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471 Cards in this Set
- Front
- Back
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how many RNA polymerases do prokaryotes have?
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1
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how would you go about finding the DNA binding specificity of a DNA binding protein?
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mix it with a DNA fragment library and allow it to bind to one of them random pieces, then sequence it.......or do DNA footprinting.. or CHIP
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regulatory proteins can recognize DNA sequence by the ______________ exposed in DNA
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chemical features of bases...... in the major and minor grooves of DNA
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RNA polymerase II must be phosphorylated in order to escape from the transcription factors and begin _________
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elongation
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single molecule tracking (using bead and laser trap) can be used to measure _______
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the motion of a single molecule
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the purpose of DNA footprinting
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to find the area that a DNA binding protein binds to....or also find the binding kinetics...nucleases will digest pieces of DNA except the part where the DNA binding protein is bound because it protects it... the pieces then can be run through a gel
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what does it mean that transcription factors can work synergistically?
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adding more of them means the total result of transcripts is greater than the sum of 1 transcription factor working alone
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why are transcription factor domains (modular) why is it defined that way?
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they all have the same general types of domains (functional parts) within them
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Zn finger, HLH, leucine zipper (bZIP), HMG box (are all what?)
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DNA binding motifs
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catalyze peptide bond formation, help align tRNAs by forming A,P,E sites, line exit tunnel to make it non stick
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rRNA
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many chaperones belong to the _____________ class of proteins which are upregulated in times of increased temperature or stress
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heat shock proteins (HSP)
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coactivator/corepressor complexes can contact the general ______ machinery and alter ________ in the vicinity of the promoter
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transcription..... chromatin'
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DNA Replication Is Fundamentally Similar in bacteria and eukaryotes (yes/no)
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yes
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do we spend energy to degrade proteins
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yes, ATP is required by the proteasome
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Dual-Color Fluorescence Microscopy:
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learning by looking
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Each cell's DNA sustains >10,000 ____________ per day
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lesions
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Electron and _____________ microscopes are Similar
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Light Microscopes
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erythromycin, clindamycin, tetracycline are antibiotics that target the ________
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ribosome
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gene activators may recruit ________________ to help transcription
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ATP-dependent chromatin remodelers
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Gene number and organism complexity (correlate how well?)
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poorly correlate
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in the nucleus, heterochromatin is near the
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Lamina
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histones are very different between species (yes/no)
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no, they are highly conserved
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Histones have MANY sites for _____________
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regulatory modifications
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histones have very stiff and rigid tails (yes/no + explain)
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no, their tails are very flexible
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Homologous recombination can result in_________
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loss of heterozygozity, for example loss of SNPs in the damaged strand (can be caused by which DNA repair mechanism?)
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Low Mutation Rates Are Necessary for life as we know it (yes/no + explain)
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yes
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makes sure that the correct amino acid is linked to each tRNA via hydrolitic editing (it is the enzyme that performs this process but also edits it)
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aminoacyl tRNA synthetase
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Mismatch repair is active immediately following replication (yes/no)
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yes
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nonsense-mediated mRNA decay
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mechanism that degrades mRNAs that have been abnormally spliced and may contain a premature stop codon
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Nuclear import receptors are encoded by _____________. The gene products recognize distinct nuclear localization sequences in cargo proteins.
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related karyopherin genes
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Nuclear Import Receptors Receptors Bind to
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Cargo Proteins, NPC Proteins, and Ran-GDP
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Nucleosomes are instrinsically dynamic, which means that they
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unwrap and rewrap DNA very quickly, constantly
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Nucleosomes can be moved by_____________ hydrolysis
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ATP
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Presence of a________ is the cause of the “w” allele that causes the wrinkled pea phenotype
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transposon
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proteins involved with translation that improve accuracy
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elongation factors
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Reactive species (ie oxygen or nitrogen) may be produced by
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cellular metabolism, or taken in from the environment
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ribosomes are made from ____# rRNAs which are cut from the preRNA
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4
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Scientists still don’t know the function of about _________of the genes.
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half
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Selective Permeability of the Nucleus is conferred by
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Conferred by Nuclear Pore Complexes (a property of the nucleus)
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The greatest biochemical diversity exists in
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procaryotes
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The nucleus is selectively ____________
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permeable
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the peptidyl transferase site is surrounded by
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rRNA
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The Proteins at a Replication Fork cooperate to form _________
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a Replication Machine
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There are multiple ___________ that bind distinct classes of cargo proteins
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nuclear import and export receptors (importins/exportins)... (karyopherins)
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things that are imported into the nucleus
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histones, regulatory factors
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Three sequences necessay for chromosome heritability
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telomere, replication origin, centromere
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transposase
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the enzyme that is encoded by a transposon and mediates its movement
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transposons encode this enzyme
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transposase (encoded by what type of DNA)
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tRNA synthetase editing, elongation factor checking, nonsense-mediated mRNA decay
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quality control mechanisms, regulation of translation
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types of DNA sequences in a genome
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repetitive sequences, satellite DNA, transposons, genes
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UV can cause DNA _________ and __________
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breaks and pyridine dimers
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Variable color in maize kernels can be caused by
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transposon mutagenesis (can cause what appearance of corn?)
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visibility in a microscope depends on _________
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contrast (and other variables too)
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We are constantly bombarded with _________ from the atmosphere and therefore our cells must cope with spontaneous double strand breaks
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ionizing radiation
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What may account for the disparity between human complexity and gene number?
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Hypothesis are: alternative splicing, or developmental regulation (optimal use of existing genes)
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what is the function of the barrel of the proteasome
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degrades proteins, contains protease active sites
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what is the function of the cap of the proteasome
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regulates entry into the destruction chamber, based on recognition of ubiquitin chains, and unfolds the substrate
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what part of the histone is modified?
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the tail of a histone
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when do chaperone molecules bind to the new polypeptide?
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as it emerges from the ribosome
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when is the x chromosome inactivated?
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in the early embryo
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cells expressing telomerase proliferate more or less?
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more
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cells regulate their telomere length (yes/no)
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yes
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difference between prokaryotic and eukaryotic mRNA
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eukaryotic has introns and processing (cap and tail), while prokaryotic don't have those
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does RNA polymerase need a primer?
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no
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does RNA polymerase require strand unwinding (topoisomerase)?
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yes
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electrophoretic (gel) mobility shift assay
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proteins bound to DNA are run through a gel... in order to study protein/DNA interactions
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epigenetic mosaics (are examples of?)
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x inactivation
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helix-turn-helix is a motif found where?
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DNA binding proteins
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how can genes be repressed by chromatin
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chromatin modification via chromatin remodeling complexes: histone deacytlases are added, HP1, H3 methyl-lys9, etc. (histone deacytlation)
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how many RNA polymerases do eukaryotes have?
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4
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in translation, the _________ catalyzes the reaction that transfers the amino acid from the tRNA in the P site to the tRNA in the A site, so that a peptide bond is formed by ________________
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rRNA, peptidyl transferase
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in translation, the amino acid is transferred from the ______ site to the ______ site in order to form a peptide bond
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P site to the A site
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is the nucleolus heterogeneous (yes/no.... why?)
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yes...... differing areas of active transcription
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major steps of transcription
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initiation, elongation, termination
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major steps of translation
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initiation, elongation, termination
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many of the steps of translation require ______ hydrolysis (for energy)
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GTP
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nascent polypeptides don't stick to the exit tunnel of a ribosome because _________
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the tunnel is mostly hydrophilic, and it is wide enough to accommodate the chain and water
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rDNA
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the DNA that encodes for rRNA... RIBOSOMAL DNA
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stabilize rRNAs, interact with incoming tRNAs, interact with elongation factors, provide structural support
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ribosomal proteins
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the genetic code is almost universal, this means that
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organisms share a common ancestor
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_____ and ______ finish and seal okazaki fragments
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DNA polymerase and DNA ligase work together to do what during replication?
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this property of DNA underlies DNA Replication and repair
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base pairing
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“Exportin”:
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Nuclear export receptor that binds a nuclear export sequence
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“Importin”:
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Nuclear import receptor that binds a nuclear localization sequence
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A DNA glycosylase of the base-excision (function is what?)
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recognizes damaged DNA bases by flipping them out of the heli, thought to scan the genome, a “surveillance” mechanism
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A free radical
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an ion that contains one or more unpaired electrons
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A Sliding Ring Called the “Sliding Clamp” does what?
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Holds Moving DNA Pol. onto the DNA
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A Strand-Directed Mismatch Repair System
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Removes Replication Errors that Slip Through (what repair system?)
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adherent cells
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cell culture that sticks to a substrate
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all of the DNA sequence for an organism
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genome
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aminoacyl-tRNA synthetase
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enzyme that binds the corresponding amino acid to a tRNA, with energy from ATP
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ATPases bind to nucleosomes and act by sliding them to expose DNA or switch out _________
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histones (may be switched out by what enzymes?)
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Bacteria usually initiate replication at how many origins?
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single origin of replication (in what organism?)
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Barr bodies in female cells are also called
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inactive X is also called
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Base excision repair
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Initiated by a DNA glycoslyase,repairs basic sites where base has been lost, removes nucleotides that were damaged
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Celera assembly strategy
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contigs, reads, read pairs, scaffold, ordering of scaffold, using Human Genome Project clone map and other maps
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cell line
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– culture derived from an ancestor, which is a single cell
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cellular senescence
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replicative senescence, loss of the ability to divide
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centromere
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point of the mitotic spindle, DNA sequence that is essential for proper chromosome segregation
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centromere
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sequence that attaches to microtubules to pull DNA apart during cell division
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chaperonins
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HSP60 family, barrel shaped protein complexes that provide a secluded environment for proteins to fold
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Chromatin (what is it made of)
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DNA and associated proteins, histone and non histone
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chromatin immunoprecipitation (CHIP)
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cell DNA is crosslinked with formaldehyde, cell is lysed, DNA sonicated (broken up), antibodies applied to bind to DNA binding proteins, the pieces that have antibodies bound are separated out, DNA purified, and measured using QTRTPCR
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chromosome conformation capture (how is it performed?)
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like CHIP, but without the DNA binding proteins: dna is cross linked, digested (no sonication), ligated, PROBED
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Chromosome Territories:
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Each chromosome tends to stay in its own nuclear neighborhood
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chromosomes are replicated in what phase
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s phase (what happens to chromosomes?)
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clonal cells
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a type of line, cells are genetically identical
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co-culture
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– cells are grown with another kind, can be for growth factors
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coactivator
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protein that increases gene expression by binding to an activator which contains a DNA binding domain. cannot bind to DNA by itself. often contains acetyltransferases
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compartmentalization of nucleus achieves what?
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clustering of molecules may facilitate biochemical reactions, be more efficient (this is called?)
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confluent cells
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culture where all cels are touching each other
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Confocal Microscopy
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uses a hole to get rid of out of focus light. Slices of specimen
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Conserved since the last common ancestor of all living things:
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ribosomal RNA (to what extent is it conserved?)
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constitutive DNA
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“never” transcribed DNA is called (not really)
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corepressor
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protein that decreases gene expression by binding to a transcription factor which contains a DNA binding domain. THE ____ is unable to bind DNA by itself..... it can recruit histone deacetylases
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Differenital Interference Contrast Microscopy - “Nomarski”
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(ΔRI/Δd) causes a Δcontrast
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Different regions of a chromosome are replicated at the same time?
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no
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DNA coils when placed in solution
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yes
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base excision mechanism
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1) recognizes alteration, 2) removes base by cleaving bond that holds sugar, 3) the beheaded doxyribose phosphate is excised by AP endonuclease,4) AP endonuclease cleaves the DNA backbone, 5) DNA polymerase fills gap using comp. Strand as template, 6) DNA ligase seals
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DNA helicase
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unwinds doublestranded DNA
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DNA looping
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a regulatory mechanism in DNA that can affect protein interactions with DNA, DNA is looped
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DNA microarray
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DNA oligonucleotide probes bind a cDNA or RNA sample in order to evaluate gene expression
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DNA polymerase cannot polymerize following ________________
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a mis-matched nucleotide pair (causes what to stop)
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DNA primase polymerizes
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RNA primer (polymerized by what enzyme?)
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DNA replication Begins at __________________
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replication origins (where _____ begins)
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DSBs are repaired by _______________ and ________________?
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non homologous end joining and homologous recombination (can repair what type of break?)
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During replication, RNA primers are replaced by _____________
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DNA (replaces what type of primers during replication?)
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Eamples of things that exported out of nucleus
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mRNA, ribosomal subunits
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Electron micrograph of H1-depleted chromatin
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“beads on a string”, a 10 nm fiber (smaller number than 30!)
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Electron Microscopy
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λ = sqrt(150/V) (i.e., 0.5 A° ). 1000 - 250,000 x magnification
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empty magnification
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magnification with no corresponding increase in detail resolution
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enhancer (definition and function)
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a short region of DNA that can be bound with proteins to increase transcription levels
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Epigenetic inheritance (mediated by chromatin state) - definition
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any change other than identity of A, T, C, or G that is inherited by cell division, and potentially (but not usually) in germ cells
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Eucaryotic Chromosomes Contain Multiple ______ whereas bacterial DNA only has 1.
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multiple origins of replication (in what organism?)
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euchromatin
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DNA that is normally loosely condensed and condensed more only during mitosis or meiosis, contains more active genes
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euchromatin
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transcribed DNA is called
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eukaryotic translation initiation
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small ribosomal subunit joins with initiation factors, initiatior tRNA (tRNAmet) is brought to P site, and mRNA bound to more initiation factors, 43s complex scans mRNA for AUG start, LARGE subunit joins the complex
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examples of nuclear bodies
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cajal bodies, GEMS, speckles, PML bodies, nucleolus (these are examples of what?)
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facultative DNA
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DNA that could be transcribed
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FISH (how is it performed?)
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DNA is denatured with formamide and hybridized with DNA binding probes that are labeled (name of process?)
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fluorescence microscopy -
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uses fluorophores/fluorochromes to visualize antibodies/proteins, or other cell componenents. A wavelength is absorbed by specimen, and wavelength emitted to receptor. GFP or its variants are commonly used
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Fluorescence Resonance Energy Transfer (FRET)
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conformation changes (cis) and regulated interactions (trans) can be detected if a donor molecule with a fluorescent tag interacts with another and transfers energy to it, causing the other to fluoresce as well. Used to study allosteric binding sites
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frameshift mutation
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an insertion or deletion of a nucleotide to DNA
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Freeze-Fracture Replication (how is it performed?)
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specimen is frozen, fractured, and a replica is made via carbon/metal shadowing, then finally viewed with electron microscopy
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gene activators can bind to ______. what is their function?
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can bind to DNA. increase the rate of transcription by enhancing the interaction between RNA polymerase and the promoter.
they increase attraction of RNA polymerase for the promoter, through interactions with subunits of the RNA polymerase or indirectly changing the structure of the DNA |
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Gene duplication (and divergence (mutagenesis)) gives rise to
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new gene families (and therefore new proteins) may be created by
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Gene duplication and mutatenesis (divergence) drive what process?
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evolution (is driven by these two events)
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gene regulatory circuit
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functional clusters ofﾠgenesﾠthat impact each other's expression through inducible transcription factors and cis-regulatory elements.
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genes are silenced due to their proximity to _______________
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heterochromatin causes ________________ when it is proximal to it
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genetic inheritance
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inheritance of DNA sequence, by cell division or germ cells
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GroEL and GroES
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proteins of the chaperonin family that work with chaperonin to fold proteins
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GST pull-down or Co-Immunoprecipitation
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antibody or protein tag coupled to an agarose bead can pull a protein out from a cell lysate, used to detect protein-protein interactions
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H1 linker histone (links what together? to form what?)
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links histones together, to form the 30 nm fiber
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half of our genome came from _______________
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transposons (make up half of our ______)
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heterochromatin
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compact regions of DNA, silenced genes, and long sequences of satellite DNA
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heterochromatin
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non-transcribed DNA that is kept in a compact state
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highly conserved DNA sequence in the promoter region of genes and is the binding site for transcription factors and other proteins. usually the most important sequence
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TATA box
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Histone Acetylation is GENERALLY Associated with
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Active Genes (are associated with what histone modification?)
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histone modifications (examples)
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acetyl, methyl, phosphoryl. can be added to what for modification?
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Histone Modifying Enzymes
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histone methyl transferases, acetyltransferases, kinases, ubiquitin ligases
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histone octamer
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found at the center of a nucleosome core particle. It consists of 2 copies of each of the four core histone proteins (H2A, H2B, H3 and H4). Makes up the nucleosome core particle.!!!
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Histone tails
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protrude from the nucleosome, contribute to chromatin folding, are subject to regulation by modification
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Histone variants (examples)
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H3.3, H2A.Z, H2A.X, CENP-A (are examples of?)
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HOMOLOGOUS RECOMBINATION mechanism
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a DNA single strand binds with a homologous region, branch migration fills in remaining DNA
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homologs
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genes with similar sequences due to shared ancestry
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horizontal transfer
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transfer of genes between species, via viruses, or within species (due to sexual reproduction)
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how are histone modifications inherited by the daughter chromosomes?
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half of daughter chromosomes DNA receive histones, the rest of the pattern is re-established by reader-writer complexes
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How is directionality achieved in nuclear import/export?
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By Ran.
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how is DNA bent during initiation of transcription
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TBP (tata binding protein) binds to the tata box and other proteins
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how is the 30 nm Fiber formed
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with core histone tails and histone H1 (what unit of structure can be formed?)
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Human genome project (HGP) sequencing strategy
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Overlapping BACs (used in what type of DNA sequencing)
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Hutchinson-Gilford Progeria Syndrome
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Premature aging, Defects in nuclearmorphology, nucleus is not round because lamina is messed up. ･In more than 80% of the gene defect responsible for HGPS is a single spontaneous mutation in codon 608 of the LMNA gene, which encodes both lamin A and lamin C
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hydrolyzing ATP (causes what unwinding-enzyme to move?)
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DNA helicase moves by ___________________
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immortalized cells
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cell culture that can divide infinitely
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in translation, the “A site”
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aminoacyl site, the charged tRNAs enter here
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in translation, the “E site”
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exit site, the tRNA that no longer is charged with an amino acid exits
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in translation, the “P site”
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peptidyl site, the peptide bond forms between the amino acid on this site and the A site
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in yeast how is mating type determined
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expression of transcription factors
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Incorrectly paired bases do not have the correct ___________, so they do not fit properly in the active site of DNA pl
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geometry, base pair angles are different when they are ?
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initiation of replication in eukaryotes
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multisubunit complex binds to origin of replication
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Ionizing radiation (e.g. X-rays, high energy UV) can cause ________ in DNA
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double strand breaks (can be caused by what?)
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Lamins
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type of intermediate filament. 10nm in diameter, form rope like networks
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lampbrush mitoticchromosome
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large chromosome with loops that are performing transcription
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Laser Scanning Confocal Microscopy
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focus a laser onto specimen and collect scattered/defracted light. uses a hole to get rid of out of focus light. View specimen in a single plane, Usually used with fluorescence optics, Bleaching can occur
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Many of the repeated sequences in the human genome are nonfunctional __________
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transposons (make up many of the _______ sequences in the human genome)
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max theoretical resolution
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? = d = (0.61 l)/[n sin (a)]
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Maximum useful magnification of a microscope
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? = (objective numerical aperture) x 500 – 1,000
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mechanism that can flawlessly repair double strand breaks
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homologous recombination (capable of fixing what?)
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mechanisms for repairing damaged DNA
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nucleotide excision repair. Base exision repair. Mismatch repair. Double strand break repair (non homologous end joining and homologous recombination)
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Mismatch repair
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removes mistakes that aren't caught by DNA pol. during replication. mismatch repair proteins look at DNA for mismatches. nucleotide from the non-methylated strand is removed
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Mismatches are cleaved by
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associated exonucleolytic activity (cleaves what?)
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Molecular Basis of Hutchinson-Gilford Progeria Syndrome
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Non-random distribution of DNA, interaction of DNA with lamins
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molecular chaperones (chaperones)
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proteins that assist the non-covalent folding or unfolding by BIINDING HYDROPHOBIC SURFACES and the assembly or disassembly of other macromolecular structures, but do not occur in these structures when the latter are performing their normal biological functions... use ATP hydrolysis to fold
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negative regulation
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a bound repressor protein prevents transcription (what type of regulation?)
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neighborhoods of chromosomes are
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statistical probabilities of where chromosomes will be located
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New genes can be generated from pre-existing genes (how?)
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mutation, dupliication and divergence, shuffling, horizontal transfer
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New Nucleosomes Are Assembled where
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behind the replication fork (what is assembled?)
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non homologous end joining and homologous recombination do what?
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repair double strand breaks (what DNA repair pathways do this?)
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non-histone DNA associated proteins
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ATP-dependent remodeleers, histone modifying enzymes, structural proteins, DNA binding transcription factors (are examples of?)
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Non-homologous end joining (mechanism)
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rings shaped protein Ku finds DSB, protein complex forms that brings ends together and recruits DNA ligase (what DNA repair pathway?)
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nonsense mutation
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DNA mutation that results in a premature stop codon
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northern blot (mechanism)
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RNA is run through a gel, blotted onto a membrane, visualized with labeled probes, and x-rayed to see it
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nuclear bodies (definition)
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sub-environments that form as needed within nucleus, sites of rRNA transcription
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Nuclear import and export work the same but in opposite directions. The receptors for both are encoded by ____________ genes
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karyopherin genes produce what type of receptors
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nuclear lamina (definition + function)
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inside/attached to nuclear envelope. made of intermediate filaments and memb. Associated proteins. gives mechanical support. anchors NPCs
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nuclear localization/nuclear export sequence?
|
A small stretch of amino acids in the cargo protein that binds to a karyopherin.
|
|
|
nucleolus
|
nuclear subcompartment where ribosomal RNAs are transcribed
|
|
|
Nucleotide excision repair
|
cut and patch mechanism. Removes bulky lesions, pyrimidine dimers, chemical adducts
|
|
|
nucleotide excision repair mechanism
|
Proteins detect bulky DNA lesions, helicase separates strands, damaged DNA cut by nucleases, segment is released, gap filled by DNA polymerase, sealed by ligase
|
|
|
nuclesome
|
basic unit of structure of chromatin
|
|
|
ortholog
|
a new set of genes created through speciation and divergence of the genes
|
|
|
paralogs
|
a new set of genes created in a single species through duplication and divergence...
|
|
|
Phase Contrast Microscopy
|
ΔRI is is caused by ΔIntensity of light, Organelles differ in refractive index, which creates interference
|
|
|
point mutation (definition and result)
|
mutation: usually means replacement of a nucleotide with another... no drastic consequences
|
|
|
polyribosome
|
multiple ribosomes translating mRNA simultaneously in a complex
|
|
|
positive regulation
|
a bound activator protein increases the rate of transcription (what type of regulation?)
|
|
|
Pre-replication complex
|
protein complex that forms at the origin of replication during the initiation step of DNA replication.
|
|
|
primary cell culture
|
cell culture that comes from a living organism
|
|
|
proteasome
|
large protein complex that degrades unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds
|
|
|
Reactive nitrogen species
|
include Nitric Oxide NO and nitrous acid HNO2, and can damage DNA
|
|
|
Reactive oxygen species (oxygen radicals) include
|
include super oxide, O2, and hydrogen peroxide, H2O2, and can damage DNA
|
|
|
regulatory nuclear shuttling
|
a way for transcription factors and other regulatory proteins (such as p53) to get into the nucleus
|
|
|
Repeat sequences (examples)
|
microsatellites,minisatellites, VNTRs, telomere repeats, etc.
|
|
|
repressor
|
a DNA binding protein that regulates the expression of one or more genes by decreasing the rate of transcription
|
|
|
Resolution
|
the shortest distance between two points on a specimen that can still be distinguished as separate entities
|
|
|
Retrotransposons (how do they get into the new spot)
|
transposons that encode reverse transcriptase so they can make DNA copies of themselves and be inserted into the genome. they are initially made of RNA.
|
|
|
Retrotransposons go through an _______ intermediate
|
RNA (what type of transposons use this?)
|
|
|
Ribosomal RNA (rRNA) (function + what do they encode)
|
catalyze peptide bond between amino acids, recognize and bind RNAs and proteins, part of ribosome
|
|
|
RNA polymerase I synthesizes what type of RNA?
|
rRNA is synthesized by which RNA polymerase?
|
|
|
RNA polymerase II synthesizes what type of RNA?
|
mRNA and small nuclear RNAs are synthesized by which RNA polymerase?
|
|
|
Scanning Electron Microscopy (how is it performed?)
|
Critical-point drying, temp and pressure where dliq = dvap. Electron beam scans the image. Image indirectly generated by back-scattered electrons. Key is to preserve surface characteristics w/o hydration
|
|
|
secondary cell culture
|
cell culture that is taken from frozen cells
|
|
|
Sequence variants of genes
|
alleles
|
|
|
short string of amino acids in the cargo protein that binds to a karyopherin (nuclear transport receptor)
|
nuclear localization signal/sequence
|
|
|
shotgun sequencing (method)
|
dna is fragmented into small pieces, pieces are sequenced, a computer finds overlapping fragments
|
|
|
sigma factor
|
a prokaryotic transcription factor that enables specific binding of RNA polymerase to gene promoters
|
|
|
silent mutation
|
DNA mutation that does not result in an amino acid change
|
|
|
Single-standed DNA binding protein
|
binds to single strands to keep them from re-annealing. stabilizes the “melted” strand
|
|
|
SNPs
|
a DNA sequence variation occurring when a single nucleotide — A, T, C, or G — in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual). For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case we say that there are two alleles : C and T. Frequency may vary with ethnicity
|
|
|
southern blot (method)
|
DNA is run through a gel, blotted onto a membrane, visualized with labeled probes, and x-rayed to see it
|
|
|
splicing (the process does what?)
|
removes introns from newly transcribed pre-mRNAs in eukaryotes. exons are joined
|
|
|
t-loop and associated protein complex is called
|
shelterin
|
|
|
t-loops
|
protective loop at the end of a chromosome
|
|
|
Tangled meshwork of unstructured protein segments lines the pore and prevents _______________
|
passage of large proteins through NPC is prevented by
|
|
|
telomerase
|
reverse transcriptase that adds repeats to the end of a chromosome and has an RNA template
|
|
|
telomere
|
repetitive DNA at the end of a chromosome, essential for maintenance of chromosome ends
|
|
|
TEM (transmission electron microscopy)
|
beam of electrons passed through specimen (what type of microscopy?)
|
|
|
The “gene” is made of the DNA that encodes protein as well as ____________
|
regulatory sequences that controls gene expression (is part of what?)
|
|
|
The down side of NHEJ is that non-matching free DNA ends could be ligated together, causing
|
chromosomal translocations or loss of entire regions of chromosomes can be caused by what DNA damage repair pathway?
|
|
|
The fingers do a “squeeze” check of the bound nucleotide before it is covalently attached to the growing strand
|
DNA polymerase (does what checking function during replication?)
|
|
|
The heterochromatic state can spread, leading to
|
“position-effect”
|
|
|
The Histone Code Hypothesis
|
Histone covalent modifications control the activities of the underlying DNA (post-translational). modification will increase or decrease affinity for specific proteins
|
|
|
The nucleus is surrounded by the
|
The nuclear envelope surrounds what?
|
|
|
The three major branches of life
|
bacteria, archea, eukaryotes
|
|
|
the wobble hypothesis
|
there are 61 codons but less than 61 tRNAs.... some tRNAs can bind with more than one codon because the third nucleotide does not have to be specific
|
|
|
topoisomerase I
|
It wraps around DNA and makes a cut , or “nick” permitting the helix to spin. Once DNA is relaxed, topoisomerase reconnects broken strands
|
|
|
Topoisomerase II deals with
|
“tangling” problems... it cuts both strands of one DNA double helix, passes another unbroken DNA helix through it, and then reanneals the cut strand . it cuts to rearrange crossed helices (what enzyme is this?)
|
|
|
transcription factory
|
specific areas within the nucleus where active transcription occurs, may remain in the absence of transcription
|
|
|
transcriptional state & ___________ are linked
|
nuclear localization
|
|
|
translation
|
synthesis of proteins from an RNA template
|
|
|
translation: elongation (what is in P site, what enters A site, what happens to amino acid, what factor is released, how does ribosome move (relative to the mRNA))
|
initiator tRNA (methionine) is in the P site, new tRNA enters A site, amino acid goes from P to A tRNA, elongation factor is released, GTP hydrolysis and another elongation factor binding causes the ribosome to move
|
|
|
translation: termination
|
release factor binds to A site (with STOP codon), other proteins and GTP hydrolysis dissociates the ribosome into two separate subunits
|
|
|
transposition of a transposon can occur by ________ or ________
|
cut and paste, or replicative
|
|
|
Transposons
|
jumping genes, mobile genetic elements
|
|
|
Transposons in the human genome (how much?)
|
half of our genome comes from this type of DNA
|
|
|
tRNA
|
small RNA with ANTICODON and corresponding AMINO ACID
|
|
|
ubiquitin
|
this protein, (1_______) adds (1________) monomers via an isopeptide bond, one example being for proteasomal degradation
|
|
|
Variable number tandem repeats (VNTRs) are used in
|
DNA fingerprinting and forensic science (makes use of what?)
|
|
|
what does it mean that the genetic code is “degenerate”
|
there is redundancy but no ambiguity (this makes the genetic code what?)
|
|
|
What does Ran bind
|
cargo protein and GTP or GDP, and a karyopherin (bind to what molecule)
|
|
|
what happens during initiation of transcription
|
transcription factors and RNA pol. assemble at the promoter, as well as histone modifying enzymes, and mediator.....the template strand is exposed, RNA Pol is phosphorylated and dissocates from the other factors
|
|
|
When transposons “hop” into the middle of genes they usually disrupt __________
|
gene function can be disrupted by these mobile genetic elements
|
|
|
a type of gene dosage compensation in females..... without it females would express double the amount of genes
|
x inactivation
|
|
|
X inactivation (mechanism)
|
One X is randomly selected in female embryonic stage, silencing is initiated by expression of Xist non-coding RNA, counting of X chromosomes, Xist coats the silenced Xi, histone 3 Lysine 9 and Lysine 27 undergoes methylation, silencing is maintained by DNA methylation and/or polycomb group proteins
|
|
|
Xeroderma pigmentosum, or XP, is
|
an autosomal recessive genetic disorder of DNA repair in which the body's normal ability to remove damage caused by ultraviolet (UV) light is deficient. defects in Nucleotide Excision Repair. This leads to multiple skinnmalignancies at a young age. In severe cases, it isnecessary to avoid sunlightcompletely. Usually caused by loss of nucleotide excision repair enzymes.
|
|
|
Xist promotes ________________ X chromosome.
|
heterochromatin formation on the X chromosome (is conferred by what RNA transcript?)
|
|
|
yeast mating (mechanism)
|
two haploid shmoos secrete pheromones, grow projections and mate
|
|
|
zigzag vs. solenoid model
|
different theories of structure for chromatin packing
|
|
|
DNA polymerase and DNA ligase work together to do what during replication?
|
_____ and ______ finish and seal okazaki fragments
|
|
|
Nuclear export receptor that binds a nuclear export sequence
|
“Exportin”:
|
|
|
Nuclear import receptor that binds a nuclear localization sequence
|
“Importin”:
|
|
|
recognizes damaged DNA bases by flipping them out of the heli, thought to scan the genome, a “surveillance” mechanism
|
A DNA glycosylase of the base-excision (function is what?)
|
|
|
an ion that contains one or more unpaired electrons
|
A free radical
|
|
|
Holds Moving DNA Pol. onto the DNA
|
A Sliding Ring Called the “Sliding Clamp” does what?
|
|
|
Removes Replication Errors that Slip Through (what repair system?)
|
A Strand-Directed Mismatch Repair System
|
|
|
cell culture that sticks to a substrate
|
adherent cells
|
|
|
genome
|
all of the DNA sequence for an organism
|
|
|
enzyme that binds the corresponding amino acid to a tRNA, with energy from ATP
|
aminoacyl-tRNA synthetase
|
|
|
histones (may be switched out by what enzymes?)
|
ATPases bind to nucleosomes and act by sliding them to expose DNA or switch out _________
|
|
|
single origin of replication (in what organism?)
|
Bacteria usually initiate replication at how many origins?
|
|
|
inactive X is also called
|
Barr bodies in female cells are also called
|
|
|
Initiated by a DNA glycoslyase,repairs basic sites where base has been lost, removes nucleotides that were damaged
|
Base excision repair
|
|
|
contigs, reads, read pairs, scaffold, ordering of scaffold, using Human Genome Project clone map and other maps
|
Celera assembly strategy
|
|
|
– culture derived from an ancestor, which is a single cell
|
cell line
|
|
|
loss of a cell's ability to divide
|
cellular senescence
|
|
|
point of the mitotic spindle, DNA sequence that is essential for proper chromosome segregation
|
centromere
|
|
|
sequence that attaches to microtubules to pull DNA apart during cell division
|
centromere
|
|
|
HSP60 family, barrel shaped protein complexes that provide a secluded environment for proteins to fold
|
chaperonins
|
|
|
DNA and associated proteins, histone and non histone
|
Chromatin
|
|
|
cell DNA is crosslinked with formaldehyde, cell is lysed, DNA sonicated (broken up), antibodies applied to bind to DNA binding proteins, the pieces that have antibodies bound are separated out, DNA purified, and measured using QTRTPCR
|
chromatin immunoprecipitation (CHIP)
|
|
|
like CHIP, but without the DNA binding proteins: dna is cross linked, digested (no sonication), ligated, PROBED
|
chromosome conformation capture (how is it performed?)
|
|
|
Each chromosome tends to stay in its own nuclear neighborhood
|
Chromosome Territories:
|
|
|
s phase (what happens to chromosomes?)
|
chromosomes are replicated in what phase
|
|
|
– a type of line, cells are genetically identical
|
clonal cells
|
|
|
– cells are grown with another kind, can be for growth factors
|
co-culture
|
|
|
protein that increases gene expression by binding to an activator which contains a DNA binding domain. cannot bind to DNA by itself. often contains acetyltransferases
|
coactivator
|
|
|
clustering of molecules may facilitate biochemical reactions, be more efficient (this is called?)
|
compartmentalization of nucleus achieves what?
|
|
|
culture where all cels are touching each other
|
confluent cells
|
|
|
uses a hole to get rid of out of focus light. Slices of specimen
|
Confocal Microscopy
|
|
|
ribosomal RNA (to what extent is it conserved?)
|
Conserved since the last common ancestor of all living things:
|
|
|
“never” transcribed DNA is called (not really)
|
constitutive DNA
|
|
|
protein that decreases gene expression by binding to a transcription factor which contains a DNA binding domain. THE ____ is unable to bind DNA by itself..... it can recruit histone deacetylases
|
corepressor
|
|
|
(ΔRI/Δd) causes a Δcontrast
|
Differenital Interference Contrast Microscopy - “Nomarski”
|
|
|
no
|
Different regions of a chromosome are replicated at the same time?
|
|
|
yes
|
DNA coils when placed in solution
|
|
|
1) recognizes alteration, 2) removes base by cleaving bond that holds sugar, 3) the beheaded doxyribose phosphate is excised by AP endonuclease,4) AP endonuclease cleaves the DNA backbone, 5) DNA polymerase fills gap using comp. Strand as template, 6) DNA ligase seals
|
DNA glycoslyase mechanism
|
|
|
unwinds doublestranded DNA
|
DNA helicase
|
|
|
a regulatory mechanism in DNA that can affect protein interactions with DNA, DNA is looped
|
DNA looping
|
|
|
DNA oligonucleotide probes bind a cDNA or RNA sample in order to evaluate gene expression
|
DNA microarray
|
|
|
a mis-matched nucleotide pair (causes what to stop)
|
DNA polymerase cannot polymerize following ________________
|
|
|
RNA primer (polymerized by what enzyme?)
|
DNA primase polymerizes
|
|
|
replication origins (where _____ begins)
|
DNA replication Begins at __________________
|
|
|
non homologous end joining and homologous recombination (can repair what type of break?)
|
DSBs are repaired by _______________ and ________________?
|
|
|
DNA (replaces what type of primers during replication?)
|
During replication, RNA primers are replaced by _____________
|
|
|
mRNA, ribosomal subunits are exported out of the ________
|
Eamples of things that exported out of nucleus
|
|
|
“beads on a string”, a 10 nm fiber (smaller number than 30!)
|
Electron micrograph of H1-depleted chromatin
|
|
|
λ = sqrt(150/V) (i.e., 0.5 A° ). 1000 - 250,000 x magnification
|
Electron Microscopy
|
|
|
magnification with no corresponding increase in detail resolution
|
empty magnification
|
|
|
a short region of DNA that can be bound with proteins to increase transcription levels
|
enhancer
|
|
|
any change other than identity of A, T, C, or G that is inherited by cell division, and potentially (but not usually) in germ cells
|
Epigenetic inheritance (mediated by chromatin state)
|
|
|
multiple origins of replication (in what organism?)
|
Eucaryotic Chromosomes Contain Multiple
|
|
|
DNA that is condensed only during mitosis or meiosis, contains more active genes (be specific)
|
euchromatin
|
|
|
transcribed DNA is called (definition dealing with chromatin)
|
euchromatin
|
|
|
small ribosomal subunit joins with initiation factors, initiatior tRNA, and mRNA bound to more initiation factors, 43s complex scans mRNA for AUG start, LARGE subunit joins the complex
|
eukaryotic translation initiation
|
|
|
cajal bodies, GEMS, speckles, PML bodies,nucleolus (these are examples of what?)
|
examples of nuclear bodies
|
|
|
DNA that could be transcribed
|
facultative DNA
|
|
|
DNA is denatured with formamide and hybridized with DNA binding probes that are labeled (name of process?)
|
FISH (how is it performed?)
|
|
|
uses fluorophores/fluorochromes to visualize antibodies/proteins, or other cell componenents. A wavelength is absorbed by specimen, and wavelength emitted to receptor. GFP or its variants are commonly used
|
fluorescence microscopy -
|
|
|
conformation changes (cis) and regulated interactions (trans) can be detected if a donor molecule with a fluorescent tag interacts with another and transfers energy to it, causing the other to fluoresce as well. Used to study allosteric binding sites
|
Fluorescence Resonance Energy Transfer (FRET)
|
|
|
an insertion or deletion of a nucleotide to DNA
|
frameshift mutation
|
|
|
specimen is frozen, fractured, and a replica is made via carbon/metal shadowing, then finally viewed with electron microscopy
|
Freeze-Fracture Replication (how is it performed?)
|
|
|
enhance the interaction between RNA polymerase and the promoter, encouraging expression of the gene.... they increase attraction of RNA polymerase for the promoter, through interactions with subunits of the RNA polymerase or indirectly changing the structure of the DNA
|
gene activators
|
|
|
new gene families may be created by
|
Gene duplication (and divergence (mutagenesis)) gives rise to
|
|
|
evolution (is driven by these two events)
|
Gene duplication and mutatenesis (divergence) drive what process?
|
|
|
functional clusters ofﾠgenesﾠthat impact each other's expression through inducible transcription factors and cis-regulatory elements.
|
gene regulatory circuit
|
|
|
heterochromatin causes ________________ when it is proximal to it
|
genes are silenced due to their proximity to _______________
|
|
|
inheritance of DNA sequence, by cell division or germ cells
|
genetic inheritance
|
|
|
proteins of the chaperonin family that work with chaperonin to fold proteins
|
GroEL and GroES
|
|
|
antibody or protein tag coupled to an agarose bead can pull a protein out from a cell lysate, used to detect protein-protein interactions
|
GST pull-down or Co-Immunoprecipitation
|
|
|
links histones together, to form the 30 nm fiber
|
H1 linker histone
|
|
|
transposons (make up half of our ______)
|
half of our genome came from _______________
|
|
|
compact regions of DNA, silenced genes, and long sequences of satellite DNA
|
heterochromatin
|
|
|
non-transcribed DNA that is kept in a compact state
|
heterochromatin
|
|
|
TATA box
|
highly conserved DNA sequence in the promoter region of genes and is the binding site for transcription factors and other proteins. usually the most important sequence
|
|
|
Active Genes (are associated with what histone modification?)
|
Histone Acetylation is GENERALLY Associated with
|
|
|
acetyl, methyl, phosphoryl. can be added to what for modification?
|
histone modifications (examples)
|
|
|
histone methyl transferases, acetyltransferases, kinases, ubiquitin ligases
|
Histone Modifying Enzymes
|
|
|
found at the center of a nucleosome core particle. It consists of 2 copies of each of the four core histone proteins (H2A, H2B, H3 and H4). Makes up the nucleosome core particle.!!!
|
histone octamer
|
|
|
protrude from the nucleosome, contribute to chromatin folding, are subject to regulation by modification
|
Histone tails
|
|
|
H3.3, H2A.Z, H2A.X, CENP-A (are examples of?)
|
Histone variants (examples)
|
|
|
a DNA single strand binds with a homologous region, branch migration fills in remaining DNA
|
HOMOLOGOUS RECOMBINATION mechanism
|
|
|
genes with similar sequences due to shared ancestry
|
homologs
|
|
|
gene function (may be inferred by a gene's _________________ in a different organism)
|
Homolog, specifically a paralog because different organism
|
|
|
transfer of genes between species, via viruses, or within species (due to sexual reproduction)
|
horizontal transfer
|
|
|
half of daughter chromosomes receive histones, the rest of the pattern is re-established by reader-writer complexes
|
how are histone modifications inherited by the daughter chromosomes?
|
|
|
TBP (tata binding protein) binds to the tata box and other proteins
|
how is DNA bent during initiation of transcription
|
|
|
with core histone tails and histone H1 (what unit of structure can be formed?)
|
how is the 30 nm Fiber formed
|
|
|
Overlapping BACs (used in what type of DNA sequencing)
|
Human genome project (HGP) sequencing strategy
|
|
|
Premature aging, Defects in nuclearmorphology, nucleus is not round because lamina is messed up. ･In more than 80% of the gene defect responsible for HGPS is a single spontaneous mutation in codon 608 of the LMNA gene, which encodes both lamin A and lamin C
|
Hutchinson-Gilford Progeria Syndrome
|
|
|
DNA helicase moves by ___________________
|
hydrolyzing ATP (causes what unwinding-enzyme to move?)
|
|
|
cell culture that can divide infinitely
|
immortalized cells
|
|
|
aminoacyl site, the charged tRNAs enter here
|
in translation, the “A site”
|
|
|
exit site, the tRNA that no longer is charged with an amino acid exits
|
in translation, the “E site”
|
|
|
peptidyl site, the peptide bond forms here
|
in translation, the “P site”
|
|
|
expression of transcription factors
|
in yeast how is mating type determined
|
|
|
geometry, base pair angles are different when they are ?
|
Incorrectly paired bases do not have the correct ___________, so they do not fit properly in the active site of DNA pl
|
|
|
multisubunit complex binds to origin of replication
|
initiation of replication in eukaryotes
|
|
|
double strand breaks (can be caused by what?)
|
Ionizing radiation (e.g. X-rays, high energy UV) can cause ________ in DNA... also reactive oxygen species can do this
|
|
|
type of intermediate filament. 10nm in diameter, form rope like networks (in the nucleus)
|
Lamins
|
|
|
large chromosome with loops that are performing transcription
|
lampbrush mitoticchromosome
|
|
|
focus a laser onto specimen and collect scattered/defracted light. uses a hole to get rid of out of focus light. View specimen in a single plane, Usually used with fluorescence optics, Bleaching can occur
|
Laser Scanning Confocal Microscopy
|
|
|
transposons (make up many of the _______ sequences in the human genome)
|
Many of the repeated sequences in the human genome are nonfunctional __________
|
|
|
? = d = (0.61 l)/[n sin (a)]
|
max theoretical resolution
|
|
|
? = (objective numerical aperture) x 500 – 1,000
|
Maximum useful magnification of a microscope
|
|
|
homologous recombination (capable of fixing what?)
|
mechanism that can flawlessly repair double strand breaks
|
|
|
nucleotide excision repair. Base exision repair. Mismatch repair. Double strand break repair (non homologous end joining and homologous recombination)
|
mechanisms for repairing damaged DNA
|
|
|
removes mistakes that aren't caught by DNA pol. during replication. __________ proteins look at DNA for mismatches. nucleotide from the non-methylated strand is removed
|
Mismatch repair
|
|
|
proteins that assist the non-covalent folding or unfolding by BIINDING HYDROPHOBIC SURFACES and the assembly or disassembly of other macromolecular structures, but do not occur in these structures when the latter are performing their normal biological functions... use ATP hydrolysis to fold
|
molecular chaperones (chaperones)
|
|
|
a bound repressor protein prevents transcription (what type of regulation?)
|
negative regulation
|
|
|
statistical probabilities of where chromosomes will be located
|
neighborhoods of chromosomes are
|
|
|
mutation, dupliication and divergence, shuffling, horizontal transfer
|
New genes can be generated from pre-existing genes (how?)
|
|
|
behind the replication fork (what is assembled?)
|
New Nucleosomes Are Assembled where
|
|
|
repair double strand breaks (what DNA repair pathways do this?)
|
non homologous end joining and homologous recombination do what?
|
|
|
rings shaped protein Ku finds DSB, protein complex forms that brings ends together and recruits DNA ligase (what DNA repair pathway?)
|
Non-homologous end joining (mechanism)
|
|
|
DNA mutation that results in a premature stop codon
|
nonsense mutation
|
|
|
RNA is run through a gel, blotted onto a membrane, visualized with labeled probes, and x-rayed to see it
|
northern blot (mechanism)
|
|
|
sub-environments that form as needed within nucleus, sites of rRNA transcription
|
nuclear bodies (definition)
|
|
|
karyopherin genes produce what type of receptors
|
Nuclear import and export work the same but in opposite directions. The receptors for both are encoded by ____________ genes
|
|
|
inside/attached to nuclear envelope. made of intermediate filaments and memb. Associated proteins. gives mechanical support. anchors NPCs
|
nuclear lamina
|
|
|
A small stretch of amino acids in the cargo protein that binds to a karyopherin.
|
nuclear localization/nuclear export sequence?
|
|
|
nuclear subcompartment where ribosomal RNAs are transcribed
|
nucleolus
|
|
|
cut and patch mechanism. Removes bulky lesions, pyrimidine dimers, chemical adducts
|
Nucleotide excision repair
|
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Proteins detect bulky DNA lesions, helicase separates strands, damaged DNA cut by nucleases, segment is released, gap filled by DNA polymerase
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nucleotide excision repair mechanism
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basic unit of structure of chromatin
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nuclesome
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a new set of genes created through speciation and divergence of the genes
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ortholog
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a new set of genes created in a single species through duplication and divergence
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paralogs
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ΔRI is is caused by ΔIntensity of light, Organelles differ in refractive index, which creates interference
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Phase Contrast Microscopy
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mutation: usually means replacement of a nucleotide with another... no drastic consequences
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point mutation (definition and result)
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multiple ribosomes translating RNA simultaneously in a complex
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polyribosome
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a bound activator protein promotes transcription (what type of regulation?)
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positive regulation
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protein complex that forms at the origin of replication during the initiation step of DNA replication.
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Pre-replication complex
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cell culture that comes from a living organism
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primary cell culture
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large protein complex that degrades unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds
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proteasome
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include Nitric Oxide NO and nitrous acid HNO2, and can damage DNA
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Reactive nitrogen species
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include super oxide, O2, and hydrogen peroxide, H2O2, and can damage DNA
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Reactive oxygen species (oxygen radicals) include
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a way for transcription factors to get into the nucleus
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regulatory nuclear shuttling
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microsatellites,minisatellites, VNTRs, telomere repeats, etc.
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Repeat sequences (examples)
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DNA polymerase (catalyzes what major function?)
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Replication is catalyzed by
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a DNA binding protein that regulates the expression of one or more genes by decreasing the rate of transcription
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repressor
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the shortest distance between two points on a specimen that can still be distinguished as separate entities
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Resolution
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usually the only type of transposons that make copies of themselves when they transpose
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Retrotransposons
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RNA (what type of transposons use this?)
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Retrotransposons go through an _______ intermediate
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help make up structure of ribosome, catalyze peptide bond between amino acids, recognize and bind RNAs and proteins, do not encode proteins
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Ribosomal RNA (rRNA) (function + what do they encode)
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rRNA is synthesized by which RNA polymerase?
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RNA polymerase I synthesizes what type of RNA?
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mRNA and small nuclear RNAs are synthesized by which RNA polymerase?
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RNA polymerase II synthesizes what type of RNA?
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Critical-point drying, temp and pressure where dliq = dvap. Electron beam scans the image. Image indirectly generated by back-scattered electrons. Key is to preserve surface characteristics w/o hydration
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Scanning Electron Microscopy (how is it performed?)
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cell culture that is taken from frozen cells
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secondary cell culture
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alleles
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Sequence variants of genes
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nuclear localization signal/sequence
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short string of amino acids in the cargo protein that binds to a karyopherin (nuclear transport receptor)
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dna is fragmented into small pieces, pieces are sequenced, a computer finds overlapping fragments
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shotgun sequencing (method)
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a prokaryotic transcription factor that enables specific binding of RNA polymerase to gene promoters
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sigma factor
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DNA mutation that does not result in an amino acid change
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silent mutation
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binds to single strands to keep them from re-annealing. stabilizes the “melted” strand
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Single-standed DNA binding protein
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a DNA sequence variation occurring when a single nucleotide — A, T, C, or G — in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual). For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case we say that there are two alleles : C and T. Frequency may vary with ethnicity
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SNPs
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DNA is run through a gel, blotted onto a membrane, visualized with labeled probes, and x-rayed to see it
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southern blot (method)
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removes introns from newly transcribed pre-mRNAs in eukaryotes. exons are joined
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splicing (the process does what?)
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shelterin
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t-loop and associated protein complex is called
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protective loop at the end of a chromosome
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t-loops
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passage of large proteins through NPC is prevented by
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Tangled meshwork of unstructured protein segments lines the pore and prevents _______________
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reverse transcriptase that adds repeats to the end of a chromosome and has an RNA template
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telomerase
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repetitive DNA at the end of a chromosome, essential for maintenance of chromosome ends
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telomere
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beam of electrons passed through specimen (what type of microscopy?)
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TEM (transmission electron microscopy)
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regulatory sequences that controls gene expression (is part of what?)
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The “gene” is made of the DNA that encodes protein as well as ____________
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chromosomal translocations or loss of entire regions of chromosomes can be caused by what DNA damage repair pathway?
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The down side of NHEJ is that non-matching free DNA ends could be ligated together, causing
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DNA polymerase (does what checking function during replication?)
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The fingers do a “squeeze” check of the bound nucleotide before it is covalently attached to the growing strand
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“position-effect”
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The heterochromatic state can spread, leading to
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Histone covalent modifications control the activities of the underlying DNA. modification will increase or decrease affinity for specific proteins. (phenomena is called?)
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The Histone Code Hypothesis
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The nuclear envelope surrounds what?
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The nucleus is surrounded by the
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bacteria, archea, eukaryotes
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The three major branches of life
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there are 61 codons but less than 61 tRNAs.... some tRNAs can bind with more than one codon because the third nucleotide does not have to be specific
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the wobble hypothesis
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It wraps around DNA and makes a cut , or “nick” permitting the helix to spin. Once DNA is relaxed, it reconnects broken strands
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topoisomerase I
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“tangling” problems... it cuts both strands of one DNA double helix, passes another unbroken DNA helix through it, and then reanneals the cut strand . it cuts to rearrange crossed helices (what enzyme is this?)
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Topoisomerase II deals with
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specific areas within the nucleus where active transcription occurs, may remain in the absence of transcription
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transcription factory
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synthesis of proteins from an RNA template
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translation
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initiator tRNA (methionine) is in the P site, new tRNA enters A site, amino acid goes from P to A tRNA, elongation factor is released, GTP hydrolysis and another elongation factor binding causes the ribosome to move
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translation: elongation (what is in P site, what enters A site, what happens to amino acid, what factor is released, how does ribosome move (relative to the mRNA))
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release factor binds to A site (with STOP codon), other proteins and GTP hydrolysis dissociates the ribosome into two separate subunits
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translation: termination
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jumping genes, mobile genetic elements
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Transposons
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half of our genome comes from this type of DNA
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Transposons in the human genome (how much?)
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small RNA with ANTICODON and corresponding AMINO ACID
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tRNA
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this protein, (1_______) adds (1________) monomers via an isopeptide bond, one example being for proteasomal degradation
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ubiquitin
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DNA fingerprinting (makes use of what?)
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Variable number tandem repeats are used in
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there is redundancy but no ambiguity (this makes the genetic code what?)
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what does it mean that the genetic code is “degenerate”
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cargo protein and Ran-GTP (bind to what molecule)
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What does Ran bind
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transcription factors and RNA pol. assemble at the promoter, template strand is exposed, RNA Pol is phosphorylated and dissocates from the other factors
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what happens during initiation of transcription
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gene function can be disrupted by these mobile genetic elements
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When transposons “hop” into the middle of genes they usually disrupt __________
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(name of process?) one of the female’s two X chromosomes is silenced as a gene dosage compensation mechanism (without X inactivation, females would express double the amount of genes on the X
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X inactivation
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One X is randomly selected in female embryonic stage, silencing is initiated by expression of Xist non-coding RNA, counting of X chromosomes, Xist coats the silenced Xi, histone 3 Lysine 9 and Lysine 27 undergoes methylation, silencing is maintained by DNA methylation and/or polycomb group proteins
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X inactivation (mechanism)
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an autosomal recessive genetic disorder of DNA repair in which the body's normal ability to remove damage caused by ultraviolet (UV) light is deficient. This leads to multiple skinnmalignancies at a young age. In severe cases, it isnecessary to avoid sunlightcompletely. Usually caused by loss of nucleotide excision repair enzymes.
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Xeroderma pigmentosum, or XP, is
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heterochromatin formation on the X chromosome (is conferred by what RNA transcript?)
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Xist promotes ________________ X chromosome.
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two haploid shmoos secrete pheromones, grow projections and mate
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yeast mating (mechanism)
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different theories of structure for chromatin packing
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zigzag vs. solenoid model
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