DNA Replication, Genes, and Proteins

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QuestionAnswerExtra Info
Model/mechanism that shows DNA daughter strands forming a new double stranded DNA moleculeParental DNA remains intact
Model/mechanism that shows parental DNA strand being permanently separated and forming a new duplex molecule with the daughter strand
Pre-existing RNA or DNA strand that must be added to DNA in order to begin chain growth in replicating DNACan be made of both RNA and DNA, or simply RNA alone. Chain growth requires this component because DNA polymerases cannot initiate chain synthesis de novo
Enzyme that produces short RNA strand in Q#3
Unwinding of DNA molecule is conducted by this enzymeConducted at the replication origins or simply origins. Origins usually contain A-T rich sequences
Torsional stress induced by the unwinding of DNA is relieved by this enzymeSimilar to transcription. Removes supercoils
One daughter strand that is able to continuously synthesize DNA from a single RNA primer in the 5'--> 3' direction
One daughter strand that must continuously synthesized from multiple RNA primersMust have an RNA primer every few hundred bases.
Discontinuous segments of DNA which have been elongated from the RNA primersCan be found on both elongating daughter strands
Enzyme that joins adjacent DNA fragmentsThese family of proteins are extremely useful in Plasmid Recombination
This viral protein is a helicase that unwinds parental DNA strands.Hexamer. SV40 DNA
Once this viral protein has unwound parental DNA, this protein binds to single stranded regionsHeterotrimeric. SV40 DNA. Binding of this protein allows a uniform conformation optimal for DNA polymerase to copy parental DNA. This protein is dislodged from parental strand by both polymerases as they synthesize the complementary strands base paired with parental strands.
The leading strand is synthesized by a complex of these three proteins. The first being:Polymerase. SV40 DNA Less likely to make errors during copying because this polymerase contains a proofreading mechanism.
The leading strand is synthesized by a complex of these three proteins. The second being:SV40 DNA.
The leading strand is synthesized by a complex of these three proteins. The third being:SV40 DNA
Primers for lagging strand synthesis are synthesized by complex of two proteins. The first being:Polymerase. SV40 DNA Together this complex synthesizes a mixed RNA-DNA primer
Primers for lagging strand synthesis are synthesized by complex of two proteins. The second being:Answer to a previous question. SV40 DNA
Another lesser known polymerase that contributes to synthesis of cellular chromosomal DNAIt's role in DNA replication is uncertain.
Removal of nucleotides at 5' ends is conducted by two proteins: The first is:These nucleotides are replaced by deoxynucleotides added by DNA Pol delta
Removal of nucleotides at 5' ends is conducted by two proteins: The second is:
This complex binds to each origin and associates with other proteins required to load cellular hexameric helicases composed of six homologous MCM proteins (MiniChromosome Maintenan
Activation of MCM helicase activity is regulated by specific protein kinases called
Proteins that compact and organize chromosomal DNA Nuclear proteins.
Complex of histones, nonhistone proteins, and DNA that exists in various degrees of compactionHalf DNA and half protein by mass (in interphase cells). Compacts long DNA molecules using proteins but has readily available sites for cell processes such as transcription, replication, repair, and recombination of DNA
Histone proteins that are rich in positively charged basic amino acids (Lysine, Arginine, Histidine) which interact with negatively charged phosphate groups of DNA5 in order. Each histone protein comprising core to the answer to Q#26 contains a flexible N-terminus of 19-39 residues extending from globular structure of answer to Q#26. Two of these proteins (order # 2 and #3 in correct answer to this question) contain a flexible C-terminus extending from the core of the answer to Q#26. These are termed histone tails which are required for chromatin to condense.
Complex of DNA and histones that are normally 10nm in diameter and are primary structured units of chromatinDNA of this answer is less susceptible to nuclease digestion than is the linker DNA. Contains a protein core, an octamer containing 2 copies of H2A, H2B, H3 and H4 histone proteins. Allows 147 base pairs of DNA to be wrapped 1 and 2/3 turns around protein core.
30-nm fiber found in isotonic buffer is said to have a ______ structure that is wound into a 'two-start' helix made from two 'strands' of nucleosome stacked on top of one another lSupplemental: The two 'strands' are then wound into a double helix, except that the helix is left handed. H1 histone is bound to DNA as it enters and exits the nucleosome core.
N-terminal tails of H4 histone on lysine ____ are critical in forming 30-nm fiber conformation (condensed form)number. Positively charged lysine (basic) residues interact with negatively charged patch at H2A-H2B interface of next nucleosome in stacked nucleosomes.
The four possible post-translational modifications of histone tails.In alphabetical order.
This form of post-translational midification tend to form less condensed 'beads on a string' conformation conducive for transcription and replicationCan be reversed as well. H4 histone lysine 16 can undergo this modification in order to form less condensed chromatin. Other sites in H4 and other histones can undergo this modification and the chromatin will have an increased sensitivity to digestion by nucleases
These enzymes in yeast are able to acetylate specific lysine residues in histones which are required for full activation of transcription of a number of genesSupplemental: folded regions of chromatin are less accessible to exogeneously added DNase 1 than genes in decondensed, extended regions of chromatin
Lysine epsilon-amino groups can be _____, preventing acetylation, thus maintaining positive charge Can undergo this modification 1,2,or 3 times, Arginine side chains can also undergo this modification
These amino acid side chains can undergo reversible phosphorylation in order to introduce a negative charge 2 main amino acids list in alphabetical order. When phosphorylated, they change the overall structure of the nucleosome and corresponding DNA which can lead to degradation by a ubiquination/proteosome pathway (substrates for E3 ubiquitin ligases). Tyrosine phosphorylation is relatively rare.
QuestionAnswerExtra Info
A single, 76 amino acid ubiquitin molecule can be reversibly added to a _____ amino acid in the C terminal tails of H2A and H2BInduces a conformation change. If more than one is present on the protein, then it can be marked for degradation by proteosomes
Name of highly condensed chromatinThe opposite is less condensed chromatin termed euchromatin. This type of chromatin does not fully decondense after mitosis remaining compacted during interphase. This type of chromatin is found at centromeres and telomeres of chromosomes. Stains very darkly.
This protein is associated with heterochromatin which bind to H3 N-terminal tail only when it is tri-methylated at lysine 9 (chromodomain)Chromodomain is the domain that binds to histone tails when methylated at the specific site.
Name the second domain of protein answer of Q#36 that is frequently found in proteins containing a chromodomain. It binds to domain of itself on other proteins and also binds the eNucleosome adjacent to a region of HP1 containing heterochromatin also become methylated at lysine 9 (H3). This spreads heterochromatin condensation until a boundary element is encountered that blocks further spreading. Boundary element = regions of chromatin where several nonhistone proteins bind to DNA
This domain binds to acetylated histone tails of euchromatin and is associated with transcriptionally active chromatinTFIID contains two of these closely related domains which maintains chromatin in hyperacetylated (Less condensed) state conducive for transcription.
Large DNA loops observed in histone depleted metaphase chromosomes from HeLa cells contain these scaffold proteins at the bases of these DNA loopsOnly abbreviation required for answer. Genes are located between these regions and may affect transcription of neighboring genes.
These proteins help condense chromosomes in metaphase and can wrap around (encircle) two 30-nm chromatin fibers in interphase Topological knots of these proteins and chromatin at the base of each loop are probably linked together in some way to produce the apparent protein scaffold shape visualized in histone-depleted metaphase chromosomes
Condensed chromatin fiber that is formed during metaphaseA 100-130 nm fiber formed from 30-nm chromatin. This fiber then folds into the 200-250 nm fiber called middle prophase chromatid. This middle prophase chromatid then folds into the 500-750nm diameter chromatid observed during metaphase
These proteins are present in large amounts and are believed to affect transcription by binding to DNA cooperatively with transcription factors. Stabilize these multiprotein complexes that regulate transcription of a neighboring gene. Exhibit high mobility in electrophoretic separation
These bands are produced when metaphase chromosomes are subjected to heat or proteolysis and then stained with a Giemsa reagentCorrespond to a large region of human genome that have an unusually low G/C content. If metaphase chromosomes are treated with a hot alkaline solution and before staining with Giemsa reagent, then it produced R bands which have unusually low A/T content.
Spectral karyotyping or chromosome painting is done by this method which makes use of DNA probes specific for sites scattered along the length of each chromosome.These probes are labelled with several different fluorescent dyes with distinct excitation and emission wavelengths. After probes are hybridized, sample is observed with fluorescent microscope in which a detector determines fractions of each dye present at each fluorescing position in the microscopic field. Information is conveyed to computer program which assigns a false color image to each type of chromosome
Phenomenon of genes occurring in the same order on a chromosome in two different species
3 functions elements that are required for correct replication and segregation. The first being:***Important Yeast transfection experiments identified the functional chromosome elements necessary for normal chromosome replication and segregation***. Ones containing a yeast autonomously replicating sequence (ARSs - 100 bp sequences)
3 functions elements that are required for correct replication and segregation. The second being:***Important Yeast transfection experiments identified the functional chromosome elements necessary for normal chromosome replication and segregation*** Introducing a CEN sequence (centromeric sequence) allows good segregation. (Greater than 90% of progeny cells contain a plasmid.
3 functions elements that are required for correct replication and segregation. The third being:***Important Yeast transfection experiments identified the functional chromosome elements necessary for normal chromosome replication and segregation*** if plasmid containing CEN and ARS is cut and the resulting linear plasmids have introduced a TEL sequence (telomeric sequence), then these linear plasmids behave like normal chromosomes.
CEN contains three regions: I, II, and III. Regions I and III bound by proteins interact with a set of 30 other proteins, which in turn bind to microtubules. Region II is bound to Essential for centromere function. In humans, centromeres = 2-4 megabase arrays of 171 bp single sequence DNA called alphoid DNA.
Telemore repeat sequence in humans is ______.6 base repeat sequence. repeated at every termini of chromosomes for a total of a few hundred base pairs in yeasts and protozoans. 3' end of G-rich strand extends 12-16 nucelotides beyond the 5' end of the complementary C-rich strand. This region is bound by specific proteins that protect the ends of linear chromosomes from attack by exonucleases.
Protein-RNA complex that adds telomeric (TEL) sequences to end of each chromosomeSpecialized form of reverse transcriptase that carries its own internal RNA template to direct DNA synthesis. RNA template is specific.
3 genetic loci on yeast chromosome 3 control mating type of yeast cells. The first, centrally mating type locus, termed ____, is actually transcribedThe other two silent loci are HML and HMR near the left and right telomeres respectively. These sequences are transferred alternatively from HML alpha to HMR A into the MAT locus by a type of nonreciprocal recombination technique between sister chromatids during division.
Repression of silent loci depends on _______ located next to the region of trnasferred DNA at HML and HMRIf this sequence is deleted, the adjacent silent locus is transcribed. Any gene placed near this sequence via recombinant techniques is repressed of 'silenced'. These sequences bind proteins that are critical for repression of these silent loci.
The RAP 1 and SIR proteins are required for _______ of silent mating type loci and telomeres in yeast. RAP 1 was found to bind within DNA sequence associated with HML and HMR and to a sequence that is repeated multiple times at each yeast chromosome telomere. SIR 2 protein is a histone deacetylase; it removes acetyl groups on lysines of histone tails, making it more condensed. RAP 1 and SIR 2,3, and 4 proteins bind to one another, meanwhile SIR 3 and 4 proteins bind to N-terminal tails of histone H3 and H4 maintained in unacetylated form due to deacetylase activity of SIR 2. In telomeres, this complex is the same, however SIR 1 is required for silencing of mating type loci, which binds to silencer sequences of HMR and HML with RAP 1. Must be hypoacetylated tails. IN YEAST
Polycomb proteins regulate ________ of genes in higher eukaryotes (examples with drosophila)Hox genes are the genes regulated by these polycomb proteins and these genes play an important role in development of specific tissues and organs in embryo. Trithorax proteins perform the opposite function of polycomb protein, instead promoting expression of hox genes. Expression of hox genes is regulated by a process that involves more than simply specific DNA sequences interacting with proteins.
These proteins are subunits of one of two multiprotein complexes, PRC1 and PRC2.PRC2 is thought to act initially by associating with specific repressors bound to their cognate DNA sequences early in embryogenesis.
PRC2 complex contains a _____ domain (enzymatically active domain of several histone methyl transferases).This domain methylates histone H3 on lysine 27.
The PRC1 complex then binds the methylated nucleosomes through dimeric _______ subunits each containing a binding domain (chromodomain) specific for H3 lysine 27Two letters. Binding of this dimeric subunit to neighboring nucleosomes is proposed to condense the chromatin into a structure that inhibits transcription. PRC2 or another methyl transferase is postulated to associate with PRC1 maintaining methylation of H3 lysine 27 in nucleosomes. Therefore, heterochromatin propagates with these proteins.
These proteins contain a histone methyl transferase as well that methylates histone H3 lysine 4, a histone methylation associated with the promoters of actively transcribed genesThis methylation is thought to create binding sites for histone acetylase and chromatin remodelling complexes that promote transcription and prevent methylation of histone H3 at lysine 9, preventing binding of HP1, and at lysine 27, preventing the binding of PRC1 repressing complex.
When promoter DNA is assembled onto a nucleosome with ________ histones, the general transcription factors cannot bind to the TATA box and initiation is repressed.Modification. In these histones, the N terminal lysines are positively charged and interact strongly with DNA phosphates. Also interact with neighboring histone octameric complexes favoring condensed, higher-order structure
For repressor-directed histone deactylation in yeast, this protein is the active deacetylase enzymePart of large multiprotein complex
For repressor-directed histone deactylation in yeast, this repressor binds to the upstream regulatory sequence and SIN3 (part of large multiprotein complex containing deacetylase)Binds the URS1 (upstream regulatory sequence and SIN3 of multiprotein complex in order to position the RPD3 deacetylase over nearby promoter-associated nucleosome. Ultimately inhibits binding of transcription factors for transcription activation.
For activator-directed histone hyperacetylation in yeast, this complex functions with GCN4 and activator protein GCN5
For activator-directed histone hyperacetylation in yeast, this protein interacts with UAS (Upstream Activating Sequence) and with multiprotein acetylase complex
For activator-directed histone hyperacetylation in yeast, this protein is the acetylase that hyperactylates surrounding N-terminal tails (ex lysine 16 on H4) from histonesAcetylation results in binding sites of bromodomain within TFIID and other transcription factors.
These modifications on histone lysines turn over rapidly, meaning they do not bind very strongly and for long periods of time.Methyl groups are much more stable.
QuestionAnswerExtra Info
The entire nucleic acid sequence that is necessary for the synthesis of a functional gene product is called a what?Includes promoters, enhancers, promoter proximal elements, coding region, sequences specifying 3' cleavage and polyadenylation sites, and sites specifying splicing of primary RNA transcripts
mRN that encodes several proteins that function together in biological processes is considered to be:ex. trp operon. Most eukaryotic mRNAs are monocistronic
Cluster of genes forming a bacterial operon comprises a single __________ that is transcribed from a specific promoter in DNA sequence to termination siteEukaryotic units have two types: single and complex. Single units yield only one particular protein from an mRNA, while complex units yield multiple proteins from a single mRNA via alternative splicing and mutations in exons
Set of duplicated genes encode proteins with similar but non-identical amino acid sequence called a what?The encoded, closely related, homologous proteins constitute a protein family.
Nonfunctional sequences found in DNA due to evolutionary weak selection and sequence drift
Why does our human genome contain large amounts of DNA that is non-coding? (Answer = evolution, explained in extra info)Because vertebrae DNA has not had any selective pressure to eliminate nonfunctional DNA. For microorganisms, synthesis of nonfunctional DNA requires time, nutrients, and energy which was heavily selected upon to lose this DNA.
Repetitious DNA which are short, tandemly repeated sequences that are found at centromeres and telomeres as well as at other chromosomal locations and are not transcribedMost of this DNA are repeats of 14-500 base pairs in tandem arrays of 20 -100 kb. They are required to form specialized chromatin structure called centromeric heterochromatin. Repeats contain 1-15 base pairs are often called microsatellites. These are thought to have originated via 'backwards slippage' of daughter strand on its template strand during DNA replication so that the same short sequence is copied twice.
These sequence elements are DNA sequences found in bacteria that are able to transpose directly in the middle of an E. Coli geneContain an inverted repeat of approximately 50 bp present at each end of this sequence. The region in between the inverted repeats encodes an enzyme, transposase, required for transposition of this sequence element to a new site. At the very ends of this sequence are short direct repeat sequences containing 5-11 bp. Transposase will make staggered cuts in target DNA and blunt end cuts in donor DNA.
In eukaryotes, the agent responsible for first class mutations in maize are called what?NOT IN FAGGOTTO'S SLIDES. Abbreviated Ac. These elements are equivalent to (answer to previous question) and also contain inverted terminal repeat sequences that flank the coding region for a transposase.
In eukaryotes, the agent responsible for second class mutations in maize are called what?NOT IN FAGGOTTO'S SLIDES. Abbreviated Ds. These elements are deleted forms of the first class mutation elements in which a portion of the sequence encoding transposase is missing. That means these elements are unable to move by itself and will require the transposase of the other element in order to move.
Eukaryotic retrotransposable mobile elements that contain 5' to 3' direct repeats, a coding region, and specific repeats to themselves are called what?Contain their own repeat units between the coding region and the short direct repeat sequences. These specific repeats are about 250-600 bp long depending on the type.
Non-LTR retrotransposons transpose by a distinct mechanism of which the most abundant and second most abundant of these retrotransposons are called:Answer in form of _____ and _____ (plural). These interspersed elements are either 6 kb long or 300 bp long depending on the type. DNA transposons and the longer type of these interspersed elemental retrotransposons occasionally carry unrelated flanking sequences when they transpose to new sites.
Mobile DNA elements: (no answer- just for understanding read extra info)(1) contribute to generations of gene families via gene duplication, (2) creation of new genes via shuffling of pre-existing exons, and (3) formation of more complex regulatory regions (enhancers) that provide multifaceted control of gene expression
Two very important molecular techniques (1) for forming thousands of repeated cDNA and (2) for identifying specific amino acid sequences of DNA are:Should understand these methods and know very well. Also understand cloning libraries, gel electrophoresis, transient and stable transfections, SouthernNorthern/Western blotting, in situ hybridization, plasmid recombination, and ******* gene-targeted knockout mice******* For proteins, understand chromatography, electrophoresis, and centrifugation
The three most abundant secondary structures in proteins include the alpha helix, the beta sheet, and the _____.The average polypeptide = 60% alpha helices and beta sheets
Highly flexible portions of a polypeptide chain that have no fixed 3D structure
The alpha helix backbone forms a spiral structure in which carbonyl oxygen atom of each peptide bond forms hydrogen bonds with amide hydrogen atom of amino acid ___ residues fartheAnswer = number. Side chains point outward. Alpha helices can often be predicted due to periodicity of hydrophobic aa. If an alpha helix is at the surface of a protein, one face will often display hydrophobic residues that will interact with the other parts of the protein while hydrophillic/charged residues will be exposed at the surface. Typical periodicity for such helices is: i, i+3, i+4, I+7 which correspond to hydrophobic residues
These two amino acids (in alphabetical order) are commonly present in beta turns.
These bonds or bridges found between side chains of cysteine residues in some proteins covalently link regions of proteins, thus restricting the mobility of proteins and increasing
Region of protein that exhibit a particular activity characteristic of the protein. ex Region of protein for catalytic activity
Region approximately 40 or more amino acids in length, arranged in stable, distinct secondary or tertiary structure independently of the rest of the protein
Region of protein that are defined by their distinctive spatial relationship to the rest of the proteinex Cell surface membrane proteins with portions in the membrane and also extending into both the cytoplasm and the extracellular space
These type of chaperones bind and stabilize unfolded/partly folded proteins preventing these proteins from aggregating and being degraded.Required otherwise unfolded/partly folded proteins that tend to aggregate with their hydrophobic side chains forming and promoting aggregation and thus the hydrophobic effect.
These type of chaperones form small folding chamber into which an unfolded protein can be sequestered, giving it time and and approximate environment to fold properlyThese are huge cylindrical macromolecule assemblies that formed from two rings of oligomers, which can exist in a 'tight' peptide-binding state and a 'relaxed' peptide-releasing state.
In bacteria, the GroEL chaperonin has the unfolded/partly folded protein inserted into its cavity (which is barrel like) where it binds to the inner wall and folds into its native
Large macromolecular machines of approximately 50 protein subunits that degrade proteins are called:Contain ATPases to provide energy needed to unfold protein substrates and selectively transfer them into the inner chamber of the proteosome. Also contains 2 active sites that cleave hydrophobic residues, acidic, and basic residues.
Cells identify proteins that should be degraded by covalently attaching multiple copies of a 76 residue polypeptide called ________.The 19s regulatory cap of 20 proteosome core recognizes these specifically labelled proteins and unfolds/transports them into the proteosome for degredation. Must have multiple binding ubiquitin molecules to undergo degradation. Ubiquitin is transferred along a pathway from E1 (ubiquitin-activating enzyme) to E2 (Ubiquitin-conjugating enzyme) which is then added to the protein via E3 (ubiquitin ligase). Subsequent additions of ubiquitin via this pathway yields a protein ready for degradation by a proteosome. Ligated by E3 ligases
Ubiquitin-Proteosome systen is regulated by degradation of proteins called _____ which control the cell cycle.Contain internal sequence Arg-x-x-Leu-Gly-x-Ile-Gly-Asp/Asn. At a specific time in the cell cycle, each cyclin is phosphorylated by a cyclin kinase. This phosphorylation is thought to cause a conformational change that exposes the recognition sequence to the ubiquitinylating enzymes, leading to polyubiquitination and proteosomal degradation.
Addition of _____ groups onto hydroxy groups of serine, threonine, and sometimes tyrosine residues changes a proteins charge and leads to a conformational change which can alter liThese groups are added by protein kinases and are taking of by phosphatases
The two properties of a protein that characterize how it binds to ligands are:Alphabetical order. 2 things. The first refers to the tightness or strength of binding while the second refers to ability of proteins to bind one molecule in preference to other molecules
Portion of the antigen that an antibody binds to Used for tagging in specific protein targeting mechanisms.
_______ refers to any change in a proteins tertiary or quaternary structure or both, induced by the noncovalent binding of a ligand.This can affect the protein in various ways. ex Binding of a ligand induces a change in conformation of an enzyme thus not allowing it to bind to its specific reagents (Termed Allosteric inhibition). Can induce increase or decrease in protein activity. ex you should know include GTPase conformations with the help of GEFs and GAPs

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