Term
| True or False: Enzymes cause reactions that would not otherwise have taken place? |
|
Definition
| False. Enzymes catalyze reactions (i.e. make them run faster) that would occur otherwise, though not always in a physiologically available timeframe. |
|
|
Term
|
Definition
| Catabolism is the degradation and conversion of ingested food and/or stored fuel into energy (produces energy to be used). |
|
|
Term
|
Definition
| Anabolism is the energy-requiring biosynthesis of large molecules (energy is used). |
|
|
Term
| What differentiates a prokaryote from a eukaryote? |
|
Definition
| The presence of a nucleus. |
|
|
Term
| What is the function of the nuclear envelope? |
|
Definition
| The nuclear envelope separates the contents of the nucleus from the cytoplasm and provides the structural framework of the nucleus. |
|
|
Term
| What is the structure of the nuclear envelope? |
|
Definition
| Two nuclear membranes, an underlying nuclear lamina, and nuclear pore complexes |
|
|
Term
| What structures create the perinuclear space? |
|
Definition
| The inner and outer nuclear membranes |
|
|
Term
| The endoplasmic reticulum of a cell is contiguous with what other structure? |
|
Definition
| The nucleus (specifically the outer membrane) |
|
|
Term
| True or False: Nuclear pore complexes are distributed equally across the nuclear membrane. |
|
Definition
| False. The nuclear pore complexes are not distributed evenly and may tend to cluster in some locations. |
|
|
Term
| What structure underlies the inner nuclear membrane and provides structural support? |
|
Definition
| A fibrous protein mesh called the nuclear lamina |
|
|
Term
| What is the nuclear lamina composed of? |
|
Definition
| 60-80 kD fibrous proteins (lamins) which associate with one another to form higher-order structures |
|
|
Term
| Three genes (A,B,C) code for the seven proteins making up the nuclear lamina. How does this happen? |
|
Definition
|
|
Term
| True or False: Chromatin may bind the nuclear lamina using specific, conserved Lamina Binding Sequences, or LBSs. |
|
Definition
| False. Chromatin may be bound to the nuclear lamina by its centromeres and telomeres. |
|
|
Term
| How do individual lamin proteins associate to form the nuclear lamina? |
|
Definition
| First, the lamin polypeptides dimerize with one another. Head-to-tail association of these dimers ensues, followed by side-by-side assocation to form the higher-order structure. |
|
|
Term
| What mediates the attachment of the nuclear lamina to the inner nuclear envelope? |
|
Definition
| Emerin and LBR (Lamin B Receptor) |
|
|
Term
| How do small polar molecules, ions, and macromolecules travel between the nucleus and cytoplasm? |
|
Definition
|
|
Term
| Name the two mechanisms by which molecules may travel through the nuclear pore complexes. |
|
Definition
| Passive diffusion and Energy-dependent transport |
|
|
Term
| Describe the structure of the nuclear pore complex. |
|
Definition
| Eightfold symmetry organized around a large central channel, spoke-ring assembly with cytoplasmic filaments and a nuclear basket |
|
|
Term
| You are told that a protein has a NLS. What does this mean? |
|
Definition
| Nuclear Localization Sequence (Signal), amino acid sequence that is recognized by transport receptors so that a protein may be transported through the nuclear pore complex |
|
|
Term
| You believe that an isolated protein may have a NLS that is divided into two separate amino acid sequences. Is this possible? |
|
Definition
| Yes, some transport receptors recognize a single unified NLS sequence while others may recognize two sequence subunits |
|
|
Term
| What are nuclear transport receptors? |
|
Definition
| Proteins that recognize nuclear localization signals (NLS) and mediate transport across the nuclear envelope |
|
|
Term
|
Definition
| Class of nuclear transport molecules (include importin, exportin) |
|
|
Term
| True or false: Importins transport macromolecules to the nucleus from the cytoplasm. |
|
Definition
|
|
Term
| True or false: Exportins themselves must be phosphorylated in order to return to the nucleus from the cytoplasm. |
|
Definition
|
|
Term
| RAN, when bound to GDP or GTP, may assist in the transport of macromolecules through what membrane? |
|
Definition
|
|
Term
| True or False: Import of a protein into the nucleus begins when an Importin binds the NES of a cargo protein in the cytoplasm. |
|
Definition
| False. …Importin binds the NLS of a cargo protein… |
|
|
Term
| The NLS of NF-?B may be hidden by I?B. What would the phosphorylation of I?B result in? |
|
Definition
| Exposure of the NLS of NF-?B and subsequent transport of the transcription factor into the nucleus |
|
|
Term
| How are RNAs typically transported across the nuclear envelope? |
|
Definition
| As ribonucleoprotein complexes, or RNPs |
|
|
Term
| True or False: Genetic material within the nucleus is organized and localized into functional processing domains. |
|
Definition
|
|
Term
| What is the difference between heterochromatin and euchromatin? |
|
Definition
| Heterochromatin is condensed, transcriptionally inactive chromatin, while euchromatin is decondensed and transcriptionally active. |
|
|
Term
| Define ARS, in a genetic context |
|
Definition
| Autonomously Regulating Sequence; consensus sequence generally functioning as an origin of replication |
|
|
Term
| True or False: Nuclear speckles are visible clusters of pore complexes in the nuclear membrane. |
|
Definition
| False. Nuclear speckles are areas in the nucleus in which mRNA splicing machinery are concentrated. |
|
|
Term
| Where does rRNA transcription and portions of ribosome assembly traditionally occur? |
|
Definition
|
|
Term
| True or False: In oocytes, the rRNA genes are dampened to support the synthesis of large numbers of ribosomes required for development. |
|
Definition
| False. The rRNA genes are amplified |
|
|
Term
| True or False: All cells contain multiple copies of the rRNA genes. Why or why not? |
|
Definition
| True. Large numbers of rRNA molecules are usually needed. |
|
|
Term
| The fibrillar center, dense fibrillar component, and granular component regions make up what structure? |
|
Definition
|
|
Term
| Morphologically, the nucleoli consist of three distinguishable regions. What are they? |
|
Definition
| Fibrillar center, Dense fibrillar component, and granular component |
|
|
Term
| What are nucleolar organizating regions? |
|
Definition
| Where nucleoli become associated with the chromosomal regions that contain the 5.8S, 18S, and 28S rRNA genes. |
|
|
Term
| True or False: Each nucleolar organizing region contains a cluster of tandemly repeated rRNA genes separated by nontranscribed spacer DNA. |
|
Definition
|
|
Term
| In higher eukaryotes, the primary transcript of the rRNA genes is the large 45S pre-rRNA, which contains… |
|
Definition
| …the 18S, 5.8S, and 28S rRNAs, along with nontranscribed spacer regions. |
|
|
Term
| What are snoRNAs and what are their functions? |
|
Definition
| Small nucleolar RNAs, they are complexed with proteins and function in pre-rRNA processing |
|
|
Term
| pre-rRNA processing involves a substantial amount of base modification. What does this result from? |
|
Definition
| Methylation of bases and ribose residues, along with uridine's conversion into pseudouridine |
|
|
Term
| True or False: Most snoRNAs function in rRNA synthesis by directing specific base modifications such as ribose methylation and pseudouridine formation. |
|
Definition
|
|
Term
| The final stage of ribosome maturation follows the export of pre-ribosomal particles to the cytoplasm, forming which subunits of the eukaryotic ribosome? |
|
Definition
|
|
Term
| Which two nucleobases are classified as purines? |
|
Definition
|
|
Term
| Which two nucleobases are classified as pyrimidines? |
|
Definition
| Cytosime and Thymine (Uracil) |
|
|
Term
| True or False: Phosphodiester linkages, such as those in DNA, are fairly unstable and have a relatively short half-life. |
|
Definition
| False. They have a very long half-life |
|
|
Term
| Contrast exonucleases and endonucleases. |
|
Definition
| Exonucleases remove nucleotide residues from one end of a polynucleotide, while endonucleases hydrolyze interior phosphodiester bonds. |
|
|
Term
| Name three stabilizing factors in duplex DNA |
|
Definition
| Stacking interactions (pi-bonds), Hydrophobic effect (bases in contact, phosphates outside), and Hydrogen bonding (specificity, stability) |
|
|
Term
| Which DNA sequence is more thermodynamically stable: ATTAGTCATC or CCGGATTCGC. Why? |
|
Definition
| The latter, CCGGATTCGC; three (G-C) versus two (A-T) hydrogen bonds per pair increase stability |
|
|
Term
| What are the three main families of DNA conformation? |
|
Definition
| A (righthand, shorter/fatter), B (righthand, thinner/longer), Z (lefthand, with zig-zag backbone) |
|
|
Term
| What are telomeres and what is their function? |
|
Definition
| DNA and protein at end of a chromosome; stabilize and protect the chromosome |
|
|
Term
|
Definition
| Through 3' single-strand invasion of the double helix |
|
|
Term
|
Definition
| Hereditary Persistence of Fetal Hemoglobin; production of fetal hemoglobin continues into adulthood |
|
|
Term
| What enzymes function in reducing torsional strain of DNA during synthesis and transcription? |
|
Definition
|
|
Term
|
Definition
| Fundamental unit of chromatin; two copies each of H2A, H2B, H3, H4 and their accompanying DNA |
|
|
Term
| What is a DNA vaccine and how might it prove useful? |
|
Definition
| Typically a bacterial plasmid engineered to include the sequence of an antigenic protein from a pathogen; may be safely expressed and recognized by the immune system |
|
|
Term
| What is the term for the mode of replication which DNA synthesis utilizes? |
|
Definition
|
|
Term
| What is the primary function of the eukaryotic enzyme Pol ?/primase? |
|
Definition
| RNA priming + a little DNA, synthesis of initial part of Okazaki fragments |
|
|
Term
| What are the primary functions of Pol ?? |
|
Definition
| Synthesis of leading strand and most of Okazaki fragments, and gap filling after primer removal |
|
|
Term
| What are SSBs and what is their function? |
|
Definition
| Single-stranded DNA-binding proteins, keep ssDNA apart following helicase's unzipping |
|
|
Term
| What are the two modes of therapeutically targeting bacterial topoisomerases and what are some examples of medications utilizing each? |
|
Definition
| I. Topoisomers inhibitors, coumermycin A1 and novobiocin, prevent catalytic activity. II. Topoisomerase poisons, Nalidixic acid and Ciproflaxacin, freeze covalent DNA-protein links, leading to dsBreaks |
|
|
Term
| What are the primary steps in DNA synthesis? |
|
Definition
| 1)Replication Protein A (RPA), 2)Pol?, 3)PCNA clamp, 4)Pol?, 5)Rnase, 6)DNA ligase |
|
|
Term
| How is the end of the DNA strand synthesized? |
|
Definition
| Telomerase; has short RNA strand as integral part, serving as template for 6-nt telomere repeat sequence |
|
|
Term
| How is Cisplatin an effective anti-cancer agent? |
|
Definition
| Bonds with two bases, crosslinking DNA |
|
|
Term
| Describe xeroderma pigmentosum (XP) |
|
Definition
| Caused by defective DNA repair, photosensitive and susceptible to skin cancers |
|
|
Term
| How is the parental strand recognized during mismatch repair? |
|
Definition
| MutS and MutL bind mismatch, MutH binds at HEMIMETHYLATED site, unmethylated strand is nicked and excised |
|
|
Term
| A defect in mismatch repair causes hereditary nonpolyposis colon cancer (HNPCC). How does this occur? |
|
Definition
| With one inactive, dysfunctional allele (by inheritance), a mutation is more likely to have a significant affect if it occurs in the remaining active allele. |
|
|
Term
| What is the primary characteristic of some DNA polymerases that are important in translesion repair? |
|
Definition
| Low specificity for a short period; Just get by |
|
|
Term
| What two proteins are integral to double-strand break repair? |
|
Definition
| Ku and DNA-dependent protein kinase |
|
|
Term
| What are the complexes between eukaryotic DNA and protein called? |
|
Definition
|
|
Term
| True or False: Histones have a high proportion of acidic amino acids. |
|
Definition
| False. High proportion of the basic amino acids, arginine and lysine, that bind to the negatively charged DNA molecule |
|
|
Term
| Approximately how many base pairs does a nucleosome core particle contain? |
|
Definition
|
|
Term
| How many subunits comprise a nucleosome core particle? |
|
Definition
|
|
Term
| What is the difference between a nucleosome and a chromatosome? |
|
Definition
| Nucleosome is 2(H2A,H2B,H3,H4+DNA) while Chromatosome is a Nucleosome+H1 linker histone (166 bp) |
|
|
Term
| How many DNA double helix molecules are in an average chromosome? |
|
Definition
|
|
Term
| During interphase, nucleosomes of euchromatin are generally packed into fibers how small in diameter? |
|
Definition
|
|
Term
| What is the general structure of metaphase chromosomes? |
|
Definition
| Large loops attached to a protein scaffold |
|
|
Term
| What is the centromere of a chromosome? |
|
Definition
| Specialized region of the chromosome that plays a critical role in ensuring the correct distribution of duplicated chromosomes to daughter cells during mitosis |
|
|
Term
|
Definition
| Site of spindle fiber attachment to the centromere |
|
|
Term
| True or False: Plasmids with functional centromere sequences may segregate equally, just like chromosomes. |
|
Definition
|
|
Term
| How might missegregation of a plasmid occur? |
|
Definition
| Absence of a centromeric sequence |
|
|
Term
|
Definition
| Enzyme utilizing reverse transcriptase activity to replicate telomeric DNA sequences |
|
|
Term
| What would a FISH show you (besides his scales)? |
|
Definition
| Fluorescence in situ hybridization; Used to identify specific gene sites (which chromosome, which arm) |
|
|
Term
| How large is the human genome approximately? |
|
Definition
|
|
Term
| Approximately how many genes are in the human genome? |
|
Definition
|
|
Term
|
Definition
| Interface of biology and computer science; focused on computational methods of analysis and extraction of useful information from genomic sequence |
|
|
Term
| What does systems biology seek to achieve? |
|
Definition
| A quantitative understanding of the integrated dynamic behavior of complex biological systems and processes |
|
|
Term
| What information does gene expression profiling offer? |
|
Definition
| Expression level of thousands of genes |
|
|
Term
| How might large-scale screening based on small interfering RNA be used to analyze gene function? |
|
Definition
| In RNAi screens, dsRNA may be used to induce degradation of the homologous mRNAs in cells |
|
|
Term
| How different are the genomes of two unrelated people on average? |
|
Definition
| SNPs (single nucleotide polymorphisms) in approximately one of every thousand bases |
|
|
Term
| True or False: RNA's 3'-OH group differentiates it from DNA. |
|
Definition
| False. RNA's 2'-OH group is the differentiating factor |
|
|
Term
| True or False: Unlike mRNA, tRNA, and snoRNA, rRNA has a specific cloverleaf tertiary structure. |
|
Definition
| False. tRNA has a cloverleaf tertiary structure |
|
|
Term
| How is mRNA capped during processing and maturation? |
|
Definition
| 7-methylguanosine is inverted, and 5'-phosphate to 5'-phosphate link is formed |
|
|
Term
| True or False: RNA is capable of self-cleaving. |
|
Definition
|
|
Term
| What is the most abundant form of RNA? Approximately what percent of total RNA is this form? |
|
Definition
|
|
Term
| How does erythromycin serve as an anti-bacterial? |
|
Definition
| By targeting the ribosome |
|
|
Term
| The ribosome is a ribozyme. What does this mean? |
|
Definition
| The ribosome catalytic center has no protein |
|
|
Term
| What are RNA aptamers? Give one example of their use discussed in lecture. |
|
Definition
| Sequences of RNA selected for tight binding to a variety of substances; may be used to purify theophylline out of caffeine |
|
|
Term
| Briefly describe how RNAi works. |
|
Definition
| miRNA are processed from primary transcripts (pri-miRNA); mature miRNA molecules are partially complementary to mRNA molecules and downregulate gene expression |
|
|
Term
| HIV is a retrovirus, while HCV is a positive strand RNA virus. What's the difference? |
|
Definition
| HIV: RNA converted to DNA and integrated into host genome - HCV: make dsRNA, then make new copies of positive strand for packaging |
|
|
Term
| What are the five phases of the cell cycle, and what is the primary activity within each? |
|
Definition
| G1:metabolism, S:DNA synthesis, G2:proteins made for mitosis, M:cell division, G0: outside of cycle |
|
|
Term
| Cell division requires a G2 amount of DNA. Therefore mitosis requires (?)C DNA. |
|
Definition
|
|
Term
| What was Sendai virus used for in studying cellular division? |
|
Definition
| Used to fuse cells in different stages of the cell cycle |
|
|
Term
| What two proteins activate condensins in a mitotic cell? |
|
Definition
|
|
Term
| What do Cyclin dependent protein kinases do? |
|
Definition
| Regulate processes of cell division; controlled by growth factors |
|
|
Term
| Four drugs inhibit the cell cycle by interfering with the spindle assembly. What are these? |
|
Definition
| Colchicine (blocks at metaphase), Vincristin-vinblastine (inhibit spindle formation), and Paclitaxel (prevents disassembly of mitotic spindle) |
|
|
Term
| Where and when does 5-fluorodeoxyuridine (5FU) stop the cell cycle? |
|
Definition
| Stalls at the G1 checkpoint, inhibits DNA synthesis |
|
|
Term
| At what point in the cell cycle does Bleomycin/Etoposide have its effect? |
|
Definition
|
|
Term
| Name the two types of continuously replicating cells. |
|
Definition
| VIM (Vegetative intermitotic), such as stem, basal/skin, intestines); and DIM (Differentiating intermitotic), such as in stratum spinosum |
|
|
Term
| What is one example discussed in class of an occasional replicator? |
|
Definition
| RPM (Reverting postmitotic), fibroblasts, liver and smooth muscle cells, astrocytes |
|
|
Term
| Name three times of FPM cells. |
|
Definition
| Fixed postmitotic/non-replicators; surface of skin, neurons, skeletal and cardiac muscle |
|
|
Term
| Describe nuclear changes present at the beginning of cell division. |
|
Definition
| Cdk1 activated by Cyclin B; leads to Chromosome condensation, nucleolus disappears; breakdown of nuclear envelope, activated Cdk1 phosphorylates lamins |
|
|
Term
| Name two nuclear changes that occur at the end of divison and describe what happens to Cdk1. |
|
Definition
| Nuclear envelope reforms, chromosome decondenses; Cdk1 is inactivated via ubiquitination and Cyclin B degradation |
|
|
Term
| How does Cdk1 function in breaking down the nuclear envelope? |
|
Definition
| Binds to lamin dimer heads and tails, preventing alignment and increasing instability of nuclear lamina |
|
|
Term
| What is the difference between cohesins and condensins? |
|
Definition
| Cohesins bind during S phase, condensins are activated by Cdk1 and replace cohesin (except at centromere), resulting in metaphasic contraction |
|
|
Term
| The cytokinetic contractile ring is comprised of what proteins? |
|
Definition
|
|
Term
| What are the stages of prophase I of Meiosis and how are they characterized? |
|
Definition
| Leptotene (condensation), Zygotene (pairing), Pachytene (recombination,tetrads), Diplotene (chiasmata), and Diakinesis (terminalization) |
|
|
Term
| The primary oocyte is arrested in what special stage of diplotene? |
|
Definition
|
|
Term
| At prophase II of Meiosis, each cell has (?)C,(?)n DNA. |
|
Definition
|
|
Term
| At the conclusion of Meisosis II, each product has (?)C,(?)n DNA. |
|
Definition
|
|
Term
| What are some clinical manifestations of meiotic nondisjunction? |
|
Definition
| Klinefelter's syndrome (XXY), Down's syndrome (trisomy 21), Turner's syndrome (XO) |
|
|
Term
| What is the primary difference between DNA and RNA? |
|
Definition
| RNA has 2'-OH group, RNA has uracil rather than thymine |
|
|
Term
| True or False: RNA is classically thought of as a single stranded molecule. This is potentially misleading. |
|
Definition
| True. RNA is, truly, a single stranded molecule, but in such cases as the 5S ribosome, it seems, by all appearances, to be double stranded |
|
|
Term
| What are the three primary families of RNA and what are their respective functions? |
|
Definition
| messenger (mRNA), produced as transcription, codes for proteins; transfer (tRNA), used during translation, recognizes aa; ribosome (rRNA), used during translation, part of ribosome |
|
|
Term
| How is positive and negative supercoiling accomodated during transcription? |
|
Definition
|
|
Term
| True or False: The RNA transcript is synthesized off the coding strand and is identical to the complementary DNA strand. |
|
Definition
| False. …synthesized off the complementary template strand and is identical to the coding DNA strand. |
|
|
Term
| E. coli RNApol holoenzyme consists of 6 subunits. What are they and and list their respective functions. |
|
Definition
| 2(?) binds UP element, ?/?' form active site for RNA synthesis, ? functions in promoter recognition and is not present during elongation, and ? subunit function is unknown |
|
|
Term
| Name two classic prokaryotic promoter sequences and their locations. |
|
Definition
| CAT (GC Rich) @ -35, and TATA @ -10 |
|
|
Term
| Where is the UP generally found? |
|
Definition
| Upstream promoter, -60 - -40 |
|
|
Term
| What subunit of the holoenzyme is primary responsible for binding the UP? |
|
Definition
|
|
Term
| What subunit of the holoenzyme is primary responsible for binding the -10 and -35 promoter elements? |
|
Definition
|
|
Term
| Briefly describe prokaryotic transcription. |
|
Definition
| 1)Pol binds nonspecifically to DNA and migrates, 2)? subunit bind promoter elements, 3)Pol unwinds DNA and initiates TXN, 4)? released and core enzyme elongates mRNA chain |
|
|
Term
| How does Rho-independent transcription termination occur? |
|
Definition
| GC-rich stem-loop (strong) forms, pulling a relatively weak Uracil-rich region away from the polymerase |
|
|
Term
| How does Rho-dependent transcription termination occur? |
|
Definition
| A stem-loop is formed, allowing rho to catch up to the polymerase, knocking it off |
|
|
Term
| What are the three Eukaryotic RNA polymerases and what does each primarily synthesize? |
|
Definition
| Pol I(pre-rRNA: precursor for 18S, 5.8S, and 28S RNA); Pol II(mRNA and some specialized RNAs); Pol III(tRNA, 5S RNA, and other small, specialized RNAs) |
|
|
Term
| At what location is the TATA box in eukaryotes? |
|
Definition
|
|
Term
| Four drugs were mentioned in lecture that inhibit transcription. What are these and how do they carry out their function? |
|
Definition
| Actinomycin D & Acridine (inhibig RNA elongation by intercalating into DNA); Rifampicin (bind ? subunit of bacterial polymerase); ?-amanitin (blocks Pol II and III at high doses) |
|
|
Term
| True or False: Eukaryotes process their RNA while prokaryotes do not. |
|
Definition
| False. Many bacterial and almost all eukaryotic mRNAs are processed; eukaryotic mRNA and tRNA from bacteria and eukaryotes are the most heavily processed. |
|
|
Term
| What are two other names for the primary RNA transcript? |
|
Definition
| hnRNA (heteronuclear RNA) or pre-mRNA |
|
|
Term
| There are two types of self-splicing introns. Describe them. |
|
Definition
| Group I, nuclear, mitochondrial, and chloroplast genes coding for rRNA, mRNA and tRNA; Group II, mitochondrial and chloroplast genes in fungi, algae, and plants |
|
|
Term
| Non self-splicing introns are found… |
|
Definition
| …in most mRNA primary transcripts (and require snRNPs, RNA+protein) and some tRNAs (require ATP an an endonuclease) |
|
|
Term
| Generally, describe the process of spliceosome-based non self-splicing. |
|
Definition
| 1)U1 bind consensus sequence, 2)U2,4,5,6, come in, 3)U5 binds 3' splice, 4)excision of the intron and ligation of the exons together |
|
|
Term
| How might a mutation in a)a promoter sequence, b)cap site, c)branch point, and d)intron/exon boundary affect the expression of a gene? |
|
Definition
| a)no transcription, b)increased degradation, c/d) affect splicing |
|
|
Term
| mRNA is always read in what direction? |
|
Definition
|
|
Term
| What is the nucleotide sequence coding for START? |
|
Definition
|
|
Term
| What three codons code for STOP? |
|
Definition
|
|
Term
| What is the primary implication of Crick's Wobble Hypothesis? |
|
Definition
| The first two bases of a codon always form strong Watson-Crick pairs, but the last one is less strict; some tRNAs can recognize more than one codon |
|
|
Term
| Protein synthesis accounts for __% of the chemical energy used by a cell for all biosynthetic reactions. |
|
Definition
|
|
Term
| What are the five general stages of protein synthesis? |
|
Definition
| 1)aa activation/tRNA charging, 2)Initiation of translation, 3)Elongation of peptide chain, 4)Termination and ribosomal release, 5)Folding and posttranslational processing |
|
|
Term
|
Definition
| Aminoacyl-tRNA-synthetases attach the correct amino acid; transfer amino acid to 3' end of tRNA |
|
|
Term
| Methionine has one codon, AUG. How many tRNAs for methionine do eukaryotes have? |
|
Definition
| Like all other organisms, two: one used exclusively for initiation, the other for internal methionine residues. |
|
|
Term
| Bacteria, mitochondria, and chloroplasts initiation translation with a special initiating tRNA for methionine. What is it called? |
|
Definition
| N-formylmethionine-tRNA (fMet) |
|
|
Term
| How is prokaryotic translation initiated? |
|
Definition
| Pairing of the 16S rRNA with the Shine-Delgarno sequence |
|
|
Term
| How is the eukaryotic initiation complex formed? |
|
Definition
| 1) 5' and 3' ends linked by protein complex, 2) mRNA scanned for first AUG in Kozak context, 3) this binds 40S ribosomal subunit |
|
|
Term
| What enzymes catalyze the formation of the bond between amino acids while they are bound to their respective tRNAs? |
|
Definition
|
|
Term
| Uncharged tRNAs leave from which site of the ribosome? |
|
Definition
|
|
Term
| How is protein synthesis terminated? |
|
Definition
| RF1 or RF2 recognizes termination codon in A site, causes peptidyl transferase to transfer polypeptide to water molecule, and complenents dissociate |
|
|
Term
| Eight compounds were mentioned that affect translation. What were these and what processes to they affect? |
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Definition
| Streptomycin, Cycloheximide (initiation, elongation); neomycins (translation); tetracyclines (aminoacyl tRNA binding); puromycin (peptide transfer); erythromycin, fusidic acid (translocation, ricin (multiple) |
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Term
| True or False: Eukaryotic transcription and translation is more efficient than that of prokaryotes because they occur almost simultaneously in the former. |
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Definition
| False. Transcription and translation are separated in eukaryotes as a result of the nuclear membrane; they are coupled in prokaryotes (however efficiency is a rather subjective term) |
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Term
|
Definition
| Region of DNA bound by RNA polymerase, signalling for the start of transcription |
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|
Term
| True or False: The UP is only present in some genes. |
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Definition
| True. When present, the UP strongly upregulates transcription. |
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Term
| True or False: The promoter regulates the basal rate of transcription. |
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Definition
|
|
Term
| What is another word for housekeeping genes? |
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Definition
| Constitutive, expressed at relatively uniform level |
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|
Term
| What are three factors having roles in regulated gene expression in bacteria? |
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Definition
| Specialty factors (alter specificity of RNApol for promoter); repressors (impede RNApol access to promoter); activators (enhance interaction of RNApol with the promoter) |
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|
Term
| True or False: Most eukaryotic genes are regulated in units called operons. |
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Definition
| False. Most prokaryotic genes… |
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Term
| What is another adjective for the genes coded for by an operon? They are said to be… |
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Definition
|
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Term
| True or False: A single Shine-Delgarno sequence initiates translation of multiple polycistronic genes. |
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Definition
| False. Each gene has its own SD sequence. |
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|
Term
| What is the primary benefit of the operon system? |
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Definition
| Allows coordinated regulation of gene involved in related processes |
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Term
| Most signal-specific DNA binding proteins make contact with the ______ groove. |
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Definition
|
|
Term
| Describe the structure of the lac repressor. |
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Definition
| Tetramer with four helix-turn-helix DNA binding motifs |
|
|
Term
| What is the significance of palindromes in the genetic code? |
|
Definition
| Usually DNA binding site for regulatory proteins; multiple subunits bind cooperatively |
|
|
Term
| True or False: Lac Repressor negatively regulates the lac operon; cAMP Receptor Protein negatively regulates the lac operon. |
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Definition
| False. …cAMP Receptor Protein positively regulates the lac operon. |
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|
Term
| CRP is to glucose as LacI is to… |
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Definition
|
|
Term
| Describe the lac operon in its repressed state (no lactose present). |
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Definition
| Lac repressor expressed from its own promoter, LacR binds to O1, blocking access of RNA pol to promoter (repressed transcription) |
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Term
| Describe the induced state of the lac operon (lactose present). |
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Definition
| Lactose is imported by glactoside permease and converted to allolactose by ?-galactosidase; allolactose bind lacR, dissociating from operator; RNA pol transcribes the gene |
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|
Term
| Describe how CRP regulates the lac operon. |
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Definition
| As glucose levels fall, cAMP levels rise and more cAMP binds CRP. CAMP binding to CRP promotes binding of CRP to CRP site, facilitating RNApol binding |
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|
Term
| How does the trp operon work at low levels tryptophan? |
|
Definition
| 1)During synthesis, ribosome pauses at two trp codons (low levels), 2)ribosome occupies sequence 1, so 2 and 3 base pair, 3)transcription proceeds normally |
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|
Term
| How does the trp operon attenuate tryptophan production? |
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Definition
| 1)During synthesis, ribosome doesn't pause at two trp codons (high levels), 2)ribosome occupies sequence 2, so 3 and 4 base pair, 4)attenuator loop halts translation |
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|
Term
| List four potential sites of eukaryotic gene regulation. |
|
Definition
| Transcription, gene amplification, gene rearrangement, RNA processing, alternate mRNA splicing, transport of mRNA from nucleus to cytoplasm, mRNA stability (half-life) |
|
|
Term
| True or False: In eukaryotes, enhancers are typically 10 to 40 bp upstream of the initiation site. |
|
Definition
| False. Enhancers can be anywhere, even with other genes between it and its target gene. |
|
|
Term
| Why would an electrophoretic-mobility shift assay prove useful in proteomics? |
|
Definition
| Elucidates the nature of specific DNA|Protein interactions. |
|
|
Term
| True or False: Transcription factors tend to be rather small and contain some redundancy. |
|
Definition
|
|
Term
| What are the four families of DNA-binding domains? |
|
Definition
| Zinc fingers, Helix-turn-helix (HTH), Leucine zipper, and Helix-loop-helix (HLH) |
|
|
Term
| How is ?-thalassemia differentiated based upon the number of mutations? |
|
Definition
| One gene: silent carrier, no symptom; Two: ?-thal minor; Three: anemia or hemoglobin H disease; Four: ?-thalassemia major, perinatal death |
|
|
Term
| What role does histone acetylation play in the formation of heterochromatin and euchromatin? |
|
Definition
| Acetylation leads to decondensed, active chromatin; deacetylation leads to condensed, inactive chromatin |
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|
Term
| How does Angelman's Syndrome arise from the loss of UBE3A expression? |
|
Definition
| Maternal-only expressed allele (UBE3A) is methylated, so no expression; mental retardation is symptomatic |
|
|
Term
| Why are Chromatin immunoprecipitation (ChIP) assays important to genomics? |
|
Definition
| Allow identification of regions of genomic DNA bound by a specific protein. |
|
|
Term
| True or False: A transcription factor (activator) can be made from the same mRNA transcript as a repressor. |
|
Definition
|
|
Term
| How is the transferrin receptor mRNA protected when presented with low levels of iron? |
|
Definition
| In scarce iron conditions, Iron Responsive Element Binding protein (IRE-BP) blocks IRE, the site of high nucleolytic cleavage |
|
|
Term
| Trans-acting factors (proteins) may bind what cis-acting regulatory DNA sequences? |
|
Definition
| Promoter, Enhancers, UAS, Hormone response elements |
|
|
Term
| True or False: While the genetic code is generally read, transcribed, and translated 5' to 3' Enhancers may only function when in a 3' to 5' orientation. |
|
Definition
| False. Enhancers can be 5'-3', 3'-5; they are position-and orientation-independent. |
|
|
Term
| MyoD is what type of regulatory element? |
|
Definition
|
|
Term
| What roles do SXL and U2AF play in Drosophila sex determination. |
|
Definition
| Sex determined by alternative splicing; If SXL is blocking access to premature stop codon, female phenotype results.Truncated, nonfunctional protein results in male phenotype. |
|
|
Term
| You have just finished analyzing a strand of DNA; the sequence is AGGTCAAGGTTCA. What could you assume about this sequence? |
|
Definition
| Most likely a general hormone receptor consensus sequence (note the AGGTCA and AGGTNCA sequences) |
|
|
Term
| How do glucocorticoids outside the cell affect transcription? |
|
Definition
| Pass through cell membrane and bind receptor, both of which are taken into the nucleus to act as transcription factors. |
|
|
Term
| How might alternative polyadenylation sites play a role in gene regulation and expression? |
|
Definition
| Cleavage and polyadenylation at specific sites may result in a nonfunctional protein. |
|
|
Term
| How is it that the apoB gene is able to code for the proteins apoB 100 and apoB 48, depending upon where it is transcribed? |
|
Definition
| RNA editing (for example, apoB 48 is formed as a result of a premature stop codon in the intestine) |
|
|
Term
| What happens to transferrin receptor mRNA during iron deficiency? |
|
Definition
| An Iron response element binding protein (IRE-BP) blocks nucleolytic activity targeted to the IRE site. |
|
|
Term
| What is another name for The Sanger Method and what is it used for? |
|
Definition
| Dideoxy DNA sequences; synthesis of a new strand complementary to one analyzed (determines sequence) |
|
|
Term
| What differentiates a deoxyribonucleoside from a dideoxyribonucleoside? |
|
Definition
| Dideoxy- denotes that the 3' OH has been replaced with an H group |
|
|
Term
| Why aren't typical dNTPs used in the Sanger method of DNA sequencing? |
|
Definition
| ddNTP lacks the 3' OH necessary for elongation, so synthesis is halted; this allows strands of varying lengths to be separated |
|
|
Term
| True or False: Only ddNTPs are used in dideoxy DNA sequencing. |
|
Definition
| dNTPs are also added; otherwise any strand would be immediately terminated |
|
|
Term
| There are three types of restriction endonucleases. Define them. |
|
Definition
| Type I(cleave at random site >1kb from recog. site, require ATP); II(cleave within recog. site, do not require ATP, most require divalent cation); III(cleave at random site ~25 bp from recog. site, require ATP) |
|
|
Term
| What does a restriction endonuclease do? |
|
Definition
| Recognize and cleave DNA at specific recognition site |
|
|
Term
| BamHI is a RE that creates sticky ends while EcoRV creates blunt ends. What's the difference? |
|
Definition
| Sticky ends are short single strand sequences capable of base pairing with another such sequence; blunt ends are double stranded breaks |
|
|
Term
| True or False: Blunt ends ligate with high efficiency. |
|
Definition
| False. They ligate correctly with low efficiency. |
|
|
Term
| pBR322, a cloning vector, has two sequences for antibiotic resistance. What are these used for? |
|
Definition
| They are markers used in selecting those colonies which have successfully taken up the targeted plasmid |
|
|
Term
| Following bacterial transformation with a recombinant pUC 18 plasmid, your resultant colonies are all blue. Do you celebrate or start over? |
|
Definition
| Start over. Blue indicates that those colonies have the pUC18 plasmid without the recombinant DNA. |
|
|
Term
| As an amazing microbiologist, you isolate 100 E. coli cells and shake them up with bacteriophage. On average, how many will get the vector? |
|
Definition
| Almost all. Phage-based vector transformation has close to 100% efficiency |
|
|
Term
|
Definition
| Bacterial Artificial Chromosome |
|
|
Term
| What is the purpose of the CEN sequence in a Yeast Artificial Chromosome? |
|
Definition
| Centromere. When linearized and inserted into yeast, allows for propagation/division |
|
|
Term
| Why does a YAC generally have two selectable markers? |
|
Definition
| One for bacteria, one for yeast |
|
|
Term
| A Yeast Artifical Chromosome has two TEL sequences. How would you remove the intervening sequence and why would you do so? |
|
Definition
| Restriction Endonucleases would be used to remove the sequence, linearizing the chromosome |
|
|
Term
| How is the dsDNA denatured in PCR? |
|
Definition
|
|
Term
| Why is Taq polymerase used in PCR? |
|
Definition
| Isolated from Yellowstone hot spring bacteria, Taq is heat-stable |
|
|
Term
| You have successfully completed a PCR cloning from a single dsDNA strand. How many exact duplicates of this dsDNA do you have? |
|
Definition
| None. You have the two original single strands (denatured from the double strand). |
|
|
Term
| While using hybridization to identify a clone with a DNA segment, you treat your nitrocellulose with alkali. Why |
|
Definition
| It denatures the dsDNA, allowing the single strands to bind the paper. |
|
|
Term
| When generating a DNA probe from the amino acid sequence of a targeted protein, what is the term for the most efficient sequence used? |
|
Definition
| Region of minimal degeneracy (that region requiring the fewest number of different probes |
|
|
Term
| When building an expression vector, why might you incorporate the lac promoter and operator? |
|
Definition
| So that you my activate the gene in bacteria |
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