Exam 2 Week 2 Flashcards
What is tetraploidy typically associated with?
Cancer
Give the 3 examples of autosomal triploidy:
- Trisomy 21
- Trisomy 18 Edward Syndrome
- Trisomy 13 Patau Syndrome
Give the 2 examples of Sex Chromosome Aneuploidy:
Turner Syndrome X
Klinefelter Syndrome XXY
Most common cause of Trisomy 21:
Nondisjunction in Meiosis 1 of Oogenesis due to increased maternal age
Main features of Down Syndrome:
- Short Stature
- Depressed Nasal Bridge
- Congenital Heart Defects
- Alzheimer’s like changes at a young age
- Single Palmar Crease
- Epicanthal Folds
Main Cause of Edward Syndrome:
Non disjunction during Oogenesis
Main features of Edward Syndrome:
Clenched Fist Low-Set Ears Intellectual Disability Microcephaly Rocker Bottom Feet Congenital Heart Defects SMALL Lower Jaw "Tiny Balloon Head"
Main Features of Patau Syndrome:
Polydactyly Intellectual Disability Microcephaly Microphthalmia (SMALL EYES) Cleft Lip Cardiac Anomalies "Oliver with extra fingers for his photography"
Main Features of Turner Syndrome:
- Primary Amenorrhea (no menstruation)
- Webbed, Swollen Neck/Feet
- Gonadal Dysgenesis
- Streak Ovaries
* PAWGS don’t go for Turner because of his SMALL gonads*
Main cause of still born/miscarriages:
Trisomy 18 Edward Syndrome (that’s why the baby has a clenched fist and looks like a mad scientist, because he almost made it to birth”
Turner Syndrome patients are often considered __________, in that:
- Mosaic
2. Some cells are 45X with NO BARR BODY, while others are 46XX or 47XXX which indicates nondisjunction
Of all the abnormal chromosome syndromes, which is commonly caused by translocation?
Patau (Trisomy 13)
Main Features of Klinefelter:
- Testicular Atrophy
- Gynecomastia
- Infertility
- Female Hair Distribution
* TGIF, even though I look like both a man and a woman*
Will Klinefelter present with a bare body seen on a karyotype?
Yes, because unlike Turner Syndrome there are 2 X-chromosomes
Two types of translocations:
- Reciprocal: Between 2 NON-homologous chromosomes
2. Robertsonian: ACROCENTRIC chromosomes only
What is the primary concern of somatic translocations?
Leads to cancer
Ex: Philadelphia Chromosome (A reciprocal translocation)
2 types of Structural Chromosome Abnormalities:
- Balanced (no loss of DNA)
2. Unbalanced (loss of DNA)
2 Types of Translocations:
- Reciprocal: NON-homologous chromosomes
2. Robertsonian: ONLY ACROCENTRIC chromosomes
4 other kinds of Structural Abnormalities of chromosomes:
- Deletions
- Inversions
- Rings
- Isochromosomes
Describe Wolf-Hirschhorn syndrome:
A micro deletion of 4p, which can be caused by a Reciprocal Translocation of Chromosomes 4 and 8 in the mother. The child gets a copy of chromosome 4 WITHOUT the normal 4p genes, so she gets Wolf-Hirschhorn
Describe the Philadelphia Chromosome:
- A reciprocal translocation, t(9:22), activates an oncogene
- Specifically, ABL is activated because if forms an abnormal protein with BCA
- Hematopoietic Cells will proliferate uncontrollably
Give an example of a reciprocal translocation that also produces cancer (like Philadelphia Chromosome):
t(8:14) —> Burkitt’s Lymphoma
Describe Robertsonian Translocation:
- Loss of both short arms of ACROCENTRIC chromosomes
- Fusion of 2 long arms = Basically trisomy, because all of the genes are on the long arm
- Occurs in Chromosomes: 13, 14, 15, 21, and 22
Effects of Alternate and Adjacent segregation in carriers for Robertsonian Translocations:
- Alternate: Balanced Chromosomes
2. Adjacent: UNbalanced chromosomes (PARTIAL TRISOMY)
How will the karyotype look for a patient with Down syndrome due to Robertsonian Translocation?
There will be 2 copies of chromosome 21 in its area of the karyotype, AND chromosome 14 will have one LONGER COPY because it will have an additional 21 attached to it
2 syndromes caused by large deletions:
How must smaller deletions be detected?
- Wolf Hirschhorn: 4p-
- Cri-du-Chat: 5p-
- For smaller deletions—>Must use FISH or ArrayCGH
When to do Cytogenomic Testing:
- Suspected deletion/duplication
- Autism/Dev. delay
- Dysmorphic Features
Main Features of Cri-du-Chat:
Speech problems
High pitched cry
Intellectual Disability
Microcephaly
What are the 2 Cytogenomic tests and what DONT they detect?
Array CGH and SNP Chip Array
They don’t detect BALANCED rearrangement
Main Features of DiGeorge:
1. MICROdeletion of 22q- Congenital Heart Defects Cleft Palate Intellectual Disability Thymus Absence CATCH22
Main Features of Wolf-Hirschhorn:
Wide Eyes Intellectual Disability Prominent Nose Cardiac Anomalies *Wide Eyed Wolf*
WAGR Syndrome:
- Deletion of 11p- = Wilm’s Tumor, Aniridia, Genitourinary Malformation, Retardation of Growth/Dev.
- Main Features:
Loss of Iris
Wilm’s Tumor
4p-:
5p-:
11p-:
22q-:
Wolf-Hirschhorn Cri-du-Chat WAGR DiGeorge *WCWD = Woman Crush WednesDAY*
15q11-:
Angelman: If maternal deletion
Prader Willi: If paternal deletion
Main Features of Prader Willi:
Hypogonadism
Obesity (eating disorder)
Failure to Thrive
Vader is failing to thrive because he’s fat and has a small dick
Angelman Features:
Happy Puppet
Jerky movements
Lack of Speech
That HJ left me speechless
Pericentric vs Paracentric Inversions:
- Peri centric: One break on each arm, flip to opposite sides of centromere (offspring will have either 2 long or 2 short arms)
- Para centric: Both breaks on same arm
Isochromosomes:
Loss of one arm, and duplication of the other
Example: X-Isochromosome = Two long arms of X leads to gene dosage imbalance. Happens in some children with TURNER SYNDROME: They only get one copy of the short arm of X, so those genes cause haploinsufficiency because they escape inactivation
Ring Chromosomes:
2 breaks occur and then it forms a ring, so essentially other entire chromosome is lost if it becomes unstable when forming a ring
Fundamental Tenant of Pharmacokinetics:
A relationship exists between the effects of a drug and its concentration in the blood
3 Factors affecting Plasma concentration:
- Rate of Input
- Rate of Distribution
- Rate of Elimination
Clearance:
Ability to eliminate a drug
Bioavailability:
The fraction ABSORBED in to circulation
Volume of Distribution Calculation:
Vd = Amount Administered / Plasma conc.
Definition of Vd:
The volume required to keep all drug in body at same conc. as in blood (Vd is a PROPORTIONALITY FACTOR)
Significance of Vd:
- It allows us to converts concentrations to amounts
2. So we can calculate a target loading dose to achieve a certain plasma concentration
When is the ONLY time the exact amount of drug in the body is known?
RIGHT AFTER the dose is given IV only
i.e. Vd = Dose / C-0
Where C-0 is Conc. at Time = 0
What are the 2 phases seen on a plot of drug plasma concentration versus time after administration?
- Distribution Phase: The RAPID decline in the beginning
2. Elimination Phase: The SLOWER phase following
What happens when we plot the log of drug plasma concentration versus time after administration?
The curve becomes LINEAR
How do we calculate C-0?
Follow the elimination curve to its Y-intercept, this will represent the plasma conc. that it would be at when FULLY distributed.
i.e. C-0 = Dose / Vd
How do we calculate a target dose to give IV?
Dose = Vd x C-T
Where C-T = Target Conc.
Define Clearance:
The volume of blood CLEARED per unit of time. Predicts the rate of elimination of a drug in relation to its concentration.
i. e. CL = Elim. Rate / Plasma conc.
i. e. (amount/time) / (amount/volume)
Total Body Clearance:
The sum of all the different drug clearances occurring at a given time
Define First Order Elimination:
- Rate of elim. is DIRECTLY proportional to plasma conc. , meaning the drug has CONSTANT CLEARANCE at any given concentration.
i. e. Elim. Rate = CL x Conc.
Three main enzymes of drug metabolism:
- CYP3A4
- CYP2D6
- CYP2C9
Drug concentration is said to decay _______, meaning that each drug ______.
- Exponentially
2. Has a HALF LIFE (t1/2)
t1/2:
The time it takes to eliminate 50% of the AMOUNT of the drug (NOT the concentration)
i.e. A CONSTANT fraction is eliminated
How do we arrange a plot to calculate t1/2?
Plot the LOG of Concentration vs Time to give a straight line
When is Half Life NOT a constant?
When a drug doesn’t follow first order kinetics
During constant infusion, describe how t1/2 of a drug is exhibited:
The drug will be increasing toward 100% of Css (Steady State Conc.) and it will reach 50% of that in the first half-life. THEN every half life will increase by half of THAT percentage.
i.e. Half-Life 2 = 75% of Css
and Half-Life 3 = 87.5% Css
THEN it works exactly OPPOSITE of that after reaching 100% of Css and infusion stops.
So first half-life after that will DROP the conc. down to 50% of Css.
How many half-lives will it take for a drug delivered over constant IV infusion to reach 100% of steady state conc. (Css)?
About 4, but technically 6 Half-Lives
Calculation for t1/2:
t1/2 = (0.693 x Vd) / CL
What is the result of doubling the Infusion Rate of a drug?
DOUBLE the Css, but the SAME t1/2 meaning that it will still only take about 4 half lives to reach 100% of the Css that is twice as high now (it won’t take any longer to reach it)
What 2 Factors affect Vd of a drug and how do they affect it?
- Obesity = INCREASED
2. Pathologic Fluid = INCREASED
What 6 Factors affect CL of a drug and how do they affect it?
- Age = INCREASE
- Heart Failure = INCREASE
- Liver Failure = INCREASE
- Kidney Failure = INCREASE
- CYP Inhibition = INCREASE
- CYP INDUCTION = DECREASE***
i. e. Stimulating CYP’s will speed up rate of elimination and therefore clearance of the drug
What 2 processes determine “saturation kinetics” because they are considered saturable processes?
- Drug Metabolism
2. Drug secretion at the kidney
When is NON-linear kinetics observed?
After a drug exceeds its Km
What is another term for saturation kinetics?
ZERO order kinetics
Give 3 drugs that exhibit zero order kinetics:
- Aspirin (at HIGH doses)
- Ethanol
- Phenytoin
* NO ORDER in AEP!*
KEY DIFFERENCE between first and zero order kinetics:
- First Order = A constant FRACTION of the drug is eliminated per unit time.
- Zero Order = A constant AMOUNT of the drug is eliminated per unit time.
(Because the Rate of elimination is at Vmax!! So it’s eliminating the same amount as fast as it can at all times because the conc. is way above Km)
Differentiate between the appearance of a plot of “Plasma Conc. of a drug vs Time” for a drug exhibiting First and Zero order kinetics respectively:
- First Order: Will show rate of elim. as EXPONENTIAL slope downward (with constant fraction eliminated every half life)
- Zero Order: Will show rate of elim. as LINEAR slope downward (independent of plasma conc.!!)
Why are drugs with zero order kinetics more dangerous in use?
Because they don’t follow the concept of “4 half lives to Css” when infusing them IV, so they can reach well above stead state conc. (Css) and achieve TOXIC doses
Difference between Loading Dose and Maintenance Dose:
- Loading Dose: Used to achieve a target plasma con. RAPIDLY
- Maintenance Dose: Used to achieve a target plasma conc. over long periods of time, without reaching toxic levels (staying within therapeutic window)
What 3 things must you know to determine maintenance doses for a dosing regimen?
- Clearance
- Vd
- Therapeutic window
What is the goal of maintenance dosing as part of a regimen?
To maintain STEADY STATE concentration of the drug for it to be optimally effective
Calculation for Dosing Rate to achieve Steady State:
Dosing Rate (ss) = Elimination Rate (ss)
i.e. “Rate In” = “Rate Out”
So Dosing Rate (ss): CL x Conc. / Bioavailability (f)
If the target conc. is known, CL will determine the dosing rate
Calculation for Maintenance Dose:
Maintenance Dose = Dosing Rate x Dosing Interval
i.e. “RATE In” x “Frequency Given In”
Calculation for Conc. (ss):
Css = Infusion Rate / CL
Calculation for Loading Dose:
Loading Dose = Vd x Therapeutic Conc. / Bioavailability (f)
What is the key point of using oral drugs with slower activity (i.e. delayed absorption and decreased Css)?
They will exhibit higher levels at LATER times than fast-acting tablets, so they are ideal for:
DRUGS WITH SHORT HALF-LIVES because they don’t have to be administered as frequently
What type of secretion do melanocytes exhibit? Describe this mode of secretion:
- Cytocrine
2. Secretion from one cell INTO another
What is the hypodermis characterized by?
Pockets of Adipose Tissue
Key Feature of Sebaceous Glands:
Fat-filled glands: Stains “clear” because of fatty sebum
Describe the action of Transdermal Patches:
The drug is LIPID soluble, so it passes readily into capillaries and exhibits CONTROLLED release
2 Types of Wound Healing:
- Epidermal Wound Healing: Only affects the EPIDERMIS
a. Break contact with Basement Membrane
b. Enlarge
c. Migrate and exhibit CONTACT INHIBITION to close wound and determine when healing can begin. - Deep Wound Healing: Affects the DERMIS, so BLEEDING occurs. Has 4 phases:
a. Inflammatory: BLOOD CLOT forms. Swollen, red appearance, while fibroblasts replace old cells. Increased Neutrophils and Monocytes.
b. Migratory: Epidermis not completely covered by scab, still reddish scab present. i.e. GRANULATION tissue is formed->Collagen/Glycoprotein Scar Tissue. BLOOW VESSELS REFORM.
c. Proliferative: Random tissue an vessel growth continues to occur.
d. Maturation: Scab SLOUGHS OFF off and FIBROTIC SCAR is left behind.
Compare Hyperkeratosis and Parakeratosis:
- Hyperkeratosis = Hyperplasia of Stratum Corneum
- Parakeratosis = Faster epidermal renewal means less maturation time, so Stratum Corneum cells RETAIN NUCLEI in the epithelium
Compare Acantholysis and Acanthosis:
- Acantholysis: Breakdown of Stratum Spinosum
2. Acanthosis: Hyperplasia of Stratum Spinosum
Describe Complement Systems:
Groups of proteins that effect lysis of cells AND effect Antigen-Antibody Complexes
What are the two main characteristics of Psoriasis and what causes each of them?
- Silvery Scales: Parakeratosis Lack of maturation time leads to RETAINED NUCLEI
- Thickened Epidermis: Acanthosis Increased proliferation of MITOTIC CELLS (aka Stratum Spinosum)
Why do patients with psoriasis often exhibit reddish regions? What can this also lead to?
- Blood Vessels are becoming more superficial due to increased length of dermal papillae and epidermal ridges
- MUNRO’s Micro-Abscesses: Causes pus filled abscesses underneath psoriatic plaques.
Describe Bullous Pemphigoid:
- Autoimmune Disease in which antibodies attack
Hemi-Desmosomes:
a. Integrins
b. Keratin - So, separation of epidermis from the basement membrane occurs and FLUID-FILLED VESICLES form.
- EOSINOPHILS increase: To endocytose antigen-antibody complexes and release proteases to destroy the surrounding tissue.
Describe Pemphigus Vulgaris:
- Autoimmune disease in which antibodies attack Desmosomes:
a. Desmoglein
b. Desmocolin
c. Desmoplakin
d. Plakoglobin
e. CADHERINS - So, junctions BETWEEN cells are destroyed and this is MORE DANGEROUS because patients can get dehydrated.
- Causes atrophy of the STRATUM SPINOSUM (Acantholysis) because THIS IS THE LAYER where desmosomes are highly formed.
What is the characteristic sign of Pemphigus Vulgaris in a histological slide?
“Fish-Net” Appearance: Because junctions are gone so cells are a little wider apart than normal and you can see DEFINITION BETWEEN THEM
What causes Albinism?
Genetic (Autosomal Recessive) deficiency of TYROSINASE: So no conversion of Tyrosine -> DOPA and therefore no DOPA -> Melanin
2 Types of Albinism:
- Ocular: ONLY affecting pigmentation of the eye
2. Oculocutaneous: Affecting BOTH the pigmentation of the eyes and skin
What happens in the cells of Albino patients due to their lack of melanin?
The melanocytes are unable to exhibit CYTOCRINE secretion of melanin into the KERATINOCYTES of the Stratum Spinosum –> So they have no protection against UV light (which would normally be melanin in the SUPRANUCLEAR portion of the cell) and they can develop cancer upon dividing with damaged DNA!! Also can cause Visual Impairment (macular hypoplasia)
Where are melanocytes derived from?
From the Neural Crest
Describe Vitiligo:
Autoimmune disease in which antibodies attack MELANOCYTES and cause patches of hypo-pigmentation
In the “rule of 9’s” for burns, which portions of the body count for less than 9% on each side (front/back)?
- Head = 4.5% on each side
- Arms = 4.5% on each side
- Genitals = 1%
* *NOTE** The abdomen and chest are TWO DIFFERENT areas in the rule of 9’s, so front/back of EACH is 9% EACH.
Differentiate between the 3 types of burns:
1st Degree: Superficial, no bleeding
2nd Degree: BLEBS of fluid, can cause dehydration
3rd Degree: CHARRED appearance, AND lack of sensation***
Describe Squamous Cell Carcinoma:
- KERATINOCYTE tumors –> Caused by UV damage leading to: P53 INACTIVATION**
- Hyperkeratosis: Hyperplasia of the Stratum Corneum
- Parakeratosis: Less time to mature, so retention of Nuclei in epithelial cells.
- Squamous cells MOVE DOWN AND FORM PEARLS that can cause ELEVATION of the skin as a whole.
Key Feature of Squamous Cell Carcinoma:
Cauliflower-like Growth (form both elevation from pearls and hyperkeratosis)
Describe Basal Cell Carcinoma:
- BASAL cell tumor –> Caused by UV damage
- Palisade Arrangements: Single layer of basal cells SURROUNDING a group of tumor cells (organized like a white picket fence***)
- Exhibits “rolled out margins” appearing like holes in the skin
Describe Melanoma:
- MELANOCYTE tumor –> Caused by UV damage
- Can be either:
a. In Situ: Not migrating
b. Invasive into dermis (lethal metastasis) - Raised bump appearance (USE ABCDE RULE)
What causes Acne?
- Sebum blocked in sebaceous glands accumulates
- Can be either filled with pus (white head) or become oxidized (black head)
- Affects areas with INCREASED SEBACEOUS GLANDS
What does “tinea” mean, and how is it treated?
- Fungal Infection
- Anti-fungal ointment MUST be used for 3-4 weeks because that’s how long it takes fungal cells to reach the surface of the skin
Defining characteristic of Multifactorial Diseases:
DON’T show mendelian inheritance, but DO show familial aggregation over generations
Describe “quantitative traits”:
The NUMBER of dominant contributing alleles determines the phenotype, NOT the specific combination of dominant or recessive alleles.
i.e. AaBb and AAbb have the same phenotype, MIXED dominance)
What is the polygenic theory of quantitative traits?
- The higher the number of genes contributing to the phenotype, the more continuous variation (different levels of the phenotype) will be produced
- This gives a more GAUSSIAN distribution (i.e. A BELL CURVE)
Quantitative trait loci produces phenotypes that are __________.
Measurable
What effect does greater environmental influence (nutrition, toxins, lifestyle, etc.) have on Gaussian Distribution produced by polygenic quantitative traits?
It BROADENS the bell-shaped curve even more, giving a wider range of phenotypes
What does the “Liability/Threshold Model” attempt to explain:
The likelihood of an individual within a population getting a disease (based on that populations genetic and environmental factors)
Define Liability:
ALL factors contributing to the “disease” (which produce a normal gaussian distribution
Define “Threshold”:
The point at which a population begins expressing ENOUGH quantitative variables (genes/environmental factors) to give rise to an abnormal/disease phenotype
How does Liability relate to threshold?
INCREASED liability indicates higher likelihood of “reaching threshold” and producing affected individuals (because some of that increased quantitative variation will be disease factors (so the RISK to the population is increased overall)
How will familial history of “bad genes” or “bad environmental conditions” shift the bell curve of the liability model?
It will shift to THE RIGHT –> More individuals within the family being affected (greater incidence)
Explain Familial Relative Risk:
The more closely related you are to someone, the more likely you are to have more of the same alleles as them.
HOWEVER –> That risk decreases by 50% with each degree of separation within the family
How would an individual determine their own Relative Risk RATIO?
RRR = (Frequency of disease alleles within familial relatives) / (Frequency of disease alleles in general pop)
What does a HIGHER RRR (lambda) indicate?
- Higher Relative Risk Ratio = HIGHER HERITABILITY
- ***KEY Concept: It indicates that the phenotype is mostly GENETICALLY determined, i.e. CF = lambda of 500 because it is a SINGLE gene disorder
4 Factors that give an individual a higher recurrence risk:
How is this different from mendelian inheritance?
- Relatives are SEVERELY affected
- CLOSE relatives are affected
- MULTIPLE relatives are affected
- SEX-BIAS
* *Different because: In mendelian the risk doesn’t change, i.e. For Autosomal Recessive diseases, offspring of heterozygous parents have a 1/4 chance ALWAYS
Give an example of a disease exhibiting sex bias in its recurrence risk:
How does the bell curve look for females vs males?
- Pyloric Stenosis: Hypertrophy of the pylorus
2. Bell curve for females = Shifted LEFT
Males are said to have a ______ liability threshold for pyloric stenosis.
LOWER (i.e. it takes less liability for them to get the disease because they’re predisposed as males)
What is difficult about calculating the recurrence risk for complex (multifactorial) diseases?
Determining the HERITABILITY (which components are genetic)
What 5 tools are used in determining the heritability (genetic components) of a disease?
- Twin Studies
- Familt Studies
- Population/Migration Studies
- Adoption Studies
- Association Studies
Explain Population/Migration Studies:
Comparing populations to see what ENVIRONMENTAL factors may be causing differences among populations
Explain Twin Studies:
Comparing the genes of monozygotic and dizygotic twins to see which has more CONCORDANCE (both twins having the disease) –> If MZ twins have HIGH concordance, but DZ twins have LOW concordance, then there must be MOSTLY GENETIC factors causing the phenotype
Explain Adoption Studies:
Comparing phenotype frequency of twins who were separated at birth, so they have the same genes but DIFFERENT environment***
Explain “Association-Analysis” studies:
- “Case-Control” studies
- Comparing a specific patient population to a normal, healthy population to see HOW MANY AFFECTED individuals also express THE SAME ALLELES (i.e. Trying to blame the disease on certain allelic expression)
Explain GWAS:
- Genome-Wide Association Studies
- Like association-analysis, but compares the entire genomes of healthy vs affected patients, looking for specific SNP’s associated with the phenotype
* i.e. Seeing more “allele D” expression in a diseased population only indicates higher CORRELATION, but not causation of the disease*
Describe the 2 types of neural tube defects:
- Anencephaly: Neural tube fails to close at ANTERIOR NEUROPORE –> Lethal, skull/brain incomplete
- Spina Bifida: Neural tube fails to close FURTHER DOWN the tube –> Incomplete closure of the spine
How can a mother reduce the risk of her children having neural tube defects?
Taking FOLIC ACID while pregnant reduces the risk by nearly 50% (seen in studies)
In the Hardy-Weinburg Equation, what do “p” and “q” represent?
- “p” = NORMAL allele (not dominant)
- “q” = DISEASE allele (not recessive)
i. e. (2pq + q^2) = Autosomal Dominant Disease Incidence
If a population has 100 individuals, how many total alleles are there for a disease in question?
200
What is “I” equal to for an Autosomal Recessive disease?
I = q^2
Because I = Incidence of diseased phenotype, and q^2 is the only diseased phenotype (“aa”).
*So q = SQUARE ROOT OF “I”
What type of genetic conditions can actually how a very low incidence (very rarely diseased) but have a relatively high carrier frequency?
Autosomal Recessive Diseases
How is Incidence calculated for X-linked Recessive Diseases?
- Males: I = q
- Females: I = q^2
* Because males are hemizygous and only need one allele
* **NOTE: Carrier Frequency does NOT apply to men, because only women can be carriers****
How is Incidence calculated for Autosomal Dominant Diseases?
I = 2Q OR q = I/2 ***HOWEVER: 99% of population will be normal, so P=1 (almost) and q^2=0 (NOT "q", just homozygous diseased) --> We reduce: I = 2pq + q^2 = 2q
4 Assumptions of Hardy-Weinburg:
- Population is large
- Mating is random (no consanguinity)
- No new mutations
- No migration of new individuals into population
How would new mutations of an allele be reflected in the hardy-weinburg equation?
There would be a steadily increasing incidence of the allele
What is meant by Heterozygote Advantage?
**NATURAL SELECTION* (trigger word)
Ex: SICKLE CELL ANEMIA: Incidence of disease allele increases steadily because the population naturally selected it due to its ability at coping with their environment (i.e. Cell must adopt sickle shape to protect people from malaria) –> So carriers (heterozygotes) have an ADVANTAGE!!
What disease, besides sickle cell anemia, exhibits heterozygous advantage over malaria?
Beta-Thalassemia
Give examples of 4 diseases that explain the importance of Reproductive Fitness in disease prevalence:
- Tay-Sachs = ZERO reproductive fitness, because of death in infancy –> Lower disease prevalence
- Turner Syndrome = ZERO reproductive fitness due to Infertility –> Lower disease prevalence
- PKU = Variable reproductive fitness depending on whether or not it is treated starting in childhood –> Variable effect on prevalence of disease
- Huntington’s Disease = HIGH reproductive fitness due to late age onset –> Higher prevalence of disease
Explain the concept of the Founder Effect in Genetic Drift:
- Genetic Drift simply implies FLUCTUATIONS of allele frequency due to random mating and passage of genes within a population, and explains that it has little effect on large populations, ONLY affecting small populations severely.
- Founder Effect: An extreme example of genetic drift, where diseased individuals enter a SMALL population and the incidence of disease rapidly increases.
What factors worsen the Founder Effect?
- Geographic Isolation
- Religious Isolation
- Social Isolation
Short Term vs Long Term Consequences of DNA Damage:
SHORT TERM: a. Reduced Proliferation b. Altered Gene Expression c. Cell Death LONG TERM: a. Aging b. Cancer
How are mutations caused in dividing cells?
DNA Replication occurs very fast, so it occurs BEFORE repair of damage*** –> Now a mutation will be passed down to dividing daughter cells
2 Types of Spontaneous Mutations:
- Replication Errors (ONLY during S phase)
Caused By: TAUTOMERISM –> Ex: Enol form of Thymine is inserted by DNA Pol. - Chemical changes (ONLY in resting cells)
What causes BLOOM syndrome?
A defect in the BLM gene, which is a DNA HELICASE Enzyme –> So chromosomes are unstable due to overwinding and aberrations occur
Main Features of Bloom Syndrome:
-
If you “unwind (helicase)” and smell the BLOOM-ing flowers, you get the SNIFL’s**
1. Smaller Than Average
2. Narrow Chine
3. Immune Diseases Frequently
4. Facial Rash
5. Lung Disease and Diabetes
What causes Fanconi Anemia?
(Autosomal Recessive) An entire gene family of DNA REPAIR genes is defective –> So genes exhibiting LOCUS HETEROGENEITY are affected, causing chromosome breakage from increased damage and high risk for tumors
Main Features of Fanconi Anemia:
-
A “falcon” attacked my ENTIRE FAMILY and now I can’t REPAIR my “SPRM”*
1. Short Stature
2. Pancytopenia (ALL blood cells have inhibited division)
3. Radial Ray Defects
4. Mental Dev. Impairment
What causes FrameShift Mutations?
“Slipping” of DNA Pol at REPEATS during replication causes DNA LOOPS/KINKS –> So a few repeats of a base aren’t copied and it will be shorter
Describe “Spontaneous Lesions”:
Chemical changes in a RESTING CELL that cause DNA damage by three main ways:
a. Oxidative Damage
b. Depurination
c. Deamination
* *Seeing lesions appear out of nowhere WHEN I’M JUST RESTING would be ODD**
Explain Depurination:
-
If you loose your “PURity”, I’m gonna break your BACKBONE*
1. Spontaneous breakage of glycosidic bond holding purine to sugar phosphate backbone
2. Leaves APURINIC sites –> Likely to cause mutation
Explain Deamination:
- Spontaneous loss of an AMINE group from CYTOSINE
2. Cytosine (still bound) is now URACIL –> Which bonds with Adenine instead
What is the key problem with Spontaneous Deamination of cytosine?
-
If you don’t take your AMINO acid supplements after doing METH, your gonna get huge THY’s instead of people just saying URACILy guy*
1. Cytosine is the ONLY base that gets METHYLATED
2. If an ALREADY METHYLATED cytosine gets deaminated, it will form Thymidine**
3. This becomes a MUTATION HOT SPOT –> And creates either A-T rich regions or G-C rich regions after repair
What 2 things will mutation hot spots likely include?
- Methylated Cytosines
2. Repeated Bases
Explain Oxidative Damage:
Too much fresh air could turn you TRANS
1. Oxidative compounds formed in many parts of the cell
2. ESPECIALLY –> Nucleotide bases affected
Ex: Formation of 8-Oxo-7-HydroxyGuanosine will pair with “A” —-> Forms a TRANSVERSION in chromosome
What are Mutagens? Give examples…
- Any factor that increases the FREQUENCY of normally occurring or spontaneous mutations
- Examples: UV light, formaldehyde, alcohol, cigarettes, etc.
Describe Ionizing Radiation:
- Radiation from X-rays, gamma-rays, etc. –> Will IONIZE molecules that will then form FREE RADICALS
- Even natural radiation from the earth can eventually cause DNA damage and mutations from this
How is UV light damaging to DNA?
Too much bright light will reflect off of your shiny RING as if it was made out of DIMEs
1. Creates DELETERIOUS photoproduct
(i.e. Cyclobutane Pyrimidine Dimer (CPD) and 6-4 Photoproduct (6-4PP), etc.)
2. These products are 2 BASES bonded together ON THE SAME STRAND to form a RING structure that will inhibit further transcription
(called “Pyrimidine Dimers/Thymine Dimers”)
Differentiate between the 3 INDIRECT repair mechanisms:
- Nucleotide Excision: A LONG PATCH of bases around the damage site is replaced (fixes Pyrimidine Dimers from UV light damage)
- Base Excision: A SHORT PATCH, of 1 or 2 nearby bases, is replaced (fixes methylation/oxidation damage)
- Mismatch Repair: (Post-Replication Repair) Replaces mis-incorporated bases that formed due to TAUTOMERISM
5 Steps of Excision Repair:
- Recognize Damage
- Recruit Endonucleases
- Excise Region
- DNA Pol replaces
- DNA Ligase seals nicks
Cause of Xeroderma Pigmentosum:
- (Autosomal Recessive) Mutations of 9 different NER (Nucleotide Excision Repair) genes
- These genes have LOCUS HETEROGENEITY, so they all complement each other
Main Features of Xeroderma Pigmentosum:
-
Too much sun will SHOC you, and it will be IRREVERSIBLE*
1. Sun-sensitivity/burns
2. Hyperpigmented Skin Lesions
3. Ocular Tumors
4. Conjunctivitis
What are the BASIC components of Base Excision Repair common to all bases?
-
EXerCISE first, then CUT OUT THE SUGAR, and then you can REPLACE it with proper diet, and PUT YOURSELF BACK TOGETHER**
1. Bases is excised by a GLYCOSYLASE
2. Sugar Phosphate is removed by an ENDONUCLEASE
3. Replacement by DNA POLYMERASE
4. Ligation by DNA LIGASE
Describe Mismatch Repair and explain how it is different than Base Excision Repair:
-
If you’ve forgotten how to MATCH CORRECTLY, it’s probably because you’ve been REPEATING the same outfits and DISCRIMINATING against your other clothes*
1. MMR (Mis-Match-Repair) proteins recognize mis-paired base
2. If MISSED by proof-reading of DNA Pol, then MMR’s repair in S-phase or G2 phase.
3. Used in removing SMALL REPEATS
4. Shows STRAND DISCRIMINATION: Since methylation should be the same on both strands, looking at where it ISN’T should indicate mis-paired bases
2 Ways of Fixing Double Stranded Breaks:
- Non-homologous End Joining: Cell RAPIDLY attempts to simply put the two strands back together normally
- Recombination Repair: Uses HOMOLOGOUS CHROMOSOMES as a template for the broken strands, causing less error in re-assembly**
Describe Hereditary Nonpolyposis Colon Cancer:
-
When the SATELLITE went down, and the REPAIR man MISMATCHED the wires when fixing my tv, I couldn’t watch MLH or MSH so I PMS’d sop hard I got COLON CANCER**
1. Mutations in genes encoding MISMATCH REPAIR proteins –> MSH2/6, MLH1, PMS1/2
2. Causes MICROSATELLITE INSTABILITY: Unstable repeats after separation (variable in size from INACCURATE replication) that cause tumors
Describe BRCA1/2:
- DNA Repair/Apoptosis mediating proteins found in Breast Cancer tissue
- Having just ONE BAD ALLELE increases your risk of making enough bad proteins –> ALLELIC heterogeneity causing breast cancer
Describe Ataxia Telangiectasia:
-
“O I C”, we can’t do ATM because you’re not ALERT
1. Defective ATM protein (11q22-23) –> In DiGeorge Syndrome as well: So it can’t alert OTHER repair proteins do fix the damage
2. It is a THREONINE KINASE that: Detects Damage, Arrests Cell Cycle, and Repairs DNA
3. Mainly Affects:
a. Ocular Telangiectasia (“spider veins”)
b. Immune Deficiency
c. Cerebellum (Ataxia)
What are ORF’s?
- Open Reading Frames, which contain:
a. Small genes potentially WITHIN other genes
b. Start and Stop sites in the same frame
What is annotation?
Annotation: Determining the FUNCTION of genes
Why does gene number not correlate with number of proteins produced?
For three reasons:
a. Alternative Splicing
b. (RNA Editing) One gene = Many different proteins
c. Post-Translational Modification
LINEs and SINEs are considered _________.
Transposons: They insert themselves into our DNA
Besides transposons, SSR’s, and Low Copy Repeats, what else is duplicated in the genome?
Pseudogenes
Describe the 3 types of pseudogenes:
- Vestigial Genes: Genes like VITAMIN C: we have the gene, but it doesn’t function anymore because it was NEVER DUPLICATED.
- Duplicated genes that are NOT expressed: GLOBIN GENES, which are TURNED OFF after duplication.
- Processed Pseudogenes: mRNA IS translated/expressed, then processed normally and CONVERTED BACK INTO DNA and re-introduced to the genome –> So NO INTRONS, and it isn’t a real gene because it doesn’t code for any protein.
Most of the repeats in DNA are from ________. These are lead to disease via 2 mechanisms:
- Transposons (LINE’s and SINE’s)
- Cause Disease By 2 Mechanisms:
a. ) Transposon “jumps” into a different spot in the genome, potentially a critical spot that disrupts a gene
b. ) Simply being a long repetitive sequence can cause MIS-ALIGNMENT during Meiosis
How can genomic testing determine paternity?
PCR of the child and suspected fathers will reveal different fragment lengths of repeats (SSR’s and VNTR’s) which will match in the child and the father
What other genetic test has PCR replaced due to its vastly more efficient technology?
Southern Blot
Describe Multiplex PCR:
- Using MANY primer pairs to examine tons of SSR’s and
VNTR’s between patients all at once - USED TO MAP SOMEONE’S TRANSPOSON PROFILE
Name a disease caused by mis-alignment of chromosomes giving unequal recombination due to repeats in transposons:
- Red-Green Color Blindness (on the X-chromosome)
2. Results in 2 copies of either: Red or Green Opsin gene
Main Idea of MicroArray Testing:
HALF A MILLION probes are ISOLATED/BOUND to a SOLID SUPPORT –> DNA is added from PATIENT AND CONTROL to see differences in resulting fragments from what hybridizes to probes
3 Main Types of MicroArray:
- CGH –> More/Less DNA than normal?
- SNP –> Same/Diff. SNP Profile?
- cDNA –> Protein Expression same/diff. between patients, tissues, diseased/healthy?
Key Point of CGH MicroArray:
It can detect duplication/deletions much SMALLER than those detected in G-banding
Key Point of SNP Chip Array:
It can give the HAPLOTYPE: personal profile of SNP’s
Define Haplotype:
- A combination of alleles at a DIFFERENT Loci that are transmitted TOGETHER to offspring
- They change/vary due to recombination
Main Point of GWAS (Genome-Wide Association Studies):
- Determination of any/all factors causing MULTIFACTORIAL DISEASES
- It scans the genome with THOUSANDS OF SNP PROBES to search for MARKERS NEARBY that might be contributing to a disease
- Looks at THOUSANDS OF INDIVIDUALS within a population to determine correlations between profiles
What are the Transcriptome and the Proteome?
- Transcriptome: ALL mRNA in a particular CELL under a particular CONDITION
- Proteome: Same, but for PROTEIN
Describe cDNA MicroArray:
- Use of cDNA to examine the TRANSCRIPTOME of cells/tissues between patients (i.e. Are healthy/diseased patients EXPRESSING genes differentially? What genes are actually being transcribed?)
- Process involves:
a. Isolating mRNA
b. Using it to prepare LABELED cDNA (DIFFERENTLY LABELED for healthy vs diseased patient)
c. Hybridizing that cDNA to patient samples with a microarray
If cDNA MicroArray revealed HIGHER expression of a certain mRNA in HEALTHY tissue than in diseased tissue, what protein might that mRNA encode?
Most likely a TUMOR SUPPRESSOR, or something meant to inhibit the disease being examined
What is the point of Proteomics?
Not all mRNA expressed may actually BE TRANSLATED into PROTEIN, so expression could be seen differentially between healthy/diseased patients
Describe the methodology that is used to isolate and determine Proteomics of a cell/tissue:
1st: Separate proteins by ISOELECTRIC POINT
2nd: Separate them by SIZE –> Run them through a MASS SPECTROMETER to determine protein of interest
(This determines the unique MASS:CHARGE ratio of every protein examined)
Describe methylation and the process by which it is inherited:
- DNMT3 methylates the unmethylated DNA
- MeCP2 will then recruit DNMT1 if the DNA is only hemi-methylated and requires further methylation
- THEN MeCP2 will recruit HDAC1/2 to de-acetylate the fully methylated DNA and make it transcriptionally active to pass the methylation pattern down to daughter cells
Differentiate between HAT’s and HDAC’s:
HAT’s: Histone Acetyl Transferases (ADD acetyl groups to histones of nucleosomes)
HDAC’s: Histone DeAcetylases (opposite effect)
Give an example of genes that exhibit changing methylation over the course of fetal development to allow variable expression:
Globin Genes
Describe ICF:
- Immunodeficiency-Centromeric Instability-Facial Anomalies (ICF) –> Mutation in DNMT-3B gene
- So methylation can’t occur properly and some genes aren’t expressed
- Specifically Instability of Chromosomes 1, 9, and 16
Main Features of ICF:
-
Need to buy ICF for the DNMT’s, but IGA is closed….FML**
1. Facial Dysmorphism
2. Mental Retardation
3. Longer Infections due to IgA deficiency
Describe Rett Syndrome:
Can’t bring METH to the ISLAND?
Man: dies in utero
Woman: Breathing Heavily, has seizure It’s a little SKEWED, but I’m alRETT with this*
1. MECP2 mutation linked to X-CHROMOSOME
2. More common in WOMEN because men DIE IN UTERO
3. Women have variable expressivity due to Skewed X-inactivation sometimes
4. If a male survives –> Klinefelter Syndrome
Main Features of Rett Syndrome:
- Seizures
- Irregular Breathing
- Motor Control Problems
What process is defined by Mono-Allelic Expression?
Genomic Imprinting
What can cause mutant alleles to behave as “dominant” or “recessive” regardless of their true nature?
Genomic Imprinting
When does imprinting occur?
During Gametogenesis
What is the cause of Prader Wili and Angelman Syndrome?
ACTUAL LOSS of the genes as a result of imprinting
Describe Beckwith-Weidemann Syndrome (BWS):
- Caused by loss of maternal 11p15 (maternal imprinting)
- OR by paternal disomy
- Is an example of how children born from In Vitro Fertilization (IVF) have a MUCH HIGHER chance of this abnormal DNA methylation –> SHOWS THAT THERE IS AN ENVIRONMENTAL FACTOR
Main Features of BWS:
-
Driving BW’S will only get you a “little head”, but a LOT of tongue*
1. Microcephaly
2. Umbilical Hernia
3. Macroglossia (large tongue)
How are restriction enzymes used to determine imprinting?
The will only cut METHYLATED DNA, so imprinted genes WON’T be cut –> LONGER/FURTHER DOWN on gel
What is an alternative name for Decitabine?
5-Aza-2-Deoxycytidine
What is the function of Decitabine?
- Once this base is incorporated into DNA it CAN’T be methylated –> Hypomethylating Agent**
- ALSO binds to DNMT’s and directly INHIBITS them
How is Decitabine used clinically?
- It prevents methylation of MUTATED TUMOR SUPPRESSOR that are causing cancer in patients (i.e. p15, p53, N-1, etc.)
- Hypo-methylated abnormal proteins will NOT be transcribed/expressed
5 Environmental Factors that disrupt methylation:
- Temperature
- Toxins
- Maternal Care
- Diet
- Hypoxia
What classical example showed that diet is an important environmental factor in determining DNA methylation?
The Agouti Mice study –> Mice needed FOLATE in their diet or methylation would not occur properly
What classical example showed that maternal care was an important environmental factor in methylation patterns?
Maternal licking/grooming in mice allowed methylation of the GLUCOCORTICOID RECEPTOR gene promoter –> So mice could deal with stress later in life
What were the findings of the Overkalix Study?
Transgenerational Effect of FAMINE: Those with grandparents that were hungry/starving in their early life = More likely to be PROTECTED from diabetes and CVD (and vice versa)
Give an example where hypomethylation (and acetylation) ALLOWED expression of a certain protein:
OREXIN = A protein in the Hexosamine Biosynthesis Pathway (HBP)
What causes Incontinentia Pigmenti?
- Mutation of IKBKG (X-linked) Gene
- Normally an inhibitor of kinases (related to light sensation)
- Females survive due to SKEWED X-INACTIVATION in favor of the normal allele
(same as example of Calico Cats)
Cancer is characterized as a disease that progress by ____________.
The accumulation of genetic alterations
What is another term for the “progressive aggressiveness” seen in cancer as genetic alterations increase?
Tumor Heterogeneity
Difference between monoclonal and polyclonal tumors:
- Monoclonal: ALL tumor cells derived from a single initially mutated cell
- Polyclonal: Multiple cells mutated to give rise to the tumor/tumors
How can X-inactivation be studied to determine Monoclonality of a tumor?
- In X-inactivation, all tissues are mosaic for their genes because some of their cells express one X while other cells express the other X.
- BUT all cancer cells will have the SAME copy of the X-inactivated, suggesting that they were derived from a single cell.
How can translocations be studied to determine Monoclonality of a tumor?
ALL cells in the tissue of the tumor will contain the same aberration/translocation
How can antibody production be studied to determine Monoclonality of a tumor?
- In Multiple Myeloma, tumors are formed from B-cells: The precursors to Plasma Cells (which produce different antibodies)
- In the mutant B-cells in the tumor –> ALL cells will have an increase in production of the SAME antibody
Difference between Proto-oncogenes and Tumor Suppressors:
THEY ARE OPPOSITES
1. Proto-Oncogenes: Promote GROWTH
Mutation = GAIN OF FUNCTION
Only ONE mutant copy causes condition
2. Tumor suppressors: Inhibit Growth
Mutation = LOSS OF FUNCTION
Requires TWO mutant copies to cause condition
What is the result of a mutation in a DNA Repair Gene?
An increase in the FREQUENCY of mutations, leading to cancer generally
5 Targets (“Proto-Oncogenes”) of Cancer-Causing Mutations:
- Growth Factor Hormone
- Receptor Tyrosine Kinase (for GF)
- Cytoplasmic Tyrosine Kinases
- GTP-ases Associated with Tyrosine Kinases
- DNA-binding proteins (TF’s) of GF pathway
What are the 2 ways that mutations can alter proto-oncogenes in the GF Receptor Tyrosine Kinase Pathway?
- Mutation results in = MUTANT PROTEIN that causes increased cell division
- Mutation results in = Increased GENE EXPRESSION that causes production of MORE of the proto-oncogene
Describe the difference between Receptor Tyrosine Kinases before and after they are mutated into oncogenes:
- Normally: They exhibit Ligand-DEPENDENT firing, and ONLY dimerize when bound by GF
- As Oncogenes: They exhibit Ligand-INDEPENDENT firing and will REMAIN DIMERIZED and fire in the absence of GF as well (CONSTITUTIVE)
What two ways can a Receptor Tyrosine Kinase be mutated into a constitutively active oncogene?
- Point Mutation
2. Truncation/Deletion mutation
Describe the cause of Burkitt Lymphoma:
- *Burkitt LYMPHoma = BETA- LYMPHocytes**
- Burkitt down Myc’y Myc*
1. Formation of a Myc Oncogene Myc is a TRANSCRIPTION FACTOR
2. Translocation which fuses Myc gene RIGHT NEXT to an active Ig Promoter sequence –> Myc is not controlled BY that Ig promoter (which is constitutively expressed)
3. Myc expression becomes CONSTITUTIVE –> So CONSTANT cell division OF B-LYMPHOCYTES
Describe the cause of Chronic Myeloid Leukemia:
- People from Philadelphia are Abl to smoke CML’s ALL THE TIME*
- Abl is a CYTOPLASMIC Tyrosine Kinase*
1. Formation of an Abl oncogene
2. Translocation of Abl RIGHT NEXT to BCR = Formation of the PHILADELPHIA chromosome –> Mutation of the REGULATORY domain of Abl
3. So uncontrolled activity –> CONSTITUTIVELY active cell growth/division
How is Chronic Myeloid Leukemia treated?
- **I’m Eatin’ A Messy Plate because I’m a Camel*
1. Imitinab Mesylate: A powerful Tyrosine Kinase Inhibitor
2. Binds to active site of BCR-ABL fusion protein product and prevents its activity
Describe the result of Ras protein mutation:
- Ras = A GTP-ase in the MAP-Kinase pathway
- It is activated BY binding GTP –> Mutation prevents it from EVER DISSOCIATING from GTP
- CONSTITUTIVELY ACTIVE = Constant growth/division
because it is constantly PHOSPHORYLATING things in its pathway
How might gene amplification by oncogenes of the MAP-Kinase pathway be determined by a genetic test?
When going FISHing, always use DOUBLE bait to catch EXTRA fish in fewer MINUTES
FISH PROBES could be used in a procedure called “Double Minutes” –> Shows EXTRAchromosomal Fragments in karyotype
What is an alternative procedure to determining gene amplification by oncogenes BESIDES double minutes?
“Homogenously-Staining Regions”: Chromosomes will appear LONGER at HSR’s but NOT as extrachromosomal fragments –> Will be seen on a G-band Karyotype
What is HER2?
Human Epidermal GF Receptor 2
What is an alternative way of defining how Homogenously Staining Regions occur?
Gene Amplification IN TANDEM
Cause of Wilm’s Tumor
Mutation in BOTH alleles of WT1 (a TUMOR SUPPRESSOR) –> So it’s a LOSS of function mutation
Difference between Familial and Sporadic Tumor Suppressor Cancers:
- Familial: 1st hit happens before birth, then 2nd happens sometime later in life
- Sporadic: BOTH hits happen sometime after birth, so symptoms present later and OCCURS IN SAME CELL
What is another term for the “2nd Hit” in the 2-hit model?
LOSS OF HETEROZYGOSITY –> Meaning you are no longer heterozygous and having one normal allele, you now have NO normal alleles
4 Mechanisms that produce the 2nd Hit:
- Gene Deletion (most common)
- Point Mutation (next most common)
- Meiotic Non-Disjunction LOSS
- Mitotic Recombination
Describe the EPIGENETIC mechanism that produces the 2nd hit:
Aberrant (abnormal) METHYLATION of the gene –> Causing one copy to be SILENCED (while the 1st hit ALREADY OCCURED via either familial or sporadic mutation)
Explain how loss of CDK/Cyclin complexes affects Rb protein:
- No CDK/Cyclin –> No phosphorylation of Rb
- So Rb can’t RELEASE E2F –> Which is a transcription factor needed to bind DNA and cause cell
growth/division
(i.e. Lack of inhibition by p16 -> Cdk4/CyclinD -> Rb -> RELEASE E2F -> E2F Binds to DNA -> Transcription)
What is the inhibitor of Cdk4/CyclinD complexes that activate Rb?
p16
What specifically causes Retinoblastoma?
Mutation of Rb protein gene on Chromosome 13
Difference in presentation of Familial vs Sporadic Retinoblastoma:
- Familial Symptoms:
a. MULTIPLE Tumors
b. Bilateral Progression (both eyes)
c. EARLY Onset - Sporadic Symptoms:
a. Single tumor
b. Unilateral or Bilateral
c. Late onset
Give a general flow diagram of the p53 pathway:
-
53 shades of killing yourself or not moving ever again after ATM breaks you**
1. dsDNA break occurs
2. ATR/ATM sense it and signal –> Chk 1/2 OR MDM2 and p53 directly
3. p53 signals Apoptosis or arrests cell cycle
What is the INTRINSIC apoptotic pathway?
In response to dsDNA breaks, p53 activates:
- Bcl-2 (pro-apoptotic) proteins
- IGFBP-3
- CD95
* Get a BIC and torch the place*
What specifically causes Li-Fraumeni Syndrome?
FAMILIAL p53 inheritance of 1st hit FROM MOTHER–> 2nd hit occurs later in life
What is similar about FAP and HNPCC?
They BOTH exhibit FAMILIAL inheritance
Normal Function of APC:
Tumor Suppressor in WNT Pathway
(WeNeedTo (WNT) BEcome CATs (b-Catenin) to GROW AsPartyClowns (APC))
1. WNT Signal Present = Activates B-Catenin to move to nucleus and complex with TCF-4 to promote growth
2. WNT Signal Absent = APC binds to B-Catenin and PHOSPHORYLATES it to target it for DEGRADATION
What happens to the WNT pathway when APC is mutated?
- APC never binds to B-Catenin to inhibit growth
2. AND B-Catenin signals growth EVEN IN THE ABSENCE of the WNT Signal
Describe the progression of mutations in FAP:
1st Hit: One APC mutation
2nd Hit: BOTH APC mutations -> Polyps Form
3rd Mutation: RAS protein -> Polyps get BIGGER
4th Mutation: p53 protein -> METASTASIS occurs
(AARP causes cancer)
Describe the HNPCC Mutation:
- Mutation in MMR genes (MisMatch Repair)
- NOT a tumor suppressor –> DOESN’T require 2 hits like FAP does
- At least 5 different genes mutated (LOCUS HETEROGENEITY) i.e. MLH1, MSH2, PMS1/2
MAIN Feature of HNPCC (Lynch Syndrome):
God gave you COLON CANCER because he saw you committing TANDEMLY REPEATED “Lynchings” from his MICROSATELLITES
MICROSATELLITE INSTABILITY: Tumors will exhibit small fragments of TANDEM REPEATS that form small satellites on a karyotype
Between FAP and HNPCC, which has accelerated tumor INITIATION and which has accelerated tumor PROGRESSION?
FAP = Accelerated INITIATION HNPCC = Accelerated PROGRESSION
What condition exhibits BOTH allelic AND Locus Heterogeneity?
Breast/Ovarian Cancer (BRCA1/2)
What is the normal function of BRCA1/2?
They are DNA Repair Genes
What is one characteristic test that can reveal breast cancer?
- FISH PROBE reveals DOUBLE MINUTES of HER2 Overexpression
2. HER2 is a GF receptor that is AMPLIFIED in 30% of breast cancers
How is amplification of HER2 in breast cancer treated?
HERCEPTIN: A drug that inhibits the receptor itself –> So GF can’t bind to it and transduce its signal
What role does miRNA play in tumorigenesis?
- miRNA INCREASE: Could be for a TUMOR SUPPRESSOR –> So there is less translation of that suppressor protein
- miRNA DECREASE: Could be for an ONCOGENE –> So there is MORE translation of that oncogene
How is the CFTR activated?
GPCR signals G-alpha subS –> AC –> cAMP –> PKA –> CFTR ACTIVATION
What is the characteristic marker of CF?
We left all the salt outside, so there’s no need to carry anything now
DECREASED SERUM ALBUMIN
What causes thickened mucous in the airways of CF patients?
- EVERYWHERE EXCEPT THE SKIN –> CFTR’s function to SECRETE salt ions into lumens
- So without CFTR function –> Ions aren’t flowing into lumen, so WATER CAN’T FOLLOW!
- So mucous secretions are viscous –> Respiratory infections more common
How does CF leads to pancreatic duct obstruction?
- Same effect as in airways: Secretions are thicker, more viscous –> Blockage is more likely
- So Pancreatic Enzymes will be LOW
What causes fatty stool (steatorrhea) in CF patients?
Malabsorption (defective digestion due to lack of pancreatic enzymes) leaves fat behind in the excreted stool
What is CBAVD with respect to CF?
Congenital Bilateral Absence of Vas Deferens (95% of males are born without vas deferens if diagnosed with CF)
How is CF caused?
- A DELETION of 3 BASE PAIRS (IN-FRAME): Causing loss of a Phe amino acid at position 508 of the LONG ARM OF CHROMOSOME 7 (7q)
- Exhibits Allelic Heterogeneity though: R117H mutation is another example
How are chloride sweat tests performed?
Use of PILOCARPINE under a pad to draw out sweat and collect it. Then simply measuring the chloride levels in the sweat
What test would you use to diagnose CF and why?
- ASO Blot = Because the allele causing it is KNOWN
2. However, due to ALLELIC HETEROGENEITY –> Patients can be compound heterozygotes
Describe Vaso-Occlusive Sickle Cell Crisis:
Blockage of capillaries due to sickled RBC’s –> Causes JAUNDICE due to INCREASE of bilirubin transport and may cause LOWER BACK AND ABDOMEN pain as well
What specifically causes Sickle Cell Anemia?
- POINT MUTATION from A->T that changes a beta chain Glutamate to a Valine: i.e. Hydrophilic –> Hydrophobic A.A. on the EXTERIOR
- So the chain has a STICKY component that forms LONG POLYMERS that distort the Hemoglobin molecule when they combine with the Alpha chain
Where specifically does the point mutation in Sickle Cell anemia occur?
At the B-6 POSITION of the beta chain ALWAYS
What might be enlarged in a sickle cell patient?
The SPLEEN: Because it functions to REMOVE the sickled blood cells, so it’s over-worked
How would gel electrophoresis indicate sickled Hb chains versus normal chains?
- Sickled chains have LESS negative charge due to the loss of a glutamate –> So the wouldn’t travel as far toward the (+) end of the gel.
- The normal chains would travel FURTHER
- Patients with BOTH chains in their gel lane would be HETEROZYGOTES: And would therefore be ASYMPTOMATIC
What 2 tests might indicate a heterozygote for Sickle Cell Anemia?
- ASO Blot: Because the gene is known so we could just observe if BOTH probes hybridize, indicating both alleles are present
- RFLP Analysis: The sickle cell mutations causes LOSS OF A RESTRICTION SITE –> So HbS will be much LONGER because the endonuclease will not cut it at the site it WILL cut normal HbA
* Longer = NOT AS FAR DOWN THE GEL* because it travels slower than normal
Main difference between DMD and Becker Muscular Dystrophy:
- DMD = Mutation causes COMPLETE ABSENCE of dystrophin because it is truncated way too short
- Becker = Mutation causes 1 of two things:
a. ) Production of ABNORMAL dystrophin
b. ) Production of LESS normal dystrophin (if it’s a PROMOTER mutation)
Why are DMD and Becker more common in males?
Because they occur as a result of mutations on the X-CHROMOSOME
Main difference regarding the mutations that specifically cause DMD and Becker:
- DMD mutation = FRAMESHIFT deletion
2. Becker mutation = IN FRAME deletion
What type of diagnostic test would reveal the specific deletion that has occurred in a DMD patient?
- MULTIPLEX PCR
- Simultaneously amplifying multiple DNA segments shows WHICH REGIONS of the gene aren’t transcribed properly
- ALL are frameshift mutations though
Does DMD or Becker Syndrome tend to be associated with Pseudo-hypertrophy of Calves?
DMD: *Remember that the pics indicating this are ALL of little boys –> Only DMD would’ve presented that early in life
What does the Gower’s Maneuver indicate in patients with DMD?
Weakness of CORE MUSCLES
What is the actual function of Dystrophin?
Dystrophin = A LINK PROTEIN between:
a. Actin cytoskeleton of Muscle
b. Extracellular Matrix
* So without it –> NECROSIS of muscle occurs because it can’t sustain the STRETCH of muscle
Upon examination of a WESTERN BLOT showing dystrophin of DMD, BMD, and “normal” patients, which protein would move FURTHER DOWN the gel?
- The BECKER PROTEIN would travel further than the control –> Because it is MORE TRUNCATED and therefore is SMALL (meaning it would be able to travel faster/further
- The DMD PROTEIN would be ABSENT completely
How would a histological staining of DMD tissue versus BMD tissue look?
- DMD Tissue: ADIPOSE would be seen accumulating –> As well as MORE connective tissue
- Becker Tissue: SOME STAINING would actually show a faded outline of a dystrophin network between myocytes
What feature would be seen in BOTH DMD AND BECKER?
- Increased levels of CK-MM
2. This marker simply indicates muscle damage
How might a female end up expressing DMD and not dying in utero?
She could be a MANIFESTING HETEROZYGOTE: Her skewed X-inactivation occurred in favor of expressing the mutated protein (so it would present more like Becker)
Females that are carriers would ALSO have increased serum CK-MM
Differentiate between Pyknosis and Karyorrhexis:
- Pyknosis: Chromatin CONDENSING and forming patches up against the nuclear envelope
- Karyorrhexis: Nuclear envelope OPENS and DNA becomes fragmented
3 Main Components of the Apoptotic Pathway:
- Regulators: Proteins that INHIBIT/STIMULATE apoptosis:
a.) Stimulate: Bak and Bax
b.) Inhibit: Bcl-2 and Bcl-xL - Adapters: Activate pro-caspases –> caspases either DIRECTLY or indirectly by causing their aggregation and SELF-ACTIVATION:
Ex: ApaF-1 - Effectors: The CASPASES that execute apoptosis via proteolytic activity.
Describe the Intrinsic Apoptotic Pathway:
- DNA damage (or other internal stimulus) causes PHOSPHORYLATION/ACTIVATION of p53
- p53 (a transcription factor) –> Increases expression of BAX and p21
- BAX inserts into the MITOCHONDRIAL membrane –> Release of Cytochrome C
- Cytochrome C binds to ApaF-1 (causes procaspase aggregates = APOPTOSOME) AND binds procaspases directly
- Caspases carry out apoptosis
* p53 -> BAX/p21 -> Cyt. C -> ApaF-1 -> Caspases*
Describe the Extrinsic Apoptotic Pathway:
- Killer Lymphocytes express Fas LIGAND –> bind Fas “DEATH” receptor (cell surface) on target cell to END immune response
- Recruits ADAPTOR molecules –> Via binding of “death domains” of receptor AND adaptor
- Procaspases aggregate TO the Death domains –> Form the DISC (Death-Inducing-Signal-Complex)
- DISC CLEAVES pro-caspases and they carry out apoptosis
* F-Lig -> F-Rec -> Adaptor -> D.D. binding -> DISC formation -> Cleavage to caspases*
How can the Extrinsic Apoptotic Pathway also make use of the Intrinsic Pathway?
It uses Caspase 8 to:
- CLEAVE BID –> tBid
a. Inhibits Bcl-2
b. Stimulates BAX - Bax carries out intrinsic pathway
Which caspases are involved in the Intrinsic and Extrinsic Apoptosis Pathways respectively?
INTRINSIC: Caspase 2 + 9
EXTRINSIC: Caspase 8 + 10
Describe the Perforin/Granzyme Pathway:
- In response to VIRALLY infected cells –> Toxic T-cells secrete Perforin/Granzyme
- Perforin –> Forms a PERFORATION in the target cell
- Granzyme B ENTERS through the pore –> Activates:
a. ) Caspase 10: Cleaves the inhibitors of apoptosis
b. ) Caspase 3: CARRIES OUT apoptosis
* PG 13 Pathway*
What extracellular molecules might bind to the cell and INHIBIT apoptosis and how might they do that?
- SURVIVAL factors
2. Activation of Bcl-2 (apoptosis inhibitor)
Besides BAK/BAX, what other proteins can p53 stimulate to cause apoptosis?
- Fas Receptor (CD95)
2. IGFBP-3: GF-Binding Protein that BINDS them and SEQUESTERS them –> So IGF1/2 CAN’T do their job
What is the “DNA Ladder” seen in gels of apoptotic cells?
It shows that DNase has cleaved the chromatin BETWEEN LINKER REGIONS of nucleosomes upon apoptosis –> Leaving behind fragments of all sizes that run the course of the gel
Describe TUNEL:
Attaching LABELED nucleotides to the NUMEROUS ends of DNA fragments that have been cut by the DNase during apoptosis –> Reveals fragmentation has occurred because normal DNA wouldn’t have so many ends
Image looks like DNA is “tunneling” into finger webbing
Besides the “DNA ladder”, what is another marker that indicates apoptosis has occurred?
- Loss of cell membrane integrity exposes PHOSPHATIDYLSERINE to the ECF –> It is bound by ANNEXIN 5
- Labeled antibodies for Annexin 5 will show its presence which indicates apoptosis has occurred
What is the “3rd” marker used to detect apoptosis?
Caspase Assays to determine if they are active or remain as pro-caspases
4 Proteins affected in Alzheimer’s disease:
- Because I have Alzheimer’s, I forgot where I put my PS1 and PS2 –> So I can only play ALP-E on my phone APP*
1. APP (amyloid precursor protein)
2. ALP-E (ApoLipoProtein E)
3. PS1/PS2 (Presenilin) - AKA TOO MUCH APOPTOSIS*
- All of these are CLEAVED by Caspase 3 (immunoactivity response like with Perforin/Granzyme)*
How is HIV-1 caused?
- TOO MUCH APOPTOSIS*
1. Inactivation of ANTI-APOPTOTIC Bcl-2’s
2. AND activation of caspases
3. Promotes Extrinsic Apoptosis in cells with CD4 (AKA T-CELLS)
4. HIV proteins: TAT, NEF, and VPR also stimulate p53 to activate apoptosis
5. TAT is taken up after release from infected cells to initiate Fas-mediated apoptosis - All of the fuck boy enzymes give you AIDS by getting rid of your CD4-presenting T-CELLS*
Define each of these 4 terms... EAR: RDA: AI: TUIL:
- Estimated Average Requirement: Intake at which risk of inadequacy is 50%
- Recommended Daily Allowance: 2-3% risk of inadequacy
- Adequate Intake: Healthy, adequate nutrient intake
- Tolerable Upper Intake Level: Risk of adverse effects with intake ABOVE this level
Difference between Water-soluble and Lipid-soluble enzymes:
- Water-Soluble: Used to form COENZYMES
- Lipid-Soluble: Lead to molecules with different functions:
Vitamin K: Blood Clotting
Vitamin D: Calcium Metabolism/Bone Health
Vitamin E: Radical Scavenging
Vitamin A: Vision and Growth
K Doesn’t Eat A…But Chows Regularly on V
3 Classes of Minerals:
- Electrolytes: Sodium, Chloride, Potassium
- Minerals: Calcium, Phosphorous, Magnesium, Sulfur
- Trace Minerals: Idoine, Copper, Zinc
Define EER:
- Estimated Energy Requirement: Dietary intake required to maintain ENERGY BALANCE (about 2000-2500kcal/day)
- LESS energy intake than EER = Weight Loss
MORE energy intake than EER = Weight Gain
Define TEE:
Total Energy Expenditure: Consists of 3 components:
- (RMR) Resting Metabolic Rate
- (DIT) Diet-Induced Thermogenesis
- Physical Activity Cost of Energy
Difference between BMR and RMR:
- BMR is heat release while at COMPLETE rest after 8 hours of sleep
- RMR is energy expenditure during POST-ABSORPTIVE state (10% higher than BMR)
What condition influences the RMR and how?
Hyperthyroidism = INCREASED RMR (weight loss) Hypo-thyroidism = DECREASED RMR (weight gain)
Rank these from highest to lowest RMR:
Organs, Fat, and Muscle
- Organs = Highest
- Muscle
- Fat = Lowest
Define DIT:
Diet-Induced Thermogenesis: The energy required to digest, absorb, transport, and store food
Only accounts for about 10% of the TEE
What percent of the TEE does RMR account for?
75% OF THE TEE
What is the BMR of the average young adult?
24kcal/kg of body weight
How is RMR calculated?
BMR + (10% of BMR) = RMR
How is TEE calculated?
TEE = RMR/0.75
Because RMR is 75% of the TEE
How many kcal/g are generated for Carbs/Proteins, Alcohol, and Fat respectively?
- Carbs AND Proteins: 4kcal/g
- Alcohols: 7kcal/g
- Fats: 9kcal/g
* Calling All Fatties 4 Seeeeven Nine*
3 Main Types of Dietary Carbs:
- Monosaccharides: Glucose/Fructose
- Disaccharides: Sucrose/Lactose/Maltose
- Polysaccharides: Starch/Glycogen
What is the recommended TOTAL plasma cholesterol?
- LESS than 200mg/dL
2. Mostly found as LDL-cholesterol
What is formed from the HYDROGENATION of vegetable oil?
TRANS-FATS
What effect do trans-fats have on cholesterol?
- They INCREASE LDL and DECREASE HDL
- Saturated fatty acids have the same effect
(i. e. Palmitate, Oleate)
What can deficiency of dietary essential fatty acids lead to? Why are these fatty acids essential?
- SCALY DERMATITIS
2. They can cross the BBB
What do DHA and EPA promote?
DHA = Brain Function and Vision EPA = Heart Function
6 Types of Bones:
- Long bones: A diaphysis with 2 epiphyses
- Short bones: Cuboidal Shape (Ex = CARPALS)
- Flat bones: 2 Layers of Compact Bone with Spongy Bone in between (Ex = SKULL bones)
- Pneumatic bones: Contain AIR spaces
- Irregular bones: Irregularly shaped (VERTEBRAE)
- Sesamoid bones: Formed IN A TENDON
Fibrous Joints:
- Bones separated by connective tissue –> Little to no movement
- Have SUTURES that fuse as they grow and make the joint more immobile in time
Cartilage Joints:
There are 2 Types:
a. Primary Cartilaginous: (Synchondrosis)
b. Secondary Cartilaginous: (Symphysis)
* Plan B = Bring in a whole SYMPHONY*
Synovial Joints:
- Covered with Hyaline Cartilage
- Has a FLUID-FILLED joint cavity
- Has a joint CAPSULE
- Has a synovial membrane
- Reinforced by ligaments
6 Types of Synovial Joints:
- Saddle: (Wrist)
- Ball-and-Socket: (Shoulder/Hip)
- Hinge: (Elbow)
- Condyloid: (Wrist)
- Pivot: (Elbow)
- Planar: (Foot)
Appendicular vs Axial Skeleton:
- Axial = Midline bones of the head, neck, and trunk
2. Appendicular = Bones of the limbs
Number of each type of vertebrae:
7 Cervical 12 Thoracic 5 Lumbar 5 Sacral (fused) 4 Coccygeal (fused)
