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100 Cards in this Set
- Front
- Back
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At which end of the tRNA is the AA bound?
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The AA is covalently bound to the 3' end of the tRNA
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Can RNAP initiate chains?
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yes
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Define transition
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Substituting purine for purine; or pyrimidine for pyrimidine
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Define Transverion
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Substituting purine for pyrimidine or vica versa
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Define tRNA wobble
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Accurate base pairing is required for the first two nucleotide positions of an mRNA codon. The third position then is the the 'wobble' position that can be different yet code for the same tRNA.
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Describe DNA replication
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Origin of replication: continuous DNA synthesis on leading strand and discontinuous (Okazaki fragments) on lagging strand. Primase makes an RNA primer on which DNA polymerase can initiate replication. DNA polymerase reaches primer of preceding fragment; 5'-->3' exonuclease activity of DNA polymerase I degrades RNA primer; DNA ligase seals; 3'-->5' exonuclease activity of DNA polymerase 'proofreads' each added nucleotide. DNA topoisomerases create a nick in the helix to relieve supercoils
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Describe euchromatin
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Less condensed than hetero chromatin and transcriptionally active
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Describe heterochromatin
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Condensed, transcriptionally inactive
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Describe the key structural differences between nucleotides
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1. Purines (A,G) have 2 rings
2. Pyrimidines(C,T,U) have one ring 3.Guanine has a ketone 4. Thymine has a methyl |
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Describe single strand excision repair
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Excision repair-specific glycosylase recognizes and removes damaged base. Endonuclease makes a break several bases to the 5' side.
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Describe the difference between eukaryotic Vs. bacterial and viral ORI
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The Eukaryotic genome has multiple ORI. Viruses and bacteria only have one
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Describe the main differences in eukaryotic and prokaryotic synthesis of RNA?
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Eukaryotes have 3 different polymerases(1,2,3 synthesize RMT) and prokaryotes have only one for all three types of RNA
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Describe the method by which introns are removed from the primary mRNA transcript?
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snRNP - small nuclear ribonucleoproteins bind to mRNA transcripts and make spliceosomes
They come and and bind to the 3' acceptor site (AG) and the 5' site (GU). They precisely splice out the introns and a lariat shaped intermediate is formed |
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Describe the number of bonds of the purine-pyrimidine pair; which one is stronger?
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AT has two bonds while GC has three and that makes GC stronger.
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Describe the structure of chromatin?
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Condensed (-)charged DNA wrapped around (+) charged histone protein beads(nucleosomes). Histone H1 ties the nucleosome together in a string(30nm fiber)
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Describe tRNA structure?
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75-90 nucleotides, cloverleaf form, anticodon end is opposite 3' aminoacyl end. All tRNAs both eukaryotic and prokaryotic, have CCA at 3' end along with a high percentage of chemically modified bases. The amino acid is covalently bound to the 3' end of the tRNA.
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Does RNA Polymerase have a proofreading function?
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No
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How do purines and pyrimidines interact molecularly?
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A with T and G with C via H bonds
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How does DNA Pol II open DNA?
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RNA polymerase II opens DNA at promoter site (A-T rich upstream sequence- TATA and CAAT)
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How is the original RNA transcript processed in eukaryotes? (3) ...
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1) Capping on 5' end (7-methyl G)
2)Polyadenylation on 3' end ( =200 As) 3) Splicing out of introns |
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In eukaryotes, what must occur before an newly synthesized RNA transcript leaves the nucleus? ...
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Only processed RNA is transported out the nucleus of eukaryotes.
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Name 3 types of RNA ...
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1) mRNA 2) rRNA 3) tRNA
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Name the charged histones around which (-) charged DNA loops (nucleosome core). ...
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H2A, H2B, H3, H4 histones
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Name the enzyme responsible for the synthesis of RNA in prokaryotes. ...
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RNA Polymerase
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Name the enzymes involved in ss-DNA repair. (5) ...
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1) specific glycosylase.
2) endonuclease. 3) exonuclease. 4) DNA polymerase. 5) DNA ligase. |
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Name the enzymes responsible for the synthesis of eukaryotic RNA. ...
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RNA polymerase I
RNA polymerase II RNA polymerase III |
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What are exons? ...
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Exons contain the actual genetic information coding for a protein
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What are four types of mutations that can occur in DNA? ...
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1) Silent
2) Missense 3) Nonsense 4) Frame shift |
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What are introns? ...
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Introns are intervening noncoding segments of DNA
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What are the four features of the Genetic Code? ...
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1) Unambiguous
2) Degenerate 3) Commaless, non-overlapping 4)Universal |
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What atoms link aa in a protein chain? ...
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Amino acids are linked N to C
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What changes occur in DNA structure during mitosis? ...
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In mitosis, DNA condenses to form mitotic chromosomes
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What codon sequence is found at the 3' end of all tRNAs? ...
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All tRNAs, both eukaryotic and prokaryotic, have CCA at 3' end.
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What direction is DNA synthesized in? ...
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5' > 3'. Remember that the 5' of the incoming nucleotide bears the triphosphate (energy source for the bond). The 3' hydroxyl of the nascent chain is the target.
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What direction is protein synthesized in? ...
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Protein synthesis also proceed in the 5' to 3' (5' > 3')
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What direction is RNA synthesized in? ...
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5' > 3'. Remember that the 5' of the incoming nucleotide bears the triphosphate (energy source for the bond). The 3' hydroxyl of the nascent chain is the target.
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What does the AUG mRNA sequence code for? ...
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AUG codes for methionin, which may be removed before translation is completed. In prokaryotes the initial AUG codes for a formyl-methionin (f-met).
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What does the P in P-site stand for? What does the A in A-site stand for? ...
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P-site: peptidyl; A-site: aminoacyl;
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What does the statement, 'the genetic code is commaless' mean? What is the exception to this rule? ...
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The code is non-overlapping. The exception are some viruses
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What does the statement, 'the genetic code is degenerate' mean? ...
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More than one codon may code for the same amino acid
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What does the statement, 'the genetic code is unambiguous' mean? ...
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Each codon specifies only one amino acid
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What does the statement, 'the genetic code is universal' mean? What are the exceptions (4)? ...
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The same code is used in all lifeforms. The exceptions are 1. mitochondria, 2. archaeobacteria, 3. Mycoplasma, 4. some yeasts
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What enzyme is responsible for 'charging' tRNA? How does it work? ...
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Aminoacyl-tRNA synthetase. This enzyme (one per aa, uses ATP) scrutinizes aa before and after it binds to tRNA. If incorrect, bond is hydrolyzed by synthetase. The aa-tRNA bond has energy for formation of peptide bond.
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What inhibits RNA polymerase II? ...
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alpha-amanitin inhibits RNA polymerase II
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What is a conservative missense mutation? ...
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Mutation results in a different aa encoded, but that new aa is similar in chemical structure to the original code
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What is a frameshift mutation? What is usually the effect on the encoded protein? ...
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A change in DNA resulting in misreading of all nucleotides downstream. Usually results in a truncated protein.
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What is a missense mutation? ...
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Mutation results in a different aa encoded.
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What is a nonsense mutation? ...
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A change in DNA resulting in an early stop codon.
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What is a promoter? ...
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Site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus.
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What is a silent mutation? What usually causes a silent mutation? ...
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Mutation results in the same aa encoded. Often the base change is in the 3rd position of the codon
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What is a snRNP? What is its function? ...
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snRNP = small nuclear ribonucleoprotein. snRNPs facilitate splicing by binding to primary mRNA transcripts and forming spliceosomes
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What is an enhancer? ...
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Stretch of DNA that alters gene expression by binding transcription facts. May be located close to, far from, or even within (an intron) the gene whose expression it regulates.
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What is an Okazaki fragment? ...
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The discontinuous DNA synthesized on the lagging strand during DNA replication
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What is hnRNA? ...
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hnRNA = heterogeneous nuclear RNA The initial RNA transcript is called hnRNA
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What is responsible for the accuracy of amino acid selection during peptide synthesis? ...
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Aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of amino acid selection.
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What is the broad classification of nucleotides? (2) ...
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Purines (A, G) and Pyrimidines (C, T, U)
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What is the difference between hnRNA and mRNA? ...
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hnRNA = the initial RNA transcript mRNA = capped and tailed transcript
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What is the difference between thymine and uracil? ...
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Uracil found in RNA Thymine found in DNA
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What is the function of DNA ligase during DNA Replication? ...
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DNA ligase seals synthesized DNA into a continuous strand
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What is the function of DNA polymerase during DNA Replication? ...
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DNA polymerase reaches primer of preceding fragment; 5' to 3' exonuclease activity of DNA polymerase I degrades RNA primer; DNA ligase seals; 3' to 5' exonuclease activity of DNA polymerase 'proofreads' each added nucleotide
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What is the function of DNA topoisomerase during DNA Replication? ...
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DNA topoisomerases create a nick in the helix to relieve supercoils
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What is the function of primase in DNA Replication? ...
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Primase makes an RNA primer on which DNA polymerase can initiate replication
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What is the function of RNA polymerase I? ...
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RNA polymerase I makes rRNA
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What is the function of RNA polymerase II? ...
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RNA polymerase II makes mRNA
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What is the function of RNA polymerase III? ...
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RNA polymerase III makes tRNA
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What is the mRNA initiation codon? ...
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AUG, or rarely GUG
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What is the mRNA stop codons? (3) ...
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UGA (U Go Away) UAA (U Are Away) UAG (U Are Gone)
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What is the result of 'mischarged' tRNA? ...
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A mischarged tRNA (bound to wrong aa) reads usual codon but inserts wrong amino acid
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What is the role of endonuclease in ss-DNA repair? ...
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Endonuclease makes a break several bases to the 5' side.
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What is the role of excision repair-specific glycosylase in ss-DNA repair? ...
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Recognizes and removes damaged base
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What is the role of exonuclease in ss-DNA repair? ...
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Exonuclease removes short stretch of nucleotides.
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What prevents an incorrect aa-tRNA pairing? ...
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If incorrect, the aa-tRNA bond is hydrolyzed by aminoacyl-tRNA synthetase.
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What role does histone H1 play in chromatin structure? ...
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H1 ties the nucleosome together in a string (30nm fiber)
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What supplies the energy for formation of peptide bond? ...
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The aa-tRNA bond has energy for formation of peptide bond.
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What would most likely be the result of a mutation of the promoter sequence? ...
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Promoter mutation commonly results in dramatic decrease in amount of gene transcribed.
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When is ATP used in protein synthesis? When is GTP used in protein synthesis? ...
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ATP is used in tRNA charging, whereas GTP is used in binding of tRNA ribosome and for translocations
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When is recombination involved in DNA repair? ...
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If both strands are damaged, repair may proceed via recombination with undamaged homologous chromosome
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Where does RNA processing occur in eukaryotes? ...
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RNA processing occurs in the nucleus.
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Which is the largest type of RNA? ...
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mRNA (massive)
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Which is the most abundant type of RNA? ...
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rRNA (rampant)
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Which is the smallest type of RNA? ...
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tRNA (tiny)
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Which nucleotide position in the codon has room for 'wobble'? ...
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Codons differing in the 3rd 'wobble' position may code for the same tRNA/amino acid
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How do you do a Northern Blot? ...
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-Electrophorese RNA on a gel --transfer to a filter
-expose filter to a labeled DNA probe -visualize the DNA probe annealed to the desired RNA |
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How do you do a Southern Blot? ...
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-Electrophorese DNA on a gel --transfer to a filter and denature the DNA
-expose to a labeled DNA probe -visualize probe annealed to desired DNA fragment |
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How do you do a Southwestern blot? ...
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Separate protein by electrophoresis
-transfer to a filter -expose to a labeled DNA probe -visualize DNA bound to desired protein |
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How do you do a Western Blot? ...
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-Separate protein by electrophoresis
-transfer to a filter -expose to a labeled antibody visualize Ab bound to desired protein |
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How do you do PCR? (4 steps) ...
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1. Heat DNA to denature.
2. Cool DNA and let the primers aneal. 3. Heat-stable polymerase replicates DNA following each premer 4. Repeat |
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What are some genetic diseases detectable by PCR?(11) ...
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SCID, Lesh-Nyhan, CF, familial hypercholesterolemia, retinoblastoma, sickle cell, B-thalassemia, hemophilia A and B, von Willebrand's dz, lysosomal storage dz, and glycogen storage dz
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What gene is involved in cystic fibrosis? ...
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CFTR
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What gene is involved in familial hypercholesterolemia? ...
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LDL-R
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What gene is involved in Lesh-Nyhan syndrome? ...
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HGPRT
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What gene is involved in retinoblastoma? ...
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Rb
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What gene is involved in SCID? ...
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adenosine deaminase
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What gene is involved in Sickle cell and beta-thal? ...
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beta globin gene
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What is an ELISA (enzyme linke immunosorbant assay)? ...
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Rapid lab test in which an antibody or an antigen (usually collected from a patient) is exposed to an Ag or Ab linked to an enzyme. A positive test results in a Ag-Ab match and is usually indicated by a color change
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What is PCR? ...
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Lab procedure used to synthsize many copies of a desired fragment of DNA
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Von Geirke's disease is a result of? ...
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Glucose-6-phosphatase deficiency; also known as Type I Glycogen Storage disease
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A build up of sphingomyelin and cholesterol in reticuloendothelial and parenchymal cells and tissues is found in what disease ...
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Niemann-Pick disease
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A child is born with multiple fractures and blue sclera what is the diagnosis? ...
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Osteogenesis imperfecta;disease of abnormal collagen synthesis resulting in fractures and translucent Conn tiss over chorioid causing the blue sclera
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A congenital deficiency of tyrosinase would lead to? ...
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Albinism, can't synthesize melanin from tyrosine
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