Bio review Lucia lecture 2-3
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| What is the central Dogma of Molecular Biology? | Replication - Transcription - Translation
DNA stores information which is transcribed to RNA then translated into protein
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| What are the purines and pyrimidines? | adenine & guanine
Cytosine, Uracil, Thymine
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| What is the correct complementary sequence to'5 AGGTCCTTAGG-3'... CCTAAGGACCT or TCCAGGAATCC | 5'-CCTAAGGACCT-3'
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| 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
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| Where is the replication fork? What melts the origin of replication? | an AT rich sequence is melted by DnaA protein
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| What keep DNA from reannealing during replication? | single-stranded binding proteins
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| What unwinds the DNA at the replication fork? What lays down RNA primer for leading and lagging strands? | Helicase
Primase
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| Why is Primase necessary? | DNA polymerase must have it to attach, cannot begin de novo
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| What removes RNA primer ('5-3' exo), replaces it with DNA (5'-3' pol) and proofreads work (3'-5')? | DNA polymerase I
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| What extends leading and lagging strands (5'-3' pol) and proofreads work (3'-5' exo)? | DNA polymerase II
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| What direction do Okazaki fragments synthesize? | way from the replication fork on the lagging strand
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| What joins DNA fragments? | DNA ligase
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| 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
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| What promotes supercoiling in prokaryotes? What relaxes supercoiling in prokaryotes? What inhibits it? | DNA gyrase coils it
Topoisomerase II uncoils it
quinolones inhibit supercoiling
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| 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
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| 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
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| What cells or disease processes often use reverse transcription? What is a reverse transcriptase enzyme? | Cancer, viruses such as HIV
enzyme: telomerase
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| Why is it hard to fight viruses that use reverse transcription? | They have no proofreading activity. Therefore, a high mutation rate exist.
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| What are three names for DNA repair enzyme? | endonuclease, excision endonuclease, excinuclease
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| 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
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| What is a rare genetic disorder that results from excision endonuclease deficiency? | xeroderma pigmentosum
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| What two diseases have bad effects due to UV-light? | porphyria (heme syntesis problem)
xeroderma pigmentosum (excision endonuclease
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| 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
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| 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
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| 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
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| 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)
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| What stays and what goes in a splice? What is the machine for splicing? | Introns go, exons stay
Spliceosome made primary transcript and snRNA
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| 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
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| 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
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| What are the three types of point mutations? | Silent mutation
Missense
Nonsense
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| If a single mutation occurs but no phenotype change happens what is the name? | silent
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| If a different nucleotide results from a point mutation and creates a different amino acid - what it be called? | Missense
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| If a different nucleotide changes from amino acid to stop codon what dat be? | Nonsense...Non-STop Fun
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| 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
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| What severe disease is caused by frameshift? What amino acid is messed up? | Duchenne and Becker Myotonic Dystrophy...problem with dystrophin
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| What happens as a result of a promoter mutation? example of disease | Usually less mRNA synthesis, less protein such as in beta Thalassemia
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| What occurs with splice site mutations? example of disease | incorrect splicing can lead to insertions or deletions, missing exons..occurs in beta thalassemia
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| 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
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| What is a conservative mutation? | missense mutation that results in amino acid with similar properties to the original (ex. non-polar to non-polar)
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| What location is the worst place for a frameshift mutation to occur? | closer to the beginning of the protein
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| What causes cystic fibrosis? | A 3 base pair deletion that codes for the choloride transporter. The missing amino acid is phenyalanine
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| What mutation occurs with Thalassemia? | deficiency in globin chain due to splice site mutation. Most common is beta thalassemia.
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| What is the most common single gene disorder in humans? | fat girls in levi's or alpha and beta thalassemias
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| What are the components of ribosomes? Purpose? | rRNA's and many proteins that translate message on mRNA into specific protein
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| What are the subunits of Eukaryotic Ribosomes | 80S ribosome = 60S + 40S
60S = 5S RNA + 28S RNA + 5.8S RNA
40S = 18S
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| What are the subunits of Prokaryotic Ribosomes | 70S = 30S + 50S
50S = 5S + 23S
30S = 16S
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| What toxin inhibits translation in Eukaryotes? | diptheria/pseudomonas
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| What does a-amanitin inhibit in eukaryotes? | RNA pol II in liver so cannot make mRNA
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| What inhibits DNA gyrase (topoisomerase) to inhibit replication in prokaryotes? | Quinolones
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| What binds RNA polymerase in prokayotes to inhibit transcrition? | Rifampin
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| What inhibits translation in prokaryotes? | tetracycline
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| What does streptomycin inhibit? | aminoglycoside that inhibits translation in prokaryotes
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| What does erythromycin inhibit? | macrolide that inhibits protein synthesis in prokaryotes
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| How is chloramphenicol different from tetracycline, aminoglycosides, and macrolides? | inhibits translation, but also inhibits mitochondrial protein synthesis
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| Who does Diptheria actualy block translation? | inactivates eEF-2, preventing translocation
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| Where do C-peptides originate in the body? What compound is also secreted from the same location? | pancreatic cells
insulin
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| What is the difference in the secretion of insulin and C-peptide? | C-peptide secreted in 5-10x higher concentration
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| Why is C-peptide useful in medicine? | Measure the levels to check insulin levels indirectly
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| What wonderful disease results from Vitamin C deficiency? Symptoms? | scurvy = collagen breakdown
bruising, bleeding gums, loose teeth, poor bone development
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| Why would collagen break down with Vitamin C deficiency? | required as cofactor for enzymes involved in hydroxylating proline and lysine residues
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| 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
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| Which type of OI is mistaken for child abuse? Why? | Type I, Type II is fatal
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| If lysly-hydroxylase collagen pepsidase goes on the fritz, what condition results? Symptom? | damn loose = Ehlers-Danlos (EDS)
hypermobile joints, hyperextensible skin
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| 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
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| What exactly is I-cell disease? | A lysosomal storage problem- post-translational modification fails. proteins never get to lysosomes for proper storage
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| 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
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| What are CREB, CRE and PEPCK | cAMP Response Element Binding Protein
cAMP Response Element
Phosphoenoylpyrvate carboxykinase
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| What does PEPCK do? | converts oxaloacetate into pyruvate and CO2
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| 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
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| What test would you use to determine the presence or absence, but NOT quantity of DNA | Southern Blot
nucleic Acid probe
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| What test would be used to test for presence and quantity of mRNA molelule? probe? | Northern Blot
nucleic acid probe
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| 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.
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| Who invented PCR? What are the four steps? | Kary Mullis: denature DNA, anneal primers to flanking regions, extend primers with DNA polymerase, repeat
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| PCR sequence and temp? What heat stable DNA pol is used? | Denature (95 C), Anneal (55C), Extend (72C)
Taq polymerase
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| Problem with Northern blot? | look for mRNA levels, but only one gene at a time
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| Benefit and drawback of Western Blot? | use gel phoresis so more specific but labor intensive and less senstive
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| What does ASO measure? | Detects DNA mutations...such as paternity
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| What does ELISA measure? | test protein or antibodies
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| What test would be used to test for Sickle Cell anemia? | ASO probes - allele specific oligonucleotids
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| Why would you like a patient with Cystic Fibrosis? | Check for elevated chloride levels in sweat
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| Why do CF patients die by 30? | lack of chloride secretions leads to dehydration of mucus in lungs, recurrent infections
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| How would a PCR mutant product for CFTR differ from the normalCFTR? | 3 base pairs shorter
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| 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
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| What is genotype? Phenotype? | genetic constitution of individual
observed expression of a gene (physical manifestation)
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| Are males circles or squares in pedigrees? | squares, females are curvy
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| What conditions are often Autosomal Dominant? | When non-catylytic proteins are involved
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| What is the recurrence risk or probablity for autosomal dominant? | each repro event is independed so 50-50
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| Which sex is affected by autosomal recessive? Are the parents affected? | can be either sex, usually parent is not affected
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| What condition only affects males? What parent is the unaffected carrier? | X-Linked recessive are inheirited from the mother.
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| What condition cannot have any male to male inheiritance? | x-linked recessive
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| 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
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| What causes alpha-thalassemia? | insufficent synthesis of alpha-chain, beta chain accumulates
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| What causes beta-thalassemia? | insufficent synthesis of beta-chain, alpha chain accumulates
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| What is the simplest form of thalasemia? genotypes? | Beta-thalassemia: 2 normal,
minor = 1 normal, 1 mutant
major = 2 mutant
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| 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
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| What is unique about dystrophin? role in cells | Huge protein (427 kD) involved in cytoskeleton of muscle cells (skeletal, smooth and cardiac)
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| What are the conditions when dystrophin screws up? What is the screw-up? | Duchenne and Becker Muscular Dystrophy caused by frameshift mutation
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| What is the heterozygote advantage? | A good reason for me not to visit africa or central or south america
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| What is aneuploidy? | a deviation from the euploid number of chromosomes = loss or gain
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| How long do autosomal monosomies live? | not long, usually lethal in utero
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| What is the only monosomy that is survivable? | Turners, -X
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| What are the three trisomies? | Patua - 13
Andersons - 18
Edwards - 21
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| What makes trisomies more likely as women age? | more frequent non-disjunction at meiosis I
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| What is most common autosomal trisomy? | Down syndrome
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| What is most common genetic cause of mental retardation? | Down syndrome
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| 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
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| What is the karyotype and only consistent finding? | 47, XXY: small, atrophic testes
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| What is a mosaic? | has different chromosomes within the same person example, a turner with 45,X and 46XX
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