KICK THE BOARDS USMLE STEP 1

GENETICS Prepared by Dr. Irfan Mir

KICK THE BOARDS. USMLE STEP 1 “GENETICS”

Prepared by Dr. IRFAN MIR

GENETICS (MOLECULAR BIOLOGY) * DNA and RNA (Nucleic acid) are composed of 1. Nitrogenous Base --------- 1. Purine ----------------- Adenine (A) Guanine (G) 2. Pyrimidine ---- Cytocine (C) Thymine (T) in DNA only Uracil (U) in RNA only 2. Sugar ----------------- Deoxyribose Ribose (only in RNA) 3. Phosphate * Centromere is a nucleotide sequence that binds to Mitotic Spindle during cell division.. * Replication Origin are nucleotide sequence that act as origination site for Replication. (human chromosome contain numerous replication origin which ensure rapid cell division. * BANDS contain gene and are identified with Fluorescent dye and Giemsa Stain. * BANDS ------------ G Bands ------ rich in A - T (stain dark) R Bands ------ rich in G - C (stain light) * Gene is a region of DNA that produce a functional RNA molecule. * Gene Region ----------- Non coding region (intron) ---- It is intervening sequence and is major part of gene, and does not express AA or mRNA. Coding region (Exons) --------- It is Expression sequence and is minor part of gene, and it code for protein and mRNA. * Chromatin is complex of histone and non histone protein that is bound to DNA. * Histone contain large proportion of lysine and arginine AA which have +ve charge thats why bind to -ve charge portion of DNA. -----------------------------------------------------------------------------------* Go (Gap phase o) is the resting phase of the cell. * G1 (Gap phase 1) -- G1 phase (last 5 hr) -- During G1 syn of RNA, Protein, Lipids, and Carbohydrates occur. * S phase (synthesis) --- last 7 hrs ---- syn of DNA and chromosome protein (histone etc) occur during this. * G2 (Gap phase 2) --- last 3 hrs ---- During this ATP syn occur ( this is interval b/w S phase and M phase) * M phase -- during this cell division occur (mitosis) it has 6 stages. 1. Prophase -- ( nucleus appear ) 2. Prometaphase -- ( Nucleus disappear, envelop disrupt ) 3. Metaphase -- ( ch aligns at metaphase plate ) colchicine inhibit microtubules here. 4. Anaphase -- ( ch moves to opposite poles ) 5. Telophase -- ( Nucleus reappear ) 6. Cytokines -- ( cytoplasm divides )

* p53 (antioncogene) supress the cell cycle at G1  S phase transition. (it is very imp to control normal cycle in normal cell) ------------------------------------------------------------------------------------* DNA polymerase require a RNA primers to begin DNA syn. * DNA polymerase copy a DNA Template in 3'  5' direction, later New DNA strand is produce in 5'  3' direction. * Replication Fork is the site where DNA syn occur. vs * Replication Origin is a specific nucleotide sequence where Chromosome Replication occur. * DNA Halicase recognize the replication Origin, unwind the DNA strand (double helix) to form replication bubble with replication fork on both end. (Topoisomerase relieve the strain imposed by unwiding)

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* Replication Fork -- contain leading strand (which add repeats of the nucleotide sequence) and lagging strand (which uses nucleotide sequence synthesize by leading strand to produce lagging strand so the DNA never shortened). Remember DNA syn occur bidirectionally on each fork. 1. Leading strand of replication fork is a template for contineous (linear) DNA syn in 5'  3' direction with DNA polymerase  (delta). 2. Lagging strand of replication fork is a template for DNA syn discontineously in 5'  3' direction with DNA polymerase  to produce okazaki fragment * DNA primase synthesize short RNA primers along lagging strand later DNA polymerase  use these short RNA primer to synthesize the DNA fragment called Okazaki Fragment. (okazaki fragment ends when it meet RNA primer downstream) * To form a continuous DNA from Okazaki Fragment, a DNA repair enz replace RNA primer with DNA. Later DNA ligase join the DNA Fragment (okazaki fragment) to form continuous DNA. * Nuclease cleave the end to form double helix DNA. * Telomere is a nucleotide sequence located at the end of chromosome which allow replication of linear DNA to its full length. In other words Telomere is the nucleotide sequence due to which DNA does not shorten with each replication cycle. * Telomerase is the enz that recognise sequence on the leading strand and adds the repeats of nucleotide sequence to the leading strand, later DNA polymerase  uses that added repeats on the leading strand as a templet to synthesize complementary repeats on the lagging strand (okazaki fragments). That is how cell prevent DNA loss with each cell replication.  Remember function of leading strand is to synthesize repeats of nucleotide sequence so lagging strand can use those repeats to produce DNA. Synthesizing repeats of nucleotide sequences by leading strand also ensure that the cell is not lossing any DNA with each cell replication cycle. Types of DNA Damage -- DNA repairs involve DNA excision of the damage site, DNA syn in correct sequence & DNA ligation. 1. Depurination is the most common type of DNA damage which is missing purine base (A or G). Depurination occur when N - glycosyl bond b/w purine and deoxyribose sugar phosphate is broken. * AP (apurinic site) Endonuclease recognize the site of missing purine and nicks the deoxyribose sugar phosphate than phosphodiesterase excise the deoxyribose sugar phosphate. * Later DNA polymerase and DNA ligase restore and correct DNA sequence and heal the nick. 2. Deamination of cytocine to uracil is another type of DNA damage  incorrect U- A base (rather than A-G base) * Uracil DNA Glycosidase recognize and remove Uracil (U) than AP (apyrimidinic site) Endonuclease recognize the missing base and nick the ribose sugar phosphate than Phosphodiesterase remove ribose sugar phosphate. * Later DNA polymerase and DNA ligase restore and correct DNA sequence and heal the nick. 3. Pyimidine Dimerization is another possible way for DNA damage by ultra violet radiation . For eg sunlights ultra voilet radiation cause covalent linkage of adjacent pyridimine  pyrimidine dimers. * uvrABC enzyme recognize the pyrimidine dimer where as DNA polymerase and DNA ligase restore and correct DNA sequence and heal the nick.

Dis Due to defect in DNA Repair ENZ :1. Xeroderma Pigmentosum - due to hypersensitivity to UV radiation and inability to remove pyrimidine dimers. 2. Ataxia Telengiectasia - hypersensitivity to ionizing Radiation due to defect in repair enz  cerebellar ataxia, oculocutaneous talengiectasia, immunodeficiency 3. Fanconi's Anemia - hypersensitivity to DNA cross linking agent due to defect in repair enz  leukemia and progressive aplastic anemia.

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4. Bloom's $ ------------------------- hypersensitivity to DNA damaging agent  immunodeficiency, growth retardation, predisposition to cancer. 5. Hereditary non polyposis colorectal cancer - human HNPCC gene (homologue to E coli gene) is involved. surgically removeable if diagnosed early. ---------------------------------------------------------------------* Many DNA viruses and other transposable element encode for a recombination enz called Integrase & Transposase respectively, Recombination is refer to process that give rise to combination of gene in offspring’s different from those of either parents * Viral Integrase recognize specific nucleotide sequence and cut the viral DNA than Cut end of viral DNA attack and break host double helix DNA and inserted into it than DNA repair occur to fill the gap. * Transposable element are mobile DNA sequences that jump from one place in genome to other ( transposition). * Human genome consist of 2 Families of transposable element. 1. Alu sequence, 2. Line-1 sequence . Both transposable element under go long quiescent (resting) period followed by period of intense movement called transposition burst which contribute to genetic variability of the genome. * Transposases is the recombination enz (in humans) similar to the integrase (in virus). It cut the transposable element in DNA and relocate it just like integrase in virus. * Transposable element undergoes transcription which produce an RNA copy that encodes Reverse Transcriptase enz. Than reverse transcriptase enz uses the RNA copy to produce double stranded DNA copy of transposable element. * If the transposable element move near the active gene it may effect the level of gene expression or mutate it or inactivate it. * Gene Transfer occur when gene b/w two transposable element move to new location during transposition. Gene transfer is imp in development of tetracycline resistance in bacteria, resistance can be spread to other bacteria through bacteriophage DNA. * Phage DNA with TetR gene infect other bacteria and confer tetracyclin resistance. -------------------------------------------------------------------------------------------* Gene Amplification occur when repeated round of DNA syn yeild multiple copies of gene. * Cancer cell often become resistant to methotrexate by amplification of the Dihydrofolate reductase gene   dihydrofolate reductase level, which overcome inhibitory effect of methotrexate. (remember methotrexate is dihydrofolate reductase inhibitor) * Restriction enz are bacterial enz that catalyze the hydrolysis of the phosphodiestrase bond in DNA molecule at specific sequence . It always produce same pattern of DNA fragment. * Gel Electrophoresis :- When DNA sample is fragmented by restriction enz it is seperated by size with Gel electrophoresis to construct and compare physical map (Restriction map) of DNA. * Restriction Mapping :- provide useful information about DNA fragment but ultimate physical mapping of DNA is in its nucleotide sequence which is establish by DNA sequencing. * DNA Sequencing :- This method is achieved by DNA syn with Dideoxyribonucleoside triphosphate that lack the 3' OH group that they normally contain, so during DNA syn addition of the next nucleotide is blocked (because of 3' OH group is missing). This blocking is the enzymatic method of DNA sequencing. (Note due to 3' OH group of dideoxyribonucleoside triphosphate DNA syn continuously) * Southern Blotting uses the DNA probe and the hybridization reaction to identify the specific DNA sequence. It is used in prenatal testing of genetic dis for eg Sickle cell anemia, huntingtun dis, neurofibromatosis, cystic fibrosis. * DNA Probe is the single stranded DNA segment that participate in hybridization reaction. * The term Cloning is used in 2 ways. 1. Making identical copies of a DNA molecules. 2. it is also isolating one gene from DNA. * The main difference b/w the genomic library and the complement DNA (cDNA) library is that genomic library uses genomic (chromosomal) DNA where as cDNA library uses DNA copied from mRNA. * Reverse Transcriptase is the critical enz in the creation of cDNA library because it produces DNA from a RNA Template. * PCR use repeated replication cycle with specially designed primers, DNA polymerase and ATPs to amplify DNA. * Another method to repeat replication is in bacterias.

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* PCR is the sensitive method that can detect even low level of viral DNA early in the course of infection. * Factor VIII can be cloned by gene expression requires a plasmid (expression) vector in bacteria. (gene transplant). * Factor X is produce in the milk of Transgenic sheep or cow by (plasmid) expression vector. (gene transplant) * Animal with gene transplant (new gene) in its genome is called transgenic. ----------------------------------------------------------------------------------------* There are two type of DNA sequences that play role in gene regulation. 1. Gene Promotor DNA sequences is usually located near the gene where initiation site is present.This is where Transcription begins. It contain TATA Box (rich in T and A) and CAAT Box (rich in G and C). 2. Gene Regulation (Enhancer) DNA sequence located far away from gene . It binds gene regulatory protein that either activate or repress the transcription initiation complex. * RNA polymease II & Transcription factor are not sufficient for transcription other factors like gene regulatory protein are also needed. * Transcription Factor and Gene regulatory protein binds to DNA are of 4 types. 1. Homeodomain protein ( Pit-1, OCT1, OCT2 etc ) 2. Zinc finger protein ( TF III A, Sp1, BRCA protien, p53 protein ) 3. Leucine zipper protein ( C/EBP, CREB, Fos, Tun protien ) 4. Helix - loop - Helix protein ( Myc protien, Myo D protien ) * Homeodomain protien regulaes genes associated with Ig Several enzymes and several hormone production. For eg Pit-1 regulate Gh, TSH & Pl gene (mutation result in combined deficiency of GH, TSH, PRL). where as OCT-2 regulate Ig gene. * Zinc finger protien is Hormone Binding protien present in Receptors; like Glucocorticoid Receptor, Estrogen & progesterone receptor, TH receptor, Retinoic acid receptor and Vit D3 receptor. * Leucine Zipper protien regulates somatostatin & Enkephalin gene and also regulate Cell cycle and cell transformation. For eg C/ERB regulate albumin and Alpha 1 antitrypsin gene. * Helix - Loop - Helix protien regulate gene involve in muscle development and cell cycle. --------------------------------------------------------------------------------------* Transcription is a process by which cell copy DNA to RNA. It occur in the nucleus. * Transcription occur by one of 3 enzs 1. RNA polymease I  produce rRNA, 45sRNA 2. RNA polymerase II  produce mRNA , small nuclear ribonucleic protein (SnRNP) 3. RNA polymerase III  produce tRNA and 5SrRNA. * RNA polymerase copy DNA template strand in 3'5' direction which produce RNA transcript in 5'3' direction. * RNA Capping is addition of methylated Guanine nucleotide to the 5' end of the RNA transcript where as RNA polyadenylation is addition of poly - A - tail to 3' end of RNA transcript they both stabilize the mRNA in order to export it from nucleus. * RNA Splicing remove all intron (non coding region) and join all exons (coding region) within RNA transcript this is perform by SnRNPs. Finally RNA transcript is export from the nucleus for translation. * Translation is the process by which mRNA nucleotide sequence is translated into AA sequence of protein in cytoplasm by decoding a set of 3 nucleotide called Codon into 1 AA eg GCA, GCC, GCG all code for alanine. * There are more than one codon for one AA. * Translation also uses Aminoacyl - tRNA synthatase for AA syn, since there are 20 different AA thats why there are 20 different Aminoacyl - tRNA synthatase. * Translation uses the enz Peptidyl transferase which help to form a peptide bond b/w AAs . * The ribosome move along the mRNA in 5' 3' direction. note - The NH2 - terminal end of a protein is synthesize first & COOH- terminal (carboxyl group) end is synthesize last.

* Translation begin always with Start Codon AUG which codes for methionine than methionine is later removed by protease . * Translation terminate always by Stop Codon (these are 3 UAA, UGA, UAG). The stop codon binds it releases factor that cause ribosome to release protein into the cytoplasm. * In  thalassemia the normal G - T sequence is mutated to A - T  incorrect RNA splicing  defective  globulin mRNA  defective protien. --------------------------------------------------------------------------------

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KICK THE BOARDS. USMLE STEP 1 “GENETICS”

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* Nucleolus contain approx 200 copies of rRNA gene per haploid genome. RNA polymerase I transcribes the rRNA gene to form 45S RNA. * There is another set of rRNA gene present out side the nucleolus. These rRNA transcribed by RNA polymerase III the to form 5S RNA. * Nucleolus contain 1. Fibrillar Center: contain transcriptionally inactive DNA. 2. Dense fibrillar component: contain transcriptionally active DNA, RNA polymerase & 45S RNA. 3. Granular component: contain 45S RNA, 5S RNA, Ribosomal protein, RNA binding protein & 5SnRNPs. -------------------------------------------------------------------------------* Silent Mutation alter the codon in nucleotide but no phenotypic changes is seen in the individual. it produce functional protein. * Missense Mutation alter a codon in a single nucleotide so that one AA replaced with another AA. This produce protein with compensated function. * Non sense Mutation alter a codon in a single nucleotide which produce altered codon or a premature Stop codon. It produce nonfunctional (truncated) protein that are unstable and readily degraded . * Frame shift mutation alter the codon by deletion or by insertion of single nucleotide which shift the reading frame with resultant change in all AA. It produce nonfunctional garbled protein. * Translocation mutation occur when a section of a gene moves from its original location to another location either on the same ch or different ch. These mutation may produce no protein. * RNA splicing Mutation alter intron part of nucleotide which change the splice site in the RNA transcript. It produce no protein because mRNA is unstable and rapidly degraded. * Transposable element mutation alter a codon in transposable element, it produce no protein (because mutation disrupt gene). Although transposition is common in human genome but it rarely disrupt a gene. * Trinucleotide Repeat Mutation results into three nucleotide sequence ( CAG, CGG, CTG) repetition some times 1000 times . These Mutation cause Kennedy $, Fragile X $, Myotonic dystrophy, Huntington dis etc. ---------------------------------------------------------------------------------------* Locus is the location of gene or DNA on ch. * Allele is alternative version of Gene or DNA occupying the same position or locus on ch. * Linkage (Coinheritance) is the closeness of two or more loci on a ch during meiosis (linkage refer to loci not allel). It is only useful in family studies (pedigree) like Adult polycystic kidney which is an example of linkage. * Polymorphism is occurrence of 2 or more allele at a specific locus in frequency greater than cant be explain by mutation only. * Polymorphism are common in noncoding region of DNA (intron). * Remember Polymorphism is not a mutation that can cause dis however a polymorphism can be used as a genetic marker of dis. For eg. Dystrophin gene in Duchenne muscular dystrophy where polymorphism and dystrophin gene are closely linked. * Polymorphism type -- 1. Restriction fragment length Polymorphism (RFLPs). 2. Variable number of tendem repeats (VNTRs). * RFLPs either create or destroy a restriction enz site & is used in gene linkage & gene mapping studies. (pedigree) * VNTRs leaves restriction enz site intact but alter the length of restriction enz fragment and are used in DNA finger printing and forensic medicine to establish paternity, zygosity, identify from blood, semens, or other DNA samples. * Since VNTRs is extremely polymorphic two unrelated people cannot exhibit the same genotype. * Genetic Drift is the random fluctuation of allele frequency in a small population because the pool of gene passed from generation to generation is small. * Founder effect is the type of genetic drift that occur in population that descends from small no of founding individuals. An allele may occur at high frequency in the population because it was present in the high frequency among the founder. ----------------------------------------------------------------------------------------

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* Autosomal Dominant Inheritance :- Individual carry one defective copy of the gene from either parents. Eg. Huntington dis. * Autosomal recessive Inheritance :- Individual carry two defective copies of the gene from each parent. eg. Cyctic fibrosis. * X - Linked Recessive Inheritance :- Usually occur in male (hemizygous), females are clinically normal but they may have subtle clinical feature because they carry two X ch (heterozygous). These dis may occur in female when one of the two X ch is inactivated during late blastocyst stage to form Barr Bodies. This process is called Dosage compensation. * During late Blast cyst stage Barr Bodies (Inactivation of X ch) formation is random and permanent event. * X - Linked Dis is genetically lethal in malebecause males are hemizygous for X ch. (female are hetrozygous for X ch) * In Duchenne Muscular Dystrophy the defective gene is on the short arm (p) of X ch in band 21 (Xp21) which code for dystrophin protein which anchor cytoskeleton (actin) of skeletal muscle cell to the EC matrix to stabilize the mem. * Mitochondrial Inheritance caused by mutation in mitochondrial DNA (mtDNA) the transmission is always maternal. It can effect all sexes. Leber's Hereditary optic neuropathy, Kearns - Sayres $, Myoclonic epilepsy with ragged Red fiber $. * Human mtDNA gene contain only exons. mtDNA encodes 2 rRNA, 22 tRNA & 13 protein. Its Mutation effect both sexes. * Multifactorial Disorder :- Mutifactorial inheritance involve gene that have a small equal and additive effect (genetic component) as well as environmental component. In multifactorial inheritance term polygenic is used. --------------------------------------------------------------------------------------* Proto Oncogene ras is a normal gene it encodes protein with intrinsic GTPase activity it stimulates cell cycle . * Oncogene is a mutated Proto - oncogne, it encodes a protein which cause cancer. * Anti Oncogene is normal gene (Tumor suppressor gene). It suppresses the cell cycle. (Rb, p53, BRCA1, NF1, WT1, VHL, APC, DCC) * Proto Oncogene and Oncogene encode such as v - ras in virus (v stands for virus) and c - ras in cells (c stands for cell). * ras gene produce Ras protien note the small r which stand for gene & capital R which stands for protien. (v for virus & c for cell) * Classes of Oncogene :1. Growth factor: sis Oncogene (Astrocytoma, osteosarcoma). 2. Receptors: erb B1 (Squmas cell carcinoma), erb B2 (Breast, ovarian, lung & stomach cancer), erb B3 (Breast cancer) 3. Signal transducer --- src (Rous avian sarcoma), abl (Chronic myeloid &Acute lymphoblastic leukemia), ras (Bladder, lung, colon & pancreatic cancer). 4. Nuclear transcription -- un (Avian sarcoma), Nmyc (neuroblastoma), myc (Berkitt Lymphoma), pmi / rar +, fos. sis is encode for PDGF. erbB1,2,3 encode for Epidermal growth factor receptor. src & abl encode for tyrosine kinase. ras encode for G protien with GTPase activity. N-myc & myc encode for Helix - loop - Helic protie * p53 is the most common target for mutation in human cancer present on ch 17. --------------------------------------------------------------------* In Dorsophilia bizarre mutation in body pattern occur ( leg sprout from the head in place of antennae) . Substitution of one body part for another is called Homeotic Mutation and gene Involve in it called Homeotic Gene and the cluster of homeotic gene called HOM complex. * In human the HOM Complex is called HOX Complex (cluster homeotic gene). * HOX Complex are organized in 4 clusters :- 1. HOX - A Cluster ----- on ch 7 2. HOX - B Cluster ----- on ch 17 3. HOX - C Cluster ----- on ch 12 4. HOX - D Cluster ----- on ch 2 * Non clustered homeotic gene are randomly dispersed through out human gene. * Homeotic gene either clustered (HOX complex) or non clustered (Dispersed) cause variety of clinical defect. eg Inner ear anomalies, Synpolydyctyly, Hand Foot Genital $, Thymic hypoplasia.

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* B cells & T cells Ag specificities develop before exposure to Ag & each B cell and T cell carries Ig for a single Ag. * B cells Immunoglobulin has 4 Protein subunit consist of ---- 1. 2 heavy chain -- gene on ch 14 2. 2 light chain -- gene on ch 2 and 22. * Variable segment (VH) , Diversity segment (DH), Joining segment (JH) and Constant segment (CH) undergoes gene rearrangement for Ig diversity. * Light chain consist of either Kappa () chain or  chain but never both. * In early Fetal development B cell differentiation occur in liver but in later fetal development and through out the adult life B cell differentiation occur in bone marrow. * Mature (virgin) B cell ( Ig M+ , Ig D+ ) express Ig M and Ig D on their surface. * Mature B cells Migrate to the spleen, lymphnode and gut (eg tonsils , payer's patches) and wait for Ag exposure. * B cell proliferate into plasma cell after Ag exposure. In early response it secrete either Ig M or Ig D. Ag after degradation in B cell lysosomes turn into fragments and some exposed Mature B cell surface in conjugation in class II MHC Complex, which is than recognized by CD - 4 Helper T cells which than secrete IL - 2. Under the influence of CD - 4 Helper T cell , B cell under go Isotype switching and hypermutation to differentiate into plasma cell. * Isotype Switching is when B cell differentiate into plasma cell which secrete Ig G, Ig E, Ig A (mediated by IL 4 & IFN ). * Hypermutation in variable segment of both heavy (VH) & light chain (VL) produce Ig G, Ig E, Ig A which binds with Ag with high affinity. ----------------------------------------------------------------------------------* T cell receptor (TcR) have two protein subunit. 1. one  and one  2. one  and one  * CD 3 function as a signal transducer on T cell surface. * CD 4 function is bind to variable protein of class II MHC and act as signal transducer. * CD 8 function is bind to variable protien of class I MHC and also act as signal transducer. * T cell develop in thymus in early fetal development untill puberty. Thymus is derived from third pharyngeal pouch. * Stem cell that originate in the bone marrow migrate into Thymus than stem cell differentiate into Pre - T - cell in thymic cortex where they are protected by blood - thymus - barrier, here +ve and -ve selection occur . After that mature T cell either with ( TcR, CD3+, CD4+, CD8-) or ( TcR CD3+, CD4-, CD8+) leaves the thymic medulla. * Mature T cell are never CD4+ and CD8+ positive togather ( it is either CD4+ or CD8+ positive but never both) . * Mature T Cell than migrate to thymic dependant zone of the lymph node and to periarterial lymphatic sheath in spleen where it wait for Ag exposure. * Immunologic disorder :1. X - linked infantile (bruton's) agammaglobulinemia :- In which pre B cell cannot differentiate in mature B cell. It effect only males, disorder occue at the age of 5 - 6 month of age and shows absence of all class of Ig. 2. DiGeorge $ (congenital thymic Aplasia) :- Hypocalcemia, recurrent viral, bacterial,fungal & protozoal infection because of developmental failure of 3rd & 4th pharyngeal pouch  absence of thymus & parathyroid gland. 3. Severe Combined Immunodeficiency dis (SCID) :- (Bubble boy) Stem cell do not differentiate embryogenically into B or T cell, other type is Adenosine Deaminase (ADA) def which result into increase ATP accumulation  viral, bacterial, fungal and protozoal infection. 4. AIDS :- selective destruction of CD4 helper T cells due to HIV infection. 5. Monoclonal gammopathies : 1. Multiple myeloma   Ig GAMED (monoclonal) due to malignant proliferation of plasma cell. Free  or  chain (Bence jones protien) in serum and urine. 2. Waldenstrome macroglobulinemia   Ig M which further cause  serum viscosity, thrombosis, bleeding & CNS problem ----------------------------------------------------------------------------------------------

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KICK THE BOARDS. USMLE STEP 1 “GENETICS”

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* Ion channel: 1. Voltage gated ion channel 2. Mechanical gated ion channel 3. Transmitter gated ion channel ** Excitatory transmitter gated ion channel : 1. Nicotinic ACh Receptor (nAChR) :- when activated become permeable to all cations Na+ , K+ , Ca++ . 2. 5 Hydroxytryptamine (5HT3) Serotonin Receptor :- when activated become permeable to Na+ and K+ ion. 3. Glutamate Receptor (N-methyl-D-aspartate Receptor) NMDA Receptor :- Which is permeable to Na+, K+ Ca+. Opening of gate require both glutamate binding & voltage dependant mem depolarization because NMDA receptor is plugged with Mg++ ion. * nAChR blocked by Bungarotoxin and curare (it act at neuromuscular junction)  muscle paralysis. * 5 HT3 serotonin receptor blocked by antiemetic, anxiolytic, and antipsychotic (imp in CNS). * Glutamate NMDA receptor blocked by phencyclidine (PCP), Dizocilpine ( MK- 801 )  Hallucinogenic behavior. * Glutamate NMDA receptor also involve in learning process in hippocampus. * Glutamate NMDA receptor hyperactivity   Ca++ influx (glutamate toxicity). Implicated in many neuro degenerative disorder. ** Inhibitory transmitter gated ion channel : are GABA and Glycine receptor. * GABA A are major inhibitory receptor in brain permeable to Cl ion channel (Anion) which hyperpolarize the postsynaptic mem. * GABA A agonist like Barbiturate, Benzodiazepine and Steroid hormone metabolites potentiate GABA binding and  inhibitory effect of GABA A receptor  sedative effect. * GABA A antagonist like picrotoxin, Bicucullin, Penecillin  inhibition of GABA A  convulsion and seizures. * Glycine is imp in spinal cord and is permeable to Cl ion (Anion)  inhibition. --------------------------------------------------------------------------------------------* G protein linked receptor are linked to GTP- binding protein, when activated it either activates cAMP pathway or Ca++ pathway. * cAMP use either Gs or Gi protien. ( cAMP level use stimulatory G (Gs) protein where as  cAMP level Use Inhibitory G (Gi) protein. * When appropriate signal binds to G protein (Gs or Gi) linked receptor; inactive Gs or Gi protein become activated by exchanging its GDP for GTP to become active (by intrinsic activity); Than active Gs or Gi protein  or  cAMP by stimulating or inhibiting adenylate cyclase which further activate or inactivate protein kinase respectively. Active protein kinase catalyze the covalent phosphorylation of serine and threonine with in the IC protein to  its activity. On other hand Gs protein is short lived which quickly hydrolyzed GTP to GDP by enz GTPase to make G Protein inactive again. This process is imp because in cholera toxin an enz that has GTPase activity is blocked (by cholera toxin) which result into continuous activation of Gs protein  Diarrhea. * Signal attach to Gi protien linked receptor (exchange GDP for GTP)  activation of Gi protien  inhibit adenylate cyclase   cAMP  inhibit response. * Signal attach to Gs protien linked receptor (exchange GDP to GTP)  activation of Gs protien  stimulate adenylate cyclase   cAMP   response. * Pertussin toxin keep Gi protien inactivated  continuous adenylate cyclase acivity   cAMP  continuous response. * Ca++ Pathway :- When appropriate signal binds with Gq receptor protein, inactive Gq protein exchange its GDP for GTP to become active Gq protein . Actived Gq protein than further activates phospholipase C which cleaves Phosphoinositol biphosphate (PIP2) into IP3 (inosotol triphosphate) and DAG (Diacylglycerol). IP3 cause the release of Ca++ from endoplasmic reticulum. This Ca++ activates enz Ca++ / Calmodulin dependent protein kinase (CaM - Kinase) which further catalyze the covalant phosphorylation of serine & threonine with in certain IC protein to  their activity. (DAG  protein kinase activity with the help of Ca++). * Muscarinic Ach Receptor (mAchR) are G protein linked receptors. imp in brain. * Adrenergic receptor :- 1. 1 --- uses Ca++ pathway 2. 2 --- uses cAMP pathway and  cAMP by inhibiting adenylate cyclase. 3. 1,2,3 --- uses cAMP pathway and  cAMP by stimulating adenylate cyclase.

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KICK THE BOARDS. USMLE STEP 1 “GENETICS”

Prepared by Dr. IRFAN MIR

* Dopamine receptor :- 1. D1 --- uses cAMP pathway and  cAMP by stimulating adenylate cyclase. 2. D2 --- uses cAMP pathway and  cAMP by inhibiting adenylate cyclase. (dopamine receptor bind with catecholamine dopamine) * Purinrergic receptor :- 1. Type A --- binds to adenosine. 2. Type P --- binds to ATP. *  - Aminobuteric acid (GABA B) receptors:- found through out CNS it is localized with GABA A receptor which is Transmitter gated ion channel. (Baclofen a muscle relaxant is GABA B agoinist & Saclofen is GABA B Antagonist). * Metabotropic Glutamate receptor (mGluR) :- Found through out CNS and has 8 types. * TSH receptors :- Defect in TSH receptor gene is implicated in hyperthyroidism. (thyroid adenoma). * LH receptors :- Defect in LH receptor gene is implicated in precocious puberty. * ACTH receptor :- Defect in ACTH receptor gene is implicated in Familial glucocorticoid deficiency. * Rhodopsin receptor gene defect is implicated in Retinitis pigmentosa  night blindness (due to rod photoreceptors degeneration). * Vasopressin receptor :1. V1 -- use IP2 Ca++ pathway as a second messenger. 2. V2 -- use cAMP pathway. Defect in V2 receptor gene is implicated in X - linked nephrogenic diabetes Insipidus ------------------------------------------------------------------------------------------* When steroid hormone diffuses across the cell mem and bind to the steroid hormone receptor inside the cytoplasm, this binding releases heat shock protein 90 (hsp 90) and hsp 56 released which exposes the DNA binding region than steroid - receptor - complex is transported to nucleus where it binds to DNA. -----------------------------------------------------------------------------------------* Enz - linked receptors : 1. Receptor Guanylate cyclase ---------- ANP, NO (produce cGMP) 2. Receptor tyrosine kinase -------------- EGF, PDGF, FGF, NGF, VEGF, Insulin. 3. Tyrosine kinase Associated Receptors ----------------------------------------------1.cytokine receptor 4. Receptor tyrosine phosphatase ---------- CD45 2. GH receptor 5. Receptor Serine - Threonine kinase ----- TGF  Receptor . 3. PL Hormones receptor, IL 2 receptor 4. Ag specific receptor on T & B cells. ----------------------------------------------------------------------* When appropriate signal bind to receptor tyrosine kinase it produce phosphotyrosine by its intrinsic tyrosine kinase activity and auto phosphorylation. IC SH2 - domain protein than binds with phosphotyrosine to interact with Son of Sevenless Protein (SOS protein) . Than SOS protein activate Ras protein (by binding GTP) which further activates Mitogen activated protein kinase (MAP) by covalent phosphorylation of tyrosine and threonine. The activated MAP kinase enter the nucleus where it phosphorylates Gene regulatory Protein, these protein cause gene transcription. * Tyrosine phosphatase cause dephosphorylation of tyrosine where as phosphorylation occur by Tyrosine kinase. -----------------------------------------------------------------------------------------* Nitric Oxide (NO) is a labile free radical gas with half life of about 5 sec . it play a role in immune function of macrophages, blood vessel dilatation, serve as a neurotransmitter in CNS and PNS. * NO form by NO Synthatase (NOS) which transform Arginine into citrulline and NO. * NO binds to heme group of cytoplasmic receptor guanylate cyclase to produce cGMP. Than cGMP activate protein kinase  catalyze phosphorylation of serine and threonine ( in smooth muscle of tunica media) which results into  cellular activity. * NO is an active metabolite that mediate relaxant effect of nitrogylcerine and nitropruside . * NO is also produce by deep cavernous artery of the penis as well as by nerve fiber around it. * NO and cGMP play a significant role in erection. sildenafil (cGMP phospodiestrase (type 5) inhibitor) that  the cGMP conc which results into vasodilation and errection. * Receptor mediated endocytosis is a process by which substance (like LDL ) endocytosed by cell. defect in receptor cause Familial Hypercholesterolemia (FH).

ONLY FOR EDUCATIONAL PURPOSE.

9

NOT FOR COMMERCIAL USE OR SALE

KICK THE BOARDS. USMLE STEP 1 “GENETICS”

ONLY FOR EDUCATIONAL PURPOSE. SALE

Prepared by Dr. IRFAN MIR

10

NOT FOR COMMERCIAL USE OR