?

21-hydroxylase

Maternal androgen excess due to maternal female pseudohermaphroditism

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ovarian tumor or drug intake also causes what type of female reproductive abnormalities with masculinized external genitalia.3 Causes in concerning deficiencies of enzyme activities for female pseudohermaphroditism are 3ß Hydroxysteroid dehydrogenase - Type 2, 11ß-Hydroxylase - type 1 and what other enzyme?

21 - Hydroxylase

The onset of puberty at an abnormal early age younger than 8 years old for boys and younger than 9 years old for female is called?

Precocious puberty

What is the link between breast cancer and the effect of estrogen?

Patients who have had surgical removal of an ovary have been given estrogen as treatment, which is a linked cause to breast cancer

Who else is at risk for breast cancer? Treatment for men with estrogen for prostatic cancer, and those going through transsexual operations have an increased risk of breast cancer

What is defined as women who have never menstruated?

Primary amenorrhea

Define secondary amenorrhea Women whom menstruation is present for a variable time and then stops

What is oligomenorrhea? Very light menstrationName 2 other female reproductive abnormalities that have not yet been mentioned

Progesterone challenge for evaluating amenorrhea, and androgen excess

Define Hirsutism Excessive hairiness of women in parts of the body where hair does not normally occur (or is minimal)

Give an example of an area where Hirsutism might occur?

Chin or Chest

What is defined as the development of male physical characteristics in females (or precociously in a boy) as a result of too much androgen production

Virilization

Give some examples of such male physical characteristics in females in Virilization

Muscle bulk, body hair, and a deep voice

What three things evaluate male infertility? Semen, obstruction, endocrine parametersEvaluation of semen includes what? Semen analysis measures ejaculate volume, pH,

sperm count, motility, forward progression, and morphology

What is included in Evaluation of obstruction? Testosterone produced after administration of hCG causes the seminal vesicles, epididymis, and prostate to increase the volume of ejaculate

Evaluation of endocrine parameters includes what?

Hypergonadotropic hypogonadismHypogonadotropic hypogonadism

What is evaluated in female infertility? Ovulation, endocrine parameters

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What is evaluated in ovulation? Female infertilityEvaluation of endocrine parameters? Hypergonadotropic hypogonadism

Hypogonadotropic hypogonadismWhat is Measurement of Total Testosterone in Blood?

Enzyme (nonisotopic) Immunoassays, Tandem Mass Spectrometry (MS/MS), Isotope Dilution Gas, Chromatography Mass Spectrometry (IDGC-MS)the reference method for testosterone measurementLiquid Chromatography MS/MS method

What is the method of choice? Mass SpectrometryWhy is mass spectrometry the method of choice?

the only method that can accurately and precisely quantify testosterone concentrations below 5.2 nmol/L

What is the analytical methodology? Measurement of Free and Weakly Bound Testosterone in blood

How is Measurement of Dehydroepiandrosterone and its Sulfate (DHEA and DHEA-S) obtained?

Mass spectrometryImmunoassaysDouble isotope derivative methodsCompetitive protein binding assays

How is Measurement of 17-ketosteroids in urine obtained?

Mass spectrometry, Zimmermann reaction

How is Measurement of Anabolic Steroids obtained?

Measurement of testosterone/epitestosterone ratiomeasurement of testosterone/LH ratio in urine

How measurement of Luteinizing Hormone and Follicle-Stimulating Hormone are?

These are must be able to recognize the unique β subunits of these hormones, serum or urine as specimens, two-site (double antibody) heterogenous immunoassays

What are the primary form the primary link between fetus and mother?

That are the placenta and the umbilical cord

What are the functions of placenta? It keeps the maternal and fetal circulation system separate, nourishes the fetus, eliminates fetal waste, and produces hormones vital to pregnancy

How many placental hormones are? These are:Human chorionic gonadotropin (hCG)Human placental lactogen (hPL)Placental steroidsProgesteroneestradiol (E2),estriol (E3)estrone (E1)

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What is amniotic fluid? Amniotic fluid is a clear, slightly yellowish liquid that surrounds the unborn baby (fetus) during pregnancy, which is contained in the amniotic sac.

What are functions of amniotic fluid? It provides a medium in which a fetus readily moves, cushions it against possible injury, and helps maintain a constant temperature

What are the tests needed during pregnancy?

• Laboratory testing• The following laboratory tests are

recommended as part of a preconception evaluation:

• Hematocrit• Blood type and Rh

compatibility• Erythrocyte antibody

screen• Papanicolaou smear (or

human papillomavirus [HPV] test)

• UrinalysisRubella titer

What are the tests required during pregnancy tests?

• Laboratory testing• Rapid plasma reagin

(RPR) test• Gonococcal and

chlamydia DNA tests• Cystic fibrosis carrier

status• Human

immunodeficiency virus (HIV) antibody

• Hepatitis B surface antigen (HBsAg)

• Screening for fetal neural tube defects and Down syndrome

fetal fibronectin (fFN)What are the clenical specimens for fetal health?

• Clinical specimens:• paternal saliva, serum

and blood• paternal saliva, serum,

blood and urine• amniotic fluid obtained

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by amniocentesis or from pools of fluid in the vagina after rupture of the fetal membranes

• chorionic villi• fetal blood obtained by

percutaneous umbilical blood sampling

fetal tissue obtained by biopsyWhat are the complications of pregnancy?

• Abnormal pregnancies• Ectopic pregnancy and

threatened abortion• Occurs when a

fertilized egg implants in a location other than the body of the uterus (e.g. – fallopian tube)

• Management is by laparoscopy (surgery) or medical (with intramuscular administration of methotrexate).

Early detection and proper management are the most effective means of preventing maternal morbidity and mortality.

What are the complications of pregnancy?

• Abnormal pregnancies• Preeclampsia and

eclampsia• Preeclampsia is a

pregnancy condition characterized by hypertension, proteinuria and often edema occurring late in the second trimester or early in the third trimester.

• The only cure for preeclampsia is delivery of the placenta.

If the mother develops convulsions, the condition is called eclampsia.

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What are the complications of pregnancy?

• Abnormal pregnancies• HELLP syndrome

• Hemolysis, elevated liver enzymes, and low platelet counts in association with preeclampsia

• Thrombocytopenia and disseminated intravascular coagulation are the most prominent features

• LD, ALT, AST are elevated

• Treatment is delivery• Postpartum

management of the patient may require plasmapheresis or organ transplantation

What are some symptoms of hyperemesis gravidarum?

It is characterized by nausea, vomiting, dehydration and malnutrition occurring in the first trimester

What are some symptoms of cholestasis of pregnancy?

Occurring in the third trimester manifested by diffuse pruritus and jaundice, and ALP, AST, ALT and Prothrombin time are elevated

What are some charactertistics of acute fatty liver of pregnancy?

- It is characterized by accumulation of microvesicular fat in the hepatocytes and AST, ALT, bilirubin are elevated.- Hypoglycemia, hyperuricemia and renal failure may occur.

What are some signs of non–pregnancy-related liver disease in pregnancy?

- Cholestasis during pregnancy may reflect the presence of hepatotoxicity from drugs, primary biliary cirrhosis, Dubin-Johnson syndrome or cholelithiasis.- Mothers who acquire hepatitis B late in pregnancy or who are chronic carriers are likely to transmit the disease to their babies.

What is neonatal thyroid function? - Low maternal thyroid hormones have been associated with preterm delivery, fetal death and a reduced intelligence quotient (IQ) in children.- If the mother has pre-existing Graves disease,

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her autoantibodies are able to cross the placenta and stimulate the fetal thyroid gland causing the fetus to develop hyperthyroidism.

What is hemolytic disease of the newborn? - It is a fetal hemolytic disorder caused by maternal antibodies directed against antigen on fetal erythrocytes.- Also called isoimmunization disease, Rh isoimmune disease, Rh disease, D isoimmunization and fetal erythroblastosis- Can be caused by erythrocyte surface antigens such as Rh(CcDEe), A, B, Kell, Duffy, Kidd.

How is Trophoblastic disease monitored? Serum hCG determinations are very useful for monitoring patients with trophoblastic disease, germ cell-derived neoplasm and other hCG-producing tumor.

What is neural tube defects? Serious abnormalities that occur early in embryonic development associated with failure neural tube formation leading to permanent developmental defects of the brain, spinal cord or both.

What are some other names for neural tube defects?

These defects are called anencephaly, spina bifida (the most common defect being a meningomyelocele) and encephalocele.

What deficiency is associated with neural tube defects?

Folic acid deficiency is associated with increased frequency of neural tube closure defects

How Fetal anomalies are detected? By prenatal screening include 1) neural tube defects2)Down Syndrome, and 3) trisomy 18

What is an initial screening test to identify women at high risk for having an affected fetus in Neural tube defects?

Serum AFP concentrations

How confirmation of Neural tube defect is done?

By high-resolution ultrasound, measurement of AFP, and measurement of acetylcholinesterase in amniotic fluid to determine whether the fetus had an open neural tube defect.

What is the most common serious disorder of the autosomal chromosomes?

Down syndrome (Trisomy 21)

What chromosome is affected in down syndrome?

An extra copy of chromosome 21

What are symptoms of Down syndrome? Moderate to severe mental retardation, hypotonia (low muscle tone), congenital heart defects and a flat facial profile.

What increases the incidence of down syndrome?

A woman’s risk of having a Down syndrome baby increases slowly up to age 30 and then steadily increases between ages 30 and 45 to a

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plateauWhat are Prenatal diagnostic testing for Down Syndrome?

AFP measurements are used as a screening test.Confirmed by unconjugated estriol (uE3), hCG and inhibin A (inhA)“quadruple test”

What chromosome is affected in Trisomy 18 (Edwards syndrome)?

extra copy of chromosome 18

What is the most common chromosome defect at the time of conception?

Trisomy 18 (Edwards syndrome)

What are Prenatal diagnostic testing for Trisomy 18 (Edwards syndrome)?

Screening is done by measurements of AFP, unconjugated estriol (uE3), hCG and inhibin A (inhA)

What is preterm delivery? Delivery before 37 weeks gestationWhat is the leading cause of neonatal mortality? Preterm deliveryDefine premature rupture of membranes (PROM)?

Rupture of the fetal membranes before the onset of uterine contractions

What is Respiratory distress syndrome (RDS)? Is the most common critical problem encountered in preterm newborns, caused by a deficiency of pulmonary surfactant.

Inhibin A is a good predictor of what defect? It is a predictor of Down syndrome.What other disorders does Inhibin A help to monitor?

It can also be applied for ovarian cancer monitoring, disorders of ovulation and early detection of viable pregnancy following IVF.

Where is Inhibin A produced during pregnancy? It is produced by the fetoplacental unit beginning in early pregnancy.

What are the storage requirements for Inhibin A?

It is stable in maternal serum with shipment at ambient temperature and storage at 4-8 C for 1 week.

What is alpha fetoprotein? It is a glycoprotein produced initially by the fetal yolk sac in small quantities, and then by the fetal liver in larger quantities as the yolk sac degenerates.

Early detection of alpha fetoprotein can be indicative of which disorders?

Concentrations in maternal serum and amniotic fluid are useful in detecting serious fetal anomalies like fetal open neural tube defects, fetal Down syndrome, and trisomy 18.

Why would alpha fetoprotein be tested if the patient is not pregnant?

AFP measurement in non-pregnant patients may be used for monitoring certain cancers.

By which method is alpha fetoprotein measured?

Measured in the laboratory by immunometric methods.

Which is the most common estrogen studied for Down syndrome?

Unconjugated estriol is the most specific of the estrogens for identifying a fetus with Down syndrome.

At which point in pregnancy is estriol production at its peak?

It is produced in very large amounts during the last trimester of pregnancy.

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Does the biosynthetic pathway require the fetal adrenal gland, fetal liver and placenta to be fully functioning?

Yes

How is estriol measured in the lab? Measured by non-isotopic, automated immunometric methods using serum as specimen. Rapid separation of serum from blood clot is a necessity.

What is human chorionic gonadotropin (hCG)? It is a glycoprotein heterodimer hormone, synthesized in the syncytiotrophoblast cells of the placenta, composed of two non-identical, non-covalently bound glycoprotein subunits – alpha(α) and beta (β).

Measurement of hCF assists in diagnosing which defecfs?

Measurement of hCG assists in diagnosing and dating pregnancy, identifying ectopic pregnancies and other abnormalities, managing certain neoplasms, and predicting the risk of Down syndrome and trisomy 18.

How is hCG measured in the lab? Measured by qualitative methods using urine or serum as specimens or by quantitative methods using serum as specimen

What are low concentrations of Pregnancy-Associated Plasma Protein-A associated with early in pregnancy?

Down Syndrome, a high rate of fetal loss, poor fetal growth, premature delivery, hypertension, and preeclampsia.

What does Pregnancy-Associated Plasma Protein-A play a critical role in?

Normal fetal growth

Why? Because of its function as an insulin-like growth factor binding protein (IGFBP) protease

What does fFN stand for? Fetal FibronectinWhat is fFN? Protein found on cell surfaces and in plasma

and amniotic fluid.What are elevated levels of fFN used as a test aid for?

In predicting a high risk of preterm delivery.

How is fFN measured? Using a membrane immunoassay using cervical or vaginal mucus swabs as specimens.

What does PAMG-1 stand for? Placental Alpha Microglobulin-1What is PAMG-1? A placental glycoprotein secreted into the

amniotic fluid during pregnancy, used as an aid for the detection of PROM.

What does PROM stand for? Premature rupture of membranes.How is PAMG-1 detected? By immunochromatographic method using

cervicovaginal fluid as specimenWhat may cause false positive results of Contamination of the specimen with large

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PAMG-1? amounts of blood.When might a false-negative result of PAMG-1 occur?

If the specimen is collected 12 or more hours after a rupture that is subsequently obstructed by the fetus.

What is presence of bilirubin in amniotic fluid an indicator of?

Fetal erythroblastosis

Why is it important to know the gestational age of the fetus when detecting bilirubin in amniotic fluid?

Because the amount of bilirubin present in the amniotic fluid changes with gestational age.

How is bilirubin measured in amniotic fluid? By a direct spectrophotometric method referred to as ΔA450 test

When are some indications that a test for evaluating fetal lung maturity should be performed?

before repeat cesarean delivery when the age of gestation is uncertainpreterm laborpremature rupture of membranesworsening maternal hypertensionsevere renal diseaseintrauterine growth retardationfetal distress

What is the counting of Lamellar bodies used for?

Assessing fetal lung maturity.

How are Lamellar bodies counted? Lamellar bodies have been counted directly using the platelet channel of whole blood cell counters (lamellar body count)

What are Lamellar bodies produced by? Type II alveolar cellsDoes the quantity of Lamellar bodies increase or decrease as gestation advances?

Increase

What are Lamellar bodies counted on? Electronic cell counters.During the counting of Lamellar Bodies, what Lamellar Body Count (LBC) indicates fetal lung maturity?

Greater than 50,000 counts/microliter

What does the contamination with whole blood do to the lamellar body count?

It decreases Lamellar Body Count

What will contamination of the smallest amount of meconium do to lamellar body count?

It dramatically increases Lamellar Body Count

How does one perform a lamellar body count? With hematology analyzers using the platelet count channel.

What lamellar body count is necessary to correspond to adequate fetal lung surfactant levels?

Lamellar Body Count of 35,000 per microliter.

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What LBC indicates immature fetal lung development?

0-15,000 counts/microliter

What LBC indicates intermediate fetal lung development?

15,000- 50,000 counts/microliter

What represents 85% of surfactants in the body? Lecithin

Why are surfactants important for assessing fetal lung maturity?

Lungs require surfactant, a soap-like substance, to lower the surface pressure of the alveoli in the lungs. This is especially important for premature babies trying to expand their lungs after birth.

During assessment of fetal lung maturity what Lecithin/Sphingomyelin ratio (L-S ratio) indicates fetal lung maturity and decrease in respiratory distress syndrome?

L-S ratio of 2 or more

What L-S ratio is considered high risk of respiratory distress syndrome?

L-S ratio of less than 1.5

How is the amniotic fluid collected and what must be done to it before determining the L-S ratio?

An amniotic fluid sample is collected via amniocentesis and the sample is spun down in a centrifuge at 1000 rpm for 3–5 minutes.

What is the best way to determine L-S ratio and why?

Thin layer chromatography (TLC) on the supernatant. TLC is good because Lecithin and sphingomyelin are relatively easy to identify and the predictive value of the test is good.

What is also tested with L-S ratio to determine the lung profile?

Phosphatidylglycerol (PG) test is comined with L-S ratio to determine lung profile.

As the gestation ages, what happens to the Phosphatidylglycerol (PG) concentration?

The concentration of PG increases as gestation ages.

What level of PG is considered positive on most TLC techniques?

Greater than 2 µmol/L.

What is Inborn Errors of Metabolism (IEM)? These are genetically determined biochemical disorders affecting an individual’s ability to convert nutrients or to use them for energy production.

They are caused by impaired activity of enzymes, transporters, or cofactors and result in the accumulation of abnormal metabolites (substrates).

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Typically present in newborn period or in infancy, but some may not be detected until adulthood.

What is Abnormal Metabolites (Substrates)? It a substrate accumulation is block or deficiency product.

What us Inheritance Pattern of Metabolic Disorders?

Inheritance Pattern Metabolic disorders are caused by mutations in genes that code for specific enzymes or transporters involved in metabolic pathway.

What is Autosomal Recessive Inheritance? It a mutation in both alleles encoding for specific enzyme or transporter. Because the mutation id a gene on a nonsex chromosome (autosome), girls are affected as often as boys.

What is the percentage of a child that inherited from their parents?

25% risk of affected child 50% chance of child who is a

carrier25% chance of child with 2 normal alleles.

What is Clinical Presentation of Metabolic Disorder?

The medical consequences of IEMs vary from failure to thrive to acute illness leading in some cases to (1) brain damage, (2) coma, and (3) death.

What is the biochemical diagnosis? Involves analysis of metabolites enzymatic activityand DNA sequence.

What is Newborn Screening test? Aims to eliminate or reduce morbidity, mortality, and disability.

Is a public health program designed to screen infants shortly after birth for a list of conditions that are treatable, but not clinically evident in the newborn period.

Most newborn screening tests are done by measuring metabolites and enzyme activity in whole blood samples collected on specialized filter paper, however many areas are starting to screen infants for hearing loss using automated auditory brainstem response and congenital heart defects using pulse oximetry.

Infants who screen positive undergo further testing to determine if they are truly affected with a disease or if the test result was a false positive.

Follow-up testing is typically coordinated between geneticists and the infant's pediatrician or primary care physician.

What is Newborn Screening? Screening (sample collection and delivery;

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testing)What is Follow-up? Follow-up (complete demographic information,

satisfactory specimens,abnormal screening results)

What is Diagnosis? Diagnosis (confirmatory tests, clinical consultation)

What is Clinical management? Clinical management (medical home, specialist physician, genetic counselor, dietitian)

Who has the access to the education? Education (healthcare professionals, parents)How does the quality assurance been verified? Quality assurance: analytical (proficiency

testing, quality controls, standards), efficiency of follow-up system, efficacy of treatment, long-term outcome)

How does the Second-tier testing involve? Involves further analysis of the same blood spotthat produce an abnormal result targeting different,more specific analytes and, using a methodologydifferent from the one used in the primary screeningtests.

How does the Second-tier testing requirement? Intended to reduce the number of infants requiring additional confirmatory testing.

What are Newborn Screening tests? Such testing includes DNA analysis for cystic fibrosis, MS/MS steroid profiling for congenital adrenal hyperplasia, and TSH for congenital hypothyroidism.

What are the three types in Inborn Errors of Metabolism disorders?

Disorders of Amino Acid Metabolism Disorders of Fatty Acid Oxidation Disorders of Carbohydrate Metabolism

What are Disorders of Amino Acid Metabolism known as Aminoacidopathies?

Aminoacidopathieso Phenylketonuriao Tyrosinemiao Homocystinuria

Maple Syrup Urine DiseaseWhat are Disorders of Amino Acid Metabolism being as Organic Acidemias?

Organic Acidemiaso Glutaric Acidemia Type Io Isovaleric acidemiao Methylmalonic acidemia

Propionic acidemiaHow are Disorders of Fatty Acid Oxidation classified?

Medium-Chain Acyl-CoA Dehydrogenase Deficiency (MCAD)

Long-Chain 3-hydroxyacyl-CoA Dehydrogenase Deficiency (LCHAD)

How are Disorders of Carbohydrate Metabolism Inborn Errors classified?

Glycogen Storage Disease Glucose-6-Phosphate Dehydrogenase

Deficiency

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Classic GalactosemiaWhat is Aminoacidopathies? Parent amino acid accumulates in excess in

blood and spills over into urineWhat is example of Aminoacidopathies? - Phenylketonuria

- Maple syrup urine disease- Homocystinuria

TyrosinemiaWhat do you called the disorder of amino acid of metabolism that’s accumulation of products in the catabolic pathway of certain amino acids?

Organic acidemias

What are examples of organic acidemias ? - Glutaric acidemia type I- Isovaleric acidemia- Methylmalonic acidemia

Propionic acidemiaWhat is PKU? A disorder of phenylalanine metabolism caused

by absence of phenylalanine hydroxylase activity leading to accumulation of phenylalanine and production of phenylketones that are excreted in urine

What do Primary or secondary impairment of phenylalanine hydroxylase cause?

- increased phenylalanine- increased phenylketone- increase phenylamines

a deficiency of tyrosineWhat might Extremely elevated levels of phenylalanine lead to?

impairs brain development and function

What are the symptoms of an untreated PKU patients?

microcephaly, eczematous skin rash, "mousy" odor, and severe mental retardation

What are the treatment for PKU? a diet low in protein and phenylalanine, and supplemented with tyrosine, minerals, vitamins and other nutrients started from 2 weeks of age

What does it mean when saying phenylalanine is teratogenic?

Results in an increased risk of spontaneous abortions or of having a child with growth retardation, microcephaly, significant developmental delays and birth defects.

Diagnosis of PKU demonstration of increase plasma phenylalanine and an increased phenylalanine:tyrosine ratio.

How is tyrosinemia characterized? By elevated blood concentrations of tyrosine.What are the three types of tyrosinemia? Tyrosinemia type I, tyrosinemia type II, and

tyrosinemia type III.Which is the most severe tyrosinemia? Type I, caused by shortage of

fumarylacetoacetate hydrolase.What are the other two tyrosinemias caused by? Type II is caused by deficiency of tyrosine

aminotransferase; type III is caused by a deficiency of 4-hydroxyphenylpyruvate dioxygenase.

How and when do tyrosinemia patients usually Usually before 6 months of age, present with

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present symptoms? severe liver involvement, or with chronic failure to thrive, mild hepatocellular dysfunction, renal involvement and rickets due to renal Fanconi syndrome.

How is diagnosis based for tyrosinemia? Through the detection in urine organic acid testing of succinylacetone, derived from fumarylacetoacetic acid, the intermediate immediately upstream of the enzyme defect.

How is tyrosinemia identified in newborns? Newborns are screened only when succinylacetone isused as the primary marker, because tyrosine usually is not elevated in the newborn period.

What is the therapy of tyrosinemia? Low dietary tyrosine, low dietary phenylalanine, and drug therapy.

What happens if it goes untreated? They develop liver cirrhosis and are at very high risk for liver cancer. Liver transplantation is indicated in these patients.

How are measurements taken in these patients? Measuring of alpha fetoprotein is used to monitor these patients, because liver cancer is a complication of this condition.

How is alkaptonuria caused? By a deficiency of homogentisic acid (HGA) dioxygenase.

What does this deficiency lead to? It leads to the presence of HGA and its oxide (alkapton) in the urine, bluish-black pigmentation in connective tissue (ochronosis), arthritis and urine that turns dark with standing of alkalinization.

What does the accumulation of HGA cause? HGA in tissues causes cartilage damage in joints specifically in the spine, leading to low back pain at a young age.

What is the treatment of alkaptonuria and how does it work?

Treatment with NTBC [2-(2-nitro-4-trifluoro-methylbenzoyl0-1,3-cyclohexanedione] prevents the formation of homogentisic acid.

How is homocystinuria characterized? By increased concentrations of the sulfur-containing amino acid, homocysteine in blood and urine and is caused by at least seven genetically different disorders. It’s the most common disorder caused by reduced activity to cystathionine β-synthase.

What else do patients usually develop with homocystinuria?

Lens dislocation (often requiring surgery) and a body habitus like that seen in Marfan syndrome (homocysteine interferes with disulfide formation in fibrillin, the protein defective Marfan syndrome).

How does homocystinuria affect blood? Patients with an increase of blood homocysteine concentration that continues to rise are at risk of blood clots that are a life-threatening

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complication.How is homocystinuria diagnosed? Diagnosis is obtained by plasma amino acid

analysis showing increase plasma concentrations of methionine (especially in children) and the presence of the disulfide homocystine. It’s detected in newborn by screening for increased concentrations of methionine in whole blood spots.

What is the therapy for classic homocystinuria? High doses of Pyridoxine (the cofactor of cystathionine B-synthase), a special diet low in methionine, and administration of betaine that donates a methyl group to homocysteine to generate methionine.

What is Maple Syrup Urine Disease (MSUD) Pyridoxine (the cofactor of cystathionine B-synthase), a special diet low in methionine, and administration of betaine that donates a methyl group to homocysteine to generate methionine.

Where did MSUD get its name from? The disease is named for the presence of sweet smelling urine with an order similar to that of maple syrup.

Individuals with classic MSUD present what symptoms?

Poor feeding and vomiting during the 1st week of life followed by lethargy and coma within a few days.

How is the diagnosis for MSUD established? By measuring plasma amino acids and finding increased branched-chain amino acids and the presence of alloisoleucine, which is characteristic of this disease.

What is the treatment for MSUD? A diet that have a restricted content of branched-chain amino acids and includes supplementation with high-dose thiamine and low doses of valine and isoleucine.

What is another name for urea cycle disorders? Urea cycle defectWhat causes urea cycle defect? It is caused by deficiency of one of the enzymes

or a transporter in the urea cycle, which is responsible for removing ammonia from the bloodstream leading to hyperammonemia.

What happens in the urea cycle? Nitrogen is removed from blood and converted to urea, which is then excreted in urine.

What happens in urea cycle disorders? Nitrogen accumulates as ammonia, a toxic substance, and is not removed from the body.

What can urea cycle disorders result into? Mental and behavioral dysfunction, coma, and death.

How is diagnosis for urea cycle disorders accomplished?

It is accomplished by measuring plasma amino acids and identifying the compound present in excess.

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How are the patients with a urea cycle disorder treated?

With a diet low in proteins and administration of nitrogen scavengers, such as sodium benzoate and phenyl acetate, which bind and remove glycine and glutamine respectively.

What results from glycine encephalopathy ? A severe condition usually caused by defect in P,T and H proteins of the glycine cleavage system

What protein is involved in glycine catabolism ? H proteinsWhat are some adverse effect patients present with glycine encephalopathy ?

Poor suckling,lethargy,severe hypotonia, hiccups, seizures, and apnea

Where is the glycine located? Found in the spinal cord and brain stemTrue or false? Toxic levels of glycine can result in glycine Encephalopathy ?

True

What is Glycine Encephalopathy also know as ? Non-ketotic hyperglycinemia -NKHGTrue or false ? Most patients die in the 1st few months of life or survive with profound developmental delays

True

What is Glutaric Academia ? Is an inherited disorder in which the body is unable to break down completely the amino acids lysine, hydroxylysine, and tryptophan

What is Glutaric Acidemia caused by? Deficiency of glutaryl-CoA dehydrogenase, leading to accumulation of glutaric acid and 3-hydroxy glutaric acid in the urine

Excessive levels of glutaryl-CoA and ___________ can cause brain damage atrophy and macrocephaly and acute dystonia

3-hydroxyglutaric

How is glutaric academia type 1 analyze? Diagnosis is confirmed by urine organic acid analysis that indicated the presence of excess 3 hydroglutaric acid and the urine acylcarnitine profile shows glutarylcarnitine as the major peak.

What is the treatment for glutaric academia ? Treatments consists of carnitine supplementation to improve glutatic acid a diet restrited in amino acids capable of producing glutaric acid and prompt administration of intravenous calories in the child who is unable to eat for any reason such as infections fever and gastroenteritis

Symptoms of Medium chain Acyl-CoA Dehydrogenase Deficiency ?

Hypoglycemia lethargy, coma and sudden death

Treatment of Medium chain Acyl-CoA Dehydrogenase Deficiency?

Consists of avoidance of fasting consumption of low –fat foods and carnitine supplementation

Glucose is stored in the form of what ? GlycogenWhere can glycogen be found ? In the liver and muscle cellsHow is glycogen storage diseases treated? Usually treated with avoidance of fasting and a

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special diet devoid of simple sugars and supplements with uncooked cornstarch

What is Glucose-6-phosphate dehydrogenase deficiency?

A disorder of carbohydrate metabolism that affects red blood cells causing hemolysis.It can cause mild to severe jaundice in newborns and in some cases hemolytic anemia.

Symptoms Glucose-6-phosphate dehydrogenase deficiency?

can be triggered by infections, certain antibiotics and antimalarial drugs, exposure to fava beans (a reaction called favism).

What is Classic Galactosemia? A disorder of carbohydrate metabolism resulting from absence of galactose-1-phosphate uridyl transferase, leading to increased concentrations of galactose-1-phosphate in cells which are toxic.

Treatment of Classic Galactosemia. removal of lactose and avoidance of all foods containing galactose.

Diagnostic Tests for Inherited Disorders of Metabolism.

-Ion-exchange Chromatography-Liquid chromatography–Tandem Mass Spectrometry-Gas chromatography–Mass Spectrometry-Tandem Mass Spectrometry (with or without liquid chromatographic separation)

What is Pharmacogenetics? It is a Combination of pharmacology (study of drugs) and genetics (study of inherited traits)

What is Pharmacogenomics? the study of how combinations of variations in several genes, potentially extended to the complete genome, influence the pharmacology of a drug(s).

What is Genotype? is the set of genes in our DNA which is responsible for a particular trait.Is the inherited set of instructions one carries within his or her genetic code.

What is Phenotype? It is the physical expression, or characteristics, of that trait. It is the composite of one's observable characteristics or traits

Medical uses for phenotype information. -Selecting or avoiding a specific drug-Selecting the optimal dose and dosing interval-Avoiding and minimizing adverse drug reactions (ADR) and drug hypersensitivity

Which factors are Responsible in drugs Pharmacogenetic?

-Drug formulation-Route of administration-Clinical status-Age-Sex-Co-medications

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-GeneticsDefine Pharmacokinetics. Pharmacokinetics: how the body acts on a

drugAbsorption, distribution, metabolism, and elimination

Define Pharmacodynamics. Pharmacodynamics: how a drug elicits responses from the body and whether the response is desirable or undesirable.

Define Predict dosing for a drug in Pharmacokinetics.

Predict dosing for a drug that is known to be clinically challenging, such as (1) due to a narrow therapeutic index, (2) due to a limited temporal opportunity to exert efficacy, or (3) requiring a long period of time to establish efficacy

Describe Utility of pharmacogenetic testing? -Alternative drugs are not available-Incorporation of testing does not clearly improve patient care-Less sophisticated or less expensive tools are sufficient for making prescribing decisions-Accommodations to specific dose or dosing strategies are not available

Which institute funded Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB) ?

Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB)Funded by the National Institutes of Health (NIH) and part of the NIH Pharmacogenetics Research Network (PGRN) Whose aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs

Two major reactions involved in what type of drugs are as followed?

Phase I Reactions mostly oxidative and are mediated by cytochrome P450 enzymes (CYPs), the major enzymes involved in drug metabolism and bioactivation, accounting for about 75% of the total number of different metabolic reactions Phase II Reactions involves enzymes that conjugate drug analytes with acetyl, glucuronosyl, amino acyl, or sulfate group.

metabolism of drugs

Phase I consist of 4 Cytochrome P450 enzymes. What are they?

1.Cytochrome P450 1A2 (CYP1A2) 2. Cytochrome P450 2B6 (CYP2B6)

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3.Cytochrome P450 2C9 (CYP2C9) 4.Cytochrome P450 2C19 (CYP2C19)

Clopidogrel Antidepressants (Amitryptyline)

True or False? The following consist of Phase I Cytochrome P450 enzymes are the following:

Cytochrome P450 2D6 (CYP2D6) Tamoxifen Codeine Antidepressant (Nortriptyline)

Cytochrome P450 2E1 (CYP2E1) Cytochrome P450 3A family ( CYP3A4, CYP3A5)

True

The following are what type of enzymes? N-acetyltransferases (NAT1 and NAT2) Thiopurine S-methyltransferase (TPMT) Uridine 5”-diphosphate (UDP) glucuronosyltransferase 1A1 (UGT1A1) Dihydropyrimidine dehydrogenase (DPD) Vitamin K epoxide reductase complex 1 (VKORC1) Human leukocyte antigen (HLA) complex, Class I, B

Phase II enzymes

What are the primary concerns of Molecular biology?

The interactions between the different types of DNA, RNA and proteins and their biosynthesis, and studies how these interactions are regulated.

What is Molecular biology? Branch of science concerning biological activity at the molecular level.

The field of molecular biology overlaps with (A)__ and (B) and in particular, (C) and (D) .

A. BiologyB. ChemistryC. GeneticsBiochemistry

What is one of the most rapidly developing areas in many diagnostic disciplines?

Molecular Diagnosis

Name the 5 branches/areas of Molecular Diagnosis.

Clinical Chemistry Clinical Hematology Clinical Immunology Clinical MicrobiologyTissue Pathology

Name 4 major developments in genetics in late twentieth century.

Decoding of the human genome Cloning of organisms Progress in stem cell researchProgress in gene therapy

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What is DNA? A nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms.

What is found in DNA nucleus? Sugar is deoxyribose and basesName the 4 bases of DNA. Adenine

Thymine CytosineGuanine

True or False: DNA is a short polymer with a deoxyribose and carbon backbone.

False[long polymer and phosphate backbone]

What are the major roles of DNA? Long-term storage and transmission of genetic information

Name the pairing of Bases: A-T (Adenine-Thymine)G-C (Guanine-Cytosine)

True or False: Deoxyribose sugar in DNA is less reactive because of C-H bonds.

True

True or False: Deoxyribose sugar is stable in alkaline conditions.

True

True or False: DNA has smaller grooves where the damaged enzyme can attach too, making it harder for the enzyme to attack DNA.

True

The helix geometry of DNA is of what form? B-FormDNA is completely protected by the what? How so?

The body i.e. the body destroys enzymes that cleave DNA.

DNA can be damaged by exposure to what? Ultra-violet raysName the 4-nucleotide building blocks of DNA. deoxyadenosine triphosphate (dATP)

deoxyguanosine triphosphate (dGTP) deoxycytidine triphosphate (dCTP)deoxythymidine triphosphate (dTTP)

What is RiboNucleicAcid (RNA)? RNA, single-stranded chain of alternating phosphate and ribose units with the bases adenine, guanine, cytosine, and uracil bonded to the ribose. RNA molecules are involved in protein synthesis and sometimes in the transmission of genetic information

Where is RNA found in the body? RNA is found in nucleus and cytoplasmWhat are the bases of RNA? RNA is a polymer with a ribose and phosphate

backbone with Adenine, Uracil, Cytosine, and Guanine bases .

What is the RNA’s main function? The main function of RNA is to transfer the genetic code needed for the creation of proteins from the nucleus to the ribosome. This process prevents the DNA from having to leave the nucleus, so it stays safe. Without RNA, proteins could never be made.

How are RNA bases paired? Pairing of Bases are: A-U(Adenine-Uracil), G-

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C (Guanine-Cytosine)Name the 3 types of RNA. mRNA, messenger-RNA

rRNA, ribosomal-RNAtRNA, transfer-RNA

What is the function of the mRNA? To deliver the information about the amino acid sequence from the DNA to the protein synthesis.

What is the function of the rRNA? To build up the ribosome together with proteins.What is the function of the tRNA? To transfer amino acids to the ribosome for

protein synthesis.Name the process responsible for the flow of genetic information from gene to protein.

Gene expression

Transcription is the process of transferring sequence information from the gene regions of DNA to a messenger RNA molecule.

Where does the Translation process of a cell take place?

Cytoplasmic ribosomes

What is Translation? Process whereby an mRNA sequence forms an amino acid sequence with the help of tRNA and eventual enzymatic peptide bond formation between amino acids to synthesize polypeptides

This is the process of producing two identical replicas from one original DNA molecule.

Replication

This protein is associated with the replication fork which helps in terms of the initiation and continuation of DNA. What is this protein which synthesizes the new DNA by adding complementary nucleotides to the template strand?

DNA polymerase

What is this first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerase?

Transcription

What are the steps in Transcription? One or more sigma factor protein binds to the RNA polymerase holoenzyme, allowing it to bind to promoter DNA.

RNA polymerase creates a transcription bubble, which separates the two strands of the DNA helix. This is done by breaking the hydrogen bonds between complementary DNA nucleotides.

RNA polymerase adds matching RNA nucleotides to the complementary nucleotides of one DNA strand

RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand.

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Hydrogen bonds of the untwisted RNA-DNA helix break, freeing the newly synthesized RNA strand.

If the cell has a nucleus, the RNA may be further processed. This may include polyadenylation, capping, and splicing.

The RNA may remain in the nucleus or exit to the cytoplasm through the nuclear pore complex.

The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. If the gene transcribed encodes a protein, messenger RNA (mRNA) will be transcribed; the mRNA will in turn serve as a template for the protein's synthesis through what next step?

Translation

RNA plays a fundamental role in the functions of a cell. It helps______ proteins. Fill in the blank.A. SynthesizeB. RegulateC. ProcessD. All of the above

D

The process in which cellular ribosomes create proteins is called..A. TranslationB. ReplacementC. DeletionD. Transcription

A

mRNA is produced by transcription from______.

DNA

A__________ decodes mRNA to produce a specific amino acid chain.

Ribosome

A polypeptide an fold into a(n) ________ protein.A. ActiveB. InactiveC. NeutralD. Denatured

A

Ribosomes contain the tRNA anticodons that sequence to mRNA ______.

codon

A string of multiple amino acids can be called a ________.

Polypeptide

Epigenetics are ________ that alter gene function or its interpretation by mechanisms other than those that rely on changes in

B

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DNA sequences.A. MethodologiesB. ProcessesC. HabitsD. proceduresEpigenetic processes include:A. DNA Methylation, Genomic ImprintingB. Histone ModificationC. Chromatin RemodelingD. Any of the Above are Epigentic

processes

D

DNA methylation is implicated in the______ and ________ of organisms. By the addition of a methyl group typically to the fifth carbon position of cytosine residues in CpG dinucleotides.A. growth, developmentB. retardation, extinctionC. stagnation, stabilizationD. None of the Above

A

Genomic imprinting Refers to the phenomenon whereby the function of each allele of a gene is determined by its parental origin. True statement or False

False

__________ are integral part of nucleosomes which are the basic repeating structural unit of chromatin

Histones

___________ are to improve accessibility of DNA to transcriptional activation.

Modifications

_________ are dynamic structures that can be remodeled according to the transcriptional demands of the cell.

A. NucleosomesB. ChromatidsC. HistonesD. Codons

A

Molecular Diagnostics requires techniques to detect sequence variations that are minute changes in complex __.

Genomes

Tools developed for molecular diagnostics include:

Selection and amplification of the nucleic acid of interestVisualization of the amplified nucleic acidsSpecific identification and often quantification of individual nucleic acid species

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Molecular diagnostics consists of the following 4 techniques:

Nucleic acid enzymesAmplification techniquesDetection techniquesDiscrimination techniques

What are nucleases? Enzymes that hydrolyze one or more phosphodiester bonds into nucleic acid polymers.

Nucleases are either DNA or RNA specific and may act on only double- or single- stranded polymers.

True

What are restriction endonucleases? Enzymes found in bacteria that degrade foreign DNA

What are restriction endonucleases used for? digesting large fragments of DNA into smaller pieces and for preparing DNA from different sources to be joined together in cloning procedures

What catalyze the formation of phosphodiester linkages between two nucleic acid chains?

Ligases

What catalyze the synthesis of complementary nucleic acid polymers using a parent strand as a template?

Polymerases

What is found in retroviruses and catalyzes the synthesis of DNA from either an RNA or a DNA template?

Reverse tranciptase

Amplification techniques involve three types of amplification these are?

Amplification of amount of nucleic acid targetAmplification of detection signalAmplification of probe

In which amplification is the sequence of interest copied many times by in vitro methods.

Amplification of amount of nucleic acid target

In which amplification does the amount of target stay the same but the signal is increased.

Detection signal amplification

In which amplification is the probe amplified only in the presence of the target

probe amplification

How long does it take to achieve more than a million-fold amplification?

Less than one hour

What is an example of a DNA amplification technique?

Polymerase chain reaction (PCR)

What are some additional amplification methods?

1) Transcription mediated amplification (TMA)

2) Ligase chain reaction (LCR)3) Strand displacement amplification

(SDA)4) Loop-Mediated Amplification (LAMP)5) Whole genome, trascriptome, or exome

amplification

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6) Branched-Chain signal amplificationSignal and probe amplification

This amplification technique in molecular biology is used to amplify a single copy or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.

Polymerase chain reaction (PRC)

PCR is a method that relies on what kind of cycling?

Thermal cycling

Describe the process of thermal cycling used in PCR

Repeated cycles of heating and cooling is used to provide a reaction of DNA melting and enzymatic replication of DNA

Short DNA fragments are also known as PrimersThese fragmets contain the sequences that are complementary to the target region along with which enzyme?

DNA polymerase

Which two components are needed to enable selective and repeated amplification?

Primers and DNA polymerase

What is one amplification technique? Polymerase Chain Reaction (PCR)As PCR progresses, the DNA generated is itself used as what?

a template for replication

How is this process beneficial? setting in motion a chain reaction in which the DNA template is exponentially amplified.

How are a wide variety of tests performed? PCR can be extensively modified to perform a wide array of genetic manipulations.

What are the methods that PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase used?

This DNA polymerase enzymatically assembles a new DNA strand from DNA building-blocks, the nucleotides, by using single-stranded DNA as a template and DNA oligonucleotides (also called DNA primers), which are required for initiation of DNA synthesis.The vast majority of PCR methods use thermal cycling, i.e., alternately heating and cooling the PCR sample through a defined series of temperature steps

What are the steps in the Polymerase Chain Reaction Test (PCR)?

• Polymerase Chain Reaction (PCR)• In the first step, the two

strands of the DNA double helix are physically separated at a high temperature in a process called DNA melting.

• In the second step, the temperature is lowered and the two DNA strands

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become templates for DNA polymerase to selectively amplify the target DNA. The selectivity of PCR results from the use of primers that are complementary to the DNA region targeted for amplification under specific thermal cycling conditions.

https://youtu.be/iQsu3Kz9NYoHow is transcription-mediated amplification advantegous?

Particularly advantageous when the target is a viral RNA from patients carrying the HIV or HCV in blood bank nucleic acid testing.

What is Ligase Chain Reaction (LCR)? A ligase replaces the polymerase of PCR, resulting in exponential ligation during temperature cycling.

When is Strand Displacement Amplification (SDA) used?

Strand displacement is used instead of thermal denaturation, allowing isothermal amplification.

What is Loop-Mediated Amplification (LAMP)?

Also uses strand displacement and is isothermal, producing a myriad of looped structures of different sizes.

This method is one of the additional amplification methods?

Whole genome, Transcriptome, or Exome Amplification

This amplification method is useful to enrich and amplify before detection or sequencing?

Whole genome, Transcriptome, or Exome Amplification

This method is one of the additional amplification methods?

Branched-Chain Signal Amplification

The following is characteristic of what amplification method?Creates branched DNA by hybridizing the target nucleic acid producing multiple copies of signal generating enzymes that act on a chemiluminescent substrate to produce light.

Branched-Chain Signal Amplification

Name two amplification techniques which belong to Signal and Probe Amplification?

Serial invasive signal amplificationRolling Circle Amplification (RCA)

The following are characteristics of what amplification method?A signal enhancing technique that combines two invasive signal amplification reactions in cities in a single tube format.The cleaved 5' arm from the target-specific primarily reaction is used to drive a secondary invasive reaction.

Serial invasive signal amplification

The following are characteristics of what amplification method?

Rolling Circle Amplification (RCA)

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A probe amplification method where, in the presence of template, a linear probe is ligated to form a circle that is replicated continuously by a polymerase and one or more primers.What are two types of detection techniques? Generic measurement and visualization and

sequence specific labels.What is sequence speficic labels? They are labels used to discriminate between

different nucleic acid sequences, using radioactive probe labels (biotin or digoxigenin).

What is one type of discrimination technique? ElectrophoresisWhat type of DNA is used for electrophoresis? Most commonly used for separating molecules

of DNA and RNA.Where would DNA/RNA migrate on the gel? Both DNA and RNA are negatively charged and

will migrate toward the positively charged electrode when an electric field is present within an appropriately buffered solution.

What is the common polymeric support media used in electrophoresis?

Agarose gels and polyacrylamide

What is PCR product length frequently used to assess?

The quality and specificity of PCR amplification.

What is PCR product length commonly used in the diagnosis of?

Inherited diseases and in identity assessment

What does RFLP stand for? Restriction Fragment Length PolymorphismWhat happens to a DNA sample in RFLP? It is broken into pieces and (digested) by

restriction enzymesWhat is done with the resulting restriction fragments in RFLP?

They are separated according to their lengths by gel electrophoresis.

What does CSGE stand for? Conformation-sensitive gel electrophoresisWhat is CSGE? A type of electrophoretic mutation scanning in

which a segment of DNA is a screened for mismatch pairing between normal and mutated base pairs.

What is Denaturing gradient gel electrophoresis (DGGE)?

DGGE is electrophoretic method for separating DNA fragments according to their mobilities under increasing denaturing conditions.

What are the denaturing conditions used for DGGE?

Increasing formamide or urea concentrations.

What is Temperature-gradient gel electrophoresis (TGGE)?

TGGE is a form of electrophoresis that uses temperature to denature the sample as it moves across an acrylamide gel.

What does Single-stranded conformational polymorphism (SSCP) determine?

Abnormal migration patterns of single stranded DNA.

What is Dideoxy-Termination Sequencing Sanger Sequencing.

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(DNA Sequencing) also known as?

What is Dideoxy-Termination Sequencing (DNA Sequencing)?

It is a method of DNA sequencing based on the selective incorporation of chain terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication.

What is Discrimination Techniques? Commonly used Electrophoresis-based techniques.

What is Electrophoresis? Provides physical separation of individual Nucleic Acid species based on molecular weight and shape.

What is Single Nucleotide Extension (SNE)? Also known as single-base primer extension (SBE) assay.

An assay performed by annealing a primer to ssDNA immediately adjacent to the single base variant.

What is Oligonucleotide Ligation Assay (OLA)?

A technique for determining the presence or absence of a specific nucleotide pair within a target gene, often indicating whether the gene is wild type (normal) or mutant (defective).

What is Multiplex Ligation-Dependent Probe Amplification (MPLA)?

A variation of PCR that permits multiple targets to be amplified with only a single primer pair.

What is the laboratory equipment used in Discrimination Techniques?

Mass spectrometry

What is Pyrosequencing in Discrimination Techniques?

A method of DNA sequencing based on the“sequencing by synthesis” principle that relies on the detection of pyrophosphate (PPi) release on nucleotideincorporation

How does the Discrimination Techniques function?

High-throughput sequencing with amplification.High-throughput sequencing without amplification

What is Discrimination Techniques? Discrimination by mass or sequence without electrophoresis

What is Hybridization assays? Hybridization is the annealing or pairing of two DNA strands

How does a specific double stranded hybrids synthesized?

Hybridization assays are based on the ability of single-stranded nucleic acids to form specific double-stranded hybrids.

What is Hybridization thermodynamics in Discrimination Techniques?

Temperature is the denaturant most easily manipulated.

How does the Hybridization thermodynamics been used in Discrimination Techniques?

The melting temperature (Tm) of a DNA molecule is defined as the temperature at which 50% of the DNA molecules dissociate or "melt” from a double-strand configuration to a single-strand configuration

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What is hybridization kinetics rate? Is 2nd order, being proportional to the concentrations of both hybridizing strands

What is the probe hybridization to a given fraction of the target is proportional to?

The probe concentration.

What influenced hybridization rates? - TemperatureIonic strength.

What is definition of probe? Is a nucleic acid used to identify a target by hybridization

What is the probe used for? To reveal the identity or abundance of a targetWhat are the probe’s types? - Cloned probes

- PCR-generated probes- Oligonucleotide probes

What are some examples of hybridization assays?

Solid-phase hybridization that include dot-blot and line-probe assays, arrays, in situ hydridization, southern and northern blotting. Solution-phase hybridization assays include real-time PCR, PCR melting analysis, single molecule visualization, as well as other classical techniques.

What is the real-time polymerase chain reaction?

The formation or dissociation of the probe target duplex (or product duplex) is monitored in real time.

When does real-time polymerase chain collect data elements?

During the nucleic acid amplification step rather than at the end of it.

What kind of instrumentation and technique does real-time polymerase chain reaction use?

Fluorescent dyes or probes and uses instruments that record fluorescence during thermal cycling.

What does the data obtained provide? Information on the identity and quantity of the nucleic acid sample.

What is Real-time Polymerase Chain Reaction? It is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR).

What does the real-time polymerase Chain Reaction do?

It monitors the amplification of a targeted DNA molecule during the PCR, i.e. in real-time, and not at its end, as in conventional PCR.

Can the Real-time Polymerase Chain Reaction be used quantitatively or qualitatively?

BothReal-time PCR can be used quantitatively (Quantitative real-time PCR), semi-quantitatively, i.e. above/below a certain amount of DNA molecules (Semi quantitative real-time PCR) or qualitatively (Qualitative real-time PCR).

What are Two common methods for the detection of PCR products in real-time PCR?(1) non-specific fluorescent dyes that intercalate with any double-stranded DNA

(2) sequence-specific DNA probes consisting of oligonucleotides that are labelled with a

(1) non-specific fluorescent dyes that intercalate with any double-stranded DNA

(2) sequence-specific DNA probes consisting of oligonucleotides that are labelled with a fluorescent reporter which permits detection only after hybridization of the probe with its

35


fluorescent reporter which permits detection only after hybridization of the probe with its complementary sequence.

complementary sequence.

qPCR measures ? measures DNA amplification; Fluorescent-baseSummary of Real-time PCR (Quantitation) Faster, more precise & reproducible › Detects

amplifiable DNA› Human-specific Highly suitable for automation› Expensive start-up instrumentation

Name some normal PCR reaction ? Denaturation, Annealing, ExtensionWhat are three types of qPCR ? 1. Probe sequences that fluorescence upon

hydrolysis or hybridization- TaqMan (FRET)2. Fluorescent hairpins- Molecular Beacons (FRET)3. Intercalating dyes- SYBR Green, no multiplexing

What is the power of PCR? Gives us an easy to use tool for targeting a specific gene or DNA region of interest amongst the thousands of genes founds in an organism's genome.

What is the purpose of PCR? Qualitative detection of the gene or region of interest or relative quantification of the target DNA.

Detecting PCR Detected via methods of gel electrophoresis or using flourescent probes during real time PCR.

What are Primers ? Designed to targetthe DNA region of interest; two primers are needed upstream and downstream; provide specificity for the region of interest.

What is PCR Incubation time Varies depending of the efficiency of the heat transfer of the thermocycler and composition of reaction tubes and size of target.

Define Detection. A fluorescent signal that increases during PCR and follows one of the expected curve shapes suggests that the specific target is present and was amplified.

Define Quantification. Real-time PCR offers a convenient and systematic approach to quantify by monitoring the amount of product produced each cycle.

Define Genome. A genome is an organism’s complete set of DNA, including all of its genes.

Which content are made The human genome? The human genome is the complete set of nucleic acid sequence for humans (Homo sapiens), encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria.

True of False? The human genome contains 3.08 billion base pairs in 23 chromosomes (46-

True

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244 million base pairs per chromosomes).How many genes do human beings have? 20,0000-25,000 genesFill in the Blank: Considered less complex done bacterial ?.

genomes

True or False? Because viruses use the host's cellular machinery, they do not need as many genes as bacteria do.

True

The viral genome consist of either 1?or 2?, and the nucleic acid may be single-stranded or double-stranded, linear or circular with one or multiple fragments and/or copies per viral particle.

1. DNARNA

Common sequence variants in viruses include what?

single-base changes, insertions and deletions.

The most common sequence variations are single-base change is also known as what?

Single nucleotide variants (SNVs)

What are the two types of variants? Copy number variants (CNVs)Single nucleotide variants (SNVs)

Which variants cover more of the genomes? CNVs or SNVs?

CNVs

What are 3 ways CNV's may be duplicated in? 1. Tandem2. Complex gainsLosses of homologous sequences at multiple sites of the genome

Since CNV regions exists in every chromosome, what percentage is involve in the human genome

5 - 12%

Most CNV's are (a) and (b), similar to single nucleotide polymorphism (SNPs)

a. InheritedBiallelic

Sequence alterations that are known to cause disease are often called?

Mutations or disease causing variants

What percent of known disease causing variants involve only a single-base?

68%

What percentage of mutation is small insertions or deletions?

24%

What percentage of mutations are complex structural variations?

8%

What are some of the variations That Cause Human Disease ?

Single nucleotide variants, Small insertions and Deletions, or Structural variants

Explain how does a single nucleotide variants cause a human disease

A Single nucleotide variants is any change in the nucleic acid that involves only a single nucleotide, including base changes, and single-base deletions/insertions.

Explain how does a small insertions and Deletions cause a human disease?

A Small insertions and Deletions is an insertion refers to the presence of extra bases, whereas

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deletion implies the absence of certain bases in comparison with a reference sequence.Insertions and deletions often cause a shift of the codon reading frame, resulting in altered amino acid sequence downstream of the variation - commonly followed by chain termination from a nonsense codon.

List some of the Structural variants Duplication or deletion of entire exons or genes, chromosomal translocations, inversions, SSR expansions (increased number of trinucleotide repeats), gene rearrangements, complex polymorphic loci related to health and disease, and Copy number variants (CNVs)

Describe the common characteristics of the bacterial genome.

Common bacteria have only one chromosome, usually a circular DNA double helix of 4 million to 5 million base pairs

What percentage, of bacterial DNA, codes for protein?

90%

What are plasmids? Bacterial accessory genes in smaller circles of double-stranded DNA

Why are plasmids important in molecular diagnosis of bacterial infections?

because they often encode pathogenic factors and antibiotic resistance.

In what way can the bacterial repertoire of DNA be altered?

DNA can be altered by gain or loss of plasmids, single-base changes, small insertions and deletions and larger segmental rearrangements.

These genomes are considered less complex than bacterial genomes.

Viral genomes

What is the difference between bacterial and viral genomes with regards to the number of genes needed to infect host?

Because viruses use the host's cellular machinery, they do not need as many genes as bacteria do

What common sequence variants occur in viruses?

single-base changes, insertions and deletions

Mycological organisms have simple genomes. True or False

False

Can fungi genomes be haploid or diploid? Yes or No

Yes

Bacteria and viral genes do not share with fungi the _________.

Introns

Rate these organisms’ complexity in general terms.

1. Fungi2. Bacteria3. VirusA. 3,2,1B. 1,2,3

B

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C. 1,3,2

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