SFM Flashcards
How much of the total volume of a cell does the nucleus take up and what is its main functions?
6% of the total volume of the cell.
Role: cell regulation, proliferation, DNA transcription
RNA Virus
Reverse transcriptase
EX: HIV
DNA is…
Double stranded and antiparallel
goes from 5’ to 3’.
What type of bond is there in A-T
Double bond
What type of bond is there in G to C
triple bond
Why are mitotic chromosomes condensed 500 times when compared to interphase chromosomes?
TO prevent physical damage to the DNA as chromosomes are separated and passed on to daughter cells.
How many hydrogen bonds are formed between DNA and the histone octamer in each nucleosome?
142 Hydrogen bond
Histone proteins….
are highly conserved across species
What are the two classes of proteins that bind to DNA?
Histone proteins and Non-histone chromosomal proteins
What makes up a nucleosome core particle?
eight histone proteins
What is Chromatin made from
Protein + DNA
“beads on a string”
What is DNA wound around?
Histone octamer
Euchromatin
lightly packed form of chromatin
highly enriched in genes
usually under active transcription
92% of the human genome
What year did watson and crick describe the helical structure of DNA?
1953
What year was the genetic code determined?
1966
What happened in Feb, 2001 in regards to the human genome project?
the sequence of the human genome was announced, but only 90% was sequenced.
Replication fork
bi-directional DNA replication
Asymmetric: leading strand is synthesized continuously. Lagging strand is synthesized in segments.
Topoismerase
Relieves overwound supercoils in DNA replication.
Called DNA gyrase in bacteria
What kind of pharmaceutical drugs are used as anti-cancer agents?
Drugs that target DNA topoisomerase.
How do Topoisomerase act as inhibitors as anti-cancer agents
block the cell cycle, generate single and double stranded breaks, harms the integrity of the genome,
Leads to apoptosis and cancer cell death.
Depurination
Guanine is removed. 5000 purine lost, bases/day
Deamination
Amino group is removed from cytosine, and C gets changed to a Uracil.
This means that when it is replicated, half the daughter cells will be normal and half will have the mutation.
100 bases/day
What does methylation of CpG islands do?
stably silences genes (Cancer/DNA repair genes)
What does deamination of methyl-C produce?
turns it into a Thymine, which gets mismatched with a T
Cross-linking and intercalating
Benzo(a)pyrene –> BPDE (an epoxide)
Pro-carginogen is changed into a carcinogen
Done by metabolism (metabolism of well-done grilled meats)
Cross-linking agents
Nitrogen Mustard
Cisplatin
Mtiomycin C
Carmustine
Alkylating agents
Dimethyl Sulfate (DMS) Methyl methanesulfonate (MMS)
Intercalating agents
Thalidomide
What are the variable outcomes of DNA damage in our bodies?
It can be repaired–> normal cellular function
Not repaired/inapropro response –> deleterious consequences–> impaired cellular function, cell death, mutations or genetic instability.
Xeroderma Pigmentosum
Skin of people with this disease is very sensitive to direct sunlight, and they are prone to developing melanomas and squamous cell carcinomas.
UV component of sunlight causes cyclobutane thymine dimers to form in DNA, which can normally be repaired by NER. But individuals with this disease have defects on carious XP proteins in the NER complex and therefore exhibit the disease.
Hereditary nonpolyposis colorectal cancer
If you have a mutation on one of the alleles of the genes in the MER complex, you are more susceptible to HNCC. An acquired mutation in the remaining copy of the good gene would render the MER system nonfunctional, allowing tumor development.
Nonhomologous end joining and what disease is it associated with?
A double strand of DNA breaks, then DNA-dependent protein kinase and Ku proteins bind to the ends of the double strand break. nucleases remove several bases from both ends and then DNA ligase joins them together.
Hereditary nonpolyposis colorectal cancer
Cockayne Syndrome
autosomal recessive, congenital disorder. Mutations in ERCC6 and ERCC8–> code for genes that are involved in TCR of DNA. If DNA is not repaired, cell dysfunction and cell death may occur. RNA polymerase is permanently stalled at sites of damage in important genes. defect in transcription-coupled repair
Symptoms: neurological delay, photosensitivity, progeria (premature aging), hearing loss, eye abnormalities. Usually die within 20 years.
BRCA associated with breast cancer
BRCA 1 ( breast cancer susceptibility gene 1) and BCRA 2 are tumor suppressor genes. Mutations of these genes increases a woman’s liklihood of getting breast cancer by 5. Also at risk for developing other cancers
Homologous recombination
linked to causing breast cancer.
Types of DNA repair
Direct repair (enzymatic repair), Base exclusion repair, nucleotide excision repair (NER), Mismatch excision repair (MER), recombination repair (non homologous end joining, homologous end joining), transcription-coupled repair, translation synthesis.
Nucleotide excision repair, type of repair, enzymes associated with it, associated disorder
Repairs chemical adducts that distort DNA (ex: pyrimidine dimers, BPDE-guanine adduced, cisplatin adducts)
NER protein complex, DNA polymerase, DNA ligase
Associated with Xeroderma pigmentosum
Mismatch excision repair, type of repair, enzymes associated with it, associated disorder
repairs mismatched base in daughter strand.
MER complex, helices/endonuclease, DNA polymerase, DNA ligase
Hereditary nonpolyposis colorectal cancers
Where is the genetic defect in colon cancer? what enzyme or process is affected?
MSH2, 3, 6, MLH1, PMS2
mismatch repair
Where is the genetic defect in skin cancer, UV sensitivity, neurological abnormalities? what enzyme or process is affected?
Xeroderma pigmentosum groups A-G
Nucleotide excision-repaor
Where is the genetic defect in leukemia, lymphoma, x-ray sensitivity, genome instability? what enzyme or process is affected?
Ataxia Telangiectasia
ATM protein, a protein kinase activated by double stand breaks
Where is the genetic defect in Breast, ovarian, and prostate? what enzyme or process is affected?
BRCA2
repair by homologous recombination
Where is the genetic defect in congenital abnormalities, leukemia, genome instability? what enzyme or process is affected?
Fanconi anemia groups A-G
DNA interstrand cross-link repair
What are histone deacetylases?
HDACs- enzymes that remove acetyl groups from the lysine on core histones and nonhistone proteins. Cancer cells are very sensitive to inhibitors of such lysine deacetylases. Inhibitors are used as anticonvulsives and anticancer drugs.
Inhibitors of HDACs
valproic acid and vorinostat
what is epigenetics
a mechanism for regulating gene activity independent of DNA sequence that determines which genes are turned off or on:
in a particular cell type
in a different disease status
in response to a physiological stimulus
What factors influence epigenetic mechanisms
development in utero, environmental chemicals, drugs, aging, diet
T/F DNA methylation represses gene transcription when at a gene promoter
true
Autosomal dominant inheritance
Only 1 allele of a gene is needed for expression.
Unaffected individuals don’t show trait (aa)
Can be transmitted via male or female.
Trait is expected in every generation
recurrent risk is 50%
Autosomal recessive inheritance
2 copies of mutant allele is needed to show expression.
Females and males affected equally
X-linked recessive
Disease allele is on X in males is called homozygous
Always expressed in male carriers
Never father to son transmission
Lyionization
x inactivation
Mitochondrial DNA
double stranded and circular.
encodes rRNA, tRNA, and 13 polypeptides.
Transcription takes place in mitochondria.
Doesn’t have introns.
Inherited exclusively through the maternal line.
Why is mutation rate higher in mitochondria DNA?
They lack DNA repair mechanisms. Damage from free oxygen radicals from OXPHOS.
Mitochondrial inheritance
all offspring is affected.
there is a threshold you have to reach in order to express the gene.
Leber’s hereditary optic neuropathy
Mitochondrial disorder.
Degeneration of retinal ganglion cells.
Caused by one of three pathogenic mtDNA point mutations affecting NADH dehydrogenase–> RGC don’t have enough energy to transmit signals to the brain.
Acute loss of central vision, blind by 20’s.
Myoclonic epilepsy and ragged red fibers (MERRF)
Mitochondrial disorder.
Caused by mutation in the gene encoding for tRNA for lysine, which disrupts the synthesis of cytochrome-C oxidase.
Pt presents with myoclonus dinated muscle movements (ataxia) and seizures. Mainly affects muscles and nerves
Has a large variability, due to heteroplasmy
Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS)
Mitochondrial disorder.
Affects brain, nervous system, and muscles. Stoke and dementia, diabetes, deafness, cognitive impairment, short stature, migraine.
Caused by single point mutation. Cant use pyruvate, so lactic acid builds up.
X-Linked dominant
No carriers. Males with disease transmit 100% to females.
Females transmit trait to males and females (50% transmission)
Euploid
cells with normal number of chromosomes
Polyploidy
Cells contain a complete set of extra chromosomes
Aneuploidy
cells contain a missing or additional individual chromosome. Can be caused by a nondisjunction during meiosis.
Genomic imprinting
We receive an active copy of each gene from each of our parents. Genomic imprinting means only one is expressed.
Imprinted alleles are silenced, and gene is expressed for non-imprinted allele.
Epigenetic process that involves methylation and histone modification of egg or sperm, while genetic sequence is unchanged.
Pattern is duplicated in all somatic cells.
Uniparental disomy
when an individual receives two copies of a chromosome or part of each chromosome from one parent and no copies from the other.
T/F for genomic imprinting, a phenotypically normal individual would only have one transcriptionally active copy of the gene
True
Where does most genomic imprinting occur?
In regions containing other clusters of imprinted genes. Through methylation of 5’ region of gene.
Epigenetic imprints in somatic cells
imprints remain throughout the lifespan of the individual in somatic cells
Epigenetic imprints in germ cells
imprints are reset at each generation. In meiosis, imprints are erased and new ones are set.
Inversion
segment of chromosomal DNA is present in its reverse orientation
Deletion
segment is lost
Duplication
segment is copied, resulting in amplification of genes contained to that region
Translocation
Different chromosomes exchange segments of their DNA. can be balanced or unbalanced.
Translocations in non-homologous chromosomes
non-homologous chromosomes exchange genetic material, it is reciprocal
Robertsonian translation
Long arm of two afrocentric chromosomes combine, the short arm is typically lost.
Karyotyping
technique that allows the determentaiton of the number, size and gross structures of chromosomes in metaphase to be examined.
Turner syndrome
Karyotype: 45, XO
female, due to absence of Y.
Symptoms: short, ovarian hypo function/premature ovarian failure, don’t undergo puberty, infertile, webbed neck, low hairline on neck, CV defects, NO cognitive defects.
Prader-willi syndrome
Deletion of a region of chromosome 15.
On the paternal chromosome.
Presentation: short, hypotonia, small hands/feet, obesity, mild to moderate intellectual ability, uncontrolled eating.
Angelman Syndrome
Deletion of chromosomes 15 on maternal chromosome.
Presentation: severe intellectual disability, seizures, ataxic gait.
Klinefelter syndrome
Karyotype: 47, XXY
Presentation is variable: cognitive-social-behavorial-learning difficulties, hypogonadism (low T), small or undefended testes, gynecomastia, infertile, tall, variability in X (XXY, XXXY) can increase symptoms.
Downs syndrome
Trisomy at chromosome 21. Increases with increased maternal age.
Most commonly from maternal meiotic nondisjunction, but can also be from unbalanced translocation.
Varying degrees of cognitive impairment.
Structural abnormalities: increased nuchal translucency, cardiac defects, duodenal atresia, ventruculomegaly, absent nasal bone, short limbs.
Edward’s syndrome
Trisomy at chromosome 18.
Often IUGR.
95% die in utero.
<10% of live births survive to one year.
Presentation: prominent occiput, malformed and low set ears, small mouth and jaw, cleft lip, rocker bottom feet, overlapped fingers.
Patau Syndrome
Trisomy at chromosome 13. Severe developmental abnormalities. 1/12,500 births. most die before birth.
Presentation: heart abnormalities, kidney malformations, CNS dysfunction, microcephaly, malformed ears, closely spaced/absent eyes, clenched hands and polydactyl, cleft lip.
Reduced penetrance
The frequency a gene manifests itself.
EX: if 100% of people who inherit a genetic defect show the clinical presentation then it is 100% penetrance.
Variable expressivity
describes the range of phenotypes that vary between individuals with a specific genotype.
EX: neurofibromatosis: patients have cafe-au-lait spots that differ in number, shape, size, and position
Marfan Syndrome
Has variable expressivity.
Affects connective tissue, have weakened or stretched aorta, may lead to aneurysm and aortic dissection.
Locus Heterogeneity
single disorder or trait, caused by mutations in genes at different chromosomal loci. Only one mutant locus is needed for the phenotype to manifest.
Osteogenesis Imperfecta
Example of locus heterogeneity.
Brittle bone disease, mutations in collagen genes (either at chromosome 7 or 17). Either mutation shows the same phenotype.
Probability independence
occurrence of one does not affect the probability of occurrence of the other.
Multiplication rule
Probability of a given outcome in multiple trials is the product of the probabilities of each trial outcome.
EX: what is the probability of producing three girls:
1/2 X 1/2 x 1/2= 1/8
Addition rule
probability of either one outcome or another summed together.
Genotype frequency
number of individuals with a given genotype divided by the total number of individuals in the population.
Allele frequency
frequency of occurrence or proportions of different alleles of a particular gene in a given population.
Hardy-Weinberg
specifies relationship between gene frequency and genotype frequency
p^2 + 2pq + q^2 = 1
Cystic Fibrosis
Recessive inheritance.
Autosomal dominant inheritance pattern
Vertical transmission of disease phenotype. No skipped generations. affect males is about the same as affected females. Father to son transmission.
Autosomal recessive inheritance pattern
Clustering of the disease phenotype among siblings. Disease is not usually seen among parents. equal number of affect males and females.
Consanguinity
consanguineous mating’s are more likely to produce offspring affected by recessive disorders.
Incest. Mortality rates increase by 9%.
Polygenic inheritance
traits in which variations are thought to be caused by combined effects of multiple genes. Ex: height.
Leads to increased variability.
Multifactorial inheritance
when environmental factors cause variation in the trait. Leads to increased variability.
For multifactorial diseases that are either present or absent, there has to be a threshold of liability that must be crossed for the disease to be expressed.
Threshold is lower for males
Pyloric stenosis
Muscular hypertrophy between stomach and duodenum. Usually in males because males need less risk genes to show the disease.
Leads to vomiting and obstruction
Multifactorial inheritance recurrence risks and transmission patterns
Recurrence risk is higher if more than one family member is affected. If expression of disease in proband is more severe, recurrence risk is higher.
Recurrence risk is higher if the probes is of the less commonly affected sex.
Recurrence risk decreases in more remotely related relatives.
How does streptomycin affect protein synthesis
Inhibits the initiation phase
What antibiotics inhibit the elongation stage of prokaryote protein synthesis
Tetracyline, shiga toxin, ricin, puromycin, chloramphenicol, cycloheximide, clindamycin, erythromycin, diphtheria toxin
How big are ribosome subunits in prokaryotes?
30S subunit
50S subunit
How big are ribosome subunits in eukaryotes?
40S subunit
60S subunit
Streptomycin
binds to the 30 S subunit to disrupt initiation of translation
Shiga Toxin
binds to the 60S subunit to disrupt elongation
Clindamycin and erythromycin
bind to 50S subunit to disrupt translocation of the ribosome
Tetracycline
Binds to the 30S subunit to disrupt elongation
Where is peptidyl transferase activity housed?
in large subunits
Diphtheria toxin
inactivates EF2-GTP and inhibits elongation
Cycloheximide
inhibits peptidyl transferase and impairs peptide bond formation
Puromycin
elongation inhibitor. causes premature chain termination.
Enters at the A site and adds to the growing chain, forms a puromycylated chain leading to premature chain release.
More resistant to hydrolysis bc it doesn’t break down as easily. Stops ribosome from functioning.
Silent mutation
does not change amino acid
Missense mutation
changes amino acid in the protein
Nonsense mutation
codon changes into a stop codon.
Also called Null mutation. protein is either degraded or formed as a truncated version.
Frameshift mutation
one or more nucleotides are deleted or inserted into ORF.
Out of frame frameshift mutation
change in the codon sequence and consequently alteration in the amino acid sequence
Sickle cell anemia
Example of a missense mutation.
Mutation of 6th allele in gene for Beta-Globing.
Changes Glutamic acid for Valine
changes causes conformational change of HbA, causing it to aggregate and form rigid, rod like structures.
Deformed erythrocytes have poor oxygen capacity and clog capillaries.
Duchenne Muscular Dystrophy
Example of a frameshift mutation. Only males can get it.
Out of frame deletions to dystrophin gene.
Little to no expression of dystrophin protein.
Leads to muscle wasting
Becker muscular dystrophy
Frameshift deletions. In frame deletion. Results in expression of truncated forms of dystrophin.
Steps after protein synthesis
Protein sorting, post-translational modifications, protein folding, proteolysis, degradation.
Cytoplasmic pathway of protein sorting
For proteins destined for cytosol, mitochondria, nucleus, and peroxisomes.
Protein synthesis begins and ends on free ribosomes in cytoplasm.
translocation signals play a role in final targeting.
Secretory pathway of protein sorting
for proteins destined for ER, lysosomes, plasma membrane, or for secretion.
Translation begins on free ribosomes but terminates on ribosomes sent to ER.
ER targeting signal sequences present on first 20 amino acid residues for polypeptide.
what is the translocation signal for proteins destined for the cytoplasm
None
in cytoplasmic pathway
what is the translocation signal for proteins destined for the mitochondria
N-terminal hydrophobic a-helix signal peptide. in cytoplasmic pathway
what is the translocation signal for proteins destined for the nucleus
KKKRK signal sequence in cytoplasmic pathway
what is the translocation signal for proteins destined for the peroxisomes
C-terminal SKL signal sequence in cytoplasmic pathway
what is the translocation signal for proteins destined for the ER lumen
C-terminal KDEL retention signal. in secretory pathway. K-Lysine D- aspartic acid E- Glutamic acid L- Leucine
what is the translocation signal for proteins destined for the Lysosome
Mannose-6-phosphate signal group. in secretory pathway.
Dysfunction in protein produces I-cell disease.
what is the translocation signal for proteins destined for the Secretion
Tryptophan-rich domain signal region, absence of retention motifs. In secretory pathway.
what is the translocation signal for proteins destined for the membranes
N-terminal apolar region (stop transfer sequence)
What is the role of chaperone proteins?
protect unfolded proteins
Mitochondrial protein import
Translocation sequences recognized by transporters present in the mitochondrial membrane.
TIM and TOM- proteins passed through
Nuclear protein import
Protein imported via nuclear pores. small proteins are able to pass through the pores. Larger proteins require nuclear localization signals - four continuous basic residues (lys and arg)
Mechanism of secretory pathway
Proteins have ER-targeting signal peptide.
Basic amino acids near N term.
Hydrophobic sequence on C term.
Signal recognition particle binds to the ER targeting signal and the ribosome during translation. it wraps around ribosome-mRNA-peptide complex, which halts translation. Translation doesn’t resume until the protein is directed into the ER lumen. Protein is cleaved and then post translational modification in ER and golgi occur.
I-Cell disease
issue with lysosomal proteins. Tagging of lysosomal proteins with mannose 6P is defective–> so proteins targeted for lysosome don’t get to lysosome.
Causes a high plasma level of lysosomal enzymes.
Presentation: failure to thrive, developmental delays, issues with motor skills are worse than cognitive delays, abnormal skeletal development, coarse facial features, restricted joint movement, stiff claw shaped hands, short trunk dwarf, clouding on cornea.
Recurrent respiratory tract infections.
Death by age 7
Protein folding
happens post-translational. Small proteins fold on their own but larger proteins can’t and are at risk for aggregation and proteolysis.
Chaperonins
barrel shaped compartments that admit unfolded proteins and catalyze their folding in an atp dependent manner.
Proteolytic cleavage
converts inactive forms to active enzymes by unmasking active site. Converts precursor proteins to mature ones (ex: proinsulin to insulin)
Post translational acetylation
covalent linkage to amine, uses amine group, Lysine is affected
Post translational glycosylation
O-glycosylation, uses -OH, affects Serine, Threonine
N-Glycosylation, uses Acid-amide, affects Asn, Gln
Post translational phosphorylation
Phosphate linked via esterification. Uses -OH. Affects Her, Try, Thr, also ASP and HIS
Post translational disulfide bonds
Oxidation to achieve covalent linkage of cysteine residues. Uses sulfhydrl. Affects Cysteine
Histone acetyltransferase (HAT)
catalyzes acetylation reaction
Histone deacetylase (HDAC)
catalyzes deacetylation reaction of histones
Ascorbic acid
Essential for activity of lysol and propel hyrdoxylases.
Defects in lysyl hydroxylases
result in skin, bone and joint disorders
Ehlers-Danlos Syndrome
defect in lysyl hydroxylase. Overly flexible joints, walls of blood vessels, intestines or uterus may rupture.
Epidermolysis Bullosa Simplex
defect in lysyl hydroxylase. Blisters on skin,
Alzheimer’s disease
Neurodegenerative disorder. comes in two forms: familial (early onset) and sporadic.
Familial caused by misfiling/aggregation of amyloid beta peptide (AB) in brain- extracellular. and by hyperphosphorylation of Tau (neurofibrillary tangles)- intracellular
Parkinson’s disease
Aggregation of a-synuclein protein forms insoluble fibrils which deposit as lewy bodies in dopaminergic neurons in substantial nigra. Results in selective death of neurons.
Due to reduced availability of dopamine. Loss of motor functions.
Huntington’s disease
Mutation in Huntington gene results in expansion of CAG triplet repeats–> polyglutamine repeats, which eventually misfold and aggregate.
Selective death of cells in basal ganglia cause symptoms: loss of movement and cognitive functions and psychiatric problems.
Creutzfeldt-Jakob Disease
Formally mad cow.
Caused by misfiling of prion proteins. Transmissible.
Belongs to transmissible spongiform encephalopathies.
Symptoms: failing memory, behavioral changes, lack of coordination, visual disturbances. late stage: mental deterioration, blindness, weakness of extremities, coma.
Characteristics of stem cells
not terminally differentiated, can divide without limit, undergo slow division, when they divide give rise to 1 cell with stem cell characteristics and another with the ability to differentiate.
Totipotency
ability to give rise to all cells of an organism, including embryonic and extra embryonic tissues. a zygote is totipotent up to about 16 cells.
in zygote
Pluripotent
ability to give rise to all cells of the embryo and subsequently adult tissues.
blastocyst
Multipotency
Ability to give rise to different cell types of a given lineage. Partially committed.
Various tissues
Founder stem cells
define the size of large final structures. controlled by short range signals. each tissue has fixed number of founder cells- proportions of the body are determined early.
Transit amplifying cells
Committed. cells that divide frequently. have limited number of divisions.
Immortal strand hypothesis
when stem cell replicates, one daughter cell gets the exact same DNA and other cell gets copies. upon further division, one daughter cell will always keep original DNA. This helps prevent mutations.
Embryonic stem cells
unrestricted development, but have to be inserted at the correct stage of embryonic development–> if not can become a tumor.
differentiate into: cartilage, bone, skin, nerves, gut and respiratory lining
Which transcription factors are responsible for pluripotent ability of ES cells?
Nanog, Oct4, Sox2, FoxD3
GCNF
required for early stages of pluripotent cell differentiation
Cripto and GDF-3
growth factors found in pluripotent cells.
Hematopoietic stem cells
differentiate into blood components
come from bone marrow
Stromal Stem cells
differentiate into connective tissues, tissues
come from bone marrow
Cord blood
undifferentiated. no gene manipulation
Somatic cell nuclear transfer
nucleus taken from somatic cell of patient and injected into oocyte of a donor replacing the oocyte nucleus.
ES cell character gene regulatory proteins
Oct3/4, Sox2, Myc, KIf4
Induced pluripotent stem cells
Prospect of introducing patient-specific iPS cells for use in treatment. Use transcription factors to induce pluripotency
Effectors
alter the activity of different components downstream and generate secondary messengers that elicit a cell response.
Endocrine signaling
signal (hormone) is transported via blood.
Long distance.
Long lasting
freely diffusing signal.
EX: epinephrine.
Paracrine signaling
signal diffuses to neighboring target cell of a different type.
Local signaling
Short lived signal
EX: testosterone
Autocrine signaling
Secreting cells express surface receptors for the signal, or release to cells of the same type.
action of growth factors in cancer cells.
EX: interleukin-1
Direct/juxtacrine
signal binds to signaling cell which then binds to receptor on the target cell. In immune cells.
EX: heparin-binding epidermal growth factor
Hydrophilic signaling
signals cannot penetrate the plasma membrane–> interact with receptors on cell surface.
Complex initiates production of second messenger.
G protein- coupled receptors…. glucagon
REceptor tyrosone kinases…. insulin
Lipohilic signaling
signals pass through the plasma membrane. binds to receptor proteins inside the cell. complex acts as a transcription factor.
Long half lives.
EX: steroid hormones, thyroid hormone, retinoids.
What is the on/off switch in GPCR signaling?
GTPase-activating protein (GAP)
Signal Desensitization mechanisms
ability to turn off signal.
Different mechanisms: drop in hormone level, remove the signal molecule, receptor sequestration, receptor destruction.
Gs
stimulates adenylate cyclase
Ligand is epinephrine and histamine
Beta-adrenergic receptor
Gi
inhibits adenylate cyclase.
ligand is epinephrine/noreepinephrine, dopamine
alpha-adrenergic receptor
Gq
activates phospholipase C
Ligand is acetylcholine
Gt
stimulates cGMP phosphodiesterase
Ligand is light
cGMP phosphodiesterase:
hydrolyzes cGMP to 5’-GMP
Inhibition of cGMP phosphodiesterase
inhibitors cGMP PDE increase concentration of cellular cGMP and prolongs its effects for a greater amount of time, leading to smooth muscle relaxation and vasodilation, resulting in an erection
inhibition of G proteins by bacterial toxins
cholera toxin prevents inactivation of Gsa (toxic water).
Covalent modification of a subunits of Gs.
ADP ribosylation of Arg in Gs alpha decreases GTPase activity. Gsa remains active and stimulates adenylate cyclase, resulting in over production of cAMP.
Overabundance of cAMP in intestinal cells open Cl channels resulting in loss of water and electrolytes.
Pertussis toxin
prevents activation of Gia ADP ribosylation of Lys on Gia prevents activation and dissociation of a subunit from the trimeric G protein complex.
Less inhibition of adenylate cyclase, more cAMP. causes excessive mucous secretion which prevents as cough.
Nitric Oxide
NO is produced in epithelial cells from arginine and is responsible for relaxation of smooth muscle.
Antihistamines
lipophilic compound that blocks the effect of histamine to the H1 GPCR
ex: zyrtec, claritin, benadryl
Hybridization
Technique to detect infectious agents.
single stranded DNA binds to another strand of DNA or RNA and makes a DNA-DNA hybrid.
First hybridized and then looked at on a solid support (blotting)
Southern Blotting
Both prob and target nucleic acid are DNA
Northern Blotting
probe is single stranded DNA and target is mRNA.
Western Blotting
target cell is protein. measures the amount of protein or antibody
Eastern blot
Target cell is PTM (lipid, carb, phosphorylation)
detects post-translational modifications on proteins
Polymerase Chain Reaction
double stranded DNA obtained from patient. First denatured by heating. Then add primers in 3’ to 5’ direction. Anneal (cool). Add dNTYPS and the Taq polymerase which extends the sample between the primers.
Quantitative PCR
Detect levels of an infectious agent.
Determine levels of gene expression.
Restriction Fragment Length Polymorphism (RFLP)
lead to different fragment patterns when looked at on a gel.
Steps of forensic analysis for DNA
extract gDNA, cleave with endonuclease, put on gel, transfer DNA to nylon membrane, add radioactive DNA probe, expose to X-ray, compare the samples.
Detection of sickle cell using RFLP
normal B-globulin allele has 3 Ddel restriction sites, sickle cell patients only have 2. loss of restriction site means that sickle cell patients are cleaved to only 1 fragment.
Variable number of tandem repeats (VNTR)
short tandem repeats occur in genome but varies in individuals. useful for recognizing severity of inherited diseases.
ex: PTs with huntington’s disease have a lot more CAG repeats.
Recombinate proteins
allow for large scale production and purification. Helps make things like insulin, growth hormone, clotting factors.
Abciximab
inhibits platelet aggregation
Baciliximbab
Prevents rejection of transplanted kidney
Cetuximab
Treats metastatic colorectal cancer
Infliximab
Treats autoimmune diseases
Retuximab
Treats lymphomas, leukemia
Enzyme-Linked immunosorbent assay (ELISA)
tests for the levels of specific antigen or antibody concentrations in biological samples using corresponding antibody.
Indirect ELISA
measures amount of antibody in sample.
Sanwhich ELISA
measures the amount of antigen in sample.
ELISA for diagnosing HIV
uses indirect.
ELISA for diagnosing MI
uses sandwich ELISA
How to diagnose HIV
use western blot
Primary elements of immune system
bone marrow, thymus
Secondary elements of the immune system
spleen and lymph nodes, mucosal tissue
Innate immunity
epithelial barriers, phagocytes, dendritic cells, complement, NK cells,
Adaptive immunity
B lymphocytes, antibodies, T lymphocytes
