Genetics 1
chromosomes and mitosis were first analyzed by __ in ___
Flemming, 1882
examples of pioneer transcription factors:
FoxA, FoxO, GATA factors
once RNA pol 2 leaves the PIC it _______ , unwinding the Double helix, and so there is a region of about ____ that is sometimes called the ______, which allows the ____to be added to the ______ of the growing RNA
cleaves the two strands apart, 30, transcription bubble, ribonucleotides, 3'
Molecular Biologist's Dream: RNA World Hypothesis-- 1, RNA molecules with _______ assemble themselves from primordial nucleotide "______." 2, RNA molecules evolve and diversity by _____ with ______ and ____ providing raw material for Darwinian selection. 3, RNA molecules begin to synthesize _________ (first, by synthesizing adapter RNAs to bind activated amino acids) which begin to improve on ribozyme-only functions 4, ____ appears with more stable information store because two strands allow for _______
catalytic activities, soup, self-replication, mutation, recombination, proteins, DNA, error correction
53BP1 influences ________ and binds to ________ to _______ transcription
cell cycle regulation, H3K79me, promote
ATP-dependent chromatin modifiers could also be considered
co-activators
the mediator complex can be considered a
co-factor (bridges TF to PIC, even if activator cannot make its own contact with the PIC, there are mediators that can bridge them)
an additional functional consequence of histone modification is _____
cofactors,
we will also note the _______, which exists to keep the CRE in proximity with ________...idea is that regulatory regions may be far away in terms of linear DNA sequence but they are brought in in proximity during transcription physically
cohesion protein, Pol 2 region
looking at cell nucleus, the darker, more stained regions are the
heterochromatin
so ____ and ______ are proteins that enforce transcriptional silencing
heterochromatin protein 1 (HP1), polycomb complex (PC)
pioneer factors play roles in
cell programming and reprogramming, often associated with cell decisions during cell development, stem cell bio, allows cells to be reprogrammed into other types of cells
chromosomes exist in cells as ___________, which is ___________
chromatin, DNA and proteins
another common modification is the ubiquitination of ______ residues
lysine
acetylation of _______ leads to partial degradation of the nucleosome
lysine 91
the nitrogenous base attaches to the sugar at the ____
1'
there ___ of each for the core histones so there are a total of ____ histones comprised of ___ types of histones
2, 9, 5
turns out there are a little over _______ protein-coding genes
20,000
some problems with the earliest, non-biotic assembly of RNA
-each nucleotide has 3 chemical moieties (complex chemistry) -contemporary nucleotides will not couple without chemical activation -phosphates (linkers) very limited (and what was available probably in stone) -adenine possibly abundant, the other bases were not -non-biotic synthesis of ribose unlikely, and ribose is unstable (so even if it did somehow spontaneously come together it would not have lasted for long) -issues with solvent: nucleotides do not self-assemble by hydrogen binds in water, polymeric RNA unstable in water -cofactor Mg +2 not available -natural RNA polymerase ribozymes not known
Chromatin immunoprecipitation with sequencing (ChIP Seq)
-isolate chromatin from whole genome -fragment chromatin into small pieces -incubate with antibody to protein of interest; precipitate antibody-chromatin complexes -purify DNA from precipitated material -sequence DNA by Next Generation Sequencing -align sequences to genome to detect regions that had been enriched for protein of interest
HMT can add ____, ____, or ___ methyl groups to lysine, forming ___, ___, ____ which all have different implications for the functioning of the histone
1,2,3, mono-methyl-lysine, di-methyl-lysine, tri-methyl-lysine
production of translatable mRNA from specific genes requires
1- accessibility of gene to transcription factors 2- interactions of transcription factors with CRE 3- initiation, elongation, and termination of RNA transcript 4- processing (capping and splicing) of newly transcribed RNA 5- transport of processed mRNA to cytoplasm
3 big takeaways from ribozyme experiment:
1-ribozymes had not been found in nature that replicated RNA by themselves, but it was possible to generate ribozymes with this capability in lab, so might have once happened back in RNA world 2-this only came about because they were dealing with RNA that had info content, they had introduced variation into the system, there were functional consequences and this selected for a particular phenotype... 3-unintentionally selected for increased complexity
_____ hydrogen bonds form between A and T, _______ hydrogen bonds form between __________
2, 3
if you have adjacent nucleosomes the DNA is
less accessible to other factors
exons account for ____ of genome
1.5%
chromatin is comprised of
1/3 DNA, 1/3 histone, 1/3 non-histone protein
salamander genome has been sequenced (treated as model organism for a while) despite it being ___X the size of a human genome but what makes it so much larger is the ____, the _____...goes to show there is more to a genome than coding genes
10, introns, simple sequence repeats
typical exon size is ______ bp, about ____% of exon have exactly that (there is tremendous variation in exon size)
100, 6
there are also about ______ Pseudogenes. A pseudogene is a
13,000 former genes, essentially broken gene, might have a premature stop codon that prevents actual translation from happening, could be reverse transcribed RNA that has gotten back into the genome
about ______ bases of DNA are able to wrap around a histone and then there is additional DNA that comes out as sequence continues and then about ______ bases till the next chromosome
160, 7-115
Darwin natural selection year____ and sexual selection year_____
1859, 1871
Mendel's big year
1865
Mendel's work was rediscovered in _____ meiotic segregation was described by _____
1902, Sutton
genetic info can be transferred experimentally discovered ______ and DNA is the genetic material discovered in _________. 3 people involved in this:
1923-1931, 1944 ...Griffith, Avery, MacLeod
evidence that genes (can) code for proteins came in ______ with an experiment performed by _____ and ________ (this is called the Central Dogma of Biology)
1941, Beadle, Tatum
genes can move on chromosomes discovered in ____ by ______ (transposable elements are mobile and can cause real time change)
1944, Barbara McClintock
first protein sequenced in ____ by ____
1951, Sanger
genes are made of DNA discovered in _____ by ______
1952, Hershey and Chase
humans have 46 chromosomes was discovered in ____ by _______
1955, Hin Trio
Isolation of DNA polymerase was done in ____ by ____
1955, Kornberg
DNA is replicated semiconservatively ___ by _____
1958, Meselson and Stahl
genetic code is a triplet in ___ by ____
1961, Brenner and Crick
genetic code cracked in ____ by ____
1966, Nirenberg
first big discovery from technological advancement: DNA sequencing in ______ by ___ and ____ (Sanger Method, di-deoxy situation,, used to use radionucleotides labeled with______, now use _____)
1975, Sanger, Gilbert, p53, fluorescent dies
PCR invented in ____ sort of by _____ (stands for ___________) 3 steps: 1-_________ (temp up, breaks _________) step 2: ________ (temp down a little, short primers that hybridize at specific location at newly single-stranded DNA template by way of _______) step 3: __________ (temp increased) extension for DNA through the activity of _____.
1983, Mullis, polymerase chain reaction, denaturing, hydrogen, annealing, hydrogen bonds, extension, Taq DNA polymerase
human genome sequenced from ___ to ____ basically the method was to chop up the genome into small pieces, Sanger sequent the pieces, then use the many areas of overlap to stitch map out...take clones and chop them up further etc.
1986-2000
during the first phase of transcription only about ________ are added then RNA pol 2 sputters out and ______. not super well understood currently but some possible explanations are _______, ______, _______. Prevailing idea is that the pause is a method of
20-60, pauses, negative energetics factor, nucleosome region, factors pulling RNA pol 2 back,
next big innovation around ______ was ________ the invention of targeted genome editing-- a lot of ongoing ethical issues with this one
2010, CRISPR-CAS(Charpentier, Doudna, Zhang)
amazingly, ______ of our genome is comprised of about ______ copies of a specific transposable element that originally moved around but may or may not be dead at this point in time
21,800,000
how many cases of malaria globally per year? how many deaths in 2015?
212 million, 429,000
there are _______ nonprotein-coding genes
22,000
introns account for _______ of genome
26%
the median size of the gene body is ______ but the range goes from as small as _____ to as large as ______
26,288 bp, 189 bp, 2.4 million bp
TATA box, sequence most often recognized by the TATA box, is often _______ upstream of the TSS
26-31
mRNAs median number is _____, ranges from __ to ___
2787 bp, 186, 109,224
phosphodiester bond forms between phosphate of one nucleotide and the _______ of the other nucleotide
3' C
during transcription the template strand is being read ______ but the new mRNA is being built ___________
3' to 5', 5' to 3'
PCR cycling-- after __ or ___ rounds you have about _____ copies of template
30, 40, billion?
a typical CRE recognized by a TF might have 8 total nucleotides but ___ of them might be variable, non-coding sequence, more free to do that
4
proximal promoter will be about ____ nucleotides from the start site
40
about ______ of our genome is comprised of _______
40%, transposable elements
what was the range of estimates for the number of genes in human genome based on various mathematical models
40,000-2,000,000
how does splicing work? sequences typically associated with __ and ___ ends of introns, as well as a particular spot within the intron (note: these sequences can also be found within exons and when they are are called _____)
5', 3', cryptic splice site
the Pre Initiation Complex is a protein-based machine comprised of _____ proteins, including_____, and the _________, which is itself a complex comprised of _____ (_____) which interacts with __ _______ (for ex: ___)
50 different, RNA Pol 2, TFIIB, TBP (TATA binding protein), 13 TATA-Binding-Protein-Associated factors (TAF), TAF6
back then, you could run ____ bases of sequenced and you could run ___ samples at a time, to get ____ bp per run...now, the _________ can generate ________ gbp per run (one human genome is only about ______) we cannot comprehend what these numbers mean! cost used go cost over ______, we can do the same for about ____ and maybe even ____
500, 32, 1600, Nova Seq 6000, 6000, 3.6, 100 million, 1000, 250
To test the possibility of a triplet genetic code in the _____, they used a ______( a virus that affects ______) and mutated this virus and examined the consequences of inserting or deleting certain numbers of nucleotides. There were 4 nucleotide bases. They knew a code of __ or __ would be insufficiency to supply the diversity of ___ amino acids. a triplet code could potentially yield ___ amino acids. The experiment revealed that while 1 or 2 insertions or deletions yield ______ proteins, insertions/ deletions of ____ yielded functional proteins.
60s, bacteriophage (bacteria), 1, 2, 20, 64, nonfunctional, 3
nucleosomes condense naked DNA
7 fold
median number of exon per gene body is ______ but some have as many exon as _____ and some have ______
7, 363, 1
there are about __________ mRNAs for only about __________ protein-coding genes
80.,000 20,000
when u look across RNA population, of the genes that have more than 1 exon to play with, ____ of them show alternative splicing
95-100
CIS regulatory elements and promoters necessary for transcription but not accessible to transcription factors can be made so by
ATP dependent chromatin remodelers
2 major methylation factors:
PRMT (protein Arginine methyl transferase), HMT (histone methyl transferase)
genes (can) code for proteins discovered by ___ in ____
Beadle and Tatum, 1941-1945
Probably simultaneously have components of PIC starting to recognize newly exposed TATA box and other components and components of mediator recognizing transcription factors that start to bind to PIC...as these things get assembled you have a initiation of transcriptional unit and the recruitment of RNA polymerase...the critical transcription factors here, beside POL 2, end up being the ones bound to _______, or sometimes bound to closer CRE, that might be just adjacent to promoter itself
CRE
who discovered A pairs with T and C pairs with G by looking at variety of organisms and noticing the ratios of A to T and of C to G were always pretty close to 1
Chargaff
one of most exciting discoveries: structure of DNA! analyzing x-ray diffraction patterns, _____ got critical high quality data about how DNA must be arranged and someone shared this data with _____ and _____, who were then able to publish the article about it in ______
Franklin, Watson and Crick, 1953
at 5' end at intron you will have a ____ and a couple of _____ on the intron side of boundary, on the exon side of the boundary you will have ______ . The ____ in particular is the sequence you would find for the _____ site On the 3' end you will have at the end of the intron a ____ and on the exon side it is a little more variable. When people say spice donor ____ and splice donor _____, they mean the ____, and the _____, respectively
GT, A, G...GT, splice donor, AG, 5', 3', GT, AG
early evidence that DNA was the critical genetic material came from ______ in ______- when he carried out the experiment with the ____________, the bacteria that causes pneumonia. Interested in the phenomena of __________, heat killed ____ strain of bacteria (has the _______ so is encapsulated and can kill) and put in the ___ strain, the mouse _______, so he knew the ___ strain had taken up something inside the ____ strain-- but what? to address this question, he treated the locate with a series of _____ that would destroy one type of molecule or another-- transformation occurred (the mouse _____) every time except when _____ was added
Griffith, 1928, Streptococcus, transformation, S, polysaccharide, R, died, R, S, enzymes, died, DNAase
core histones are
H2A, H2B, H3, H4 (HI is not a core histone it is below)
histone mark involved with DNA breathing
H3lysine56 acetylated (DNA wraps around histone at a looser angle)
histone acetyl transferase
HAT
histone deacetyltransferase
HDAC
real world examples today of DNA's double-stranded structuring conferring more stability than RNA's single-stranded structure, examples of single-stranded RNA viruses are: ___ and _____, which are really dangerous and highly mutable
HIV, influenza
DNA was first isolated by _____ in _____
Meischer, 1869
________ GROOVE INTERCALATORS: _______ is a positive example. ____ is a stain that will go specifically into the ______ groove and can be visualized under the microscope, so it can indicate where the ___ and the _____ are
Minor, Dapi, Dapi, minor, nucleus, DNA
_________ GROOVE INTERCALATORS: a not so nice example is the _________, which contains a classic compound called _______. This compound goes into the ____ groove and in the presence of ______ forms _____ between DNA strands, and in your ____ where you have _______ this __________ is super problematic, which the cells realize and undergo ______.
Minor, giant Hogweed/ Furanocoumarins, psoralen, minor, UV light, cross-links, skin cells, internal stem cells, cross-linked DNA< programmed cell death
_______ did a series of experiments in which he synthesized artificial ______ and asked which ______ came out the other end. When he put in a poly-U RNA, what came out was _______. When his mRNA sequences were made a little complicated based on repeating di-nucleotide or tri-nucleotide sequences, it was possible to see repeated amino acids incorporated into the polypeptide chain...analysis of frame-shifting allowed for the allucidation of the genetic code
Niremburg, mRNAs, amino acids, Phe
on one side the mediator complex is interacting with _______ , on he other side interacting with __________, this interaction promotes stabilization of this region, as long as this is happening, more Rna pol2 can be recruited
PIC, TF bound to CRE,
termination of transcription is important because if no termination signal then the _______ will just keep going and could be ___________. The termination depends on the presence of a ______ rich region with the _____ transcript, which, when transcribed, is recognized by a particular type of ________, which essentially clips it off....then there are sequences that bring the ________ itself to a halt but these sequences are not well understood
RNA pol 2, energy inefficient, GU, mRNA, ribonuclease, RNA pol 2
in mediator diagram, we see an _______ out there doing something, transcribing ________, the function of this ___ being transcribed is to____
RNA pol 2, noncoding RNA, noncoding RNA, interact with mediator complex/ hold bridge in place
major families of ATP-dependent chromatin remodelers
SWI/SNF, CHD (chromodomain), ISWI
hallmarks of cancer (in general demonstrate grossly disregulated gene expression)
Sustaining proliferative signaling Evading growth suppressors Activating invasion and metastasis Enabling replicative immortality Inducing angiogenesis Resisting cell death
in zebra fish genes that were transcribed during really early development were transcribed based on the _____ but genes transcribed only a few hours later were transcribed based on the _____
TATA box, INR
the PIC is assembled near the transcriptional start site through interactions with _______ box, it recruits RNA pol 2, and at some point _________ can leave that and start to transcribe RNA but ______ remains in place as long as gene is active and remains complexed with that ________
TATA, RNA Pol 2, PIC, mediator complex
BRE (______) tends to be roughly _____ bases upstream of the ____
TFIIB, 30, TSS
NASA 1970s definition of life
a self-sustaining chemical system capable of Darwinian selection
one aspect that can help dictate whether or not particular introns or exons are spliced is presence of ________ that can act as enhancers or suppressors of splicing. These factors recognize________ , so this is somewhat analogous to CRE in DNA, except these motifs were in the ____. The motifs are classified in ___ ways to generate ___ types: ___or ___ and ____ or _____.
accessory splicing factors, particular motifs, RNA, 2, 4, exonic/ intronic, enhancer/ suppressor
the gene fibroblast birth factor receptor 3 has active mutations that can result in ___________ we can see in this gene a fair amount of diversity for the composition of the _________ predicted, different transcripts can be made for this gene based on which exon will be maintained
achondroplastic
a method of regulating gene expression that doesn't involve histone modifications or post-translational modifications or changes in protein distributions but rather _________, the type of modification we are talking about is ________, not of _________, but of ________, in regions termed ___________, which tend to be close to the __________. The ______ can be recognized by ________, short-termed__________, which do what their name suggests and __________If a gene is being actively transcribed the TFs of the PIC will block access, but if gene is not transcribed, the _____ can recognize _______, do their business, and this will _______, which will eventually__________. So, this very common phenomena laters DNA in a _________. But, these changes to the DNA itself can induce changes to the histone. proteins, _________, recognize that state of the methylated CPG islands and bind to them, when bound, the _______ recruits other factors, like __________, which will ___________ the histones, thus leading to tighter binding of DNA around the nucleosomes...the _______ can also recruit ____________, also causing highly compact chromatin no longer accessible to activators (reminder, the ________ protein we have seen before, when talking about proteins that bind to particular histone marks, this protein can work along side the ________ in recognizing the methylated CPG state and recruiting______
actual changes to DNA itself, methylation, histones, DNA, CPG islands, proximal promoter, CPG islands, DNA nucleotide methyl transferase, DNMT, methylate the nucleotides, DNMT, CPG islands, spread around region, block ability of activation factors to bind to target sites, non-covalent, MCPGBP (methyl-CPG-binding proteins), MCPGBP, histone de-acetylase/HDA, de-acetylate, MCPGBP, histone methyl transfersase/ DMT, HP1 (heterochroamtin protein), MCPGBP, HMT and HDA
chromatin remodelers share
affinity for nucleosome domains to recognize histone modifications similar ATPase domains for overcoming histone-DNA interactions domains for interactions with other proteins
________ can account for about 4x extra the number of mRNAs
alternative start sites
specific sequences in the DNA are recognized by ______ in these proteins that assemble to form the PIC
amino acids
a series of really elegant experiments a while back showed that ____ and _____ can assemble if you give them the ingredients (water/ methane, ammonia, hydrogen) and add energy to the system (electrical spark)-- this was kind of an amazing find, these things we imagine as exclusive to life can self-assemble. So, we at a time imagined that _______ were the earliest genetic material, but we do not think so now because there haven't been plausible mechanisms found that would suggest ___ was able to ____ or _____
amino acids, small peptides, proteins, protein, convey information, self-replicate
2 general classes of proteins known to bind at these regulatory RNA motifs- __________ are proteins that are ______ and act as ____, so they recognize ___ and ______. These proteins will have a positive effect on the spliceosome, tending to promote removal of whatever is in between both sides... the other type of binding proteins here is _______, which bind to ____ to _____ splicing by interfering with the activity of the spliceosome
arginine serine-rich proteins, rich in arginine and serine, enhancers, ESE, ISE, promote the removal of whatever is in between both sides, HNRNP (heterogenous nuclear ribonucleic proteins), ESS, ISS, suppress
the other proteins that bind with RNA pol 2 in PIC are called
basal factors/ general transcription factors
a standard place to find some regulatory sequence would be in the __________, usually right upstream of the _________, just before the _____. There are also regulatory regions within _____ and _____ of gene. Only place you will not find CRE is _______.
basal promoter, first exon, TSS, introns, downstream, exon
famous example of ______ method of alternative splicing is in the gene that encodes for a particular type of _______ molecular...way this works is the splicing material generates RNA then picks ____ exon from each _____ (represented on slide by different colors) to maintain, so really the majority of exons are ___________. This is a critical gene to establish connections between ______ and the ______ so , thanks to this method, has very specific recognition, a code for connectivity
battery, salivary, 1, battery, discarded, CNS neurons, other CNS neurons
3 general discoveries of Mendel's
both parents contribute to offspring genes and alleles dominance and recessivity (law of independent assortment, law of segregation)
the site in the middle of the 5' and 3' splice donor and splice receptor is a 3rd site called the _______,. which is slightly closer to the _____ but not all the way there, this has _____ and also _______, and some other typical nucleotides associated with it. because the core of these sequences is ________, it is possible for the splicing machinery to look at these sites in a variety of ways: __or ___ for ex
branching site, 3' AC, AGC, invariant, 2 at a time, every intron
genetics around 10,000 BCE
breeders and farmers used genetics to select for preferred characteristics
the splicing itself is done by a complex molecular machine comprised of ___ and ______ , that is called a ______. The units are coming together to form a ________ and the ribbon is the ______ that is being processed. ______ and just under _______ participating. first thing that happens is the RNA is cleaved at the site of the _______, and the splicosome holds on to this and generates a _________ structure so the region from the intron that was connected to the exon region folds back on itself and you have the formation of kind of an unusual _____ bond. Key point is that ________________
bunch of proteins, noncoding RNA, spliceosome, tetramer, mRNA, small nuclear RNA 20 proteins, spliced donor, lariat, 5'-2', distinct 3' and 5' sites have branch site that allows formation of lariat structure when cleavage happens
where are the genes producing the transcription factors?
could be anywhere-- could be on different chromosome could be right next door
there are a lot of ways alternative splicing can happen and it depends on where _______ are
critical recognition sequences
which base of the CPG island is the one that is actually methylated
cytosine
DNA adenine nucleoside would be called _______ and shortened as ______ in RNA adenine nucleoside would be called ______ and be shorted as _____ in DNA adenine nucleotide would be called ______ and be shorted as ____ in DNA adenine nucleotide would be called ______ and be shortened as ______
deoxyadenosine, dA adenosine, A deoxyadenosine triphosphate, dATP adenosine triphosphate, ATP
cancer associated with mutations histone 3: _________ affects _____ structures and has a median survival of _____ months after diagnosis, the mutation is in H3 in _____ of cases...when the tumors whole genome was sequenced it was found that in tumors primarily localized in the _______ they found the mutation _________, a lysine was changed to a ______, which cannot be acetylated or methylated, thus chromatin state was altered
diffuse intrinsic pontine glioma (DIPG), midline, 9-12, 80%, G34R/V
the DPE (________), typically _______ of the TSS
downstream core promoter element, 28-32 downstream
Thyroid hormone receptors (TR) are examples of ________. the _________ is required for ___________, and in its native form, _____, it converts TR from a ______ to an _______ for hundreds of target genes (the dimer of of TR is ______)
dual-function activator/ repressor, thyroid hormone, T3, repressor, activator, RXR
back in the early 60s it was discovered that genes and proteins are collinear. scientists were curious about the relationship between the gene and the particular place of the protein it affects, so they went to study ______ and in particular a gene that codes for a sub unit of ______. They mutagenized the ____ and produced lots of mutants, then roughly mapped mutations relative to one another within the gene. They then examined the consequences for the protein the gene encodes and found the arrangement of mutations in the gene to be ____ with the arrangements of changes in the protein (e.g the most 5' mutation in the gene corresponded to the most ____ mutation in the protein). They also noticed that sites on the genes were _________, meaning they code encode __________ (where there was a mutation there would either be the substitute of one different amino acid, or a third amino acid). Another thing they noticed was that there could be 2 mutations within one or 2 nucleotides of each other that could __________, which suggested some sort of genetic code
e.coli, tryptophan synthase, e, coli, colinear, amino, multi-functional, more than 1 amino acid, affect the same amino acid
why is RNA such a good candidate? _________, ___________ (DNA is _______, which removes potential for other interactions and inhibits it from _________)...this also raises possibility of RNA acting as a ______ on itself and other RNAs (because of its potential to bind) lastly the ______, in the case of ______ RNAs, subunits can be identified across ____, _____ and _____ so deep evolutionary origins because clearly convergent evolution among the 3 groups
encodes info, capable of complex folding, double-stranded, forming shapes RNA can form, catalyst, phylogenic conservation, ribosomal, archea, bacteria, eukarya
as we said, the tertiary structures of RNA suggest that it could have been capable of acting as an ________ (and in order for it to have been the first genetic material, it would have needed enzymatic capabilities in order to achieve self-replication). In the _____, the first catalytic RNAs were identified: ___________. Tertiary structure of _____ includes regions where the RNA is forming circles bound to itself, called a ____ structure. __________ cleaves the ________ bonds on _____ and other _______. It normally works with the aid of other proteins but it was discovered in lab that it can have catalytic capabilities on its own in vitro. Also interesting to note that these RNAs on their own could ________. This is an intriguing activity on its own, but also raises possibility that if the RNA is acting on itself like that, there might be ______, which would allow for the _________
enzyme, 80s, ribonuclease-P, ribonuclease-P, hairpin, ribonuclease-P, phosphodiester, tRNAs, small RNAs, cut themselves out of the sequence and allow the sequence to be sequenced back together, errors in how that process is carried out, introduction of new variations in a system
Beadle and Tatum had the hypothesis that each gene in the genome coded for a specific _______, and each enzyme impacted a specific step in a metabolic pathway. to test this, they grew ______. They shined a ______ on a colony of bacteria in the hopes of mutating them. The WT could grow just fine in __________ because they are able to synthesize what they need (arginine, final product) from what is in the medium, so mutants were identified as the bacteria that could not grow on the minimal medium. Depending on which _________ a class of mutants needed in order to produce the final product arginine, it could be determined at which step in the metabolic pathway there was a default/ which enzyme's gene had been mutated
enzyme,yeast , UV light, minimal medium, precursor
histone modification and cytosine methylation are examples of ________ that affect gene expression. Cross-generational, sex-specific DNA methylation for a few hundred genes results in "_________" that affects gene expression in offspring
epigenetic modifications, genomic imprinting
histone sequences have been ______ across species
extremely
heterochromatin is often ____ poor and ____ rich, darker stained, and localized to the _______ of the nucleus
gene, repeat, periphery
methylation is not as straight forward as acetylation because acetylation has predicable consequences in terms of accessibility, whereas methylation can either increase or decrease accessibility depending on the
histone site being modified and the methylation state
sites of extensive post-transcriptional modification
histone tails, pointing outward from DNA
there are a variety of other ______ he didn't discuss: histone ____, ____, ______, ______...histone ____is a core histone but histone ____ is involved in DNA repair and recombination (______ experiment used to show this)
histones, 3.3, 2a,2ax,2z, 2a, 2ax laser DNA damage
the INR (_______ motif) , present in only some organisms, is _____ and ______
initiator, highly variable, spans the length of the TSS (starts upstream and continues downstream of it)
the addition of a _______ at the 5' end of mRNA helps to protect it from _________ (there are a zillion ____ that specifically target RNAs partly to regulate their abundance, also in context of protecting cell from RNA viruses) there is so much surveillance in the cell regarding RNA that for mRNA to persist it has to evade that surveillance, the cap of ___________ is joint by _________, it is added on the 5' end only after the 5' end is synthesized by RNA pol 2. The particular enzyme that adds the methyl group is ____________
inverted methylated guanine, being degraded by RNAses, RNAases, inverted methylated guanine, tri-phosphate bride structure, guanine 7 methyl transferase
H336Kme ___ associated with transcription, H327Kme is______
is, is not
following the _____ most significant genetic discoveries/ contributions are a result of ________
late 60s, technological advances
things Mendel did that were super lucky/ could've been potential complications
many traits are continuous, not concrete alleles not always transmitted at expected ratios many alleles not D or R but additive in their effects independent assortment not always observed (linkage) heritable material unidentified
elongation depends on ______ protein complex, a machine that can zip along the template DNA and produce RNA at _______________ depending on the specifics of the chromatin state
multi-miraic, 1000-4000 bases a minute
do transposable elements count as pseudogenes?
no
is the start codon at the TSS?
no, TSS is where 5' UTR starts, the start codon is where the translated part of sequence starts
nucleotides on opposite strands are attached by ___________
non-covalent hydrogen bonds
acetylation can change the interaction between ___ and _____, but can also lead to the __________
nucleosome DNA disassociation of the nucleosome itself
there is a correlation between complexity of organism and _______, but no correlation between complexity of organism and _______ largely because of_____________ (algae have no more than 10 or 11 cell types but can have largest genomes known, or some of the smallest) ______ have larger genomes than humans do
number of cell types, size of genome, noncoding sequences, amphibians
where is the additional O on RNA, that DNA is lacking?
on the 2' C
a cancer that is growing really rapidly might _________ to make sure there is no transcriptional pausing
overproduce EFs
but the really big generator of diversity that explains why there is so much more mRNA than protein-coding genes is
paritucular transcriptional machinery and splicing factors that can remove introns selectively and maintain exons selectively
compared to a nucleotide, a nucleoside lacks the ___________ attached at the ____
phosphate group, 5' C
nucleotides having all 3 components give them special characteristic-- now they can join up with nucleotides through _________
phosphodiester bonds
one more way transcription can occur/ access can be maintained: class of proteins called _______ that some times recognize histone modifications and sometimes use other methods, they are evolutionarily distinct from one another in certain cases but share common properties:
pioneer factors, can bind to DNA even in closed chromatin (very odd), can initiate chromatin remodeling, permit the binding of other transcription factors, can swap histone variants in or out, permit binding to other transcription factors, usually stabilize open state
Malaria: _______ parasite gains entry to the _______ by exploiting cell surface ___________...a lot of TF need to be recruited to Duffy gene to get transcription going, like ______. the ____ site is recognized by a ______ (which u remember is a type of _______) this is an important step for transcription of the Duffy Gene to begin. People who have developed resistance to malaria have a _______ in the _______....so the gene is not transcribed and the parasite cannot get into the cell
plasmodium, RBC, chemokine receptors/ Duffy, SP1, GATA, GATA factor, pioneer factor, mutation, GATA sequence
once termination happens and elongation has stopped, there is opportunity for final post-transcriptional modification which is addition of __________, which is also important for protecting _____ from degradation, it is a way of escaping RNA surveillance mechanisms that would otherwise chew up RNA quickly. Initially, the tail is not present in the transcript, and the template for the tail is not initially present in the DNA. But, there is a ___________(_________) that is recognized by ____________, which binds to the signal in the transcript and then added typically a _________ ________ to the end of the transcripts, and that signal helps to protect against degradation
poly-A tail, mRNA, signal in the transcript (AAUAAA) pol-A polymerase, couple hundred As
if a histone (lysine particularly) is not acetylated, it has _______ charge. If the histone is acetylated, the charge becomes _________. DNA has a _____ charge, so DNA is more likely to interact with the _______ histone, thus decreasing accessibility and preventing transcription.
positive, neutral, negative
any prototypical genetic material must be able to:
store information, express information, replicate, accommodate the introduction of new variation
Solutions to prebiotic chemist's worse nightmare
possibly had different types of bases doing job-- hypoxanthine other, more stable sugars than ribose may have arisen spontaneously and been able to get job done-- threose, glutamine, aspartate if you don't have phosphate, aspartate could have been the linker in terms of solvent, periodic evaporation and condensation between water and formamide could have allowed for different. chemistries within solvents instead of magnesium iron could have been the cofactor (not toxic in an environment without oxygen)
3 proposed theories of inheritance
preformationism (debunked by technologies) inheritance of acquired characteristics (sometimes incorrectly referred to as Lamarckism, debunked by Weissman's experiment with the mice) Blending inheritance (debunked because offspring not perfect mix of parents and also everyone would eventually look the same, they don't)
assuming the pause state ends, the second phase is ______ and during this phase the RNA pol 2 goes _________. There needs to be an escape from pausing, so _________ interact with RNA pol 2 to detach them form whatever is holding it back so it can zip right through, some _____ are known to act on nucleosomes in this process
productive elongation, quickly right through to the end, positive transcription elongation factor, EFs
where will RNA pol 2 be assembled
proximal promoter just upstream of TSS
ribosomes are complex machines of ____ working with ____ and _____ as well
rRNA, tRNA, proteins
RNA Pol 1
rRNAs
DNA may assume different forms: the B-form spirals _______ (_______) and the z-form spirals _______(_______)
right, typical left, weird
pioneer factors work by ________ the chromatin, finding the ______, and once they've done that, doing local _______ that makes that particular site more available to transcription factors and other more complicated proteins
scanning, binding site, remodeling
RNA polymerase ribozymes were evolved in the lab but at first the_________ blocked activity...one nucleotide could be added at a time but in event template had secondary structure, the ribozyme would soon _________. The electrophoresis diagram shows that when no nucleotides are added, _______. When nucleotides are added, if the sequence is repeated 1 time it ________, if the sequence is repeated 2+, _______. They had the idea that maybe they could overcome that by selecting for a ribozyme that added not one nucleotide at a time but rather added _________. After ____ rounds of selection, they saw 6 types of ribozymes and the strands are getting higher so we know they are replicating longer strands/ more repeats. So triplet add ons are working. Type ___ was surprisingly a dud on its own, but when combined with any other type (_ -_) it served as a _______, thus a ________ had been created that maximized efficiency.
secondary structure, stall out, nothing happens, replicates, it stalls out, triplets, 21, 1, 2-6, cofactor, hetero-dimer
the the ChipSeq graph the graph shows a lot of something stacked up-- we are saying there are a lot of "marks" there (like oh a lot of H3K27 or whatever) but really, we are counting the
sequence repeats
one common modification is the phosphorylation of ____residues
serine
HP1 is involved with _____, recognizes_____ and _______
silent transcription, H3K9me, prohibits transcription
often times _________ act as CRE so gene has multiple motifs recognized by the same transcription factor, so you have potential to recruit a bunch of the same TF at once
simple sequence repeats
repeated regions called _________ tend to ______ very quickly because replication is _____ and it is easy to add or subtract one unit to this...there is 1 simple sequence repeat every ______ bases in our genome..highly variable, some repeats of ___ nucleotide and some repeats of _____
simple sequence repeats/ micro-satelites evolutionarily expand and contract sloppy 2000 1 11
since 2015 the interest has been in _____________ we can now not only sequence a whole genome from organism but we can go in and isolate a single cell and figure out what genes that cell is expressing at a particular time...according to graphs we can go in and say...very fast moving field with about _____ cells a couple years ago and now we can do ____ cells per experiment...moving into personalized genomes now too, can take a swab of DNA and get a representation of genome sequence back
single cell RNA or DNA sequencing, "we think these cells are run development to be this type of cell", 20,000, 200,000
PRMT may add a _____ methyl group to _____ , forming or, through the activity of different __________, it could add a ________ methyl group in different locations, which can have different consequences
single, mono-methyl-arginine, subtypes of PRMT, second
additional mechanism proposed for how alternative splicing is carried out is related to _____. If RNA pol 2 is moving faster than normal, and splicosome cannot keep up, the lariat structure keeps extending and there is an opportunity for the splicing donor to match with a splicing acceptor much farther down the line than would normally be the case-- presents more choices. In contrast, if the RNA pol 2 is moving more slowly, the splicosome is able to keep up and splice in real time so there is less likelihood of an ____ ever being vulnerable outside of the splicosome/ being in the liriate structure...so in general:
speed, exon...fast moving RNA pol 2 makes it more likely exon will get spliced out, slowly moving reduces options...makes it more likely the intron will just get cut out and then move on to next intron
RNA Pol 3
tRNAs and other small RNAs
a variety of additional RNA types-- microRNA involved in ________, there is also ______ and _______ RNA, which can lead to ______
targeting mRNAs and leading to their degradations, floating RNA, retrovirus, reverse transcription
DNA Breathing experiment: put censors at two different points of DNA, if they are closer to each other _________....they used ________, 1 was ____ and 1 was _______ and if they were close enough together the _____ can interact with each other and produce a ________ (also they made a certain lysine 56 that was either always or never acetylated)...in WT (no acetylation at H3K56) the fret signal was expressed at a ________, whereas in the acetylated type the fret signal is _____
the DNA is more tightly bound to the nucleosome, fluorescent reporter, green, red, photons, fret signal, relatively high efficiency, lower
As shown, in Drosophila there are eight Hox genes in a row, and the genes' order within that row reflects their order of expression in the fly body. The gene found on the left or 3' end of the DNA strand, denoted lab (labial), is expressed in the head; on the other hand, the gene at the right end of the DNA strand, Abd-B (Abdominal-B), is expressed at the end of the fly's abdomen. so Hox gene clusters, which are close to each other and regulated close to each other, are essential for laying out
the body pattern
striking find from the pediatric cancer study-- in case of DIPG5, the mutation present in all sites was _____ and then depending on which part of the brain there were additional mutations
the histone mutations can represent the onset of cancer, H2F3A
CHD1BPTF is involved with _______, recognizes_________, and
transcriptional activation, H3K4me, activates transcription
EAF 3 is involved with _________, recognizes _______________, in order to __________
transcriptional elongation, H3K38me, promote transcription
PC is involved with __________, recognizes_______ and _________
transcriptional memory, H3K27me and H3K27ac, in case of me prohibits and in case of ac promotes
facts about genetic code
triplet, non-overlapping, 3 stop codons, degenerate (more than 1 codon can specify the same amino acid), initiation codon (AUG) marks start of reading frame, mutations (frameshift, nonsense, missense) can affect message or be silent, polarities of codons and amino acids correspond
3 tenants of natural selection
variation, differences in fitness, heritability
classic example of DNA methylation? _____________. ______ are a class example of x-chromosome inactivation, which ends up producing a _________ that is ____ and ________. The DNA methylation becomes critical for genomic _______ or ________ in the _____ switching to an _______ in terms of _________. At 6 weeks, the _________ gene is being transcribed (unmethylated promoter) and the y-globin gene is methylated, at ______ weeks, this switches and the _______ gene is not methylated and the ______ gene is methylated (this phenomenon happens because the embryo requires a really strong hemoglobin that will rip oxygen from the maternal circulation
x-chromosome inactivation, tortoise shell cats/ calico cats, mosaic, random, permanent, "imprinting," "silencing," hemoglobin, sigma, 12, y, sigma
SWI/SNF are common in ______, BAF are common in _______
yeast, human
particular TF that bind to CRE and are critical in forming mediator
zinc finger (has helices binding to specific DNA) leucine zipper (has two helices that interact with specific sequences) helix-turn-helix, and a dimer...each of these has a DNA-binding domain and an activating domain