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BCHM 4360 ACTUAL EXAM 1 2025 VERIFIED RATIONALES WITH COMPLETE
SOLUTIONS |GRADED A
In eukaryotes, the basic binding proteins are called ________. histones How many core histones are there and what are they called? 4, H2A, H2B, H3, H Which two amino acids are histones rich in and why? lysine and arginine due to positive charges DNA wraps around a histone complex in a ____-handed manner to form a __________. left, nucleosome Which two histone dimers associate with DNA first? H3, H Which two histone dimers associate last to form the octamer? H2A, H2B
About how many base pairs of DNA wrap around the histone octamer to form the nucleosome? 146 Removing the histone octamer leaves what kind of supercoiled DNA? negative Each core histone has a(n) _-terminal tail that extends outward between the DNA and coils. N The histone tails are up to __ amino acids long and have an _________ structure. 25, undefined Why do the histone tails interact with other nucleosomes? to help compact DNA further What are the five mutant variations of histone H2A? H2A.X, H2A.Z, MacroH2A1, MacroH2A2, H2A-Bbd
True or False: nucleosomes prefer some types of DNA sequences over others. true DNA is generally ________ bent around histones but has _______ bends in some places. smoothly, sharper The sharp bends in DNA usually occurs in which groove and at which sequences? minor groove, pyrimidine-purine sequences such as TA and CG The _____ groove needs to narrow during DNA bending, and this is more favorable in which regions? AT-rich regions The first level of chromatin packing is the __nm fiber, which arises from nucleosome association with DNA, and has what kind of appearance? 10, beads on a string The 10nm fiber is folded further into the __nm fiber, a regular arrangement that does what? 30, brings nucleosomes together
Which histone is involved in the formation of the 30nm fiber? H What is H1? a linker histone that binds to the linder DNA in between successive nucleosomes, helping compaction The 30nm fiber is lastly compacted further into _______ ___________ in which large loops of chromatin are anchored to a central scaffold. compact chromosomes What are two characteristics of interphase? Chromosomes are relatively uncondensed and genes are being transcribed Which is denser: euchromatin or heterochromatin? heterochromatin True or false: some transcription can occur in heterochromatin regions. true
acetylation, methylation, phosphorylation, ubiquitination What are histone modifications though to do for the histone? recruit specific proteins to the chromatin Genetic information is packaged into at least one very long DNA molecule -- a __________. chromosome Each chromosome contains ___ double-stranded DNA molecule one Each chromosome has many _____ and other regions of DNA within a single molecule. Regions between genes are __________. genes, intergenic Eukaryotes have ______ chromosomes, most bacteria and archaea have ________ chromosomes. linear, circular ____ complex organisms tend to have more _______ arranged genes. Example is _____. less, densely, yeast
Humans have __ chromosomes while the kingfisher has ___ and fission yeast have _. 46, 132, 6 Ploidy refers to how many sets of identical chromosomes an organism has What is ploidy of humans and human sex cells? diploid, haploid Each individual chromosome is __________ between the mother and the father. homologous _________ cells have multiple sets of chromosomes and are common in some plants. However, some human cells such as _____ cells are also _________. Polyploid, liver, polyploid True or false: histone modifications are reversible. True: specialized enzymes add and remove the chemical groups True or false: the side chains of the globular regions of histones can not be modified.
Histone acetylation generates binding sites for which type of proteins that bind to specifically to certain acetyl-lysines? bromodomain Why is acetylation associated with active transcription? What does it do? Acetylation removed the positive charge from the lysine side chains of the histone, weakening the affinity for the DNA wrapped around it What do bromodomains do? recruit other proteins like nucleosome remodeling complexes How many methyl groups can be added to a lysine and an arginine residue respectively? three, two True or False: Methylation is only associated with transcription repression. Explain the correct answer. False: It depends on the residue that is methylated Give an example of a residue that is methylated to silence chromatin. Methylation of Lysine 9 in the H3 tail.
Give an example of a residue that is methylated to activate chromatin. Methylation of Lysine 4 in the H3 tail. ____________ bind to specific methylated lysines, and are most often associated with transcriptional _________. Chromodomains, silencing Chromodomains are usually associated with ___________ and bromodomains are usually associated with ___________. methylation, acetylation Phosphates are added by _______ and removed by __________. kinases, phosphatases Phosphorylation of which residue allows cell growth transcription? H3 serine 10 Phosphorylation of which residue correlates with chromosome condensation in mitosis? H3 serine 10 and serine 28
- Sliding the histone octamer along the DNA
- Removing the histone octamer or transferring it elsewhere
- Introducing loops into the DNA wrapped around a histone core Which method of nucleosome remodeling is least favored and why? Removing the histone completely is the least favored because the nucleosome must be reassembled after destruction What are the two main classes of nucleosome remodeling complexes and what are their main functions? SWI/SNF disrupts nucleosome positioning, ACF (ISWI) positions nucleosomes during chromatin assembly What are the four main nucleosome remodeling complex subunits? ATPase domain (two parts Dexx and HELICc), bromodomain, chromodomain, and SANT- SLIDE If SWI/SNF fails, what usually happens to the cells? Substitute with INO80 family, which is very similar. The cells will continue to live but will operate poorly Eukaryotic cells can have __________ DNA to the chromosomal DNA found in the _______. additional, nucleus
____________ have their own, usually ________, chromosomes. Mitochondria, circular ____________ also have their own chromosomes. Chloroplasts ____________ and ____________ are thought to have derived from ancestral free-living bacteria that were absorbed and maintained by other single-celled organisms. Mitochondria, chloroplasts Bacterial cells often have additional DNA within their cells -- small circular molecules known as ________. plasmids Viruses are infectious agents and carry genetic information as small ___ or ___ chromosomes. These chromosomes can be ______ or _______, and ______ or ______ stranded. DNA, RNA, linear, circular, double, single Chromosomes must be ______ and ___________ to the next generation of cells faithfully.
Describe what happens in G2. The cell prepares for mitosis Describe what happens in M. Sister chromatids are separated and a full set of chromosomes is moved to each pole of the cell. On entry to which cell cycle phase does the nuclear envelope break down? M In condensed chromosomes, DNA appears as large _____ anchored near the middle of the chromosome. loops Chromosomes consist of ___ plus __________ proteins that help condense the DNA into a smaller space and _______ the genome. DNA, packaging, protect The DNA-protein complex that makes up chromosomes is called _________. chromatin
What occurs in the first packing stage of the chromatin? Small positively-charged proteins bind to counteract the negative charges on DNA backbone In bacteria, the first packing stage of chromatin _____ the DNA forming the _________, and the bending induces ____________. bends, nucleoid, supercoiling What are the two possible models that explain how nucleosome remodeling complexes might work? Pushing and sliding the DNA (propagation), twisting the DNA (global distortion) How do cells recruit remodeling complexes? Via proteins that bind in a sequence-specific manner What two ways do cells recruit nucleosome remodeling complexes? Transcriptional regulators and histone modifications Why doesn't the brain cool down as efficiently as the rest of the body? There isn't an overexpression of heat-shock proteins like there is elsewhere in the body so it takes longer to activate heat-shock system
Just after replication, only the parental strand of DNA is methylated (called hemi- methylated). When mismatch repair enzymes detect a mismatch, the methylation status is read, allowing the repair machinery to identify the parental strand and correclty repair the mismatch Explain how DNA methylation allows bacteria to distinguish genomic DNA from invading bacteriophage DNA. Restriction enzymes cut DNA at specific recognition sites so bacteria defend their own DNA from being cut by methylating the recognition sites. The bacteriophage DNA is not methylated and will therefore be cut by the restriction enzymes and destroyed. True or False: Methylation in eukaryotes is only used to silence transcription, not activate it. False Eukaryotic methylation is usually at which two sites? CpG or CpXpG Up to __% of human CpGs are methylated, and methylation state can be _________. inherited What is an example of epigenetic silencing in mammals and how does it work? X-chromosome inactivation, one X chromosome in each cell is inactivated in females so they have the same amount of gene product as in males
Some gene activity is affected by __________, which is thought to control expression of genes from mother and father in the embryo. imprinting True or false: If one copy of a gene is silenced and the other is absent, there is still some gene expression due to recombination. False, there will be no gene expression and no recombination Explain how fruit flies occasionally have white eyes. Fruit fly eyes are normally red, from expression of white+. Occasionally, white eyes are seen as a result of white+ moving near to heterochromatic regions and being silenced How do boundary elements work to silence some genes? They slide down the chromosome, shutting down genes due to the heterochromatin being able to spread True or false: Boundary elements can both allow and prevent heterochromatin spreading. True Give an example of how boundary elements prevent heterochromatin spreading.
