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Biofinal 2-3

Bio review Lucia lecture 2-3

What is the central Dogma of Molecular Biology? Replication - Transcription - Translation DNA stores information which is transcribed to RNA then translated into protein
What are the purines and pyrimidines? adenine & guanine Cytosine, Uracil, Thymine
What is the correct complementary sequence to'5 AGGTCCTTAGG-3'... CCTAAGGACCT or TCCAGGAATCC 5'-CCTAAGGACCT-3'
What is Tm? Which DNA base pairs have a higher Tm? Why? Tm is the temp required to melt 50% of the DNA in a sample. GC have high TM because triple bond verses AT with double bonds
Where is the replication fork? What melts the origin of replication? an AT rich sequence is melted by DnaA protein
What keep DNA from reannealing during replication? single-stranded binding proteins
What unwinds the DNA at the replication fork? What lays down RNA primer for leading and lagging strands? Helicase Primase
Why is Primase necessary? DNA polymerase must have it to attach, cannot begin de novo
What removes RNA primer ('5-3' exo), replaces it with DNA (5'-3' pol) and proofreads work (3'-5')? DNA polymerase I
What extends leading and lagging strands (5'-3' pol) and proofreads work (3'-5' exo)? DNA polymerase II
What direction do Okazaki fragments synthesize? way from the replication fork on the lagging strand
What joins DNA fragments? DNA ligase
What cuts on strand of DNA while a second type cuts both strands to relieve supercoiling ahead of replication fork? Topoisomerase I - cuts one strand Topoisomerase II - cuts two strands
What promotes supercoiling in prokaryotes? What relaxes supercoiling in prokaryotes? What inhibits it? DNA gyrase coils it Topoisomerase II uncoils it quinolones inhibit supercoiling
What is the first thing put on the lagging strand for replication? What is the second thing? primase lays down an RNA primer then DNA polymerase III recognizes the RNA primer and begins synthesis
To complete replication of circular DNA and joining of Okazaki fragments, what removes RNA primer and adds dNTPS? RNA primer extended by Pol IIIuntil another RNA sequence encountered. DNA Pol I cuts out the primer, inserts dNTPS, DNA ligase seals nick
What cells or disease processes often use reverse transcription? What is a reverse transcriptase enzyme? Cancer, viruses such as HIV enzyme: telomerase
Why is it hard to fight viruses that use reverse transcription? They have no proofreading activity. Therefore, a high mutation rate exist.
What are three names for DNA repair enzyme? endonuclease, excision endonuclease, excinuclease
How do excinucleases work? cut DNA on both sides of damage, remove it, gap filled by DNA polymerase in Eukaryotes, DNA pol I in prokaryotes
What is a rare genetic disorder that results from excision endonuclease deficiency? xeroderma pigmentosum
What two diseases have bad effects due to UV-light? porphyria (heme syntesis problem) xeroderma pigmentosum (excision endonuclease
What is the difference in RNA transcription and DNA replication? RNA polymerases do not require a primer while DNA polymerases do RNA pol synthesizes '5-3' only
RNA polymerase is constructed of what subunits? What is required for RNA polymerase to recognizes and bind promoter sequences? two alpha subunits, one beta subunit, one beta' subunit Needs Sigma factor to bind
What is the compound that binds to prokaryotic RNA polymerase and prevents transciption initiation? What condition is this used to treat? Rifampin (rifamycin) used to treat tuberculosis
What are the three Eukaryotic RNA polymerases? Activity of each? RNA pol I - make rRNA RNA Pol II - make mRNA, some snRNA RNA Pol III - make tRNA, small rRNA (5S)
What stays and what goes in a splice? What is the machine for splicing? Introns go, exons stay Spliceosome made primary transcript and snRNA
A patient comes in with a butterfly rash on her body. What might be her condition? Cause? Systemic Lupus Erythematosus caused by autoimmune reaction produces antibodies against dsDNA, especially snRNP's
You want to kill an irritating member of your class. What should you put in their salad? Why will that work? Add Amanita mushrooms. The alpha-amanitin noncompetively binds to RNA pol II in Eukaryotes. This prevents any mRNA synthesis
What are the three types of point mutations? Silent mutation Missense Nonsense
If a single mutation occurs but no phenotype change happens what is the name? silent
If a different nucleotide results from a point mutation and creates a different amino acid - what it be called? Missense
If a different nucleotide changes from amino acid to stop codon what dat be? Nonsense...Non-STop Fun
A Frame shift occurs with what sort of mutation? What frequently happens with frameshifts? An insertion or deletion that is not in a multiple of 3...these often create a stop codon
What severe disease is caused by frameshift? What amino acid is messed up? Duchenne and Becker Myotonic Dystrophy...problem with dystrophin
What happens as a result of a promoter mutation? example of disease Usually less mRNA synthesis, less protein such as in beta Thalassemia
What occurs with splice site mutations? example of disease incorrect splicing can lead to insertions or deletions, missing exons..occurs in beta thalassemia
Where are the three regions for Trinucleotide repeat expansions and a disease related to each? 5' noncoding region = Fragile X Coding Region = Huntington 3' noncoding region = Myotonic dystrophy
What is a conservative mutation? missense mutation that results in amino acid with similar properties to the original (ex. non-polar to non-polar)
What location is the worst place for a frameshift mutation to occur? closer to the beginning of the protein
What causes cystic fibrosis? A 3 base pair deletion that codes for the choloride transporter. The missing amino acid is phenyalanine
What mutation occurs with Thalassemia? deficiency in globin chain due to splice site mutation. Most common is beta thalassemia.
What is the most common single gene disorder in humans? fat girls in levi's or alpha and beta thalassemias
What are the components of ribosomes? Purpose? rRNA's and many proteins that translate message on mRNA into specific protein
What are the subunits of Eukaryotic Ribosomes 80S ribosome = 60S + 40S 60S = 5S RNA + 28S RNA + 5.8S RNA 40S = 18S
What are the subunits of Prokaryotic Ribosomes 70S = 30S + 50S 50S = 5S + 23S 30S = 16S
What toxin inhibits translation in Eukaryotes? diptheria/pseudomonas
What does a-amanitin inhibit in eukaryotes? RNA pol II in liver so cannot make mRNA
What inhibits DNA gyrase (topoisomerase) to inhibit replication in prokaryotes? Quinolones
What binds RNA polymerase in prokayotes to inhibit transcrition? Rifampin
What inhibits translation in prokaryotes? tetracycline
What does streptomycin inhibit? aminoglycoside that inhibits translation in prokaryotes
What does erythromycin inhibit? macrolide that inhibits protein synthesis in prokaryotes
How is chloramphenicol different from tetracycline, aminoglycosides, and macrolides? inhibits translation, but also inhibits mitochondrial protein synthesis
Who does Diptheria actualy block translation? inactivates eEF-2, preventing translocation
Where do C-peptides originate in the body? What compound is also secreted from the same location? pancreatic cells insulin
What is the difference in the secretion of insulin and C-peptide? C-peptide secreted in 5-10x higher concentration
Why is C-peptide useful in medicine? Measure the levels to check insulin levels indirectly
What wonderful disease results from Vitamin C deficiency? Symptoms? scurvy = collagen breakdown bruising, bleeding gums, loose teeth, poor bone development
Why would collagen break down with Vitamin C deficiency? required as cofactor for enzymes involved in hydroxylating proline and lysine residues
What condition is caused by mutations to collagen genes? What amino acid is most commonly affected? Osteogenesis imperfecta - glycine is substitued for bulky R-group amino acid
Which type of OI is mistaken for child abuse? Why? Type I, Type II is fatal
If lysly-hydroxylase collagen pepsidase goes on the fritz, what condition results? Symptom? damn loose = Ehlers-Danlos (EDS) hypermobile joints, hyperextensible skin
How soon will you die if you cannot phosphorylate Mannose? Why? symptoms I-cell disease kills by age 8 severe physcomotor problems, joint restriction, coarse facial features
What exactly is I-cell disease? A lysosomal storage problem- post-translational modification fails. proteins never get to lysosomes for proper storage
What is the pathway for the control of gene expression in gluconeogenesis? glucagon binds receptor, induces signal transduction - cAMP increase - Protein Kinase A activated - CREB activated - CREB goes in Nucleus to bind CRE - PEPCK gene induced
What are CREB, CRE and PEPCK cAMP Response Element Binding Protein cAMP Response Element Phosphoenoylpyrvate carboxykinase
What does PEPCK do? converts oxaloacetate into pyruvate and CO2
What test would you use to determine the presence or quantity of a protein? What type of probe would you use? Western blot Antibody probe
What test would you use to determine the presence or absence, but NOT quantity of DNA Southern Blot nucleic Acid probe
What test would be used to test for presence and quantity of mRNA molelule? probe? Northern Blot nucleic acid probe
What are probes? How do they show the results? single strand DNA molecules are labeled with radioactive material,exposed to a targe that is immoblized on nitrocellulose membrane. Complementary sequences bind - autoradiography shows target.
Who invented PCR? What are the four steps? Kary Mullis: denature DNA, anneal primers to flanking regions, extend primers with DNA polymerase, repeat
PCR sequence and temp? What heat stable DNA pol is used? Denature (95 C), Anneal (55C), Extend (72C) Taq polymerase
Problem with Northern blot? look for mRNA levels, but only one gene at a time
Benefit and drawback of Western Blot? use gel phoresis so more specific but labor intensive and less senstive
What does ASO measure? Detects DNA mutations...such as paternity
What does ELISA measure? test protein or antibodies
What test would be used to test for Sickle Cell anemia? ASO probes - allele specific oligonucleotids
Why would you like a patient with Cystic Fibrosis? Check for elevated chloride levels in sweat
Why do CF patients die by 30? lack of chloride secretions leads to dehydration of mucus in lungs, recurrent infections
How would a PCR mutant product for CFTR differ from the normalCFTR? 3 base pairs shorter
What is a gene, locus, allele 1. basic unit of inheritance 2. physical location on gene of chromosome 3. alternative form of gene at given locus
What is genotype? Phenotype? genetic constitution of individual observed expression of a gene (physical manifestation)
Are males circles or squares in pedigrees? squares, females are curvy
What conditions are often Autosomal Dominant? When non-catylytic proteins are involved
What is the recurrence risk or probablity for autosomal dominant? each repro event is independed so 50-50
Which sex is affected by autosomal recessive? Are the parents affected? can be either sex, usually parent is not affected
What condition only affects males? What parent is the unaffected carrier? X-Linked recessive are inheirited from the mother.
What condition cannot have any male to male inheiritance? x-linked recessive
Who inherits the disease in mitochondrial inheritance? Who give it? Can it have male to male all children are affected. Mothers give it. No male to male
What causes alpha-thalassemia? insufficent synthesis of alpha-chain, beta chain accumulates
What causes beta-thalassemia? insufficent synthesis of beta-chain, alpha chain accumulates
What is the simplest form of thalasemia? genotypes? Beta-thalassemia: 2 normal, minor = 1 normal, 1 mutant major = 2 mutant
What are the six genotypes of alpha thalassemia? aa/aa - normal -a/aa = silent carrier --/aa and -a/-a = alpha thalassemia trait --/-a = HbH disease -/-- = hydrops fetalis
What is unique about dystrophin? role in cells Huge protein (427 kD) involved in cytoskeleton of muscle cells (skeletal, smooth and cardiac)
What are the conditions when dystrophin screws up? What is the screw-up? Duchenne and Becker Muscular Dystrophy caused by frameshift mutation
What is the heterozygote advantage? A good reason for me not to visit africa or central or south america
What is aneuploidy? a deviation from the euploid number of chromosomes = loss or gain
How long do autosomal monosomies live? not long, usually lethal in utero
What is the only monosomy that is survivable? Turners, -X
What are the three trisomies? Patua - 13 Andersons - 18 Edwards - 21
What makes trisomies more likely as women age? more frequent non-disjunction at meiosis I
What is most common autosomal trisomy? Down syndrome
What is most common genetic cause of mental retardation? Down syndrome
What condition has lack of secondary sex characteristics, gynemastia, low IQ, long arms and legs, sterile due to atrophy of seminiferous tubules, small atrophic testes Klinfelter syndrome
What is the karyotype and only consistent finding? 47, XXY: small, atrophic testes
What is a mosaic? has different chromosomes within the same person example, a turner with 45,X and 46XX
Created by: El Diablo