Week1 Part2 Flashcards
define screening
used to identify those at a high probability of disease, not for diagnosis and done on healthy people (asymptomatic)
define diagnostic testing
used to establish diagnosis, administered to individuals suspected to be sick
questions, clinical exam, lab tests, genetic tests, and x-rays are all examples of
screening tests
what is the purpose (2) of screening
delay onset of disease, prolong survival
What are the three requirements for screening?
suitable disease, suitable test, suitable screening program
what is a suitable disease
a disease that has serious consequences, progressive, effective treatment, detectable
what is the natural history of disease (4 stages)
biological onset–>detectable by screening–>symptoms develop–>death
what is primary prevention
prevent disease before it starts (before biological onset)
what is secondary prevention
delay symptoms (after biological onset, before symptoms develop)
what is tertiary prevention
aims to delay death (symptoms already present)
what is detectable pre-clinical phase of disease
screening for disease before symptoms arise
what is lead time
the amount of time you gain by catching a disease before symptoms appear
validity
does the test measure what its supposed to measure
reliability
does the test give them same result over and over
internal validity
does the test measure what its supposed to measure
external validity
are the results generalizable
how do you calculate test sensitivity
TP/(TP+FN)
how do you calculate test specificity
TN/(TN+FP)
what is the relationship between validity, specificity and sensitivity
a valid test will have a high specificity and sensitivity
if specificity increase what occurs to false positive rates
false positive rates decrease
if sensitivity increases what occurs false negative rates?
false negative rates decrease
when is sensitivity favored over specificity?
to prevent disease transmission
when is specificity favored over sensitivity?
TPfor fatal diseases with no treatment. don’t want to tell someone they have HIV if they done
what is the eqn for accuracy of a screening test
(TP+TN)/(TP+FP+TN+FN)
eqn for positive predictive value
(TP)/(TP+FP)
eqn for negative predictive value
(TN)/(TN+FN)
what is erythropoeisis
the formation of RBCs
Where does erythropoeisis occur?
bone marrow of sternum, ribs, and pelvis
what is the main difference between erythroid cells in the bone marrow vs. in circulation
erythroid cells in circulation lack a nucleus
what is the color change associated with maturing eryhthroid cells? why?
as they mature the cytoplasm changes from blue to orange due to increased Hb being present
how long does it take an erythroid cell to mature in the marrow?
7 days with 2-5 cell divisions
what are reticulocytes?
the first stage of immature RBC to enter circulation and not have a nuclues
how long do reticulocytes circulate for? how many are produced/second
- 1-2 days
- 2 million reticulocytes produced per second
what is the lifespan of a mature RBC?
120 days
EPO: role, produced?,MOA
stimulate RBC production, produced in kidneys, binds EPO receptors on progenitor cells that differentiate into RBC
what is anemia
a lack of RBCs or a decreased amount of Hb in each RBC
What are the two most essential enzymes present in RBCs? why are they important?
Recall: RBCs dont have a nucleus so they need to fend for themselves (proteins, stored up RNA) or die. G6PD of the PPP ensures a steady supply of NADPH to compat free radicals. Pyruvate Kinase of glycolysis (PEP–>Pyruvate) to ensure adequate ATP production
how are old/damaged RBCs removed?
macrophages of reticuloendothelial system found in liver, spleen, and bone marrow
what is the structure of a RBC? how does this relate to function
biconcave disk (7 um). Large SA:V ratio for gas exchange
Do RBCs have organelles?
No! has stores of lipids, proteins, and carbs that were made when it still had nucleus
describe the lipid bilayer of RBCs
external surface is different in composition than inner surface, but cholesterol is evenly distributed between both layers
Role of flipases
movement of molecules (phosphatidylserine and ethanolamine) from the outer membrane to the inner membrane (flip in)
role of flopases
takes phospholipids from inner membrane to outer membrane (flop out)
Role of scamblases
move phospholipids in both directions in the phospholipid membrane
where are spectrin and ankyrin found?
interacting with membrane proteins to provide a system of vertical linkages within the cell/cytoskeleton
disruption in membrane composition or cytoskeleton (shape) can cause what in a RBC?
hemolysis
the formation of Hb is limited by what?
availability of iron and level of intracellular heme
where is heme synthesized?
mitochondria
where are globin (alpha, beta, gamma) chains formed?
ribosomes of the cytoplasm
what is the range of RBC concentration?
4-6 million/uL
What is polcythemia?
increased numbers of red blood cells or increased amount of Hb
what are hemoglobinpathies? what are the two we discussed in detail? why are they bad?
qualitative disorders of Hb. Hemoglobin S (sickle cell) and Hemoglobin C disease. these morphological changes DONT impact oxygen carrying capacity, but they are destroyed sooner than 120 days
qualitative Red cell abnormalities could include abnormal 1,2,3
Hb, cytoskeleton, enzymes
How do Thalassemias appear under a microscope?
small, hyperchromic (less orange/color)
how does hereditary spherocytosis appear under a microscope? what is it caused by?
RBC appear as spheres. abnormality in ankyrin band 3 and spectrin genes
how does hereditary ellipctocytosis/ovalocytosis appear under a microscope? cause?
RBCs appear as ovals. abnormality in spectrin and ankyrin protein 3.1 genes (spectrin dimer-dimer interactions)
how does hereditary pyropoikilocytosis appear under a microscope? cause
RBC looks like heat was added and cells fell apart in blood (this morphological disorder does impact oxygenation b/c cells degrade in circulation). spectrin and ankyrin protein 4.1 genes. spectrin dimer-dimer interactions
how does hereditary stomatocytosis appear under microscope? cause?
swelling of RBC. caused by increased intracellular sodium
how do G6PD defficencies appear under a microscope? casue (RBC)
looks like RBC have a bite taken out of them (bite cells). due to Hb oxidation
how does pyruvate kinase deficiency manifest itself in RBC? why
RBC appear spikey, termed acanthocytes. lack of ATP causes a loss of K and water and accumulation of Na
what does in vitro refer to
in a test tube
how do proteins know how to fold?
info required to fold is inherent in the primary structure of the protein
does protein folding require energy?
no, it is a thermodynamically favorable process
what drive protein folding
hydrophobicity (burying of hydrophobic residues, hydrophobic effect) and increasing the disorder of surrounding water molecules
What does Levinthal’s Paradox State
Proteins cant fold by random sampling of all possible confirmations (it would take too long), folding is therefore a stepwise, ordered event
urea does what to proteins?
denatures them
what abnormal/detrimental process competes with the normal folding of proteins?
protein aggregation (proteins fold with each other instead of with itself)
why is protein aggregation a real problem in vivo?
the intracellular environment is very crowded leaving larger macro-molecules with little room to fold
what is the excluded volume effect?
the term used to describe the increased likelihood of protein aggregation due to the minimal intracellular room
what four types of polypeptides are especially at risk for protein aggregation?
- nascent chains synthesized by polysomes
- nuclear proteins: crowded, highly charged environment
- mutant proteins
- unfolded proteins arising from conditions of stress (heat shock)
what are the cells 3 solutions to protein aggregation?
- peptidyl-prolyl cis trans isomerase (PPI)
- protein disulfide isomerase (PDI)
- molecular chaperones
what do peptidyl-prolyl cis trans isomerase (PPI) do?
catalyze/accelerate folding of proteins by interconverting between cis and trans proline bonds to avoid protein aggregation
what do protein disulfide isomerases (PDI) do? where are these proteins found?
catalyzes the quick breakage and reassembly of disulfide bonds as proteins fold so they can quickly find the correct configuration and avoid aggregation. found in the ER
what is the role of molecular chaperones
prevent and revers incorrect interactions that may occur in the crowded intracellular environment
what are the three classes of chaperones and their sizes
small heat shock protein (14-45kDA), low MW (200kDa)
how do small heat shock proteins fxn
ATP independent, form small oligomeric complexes to help fold aggregation hot spots
how do small MW chaperones function
ATP dependent that act through cycles of polypeptide release and binding
high mw chaperones: alternate name, role/fxn
chaperonins. sequester polypeptide and prevents anggregation through forming the Anfinsen Cage. Protein is release from cage when folded
Mutated proteins either fold ____ or ____
incomplete folding
aggregate protein
inappropriately Aggregated proteins are typically very _____ and result in a _______
stable
Gain of function (toxicicity)
proteins that do not fold properly are generally _____ and result in _____
unstable
loss of fxn (accumulation of non-functional proteins or decreased levels of protein)
Sickle cell disease is an example of what type of protein folding? GOF or LOF
HbS aggregation, GOF
Cystic fibrosis is an example of what type of protein folding? GOF or LOF
Incomplete folding of CF transmembrane conductance regulator. LOF
are chaperones extracellular, intracellular, both?
only intracellular
What is systemic amyloidosis
extracellular deposition and accumulation of insoluble protein, evade chaperones in extracellular space
what is a prion?
an infectious agent composed of misfolded protein, this is an example of a GOF mutation
why are prions so deadly?
prions can convert normal folded proteins to misfolded proteins
what are localized amyloids? what is a common example of disease they cause
protein aggregations that develop near site of the original protein production. Alzheimers disease is caused by beta amyloid plaques
contrast role of foldases and chaperones
Foldases: speed up rate of protein folding
chaperones: decrease rate of protein aggregation
aggregated proteins are dominated by what secondary structure?
beta sheets
in sporadic AD, amyloid plaque formation follows:
abnormal post-translational modification of precursor proteins
what are two exceptions to the “flow” of the central dogma?
The production of DNA from RNA with reverse transcriptase. non-coding RNA that can function on its own w/o producing a protein
what two major biological processes depend on coordinated regulation of gene expression
homeostasis and development
what are the steps from DNA to protein in eukaryotic cells?
DNA>Transcription to RNA>RNA processing>export of mature RNA into cytoplasm>translation>post-translational modifications
compare eukaryotes to prokaryotes: nucleus, genome, histones,introns, transcription/translation
Euk: have nucleus, germ line cells are haploid, somatic cells are diploid, have histones, have introns, transcription and tranlation are separate processes
Pro: no nuclues, haploid genome, no histones, no introns, T+T are coupled
what type of RNA is capped at the 5’ end?
mRNA
what are 4 mechanisms to regulate gene expression
physically modify DNA, chemically modify DNA, transcriptional regulation by proteins, post-transcriptional regulation
Physical modifications of DNA include (3).. and an example
DNA/gene loss: when RBC eject their nucleus
DNA/gene amplification: often seen in cancer
DNA rearrangement: segments of DNA are moved from one place to another so different proteins are made (production of antibodies by B cells). note this is not alternative splicing because the DNA is being altered not mRNA
what is a type of chemical modification to DNA, which residue is modified? what is the effect?
methylation. cytosine. methylated sections of DNA are less transcribed.
what are CpG islands?
regions in DNA that are hotspots for methylation. (p indicates a phosphodiester bond connecting C and G) these sequences are palindromic. meaning the C of the complementary is also methylated
how is X-inactivation attained in females?
methylation!
what is genomic imprinting. how can it be attained?
one copy of a gene is silenced due to parental origin. could be a result of methylation.
what role do histones play in gene expression
histones ca regulate chromatin condensation. the more condensed chromatin is, the less transcription occurs
how do transcription factors regulate gene expression?
in order for transcription to occur in eukaryotes, a multi-unit transcriptional apparatus must assemble. this apparatus includes TFs
Uniquely, a steroid hormone receptor is a…
Transcription factor, and when activated transcription is altered
what are 5 forms of post-transcriptional regulation
alternative splicing, alternative polyadenylation, mRNA editing (changing mRNA after it is made), mRNA transport, mRNA stability
what is mRNA transport and how does it impact gene expression. give an example
in eukaryotes mRNA must travel out of the nucleus before being translated. if the RNA is not allowed to leave, no protein is made.
HIV RNA produced in the nucleus must be assisted out of the nucleus
what is mRNA stability and how does i impact gene expression?
proteins can bind to mRNA and prevent their degradation.
Give an example of translational regulation
the translation of globin mRNA is regulated by heme. if heme is not present, globin is not translated. this causes iron deficiency anemia
as red blood cells mature what occurs to their histones?
histones condense chromatin and prevent their transcriptions
How does HIV work? how does it kill?
HIV infects and kills T lymphocytes (destroys immune system). people with HIV/AIDS generally die from opportunistic infections
why is it so difficult to cure/treat HIV?
HIV reverse transcriptase has very low fidelity whcih results in a high rate of mutations in the virus. The frequent mutations causes resistance to drugs such as AZT, and avoidance of immune surveillance
what is AZT
a drug that targets rverse transcriptase, used to treat HIV
Rank the fidelity of RNA pol, DNA pol, and reverse transcriptase
DNA pol>RNA pol>reverse transcriptase
what is the new approach to preventing AIDS?
treat the host instead of the virus
Antinomycin D: what does it do?
antibiotic that inhibits RNA synthesis (transcription) in both eukaryotes and prokaryotes
Rifamycin and rifampicin: what do they do
an antibiotic that inhibits transcription in prokaryotes
alpha-amanitin: what does it do?
blocks eukaryotic transcription
what is LD50?
the oral does that kills 50% of people
what 7 compounds inhibit translation in prokaryotes?
Tetracycline Chloramphenicol Erythromycin Streptomycin Neomycin Kanamycin Gentamycin
what 3 compounds inhibit translation in eukaryotes?
Cycloheximide
Diphtheria toxin
ricin
what compound inhibits translation in prokaryotes and eukaryotes
puromycin
what is the function of snRNPs?
regulate splicing
what is systemic lupus erythematosus
an auto-immune disease that targets snRNPs. joint pain, swelling and butterfly rash on cheeks are symptoms
what is the only gene expressed in mature mRNA
globin (all globin mRNA is deposited prior to enucleation)
what is the most common gene disorder in the world?
thalassemias
what is methotrexate used for?
it is a drug for cancer treatment.
how do some cancer patients become methotrexate resistant?
cancer cells will amplify gene of the enzyme inhibited by methotrexate
What is the actual problem sickle cells cause?
this is not an oxygen carrying problem. the problem is that their sickled shape causes them to be prematurely lysed (life goes from 120 day to 10-20 days) and that their shape prevent them from moving through capillaries.
what are the clinical manifestation of sickle cell?
anemia, dyspnea (labored breathing), joint pain, infections (spleen removed)
what will lab tests show for a person with sickle cell?
decreased hematocrit, decreased Hb, increased reticulocytes, increased serum iron and bilirubin (products of heme recycling)
What are some short term treatments for sickle cell
hydration, oxygenation, exchange transfusion, antibiotics
what are some long term treatments for sickle cell
gene therapy, bone marrow transplant
what is sickle cell trait? benfit?
a person with one defective beta-globulin gene. a carrier. confers malaria resistance.
how does sickle cell anemia arise? what is the mutation
a point mutation of the Beta globulin gene that is located on chromosome 11. this mutation causes a change in AA from glutamate (-) to valine (hydrophobic) at position 6. The hydrophobic residue creates a sticky patch on HbS which polymerizes with other HbS strands into 14 strand fibers
What favors the polymerization of HbS?
low oxygen levels (T state!), high concentration of HbS, high composition of HbS (low levels of HbA, HbF)
If HbS polymerization is favored by the T state, what allosteric effectors will favor polymerization?
T is deoxy state (low Oxygen affinity) So…a low pH, high CO2 or high BPG will favor polymerization
what diagnostic tests can be used to diagnose sickle cell anemia?
Hb electrophoresis, genetic testing (use PCR, restriction enzymes, gel)
fetal Hb has which subunits?
alpha and gamma
In what DNA repair pathway is PARP1 involved? HOw can it be used to treat cancer?
PARP1 is involved in ssDNA repair (and BER), PARP1 inhibitor is used to treat patients with mutated BRCA1/2 genes (repair of dsDNA). disabling both these pathways promotes cell death
what does SMA stand for?
Spinal muscular atrophy
How is SMA inherited? GOF or LOF
LOF, autosomal recessive
what is the genetic basis of SMA
A loss of SMN Protein caused primarily (95%) by a deletion in of the SMN1 gene or replacing SMN1 with SMN2 gene
What is the role of SMN protein
Survival motor neuron protein. Keeps motor neurons in brain and spinal cord alive. A loss of SMN protein causes SMA
What are the different types of SMA?
Type I: AKA Werdig-Hoffman Disease, most sever, floppy baby, feeding and breathing problems,
What account for the varying severities of SMA?
extra copies of the SMN2 gene can modify the severity. More copies=less severe (SMN2 produces low levels of functional SMN protein)
