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BrdU
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Bromodeoxyuridine
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GAL10
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UDP-galactose-4-epimerase, converst UDP-galactose to UDP-glucose.
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Polysaccharide
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• Many monosaccharides linked together• Store energy: starch/glycogen• Structure: cellulose, chitin (exoskeletons in insects, spiders, crustaceans)
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Melting temperature(Tm)
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85 degrees C
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Nucleic Acid
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• Mainly RNA, DNA• Instructions for life! Basis of inheritance• Polymers made of nucleotides
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E. Splicing intermediate
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Spliceosomal lariat is
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Barbara McClintock discovered the first eukaryotic transposable element in
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maize
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Gal80p
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inhibits transcriptional activation by GAL4 in the absence of galactose; gal80 mutants consitutively transcribe GAL genes even in glucose.
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vimentin
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intermediate filaments of endothelial and vascular smooth muscle cells, fibroblasts, chondroblasts and macrophages
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DNA ligase
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enzyme that joins sugar-phosphate backbones of Okazaki fragments
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B. gp28
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Which of the following sigma specificity factors is involved in middle gene transcription during SPO1 phage infection of bacteria?
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what are the subcellular genetic elements?
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virusviroidplasmidtransposonprions
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Which of the following scientists provided definitive evidence for the chromosomal theory?
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Morgan
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Enhancer function
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Orientation independent and distance independent. These characteristics distinguish it from promoters
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SDS
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sodium dodecyl sulfate: a detergent (denatures proteins) that coats proteins with negative charges, which serves to make then migrate to the anode and masks original charge so they migrate by size.
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What is the direction of transcription?
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5'-3'
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Replication Bidirectionally
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Replication in both direction simultaneously. Two sites opposite direction.
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origins of replication
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sites where DNA begins replication
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Cellulose
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• Main part of cell walls in plants• Polysaccharide• Very strong good for structure and can’t be disested by most organisms
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what is the lifecycle of A.thaliana?
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6-10 weeks
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what repetitive sequences used in DNA fingerprinting?
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VNTRs
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Mapping is used to determine the composition of a gene.
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F
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The e-subunit of DNA Polymerase III core enzyme functions in proofreading by having 5¢®3¢ exonuclease activity.
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False
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CTD
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Carboxy Terminal Domain. Part of the largest subunit (RPB1) of RNA pol II. when unphosphorylated it is in the IIA form and called the initiating form. When phosphorylated its in the IIO form and is in the elongation form.
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bHLH
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basic helix loop helix. Similar to bZIPs, but they form an additional globular-like domain that provides a second module for dimerization. the end result is the same, as tow basic helices are positioned into the major groove to make base-specific contacts.
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Hyperchromic shift
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The increase in DNA's solution absorbance of 260nm light upon denaturation.Sigmoidal plot
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screening
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- A genetic sorting procedure that allows one to distinguish desired organisms/genes from unwanted ones
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L-type Ca channel
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also called dyhydropiridine receptor; allows Ca influx and depolarization of cardiac and smooth muscle and interacts with ryanodine sarcoplasmic channels of smooth, cardiac and skeletal muscle
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The end-replication problem
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Conventional DNA polymerases cannot fully replicate linear chromosomes. No primer, and the strand will continue to get shorter.
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DNA is coiled around proteins and packaged as _____ within the nucleus of cells.
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chromatin
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leading strand
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strand of DNA replicating in the continuous 5'-3' direction towards the replication fork
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Life Elements
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•92 natural elements, but only 25 needed for life•96% of living matter is carbon, oxygen, hydrogen, nitrogen
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B. linker scanning mutations
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Which of the following techniques would you use to study the role of the BRE?
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what is a ribozyme?
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an enzyme made of RNA
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what are the 5 nucleosides?
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adenosine, guanosine, cytidine, thymidine, uridine
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Thymine dimer
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- means there are two thymines occuring right next to each other on the same strand and the DNA molecule is arranged in such a way that a bond can be formed within these two ringed systems
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RT-PCR
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cDNA =a DNA copy of an RNAReverse transcriptasePrimer
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crossover
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the site of breaking and rejoining of two DNA molecules during homologous recombination. Breaking and rejoining requires endonucleases, DNA polymerases, and DNA ligases.
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liquid scintillation counting
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uses radioactive emissions from a sample (inside scintillation fluid) to create photons of visible light that a photomultiplier tube can detect.
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Phosphoester bond
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Removal of 5' sugar alcohol + phosphoric acid H
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What does acetylation of histones do?
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Increases gene expression
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carcinogen
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any substance or agent that tends to produce a cancer.
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C. in vitro transcription
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Which of the following would you choose to study the role of polymerase subunits in elongation?
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what is the name for stable, flexible, non-repetitive regions of polypeptide chains?
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random coils
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what is the process of translation?
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mRNA made into protein
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Peripheral Membrane Proteins:
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at surface of the bilayer
bound to exposed integral proteins
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Which has proof-reading activity?
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subunite of pol enzyme III ε
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transcription factor
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proteins that bind DNA (usually to a specific sequence) and regulate transcription of their target genes.
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What pathogen is PCR mostly used for detecting currently?
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Chlamydia trachomatis.
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exons
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- A region of a gene that is ultimately represented in that gene's mature transcript
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Mention 4 post-translational covalent modifications
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1. Glycosylation: addition of oligosacchrides; 2. phosphorylation: addition of phosphate by kinases; 3. proteolysis: cleavage and activation of peptide bonds (proinsulin, trypsinogen, prothrombin); 4. y-carboxylation: produces Ca+ binding sites (vitamin K dependant)
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Lagging Strand
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Make the process start all over again. Discontinuous
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nucleotide
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any of a group of molecules that, when linked together, form the building blocks of DNA or RNA: composed of a phosphate group, the bases adenine, cytosine, guanine, and thymine, and a pentose sugar, in RNA the thymine base being replaced by uracil.
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B. export to the cytoplasm.
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Although snRNA U1 functions in the nucleus, it receives a 5' Cap to enhance its
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when was dna first isolated? who? what was it called?
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nuclein. F.Miescher 1869
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waht is the process of transcription
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exact compliment of dna made
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Promotor site on DNA
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segment of DNA where the RNA Polymerase binds
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Problems with the holliday model
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requires that both strands are prealigned and cut at the same site to initate recombination. there is no evidence for proteins that specifically carry out this function.
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What are 3 uses for RFLP?
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1. Epidemiology2. Infection control3. Forensics
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What does phosphorylation of manose residues do? I-cell disease?
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Manose residues on oligosacchride chain are phosphorylated in golgi aparatus to direct the enzyme to lysosome. In I-cell disease, lysosomal enzymes are secreted into extracellular space due to inappropriate phosphorylation of manose residues
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External Proteins (regulation of initiation)
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may bind and down-regulate the initiator directly.
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B. contains zinc fingers
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Select the feature that is not true of the GAL4 protein.
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which aa prevents formation of the alpha helix conformation? why?
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proline- ring causes steric interference. amide is part of ring, no H available for hydrogen bonding (the one H would be used in peptide bond)
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crick's experiment with ribosomes
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1.E. coli is labeled with a heavy isotopes of of 13C and 15N =heavy ribosomes
2.The bacteria are infected with T2 phage and grown with a light isotopes of 12C and 14N = light ribosomes, + 32P = RNA.
3.The heavy and light ribosomes are analyzed with density gradient
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Choosing a library: which host?
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E. coli or S. cerevisiae (if eukaryotic equipment needed for protein modification)
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What is a Probe?
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A labeled sequence of ssDNA or ssRNA that hybridizes with its complement by base pairing.
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DNA repair: Mismatch repair
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1. During G2 phase; 2. Produced by mutations of MSH2 & MLH1 genes; 3. Associated with HNPCRC
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Consequence of anti-parallel DNA strands and direction of DNA synthesis:
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Two strands are synthesized in the opposite direction.
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which aa destabilizes the alpha helix conformation? why?
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Glycine. b/c sidechain (H) freely rotates, very unconstrained
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which end of a nucleic acid has a free OH group?
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the 3' end
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In experiments conducted by Griffiths, the inability of the avirulent strain to produce a lethal infection was due to
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destruction by the host's white blood cells
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gel mobility shift assay (EMSA)
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since small DNA has a much higher mobility than DNA bound to a protein, one can label a short DNA fragment, mix it with protein, and electrophorese it. Detect with autoradiography.
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What are the 5 steps involved in constructing a DNA probe?
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1. Identification 2. Isolation3. Reproduction4. Seperation5. Labelling
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Unwinding of double helix at the origin of replication...
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causes supercoiling of the DNA helix.
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B. It occurs before the mRNA reaches a chain length of 30 nt.
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When does capping of the pre-mRNA occur?
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how does SDS act to denature proteins?
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has long hydrocarbon tail wraps around protein. negatively charged head keeps refolding from happening
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What insert size can the lambda phage accomodate?
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12-20kbCan package 78-105% of DNA (37-52kb total)
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What is the direction of translation of the ribosome?
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reads mRNA 5'-3'; Amino to Carboxyl group.
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C. The level of fluorescence would be very high in the assay buffer.
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In an in vitro transcription assay to detect the level of transcription from a lac operon, one of the RNA precursors was tagged with a fluorescent label on the γ-phosphate. Which of the following is a likely outcome if transcription occurred?
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what are 2 ways that proteins bind to DNA?
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1. binding regions - palindromic sequeces (usually)
2. binding domains - motifs
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using a Ni affinity column to purify proteins
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1. lyse cells to release proteins2. pour lysate through affinity column, where the Ni binds His + your protein and lets all other proteins pass through.3. Release fusion protein with histidine or imidazole.4. Cleave fusion protein with enterokinase5. pass through column once more
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explain the hydrogen bonding in the secondary structure of proteins.
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the O in the carbonyl (C=O) bond of one peptied bond bonds with the H in the amide (N-H) of another peptide bond. occurs between every 4th peptide bond
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There are three types of RNA involved in the translation process.. what are they and what do they do?
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mRNA which carries the code for the gene, rRNA which aids in the formation of the ribosome, and tRNA which brings individual amino-acids to the ribosome.
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