Molecular/Cell Bio Flashcards
What is alternative splicing?
Exons of a gene are reconnected multiple ways during post transcriptional processing, creates diff mRNA sequences and contributes to biodiversity
What elements are needed for PCR?
DNA template that includes target region, flanking sequences adjacent to target region ( the oligotide sequences of flanking must be known to make primers)
What happens to tRNA that is mischarged with the wrong amino acid and not corrected by aminoacyl-tRNA at the tase proofreading?
It will incorporate into the growing polypeptide chain
What Is DNA laddering a marker of?
Is a sensitive marker for apoptosis and refers to DNA fragments in multiples of 180 base pairs
In bacteria, what functions to remove RNA primers and replace them with DNA?
DNA polymerase I
What refers to gene exchange that occurs through the crossing over of 2 double stranded DNA molecules?
Recombination
Nonsense mutations tend to move ______ in electrophoresis due to their dec size
further
trinucleotide expansions tend to move ____ in electrophoresis due tot heir inc sezie
less
Speed of hemoglobin in gel electrophoresis between HbgA, HgbS, HgbC
Hgb A>HgbS>HgbC
Explain the intrinsic pathway mitochondrial pathway of apoptosis
- mitochondria become more permeable and pro-apoptotic substances are released in the cytoplasm under stress/ cessation of survival signals
- the anti-apoptotic proteins Bcl-2 and Bcl-x that reside in the mitochondrial membranes and cytoplasm are replaced with pro-apoptotic proteins such as Bax, Bak, and Bim
- The proapoptotic proteins allow for the inc permeability of the mitochondria which results in release of caspase activating substances like cytochrome C (can see many shrunken eosinophilic cells in the tumor b/c nucleus condensed and made it all pink)
Explain the extrinsic receptor ligand pathway of apoptosis
This requires engagement of death receptors on the cell surface. These death receptors are in the tumor necrosis family (TNFR1 and Fas=CD95).
- After cross linking of Fas with ligand, multiple molecules of Fas come together to form a binding site for a death domain containing adapter protein called FADD
- FADD then binds an inactive caspase bringing multipole caspases together–> activates caspases
Caspases are a family of proteins that cause?
apoptosis
The _______ is the site of ribosomal subunit maturation and assembly. What enzyme functions exclusively in this area? Howdoes it stain?
nucleolus, RNA polymerase I, basophilic
What is the hallmark of initial phase of injury and is it reversible?
cellular swelling (membrane blebbing,loss microvilli, swelling of RER), yes -b/c build up of Na in cell-->water follows
When membrane damage occurs cell injury is
irreversible
- ex: why we do troponin tests in MI is to basically see if enzymes leaked into the blood=irreversible myocyte damage
- ex: ETC is in INNER mitochondrial membrane and once its damaged can’t go back and giving O2 wouldn’t help, cytochrome C can lead out–> apoptosis
Causes of damage for FiO2–>PAO2—>PaO2–>SaO2
FiO2: high altitude
PAO2: anything that inc PACO2= COPD, hypoventilation
PaO2: affected by previous
SaO2: CO poisoning, Methehemoglobinemia(Fe3+ binding Hgb) (normally FeTWO binds O2)
Morphologic sign of cell death is loss of _____
nucleus
-pyknosis(nucleus shrinks), karryohexis (nucleus breaks up into small pieces)< karyolysis
In ______ necrosis, tissue remains firm, cell shape/organ are preserved and the nucleus disappears. This is characteristic of ____infarction of any organ except the _______
coagulative necrosis, ischemic, brain
In _________necrosis, tissue becomes liquified through enzymatic lysis of cells. What 3 situations do you see it in?
liquefactive
-brain infarction(mediated by microglia), abscesses(neutrophils mediate), pancreatitis(enzymes in pancreas digest itself)
_______necrosis resembles mummified tissue, and is characteristic of lower limb and GI tract. Can be superimposed with what other necrosis
Gangrene, liquefactive
________ is a combo of liquefactive and coagulative necrosis, it has a ______ like appearance, and is characteristic of __________ inflammation
Caseous, cottage cheese, granulomatous (from fungal or TB infection)
______necrosis has adipose tissue with chalk white appearance due to deposition of ____?
fat, calcium (fatty acids bind to Ca=saponification)
- ex: trauma to breast, damage of peripancreatic fat
- see giant cells, fat, calcifications
saponification is an example of ________ calcification
dystrophic
-ex: psammoma bodies
_______ necrosis is from damage to the blood vessel walls and leads to ______ of proteins into vessel wall with a ______ stain.
Fibrinoid, leakage, bright pink
-malignant HTN, vasculitis, preeclampsia (fibrinoid necrosis of placenta)
Apoptotic bodies are removed by ______ and is there subsequent inflammation?
macrophages,no
In the _________ pathway, performs create pores in membrane of target cell. Granzyme enters pores and activates caspases
cytotoxic CD8+ T cell mediated pathway
Which 3 enzymes are important for the removal of free radicals?
superoxide dismutase, catalase, glutathione peroxidase
O2-, H2O2, OH-
OH is most damaging
CCl4 is metabolized to what by what organ? What happens to hepatocyte
CCl3 by liver
hepatocytes have dec protein synthesis from cellular damage and apolipoproteins can’t work–> fatty change in liver
Amyloid is a ______ protein that deposits in the _______ space. It tends to deposit around? How does ti stain?
misfolded, extracellular, blood vessels, congo red and apple bifringence
Primary amyloidosis is systemic deposition of __________ derived from ____ light chain. What is it associated with?
AL amyloid, Ig, plasma cell dycrasias: overproduce light chain that leaks out and deposits everywhere
Secondary amyloidosis results from systemic deposition of ________ derived from SAA. SAA is an _______ reactant that is increased in ________ inflammatory states, malignancy, familial Mediterranean fever
AA amyloid, acute phase, chronic
Familial Mediterranean fever is a dysfunction of _______ and presents with fever and acute ______ inflammation. High _____ during attacks deposits as __ amyloid
neutrophils, serosal, SAA, AA
Amyloid depositing in kidneys leads to _______ syndrome
nephrotic
Amyloid depositing in heart leads to ________ and _______
restrictive cardiomyopathy(heart becomes less compliant and bendable) and arrhythmia
Diagnose amyloidosis through _______. Damage organs must be ______ because amyloid can’t be removed
abdominal fat pad and rectum, transplanted
In senile cardiac amyloidosis, _____ deposits in heart. It’s typically asymptomatic
non-mutated transthyretin,
In familial amyloid cardiomyopathy, _________ deposits in the heart. This leads to _______
mutated serum transthyretin, restrictive cardiomyopathy
In type 2 diabetes, _______ deposits in islets of pancreas
amylin (derived from insulin)
Alzheimer’s disease has _____ amyloid deposits in brain. This is derived from Beta-amyloid precursor protein on what chromosome?
AB, 21
Dialysis associated amyloidosis has _____ deposits in joints. This provides structural support for which MHC molecule?
Beta2 microglobulin, MHC class 1
-in CKD, beta2 isn’t filtered well so builds up in blood and deposits
Tumor cells with an amyloid background in the thyroid suggests
medullary thyroid carcinoma
With acute inflammation, how are these all affected: endothelial intracellular cGMP, blood velocity, RBC concentration, arteriolar resistance, endothelial transcytosis
increased cGMP, decreased velocity(b/c as you dilate/inc cross section–> dec vel), increased concentration, decreased resistance, increased transcytosis (collects fluid from vascular side and releases it on interstitial side)
example of tertiary structure
disulfide bonds
example of quartenary structure
alpha and gamma chains of Hgb (when 2/more polypeptides form a single protein)
Periodic acid Schiff (PAS) stain detects what in cells?
glycoprotein
splicesomes remove introns containing __ at the 5’ splice site and __ at the 3’ splice site
GU, AG
When is translated initiated in eukaryotes
when the small ribosomal subunit attached to the 5’ cap of mRNA and then scans for the AUG sequence within the Kozak sequence
What are the 3 stop codons
UGA, UAG, UAA
Receptors for thyroid hormone and vitamins A and D are located in the _______ at all times. Where is progesterone?
nucleus,
-progesterone is in cytosol and can go to nucleus
Fas ligands mediate the extrinsic pathway of? The Fas receptor is expressed on which lymphocytes
apoptosis, T lymphocytes
Kozak sequence indicate the start of ____________
translation, AUG sequence
CD8+ cells use the _________ to target viral proteins for destruction
ubiquitin ligase
The ______ has ribosomal RNA
nucleolus
______ may be located upstream, downstream, or within a transcribed gene. These function to inc and dec the rate of __________
enhancers/silencers, transcription
________ are typically located 25-75 bases upstream from their associated genes and function to initiate _________
promoters, transcription
________ have one origin of replication while _______ have multiple origins of replication
prokaryotes, eukaryotes
what would bind multiple deoxythymidines
poly A tail
Patients with ___ have antibodies against snRNPs (anti-______) and these are an essential component of ________
lupus, Smith, spliceosomes=removal of introns from RNA transcripts
_________ of RNA transcripts is performed by ____________. This process stabilizes mRNA helping it exit the nucleus
polyadenylation, polyadenylate polymerase
______ bodies play an important role in mRNA translation regulation and degradation
P bodies
________ recognize stop codons
releasing factors
_________ facilitate tRNA binding and the translocation steps of protein synthesis
elongation factors
Transcription factor 2 D binds the ________ to initiate transcription
TATA box
Explain PI3K/Akt/mTOR pathway
bind growth factor—>autophosporylation of tyrosine residues—>activation of PI3K–>activation of protein kinase B–>translocation to nucleus and gene transcription
________ functions for remove RNA primers (5’ to 3’ exonuclease activity) and replace them with DNA
DNA polymerase I
The TATA and CAAT boxes serve as ________ for transcription and serve as binding sites for _________ and __________
promoters, transcription factors, RNA poly 2
what stabilizes unwound template strands
single stranded DNA binding protein
what removes the RNA primer and replaces it with DNA
DNA poly 1
frameshift are caused by while missense/nonsense/silent are caused by
insertions/deletions, substitutions
mitochondrial disorder that leads to bilateral vision loss
leber hereditary optic neuropathy
myoclonic epilepsy
myoclonic seizures and myopathy with associated exercise, skeletal muscle biopsy shows red ragged fibers
MELAS
mitochondrial encephalopathy with lactic acidosis and stroke like episodes
nuclear fator kappa b is a transcription factor with a critical role in _________. Where is it normally present and what is it bound to?
immune réponse to infection
- found in the cytoplasm in a late state and bound to it’s inhibitor protein: IkappaB
- extracellular signals like toll like receptors or LPS can lead to IkappaB destruction and this allows NFkb to go to the nucleus and leads to production of numerous cytokines
microsomal monooxygenase does what
its a cytochrome P450 enzyme that can convert pro-carcinogens into carcinogens
lipoma v liposarcoma
lipoma: benign and soft rubbery subcutaneous nodules but have mature fat cells without scalloping
liposarcoma: have numerous lipoblasts (
DNA polymerase can only add primers to the _____’ end
3’ so these pieces would lead to complementary DNA strands
nonpathogenic and pathogenic influenza virus are both grown in culture and progeny of nonpathogenic virus is shown to have wild type enhanced infectivity
genetic shift=reassortment
a host cell is connected with 2 viral strains and progeny viruses exhibit coat or envelope proteins not coded for by the genetic material packaged within them. Get additional traits but there is a change in genome
phenotypic mixing
point mutations in viruses can lead to antigenic _______
dirft
gene exchange that occurs through the crossing over of 2 double stranded DNA molecules, resulting progeny can have recombined genes not present simultaneously in either parent virus
recombination (occurs less frequently than reassortment)
uptake of naked DNA by a prokaryotic or eukaryotic cells, alters the genetic composition of the host cell by typically causes no genomic change in progeny visions
transformation
In a petri dish, a normal line of cells will show _________ and stop growing and this is mediated by _______ and ______. Malignant cells will continue to divide and even pile up like __________
contact inhibition, cadherins and catenins, mounds
cells like hepatocytes and steroid producing cells of adrenal cortex are rich in what in the cell?
smooth ER because it plays a huge role in steroid synthesis and detoxification of drugs
scaly skin, ataxia, anosmia, night blindness
refsum disease
-defect in alpha oxidation in peroxisomes
hypotonia, seizures, hepatomegaly: auto recessive disorder of mutated PEX gene
Zellweger syndrome
x linked recessive disorder of B oxidation of VLCFAs–> VLCFA build up in adrenal glands, white (leuko) matter of brain, testes–> adrenal crisis
adrenoleukodystrophy
Bloom syndrome is from a defect in _____ and is characterized by?
helicase, photosensitivity, short stature, erythema, telangectasias
-predisposed to lymphoproliferative and GI malignancies
In an agglutination inhibition test, the presence of agglutination is a ________ result and the absence of agglutination is a _________ result
negative, positive
Characteristic of _______ receptors is that they have 7 transmembrane domain hydrophobic alpha helical domains
G protein
Defective proline hydroxylation by prolyl hydroxylase inhibitor –> failure of __________ and stabilization by pro-alpha chains during collagen synthesis
triple helix formation
As translation begins in the cytoplasm, a hydrophobic AA sign sequence at the N terminal of the _____ chain facilitates ribosomal binding to the _______ and the growing polypeptide chain to the ________. Absence of this single can leda to __________
alpha, rough ER, rough ER, polypeptide accumulation in the cytosol
Inside the rough ER, the signal sequence is cleaved to yield the _______ chain, Next, many of the proline and lysine residues at the Y position are hydroxylated to hydroxyproline and hydroxylysine by ___________. This step requires what vitamin
pro-alpha, prolyl hydroxylase, vitamin C
What is vitamin C necessary for in collagen synthesis. What further stabilizes this change
proper assembly of pro-alpha chains into tropical helical collagen, hydrogen bonding
After pro collagen is formed, it is secreted from the cell and the N and C terminals are cleaved by ________ making less soluble collagen=_________
pro collagen peptidases, tropocollagen
These collagen molecules spontaneously assemble into ________ which then cross link to form _________. Cross linking is facilitated by _______
fibrils, collagen fibers, lysyl oxidase
the process by which bacterial DNA is transported from one bacterium to another by a virus (bacteriophage)
transduction
Carbon dioxide/ carbon isotopes are used in the synthesis of __________ in the cytosol
pyrimidines
-uses carbamoyl phosphate synthetase 2
urea cycle sues carbomyl phosphate synthetase ___ and takes place in the _______
1, mitochondria
Which cell type is responsible for vibratory sense/pressure and diabetics often lose sense of these at their feet
Pacinian corpuscles
What cell type are responsible for fine/light touch and position sense
Meissner corpuscles
Which cell type is responsible for pressure, deeps static touch (sharps, edges), position sense
Merkel discs
Which cell types are responsible for pressure, slippage of objects along surface of skin, joint angle change
Ruffini corpuscles
Nonsilent mutations of an exon of the mRNA are translated into protein and lead to __________
abnormal/non functioning protein
mutations in promoter region of mRNA that is from introns leads to ______
affect regulation of mRNA translation–>leading to higher or lower levels of the protein
palindromic sequence of DNA
where reading 5’–>3’ one end is the same as the complementary strand so
5’TGTACA3’–>3’TGTACA5’
________ is the need for cells to be attached to or in contact with another layer of cells
anchorage dependence (they can effectively grow floating unattached to a solid surface) -is important when it comes to metastasis
Find out HER2 positivity in breast cancer by what method
FISH
