Genetic exam 4
1. Histone protein a. Composed of _________________. b. Then __________ comes in after DNA wraps around almost twice and puts everything together 2. The tails that stick out of the _________ and _________ histone proteins are highly modifiable a. They have _________ and _________ that can be methylated b. The methylation state of the histone tail affects the compaction state of the chromatin itself
1 H2A, 1 H2B, 2 H3, and 2 H4 H1 H3 and H4 arginine and lysine
DNA methylation can stop transcription in 2 ways. 1. 2.
1. DNA methylation can block activator binding 2. DNA methylation can recruit heterochromatin proteins
one possible situation that happens when the gRNA pair with pre-mRNA is that the gRNA has extra ______ residues that do not pair with the mRNA. The complementary ________ are added in a 3 step process. Name what happens
A Us i. Endoribonuclease cleaves in the pre-mRNA to form a 3' end to allow the edition of U ii. Then TUTase is used to put U's on the end iii. Then ligase is used to seal it
Molecular determinants of heritable expression patterns 1. ___________ 2. ____________
DNA methylation heritable chromatin states
1. What happens when there is a mismatched base-pair in DNA? a. ______________ comes to fix it i. 3 subunits: MutH, MutL, MutS ii. MutS: ___________ iii. MutH:______________ 1. When it finds a methyl group, it making a nick at the methyl group and on the other side of the mismatch on the new strand i. The ___________ comes in a fill it
DNA mismatch repair (MMR) find the mismatch in DNA base pairing looks for the methyl group to determine which one is the old strand DNA polymerase I
DNA mismatch repair (MMR) i. replication errors by __________ not recognized by ___________ ii. detects distortion in ____________ iii. bacteria and eukaryotes use a similar mechanism
DNA polymerase proofreading DNA helix
1. heritable changes in DNA other than sequence methylation, phosphorylation, acetylation
Epigenetics
Long-term expression patterns 1. When a cell differentiates, we want that cell to stay that type a. Cells differentiate into lung cell; we want it to stay a lung cell 2. Trithorax and Polycomb proteins maintain transcriptional states a. ____________ proteins i. Lead to transcriptional repression ii. Changes euchromatin into heterochromatin i. Polycomb recognizes methylation on a histone H3 at lysine 27 and binds b. ____________ i. Leads to transcriptional activation ii. Changes heterochromatin into euchromatin i. Trithorax protein recognizes methylation on a histone H3 at lysine 4 and binds a. These are responsible for differentiation of stem cells during development, because the chromosome is marked with these b. These states are heritable as cells divide
Polycomb Trithorax
Splicing involves two ___________ Reactions 1. The ___________ is connected to the first nt (G) on the _________ end of the intron a. Forms a loop called the __________ 2. Then we connect the 3' end of the ________exon and the 5' end of the __________ exon 3. Then the lariat intron is released a. The lariat does not have a 5' end so it's to stable in the cell so we would have a build-up of introns and waste nucleotides b. So, a ___________ enzyme cleaves the branch apart to make it linear again c. Then exonuclease comes and recycle the nt
Transesterification bulge A 5' lariat 5' 3' debranching
one possible situation that happens when the gRNA pair with pre-mRNA is that the mRNA has extra ________ that doesn't pair with the gRNA. These Us are _______. NAME WHAT HAPPENS
Us removed i. Endoribonuclease cleaves it ii. Exonuclease chews it off iii. the Same ligase seals it up
2. Ionizing radiation: a. includes __________ and ___________ b. has ___________ wavelength and _________ energy c. can penetrate deeply into biological molecules d. creates chemically reactive molecules termed free radicals e. can cause: i. ______________ ii. base deletions, oxidized bases, single nicks in DNA strands, cross-linking, chromosomal breaks
X-rays and gamma rays short high breaks double stranded DNA
Physical mutations - radiation 1. Two main types: a. b.
a. ionizing radiation b. nonionizing radiation (UV light)
1. Euchromatin: a. transcriptionally __________ regions of DNA b. far fewer nucleosomes c. histones are more highly ___________ and ______________ i. e.g. Ser10 phosho of H3 recruits HATs a. the phosphorylation of the tail can end up recruiting histone acetylation (HAT) 2. Heterochromatin: a. transcriptionally ______________ regions of DNA b. more nucleosomes c. histones less acetylated d. histones usually more highly __________ i. not DNA
active phosphorylated and acetylated inactive methylated
The _________ test is used to evaluate mutagenicity. 1. We use 3 strain of salmonella bacteria that has a mutation for ____________ a. These mutations are caused by either _____________, _____________, or __________ in the 3 strains. 2. We expose these bacteria to potential _______ then plate them on media without histidine (minimal media) to test for ___________ 3. If a lot of the salmonella ends up ____________ on the plate, this means that a mutation occurred because they should not be able to grow. Little growth could be due to random mutations so need a lot of growth. 4. Control is the use of water, not the mutagen
ames histidine (cannot produce histidine) transition mutation, or transversion mutation, or frameshift mutagen reversion growing
Induced mutations - base modifier 1. base modifiers are ___________ mutagens that enhances the ________ process or covalently modify the structure of a ____________ 2. example: _________ (deamination) a. replaces ________ groups with _______ groups (-NH2 to =O) (oxidative deamination) b. Changes the base and the base-pairing! c. Can deaminate ______, __________, and _______ i. Note: we can fix C --> U because we have __________ but nothing to fix the other 2 ii. Can be fixed by DNA mismatch system but not the best 1. example: ____________ a. covalently add _________ or _________groups to bases i. nitrogen mustard (a type of mustard gas) ii. ethyl methanesulfonate (EMS)
chemical deamination nucleotide nitrous acid amino groups with keto groups A, C, and G Uracil DNA glycosylase alkylating agents ethyl or methyl
Why have Introns? 1. Its good for __________ 2. One benefit of genes with introns is a phenomenon called __________ 3. A pre-mRNA with multiple introns can be spliced in different ways a. This variation in splicing means that we don't need to have a huge genome, we can splice introns at different parts to form different proteins 4. This variation in splicing can occur in different cell types or during different stages of development 5. One very important biological advantage of __________ in eukaryotes is the phenomenon of alternative splicing a. Alternative splicing increases the number of ________and it's the proteins that make us more complex more so than more genes
complexity alternative splicing introns proteins 7. Baker's yeast contains about 6,300 genes 8. Humans contain ~ 22,000 genes
X-chromosomal inactivation 1. early embryo — both Xs active 2. due to ____________, one RANDOM X-chromosome is silence and turned into a Barr body happens around the ___________ cell stage 3. one that X is silenced, it is now permanently silenced 4. this is heritable through cell division
dosage compensation 1000
Duchene Muscular Dystrophy and RNA splicing 1. In skeletal and cardiac muscles, ___________ is part of a group of proteins that work together to strengthen muscle fibers. In Duchene Muscular Dystrophy, Dystrophin doesn't work properly leading to muscle loss and until recently boys with DMD usually didn't live past their teens 2. Exondys 51 is for patients who have a mutation of the dystrophin gene amenable to _________, which affects about 13 percent of the population with DMD. SOME DMD deletes exon ______________ which leads to an incorrect ________ for the rest of the exons. 1. We can use little pieces of nucleic acid called __________to prevent splicing of exon 51 to move translation back into the frame a. These are not really RNA; these are chemically modified RNA to make it more stable in the cell so that it does not get degraded b. These are called __________ oligonucleotides c. These bind to that RNA splice site to prevent splicing of exon 51
dystrophin exon 51 skipping 50 reading frame oligonucleotides antisense X-LINKED 79 EXONS LARGE SIZE MAKES IT PRONE TO MUTATION THAT CAUSES PROBLEMS
a. ____________: insertion or deletion of several nucleotides that is not divisible by three
frameshift mutation
1. The Iron Paradox a. Iron is an essential element for living organisms. b. It is required for the function of many enzymes and carries oxygen on hemoglobin. c. Too much Iron can also be dangerous by generating _________. 2. There is a system that keeps the level of iron at a correct level a. _________ protein carries iron through the bloodstream and transferrin receptor brings iron into cells by binding to transferrin b. Too much or too little iron is detrimental. c. Too much improperly stored iron can generate toxic reactive oxygen d. Excess iron is stored within __________, a hollow spherical protein
free radicals Transferrin ferritin
Epigenetics at the organismal level 1. Individuals have same/similar DNA but distinct __________ patterns: a. these patterns result from environmental exposures b. these changes are not necessarily heritable in the next generation
gene expression
1. The entire DNA sequence of many (1000's) of organisms is known
genomics
There are 4 motifs seen in Eukaryotic DNA binding Gene Regulatory Proteins (used to bind to specific sequences in the DNA). NAME THEM?
helix turn helix helix loop helix zinc finger leucine zipper
Frameshift mutagens 1. Hydrophobic planar compounds slip in between the base pairs in a process known as __________ 1. This confuses DNA replication causing it to __________ or ___________ bases. example: proflavin
intercalation put in extra or to take out
1. Introns also called ___________ a. Start out in the ________ but do not end up in the final mRNA to be ____________ 2. This means that you cannot read the DNA and know the order of amino acids because you have to get rid of the introns
intervening sequences DNA translated
1. One of the big differences between prokaryotes and eukaryotes is that transcription factors can work from a ________ distance away. a. For bacteria, CAP was -65nt b. For eukaryotes, it can be thousands 2. How is this possible? a. These regulatory factors (aka transcription activators) work through __________ b. Transcriptional activator stimulates the function of ____________ i. Allows regulator to work far away in terms of nucleotide sequence but not so far away through 3-dimensional space ii. Can directly change the __________ state of RNA polymerase II on the __________ iii. Same deal with repressor binding to silencers, it inhibits the mediator from functioning
long space mediator phosphorylation the carboxy-terminal domain (CDT)
1. Transferrin receptor imports iron into cells when levels are _________ a. When iron levels are low, the _________ binds to _______ but this time on the _________ end b. This protects the 3' end of the mRNA from _________ c. When iron levels get high. Iron binds to IRP to let go of the 3' end and allows it to be degraded
low IRP IRE 3' degradation
1. an organism's physical traits. a. _________ has only simple nutritional needs b.__________ requires one or more complex biomolecule c. lethal (death as a phenotype) d. conditional lethal (temperature sensitive)
phenotype prototroph auxotroph
Methylated lysine and arginine 1. Basic amino acid with ___________ charge 2. Methylation does not neutralize the positive charge 3. All it does it add hydrophobic bulk to the end of the side chain a. This changes the ___________ that can bind to it. a. Methylation of __________ residues within the histone leads to the recruitment of different proteins
positive protein different
Another way to control gene expression in a eukaryote is to localize where the regulator is. If we keep the regulator in the cytoplasm, then it cannot regulate transcription. So instead of changing the regulator itself, you can change the localization of it. (eukaryotes) 1. An example is glucocorticoid hormone 2. Prednisone is a synthetic drug used as an immunosuppressant to treat certain inflammatory diseases 3. These drugs crossed the membrane and bind to ___________ that is already present in the ___________ a. This protein without the drug has a partner protein called HSP90 b. The receptor exists as a monomeric unit in complex with _________ when no drug is around 4. When drug is present, the HSP90 is removed and allow the receptor to form a ________ which is important to ____________ and _________ a. NLS = ____________ Uncovered after dissociation of HSP90 which allows it to go into nucleus
receptors protein cytoplasm HSP90 dimer bind to a site on the DNA and to go into the nucleus nuclear Localization Signal
1. DNA methylation can block activator binding a. Leads to transcription ________ because the activator protein can't bind.
repression
How do you control which exons are included? 1. There are proteins that bind to the RNA that either prevent splicing or activate splicing (similar to transcription regulation) 2. These are called _________ to prevent the exon from being present and___________ to which causes a certain exon to be expressed.
splicing repressors splicing enhancer
1. The one class of RNA that are processed after being transcribed in bacteria are the __________ 2. 3' of all tRNA has the sequence __________ a. This is sometimes encoded in the DNA and sometimes not. Even if it is, it sometimes gets lost in the lifetime of the tRNA. When this happens, there is an RNA processing enzyme that puts it back on. b. _______________ is the enzyme responsible for putting the CCA nt back on or add it if it's not in the DNA sequence.
tRNAs CCA CCA Terminal nucleotidyltransferase
1. nonionizing radiation (UV light) from the sun a. UV light-induced ______________ i. Happens only when thymine is ___________ other on DNA ii. Forms a ________-member covalent ring c. Do not base pair properly during DNA replication!
thymine dimers next to each four
1. Eukaryotic gene expression can be regulated after the RNA is made: a. splicing b. regulation of ____________ c. regulation of RNA stability (half-life) i. this is done via _____________ 1. double-stranded RNA can silence expression of certain genes
translation RNA interference (RNAi)
Spontaneous deamination of the amino group of cytosine 1. Cytosine and react with water and undergo a deamination reaction to form __________ and ___________ a. The amine group on the cytosine changes to a _________ group
uracil and ammonium keto
Editing via gRNA proceeds ________ on the mRNA completing one round of editing creates the binding site on the RNA for the _______of the next gNRA. Does this over and over until it goes through the whole pre-mRNA.
3' to 5' anchor a. A large portion of base pairs are changed using the gRNA 1. The theory for why this organism does this is so that the host will have a harder time killing it
motifs seen in Eukaryotic DNA binding Gene Regulatory Proteins 1. Zinc finger (only seen in eukaryotes) a. _________ strands in the protein bind to the metal __________ b. This positions the leading head into the major groove of the DNA
Beta zinc
Some chromatin types are heritable 1. During replication, the octamer of histones can go in 2 ways a. ____________ b. __________________ 2. Either way at the end of the day machinery comes and makes them identical again
Conservative: It can all go to one helix of DNA then the next histone octamer goes to another stand Semi-conservative: It can go half and half
Complex mutagens 1. intercalate and alkylate 2. not mutagenic until activated (oxidized) by __________in the liver 3. These mutagens intercalate and covalently bond to DNA
CytP450 mono-oxygenase a. CytP450 mono-oxygenase participate in the detoxifying of ingested food
1. heritable change in the genetic material (DNA or RNA)
Mutation:
Xeroderma Pigmentosum i. defects in genes involved in _____________ linked to several human diseases ii. extreme sensitivity to sunlight predisposition to skin cancer
NER (nucleotide excision repair)
1. There is also activator and repressor proteins that control transcription in eukaryotes a. The difference is that these proteins DON'T affect __________ DIRECTLY unlike in bacteria instead they affect _________ . 2. These proteins bind to DNA sequence but they are not called operator sequences instead they called _________ in the case of activator protein and __________ in the case of repressor proteins a. Transcriptional activators can work in 2 ways: 1. 2. 4. THESE PROTEINS CAN ALSO EFFECT TFIIB a. For example, maybe TFIID can bind without the activator but for TFIIB to bind an activator needs to be present
RNA polymerase II transcription factor (TFIID and TFIIB) enhancers silencers i. It can recruit TFIID to the core promoter and/or activates its function. Thus, transcription will be activated ii. It can also function by helping TFIID recruit TFIIB b. Transcriptional repressor inhibits TFIID binding to the core promoter or inhibits its function. Thus, transcription will be repressed i. Or I can prevent the recruitment of TFIIB
The ribosomal RNAs are also processed by ___________ in eukaryotes 1. There are ____ ribosomal RNA in ribosomes, but these are initially transcribed as one long rRNA. The long sequence is then cleaved to form the 3 ribosomal RNA 2. The long rRNA base pair into the structure that they are going to exist in. Then RNase III recognize specific____________ and cut them. a. Base pair structure is key, not specific sequence.
RNase III 3 base-pair stems
SOS DNA repair system 1. remember induction of lambda lysogen 2. when DNA damage occurs in bacteria leading to stop of replication, the SOS DNA repair system is activated a. ________ first gets activated i. Note: RecA causes CI (Lambda repressor) to cleave itself b. RecA then cleaves a repressor called __________ which is responsible for turning off a bunch of genes that are involved in ___________ 3. One of the gene in the SOS repair system is an ____________ which is a polymerase with no proofreading but it gets around problems in the DNA and finish the job so cells can divide. a. Regular polymerase has a lot of proofreading and does not make a lot of mistakes. When it reaches something that is not right it just stops, and the cell dies
RecA LexA SOS repair error prone polymerase
1. Two possible situations when the gRNA pairs with the pre-mRNA: explain This process is performed by _________ which is composed of many proteins including _________, __________, _________ and __________
The gRNA has extra A residues that do not pair with the mRNA. The complementary Us are added The mRNA has extra Us that don't pair with the gRNA. These Us are removed a. The system is called editosome i. Composed of many proteins including TUTase, endonuclease, exonuclease, and ligase
Pre-spliceosome 1. Consist _________ snRNP when they bind to 5' splice site and branch-site respectively 2. The full spliceosome is formed when ___________ are added to the pre-spliceosome
U1 and U2 U4, U5, and U6 (tri-snRNP)
first step in mRNA splicing is done by __________. It uses its ____________ to base pair with the ___________.
U1 snRNP U1 snRNA 5' splice site 1. So splicing start at the 5' end of the pre-mRNA with the U1 snRNP base pairing its U1 RNA with the 5' splice site
third step in mRNA splicing uses ______________ snRNPs. Also called the ___________
U4, U5, and U6 (the three work together) tri-snRNP
motifs seen in Eukaryotic DNA binding Gene Regulatory Proteins 1. Leucine zipper a. Long _________ that wrap around each other through the amino acid __________ i. Leucine is hydrophobic and has a moderate size b. The leucine zipper doesn't bind to DNA, but it positions alpha-helices into the major groove of the DNA. a. The other motifs are dimers, but for this, they can come from different polypeptide subunits. This means that each one of these alpha-helices can recognize different unrelated sequences. This is unlike the other motifs where they bind to repeats (inverted repeats or direct repeats). i. This makes it harder to find these sequences in the DNA
alpha-helices leucine
1. DNA methylation can recruit heterochromatin proteins a. A __________ bind to the methylated CpG island. b. The methyl-CpG-binding protein recruits other proteins that convert the chromatin to closed conformation.
methyl-CpG-binding protein a. One of the proteins can be histone deacetylase
second step in mRNA splicing is done by ____________ 1. U2 snRNP binds to the ____________ via RNA/RNA base pairs to create a ________ residue. This forms the ___________ complex 2. This bulge is created because one of the nucleotide sequences is skipped and does does not get ___________
U2 snRNP ranch point bulged A pre-spliceosomal "A" base-paired
Epigenetics changes influenced by the environment 1. diet a. _________ and ___________ with 2 little cofactor called betaine and choline are required to make __________ b. SAM is the __________ donor used during methylation of DNA and protein c. If you do not have enough folic acid and B12 it will make it harder methylate genes d. The Agouti Avy allele is especially sensitive to changes in methylation i. Agouti gene promotes the synthesis of yellow fur pigment ii. Giving mice folic acid increase the number of brown (pseudo-agouti mice) iii. Little methylation -> _________ iv. High methylation -> ____________ v. DNA methylation leading to transcriptional repression of the agouti gene 2. Toxins a. environmental toxins can affect DNA methylation and gene expression b. does not only affect DNA mutation (change of sequence)
folic acid and vitamin B12 s-adenosylmethionine (SAM) methyl more yellow brown
1. The genetic makeup of an organism
genotype
5 prime 7-methylG cap 1. 5' triphosphate is converted to this via an enzyme called __________ 2. The cap is put on __________
the capping enzyme backwards (5' to 5')
Why is T in DNA and U in RNA? 1. DNA repair enzymes can recognize uracil as an inappropriate base in DNA and remove it 2. There is a repair system called ____________ which know uracil does not belong on the _________ a. This enzyme is zooming around on the DNA looking for __________. If it finds it, then it removes the U base b. Then an _____________ finds any place in the DNA that has no base but has a sugar and cuts out the sugar which leaves a nick c. Then ____________ puts in the right base via proofreading d. Then __________ seals the nick 3. Deamination of C goes on all the time, but it usually doesn't cause mutation because we have a system to fix it.
uracil DNA glycosylase DNA U AP endonuclease DNA polymerase I DNA ligase
Tautomeric shift 1. results in _________ base pairing due to the shift from the common _________ form to the _________ form in the inol form T pair with ___________ and C pair with ___________
erroneous keto/amino enol/imino G A
An individual, organism, or new genetic character arising or resulting from mutation
mutant
1. Scientist plated lots of E. coli on cell 2. Looked for mutation in the LAC I gene which code for lac operon repressor protein 3. When in the absence of lactose, the repressor should bind to repress the expression of beta-galactosidase 4. The mutation on the LAC I gene causes it to turn blue on the agar plate 5. Scientist took those cells and looked at where the mutation was in those genes 7. From this graph we can clearly see that the mutation in the LAC I gene occurred very frequently at 3 spots which are 5-methyl C regions a. Note: scientist did not induce any of these mutations
1. From this graph we can clearly see that the mutation in the LAC I gene occurred very frequently at 3 spots which are 5-methyl C regions a. Note: scientist did not induce any of these mutations
Translation is regulated by controlling access to the Ribosome Binding Site (RBS) in bacteria by 2 ways name them.
1. Regulatory protein binds to the mRNA and blocks access to the RBS 2. Regulatory protein binds to the mRNA and alters RNA structure by changing base pairing of the 5' RNA to block or provide access to the RBS
Consensus sequences 1. Important sequences in pre-mRNAs for splicing (3 sites) 2. 1 at the 5' of the pre-mRNA right between the end of the first exon and the start of the first intron a. This is called __________ b. Note that the first nucleotide in the intron is a __________ 3. In the middle of the intron is the second site a. Called __________ b. Important nucleotide is the _________ 4. The last site is at the 5' end of the intron a. Called ____________
5' splice site G branch site A 3' splice site
There are two forms of mutagens. what are they and give examples of them?
Chemical a. Base modifiers: enhances deamination or react with the base b. Intercalating agents: slip in between the base pair and can be really deleterious because it can change the reading frame c. Base analogues: chemicals that fool DNA polymerase by allowing it to be incorporated into the DNA but has a property that causes mutation physical a. X-rays b. Gamma rays c. Ionizing radiation d. UV light
1. Deamination of 5-methyl cytosine can also occur 2. 5-methyl C is created as part of the ____________ system similar to the DAM methylation system 3. There is another sequence in which the C is methylated a. 5′-___________-3' 4. 5-methyl C when deaminated turns into ____________ a. Thymine is a normal constituent of DNA and is not recognized by the repair system. b. But this will change the DNA sequence and generate a mutation! c. Locations with 5-methylated cytosine tend to create ___________ for mutation
DCM methylation (DCM = DNA cytosine) CCWGG (W stands for A or T) thymine hot spots
Induced mutations - base analogs 1. Base analogues fool _________ and become incorporated into DNA during __________ a. ___________ looks like thymine i. incorporated into DNA instead of thymine ii. has a higher propensity to undergo ____________ than uracil or thymine leading to improper base pair iii. they base-pair with _________ instead of A which is wrong
DNA polymerase replication 5-bromouracil rearrangement (tautomerization) G
1. ___________: from Wild-Type to mutant 2. ______________: from mutant back to WT 3. __________: return to original amino acid at mutant site 4. ____________: change at a second site compensates for the first change
Forward mutation Reverse mutation True reversion Second site reversion
1. METHYLATION OF ___________ AND __________ ARE USED TO REGULATE THE TRANSCRIPTIONAL STATE OF GENES
HISTONES DNA
a. ____________: changes codon for one amino acid to another i. Changing one sense codon to __________
Missense mutation another sense codon
a. ___________ changes a codon for an amino acid to a stop codon i. Sense codon to a __________ i. The closer they are to the start of the gene the worst it is. ii. End up with a ___________ protein (non-complete)
Nonsense mutation nonsense codon truncated
3 prime poly-A tail 1. Transcription goes pass what is going to end as the 3' end of the mRNA a. Anything pass the eventual poly-A tail is degraded 2. ___________ recognizes a certain sequence and add A residue a. The nt signal is ___________
Poly-A polymerase AAUAAA
Overview of synthesis of eukaryotic mRNA 1. We start with the transcription of ________ via ____________ 2. We put a ___________ on the 5' end a. The cap signals to the ribosome that this is an ___________ 3. Put a bunch of A's called the ________ on the __________ a. The 3' tail is involved in regulating the _________ of the mRNA b. Some mRNAs are around for a long time meaning you will make lots of protein form it other have a very short life 4. We also need to remove the __________. a. The process to remove introns are called ____________ b. Introns are not present in bacteria DNA
Pre-mRNA RNA polymerase II 7-methylG cap mRNA poly A tail 3' end lifetime introns splicing
a. _____________: changes the sequence of the gene but does not affect the _________ of the ___________ or _________ encoded by that gene i. You can actually have a change in AA and it will still be a silent mutation. 1. This is possible because __________
Silent mutation function protein or RNA not all AA in all protein are absolutely required to be that AA
1. Second site reversion: change at a second site compensates for the first change give an example?
There is a bond between a + and - charged amino acid. the positive mutate to a negative charge leading to improper conformation. The other AA which is - charge is mutated to a + charge leading to the bond formation and return of conformation. These take place in the same nucleic acid sequence
4th step of mRNA splicing 1. After the formation of the full spliceosome, the _______ and __________ snRNPs are detached and the remaining ________, _________ and __________ snRNAs are rearranged. This conformational change creates the catalytic spliceosome. 2. _____________ : OH, from __________ in Branch Point attacks the Phosphate of the first ______ in the________ end of the intron a. In total we are breaking 2 phosphodiester bond and make 2 phosphodiester bonds 4. Then you link new phosphodiester bonds between the ________________
U1 and the U4 U2, U5 and U6 Transesterification: bulged A G 5' 3' end of the 5' exon and the 5' end of the 3' exon
Epigenetics at the cellular level 1. _____________ a. at some point of development our cells choose a developmental pathway 2. ______________ 3. Two alleles of the same gene (or chromosome) are expressed differently: a. expression pattern stable upon cell division b. expression pattern can change in next generation
cellular differentiation during development transformation of normal to cancer cell
RNA editing by deamination in humans 1. Cytosine is deaminated via ________ to form __________ a. There is a protein called __________ that is made in the liver and intestine b. This protein is made from the same gene c. A C residue is converted to a U residue in the intestine instead of alternate splicing d. This conversion creates a _________ codon which in turn creates a smaller protein (about half the size) compared to the one in the liver 2. Adenine is deaminated via __________ to form ________ a. So, it went from the ribosome thinking its an A to thinking it's a G
cytidine deaminase uracil apolipoprotein B stop adenosine deamination acting on RNA (ADAR) inosine
1. Given that Iron is both essential and that excess iron can be toxic, its levels must be carefully regulated 2. Translation of the two mRNAs that encode ________ and the _________ are both regulated by an RNA-binding protein known as the __________ 3. IRP binds to a regulatory element within these two mRNAs known as the___________ in the _______ of iron. a. The IRE in ferritin (storage) mRNA is in _____ Untranslated Region (UTR) b. IRE in transferrin receptor (uptake) mRNA is in _____ Untranslated Region (UTR) a. When free iron levels increase, it binds to the ________ and causes it to dissociate from the ______
ferritin (storage) transferrin receptor (uptake) iron regulatory protein (IRP) (trans acting) iron response element (IRE) (cis acting) absence 5' 3' IRP IRE
1. Igf2 gene a. This gene is __________ and is differentially expressed based on whether you got it from mom or dad b. Imprinting occurs during _____________ c. Normally methylation of DNA _________ gene but this is an exception i. This is because of the __________ region 1. In females during _________ the Igf2 locus is not methylated so it is ___________ a. The 2 insulator regions with the insulator proteins bound cuts off access to the Igf2 sequence 2. In males during ______________, the insulator region is methylated. a. This prevents insulator protein from binding and allows igf2 to be ____________.
imprinted gametogenesis silences insulator oogenesis silenced spermatogenesis expressed
Epigenetics at the chromosomal level 1. ____________ a. one allele used over the other. DNA methylation specifically on cytosine residue b. some gene use maternal some use paternal allele 2. _____________ a. the use of one X-chromosome or the other b. each individual cell will randomly choose which X-chromosome it uses i. the other become __________ 1. Two alleles of same gene (or chromosome) are expressed differently: a. expression pattern _________ upon cell division b. expression pattern can change in the next generation
imprinting x chromosome inactivation Barr body stable
1. Ferritin stores excess iron a. Translation of ferritin mRNA is inhibited when iron levels are ______ due to the binding of _________ to _______ in the _______ region of the mRNA to inhibit translation by ribosome. b. At high iron levels, iron binds to ______, which is released from the IRE; translation can occur to make more ferritin to store the iron
low IRP (Iron Regulatory Protein) IRE 5' IRP
non-coding RNAs (ncRNAs) 1. In a typical human cell: a. only ~20% of transcription produces __________ b. ~80% of transcription devoted to ___________!!! c. ncRNA abnormalities associated with disease i. (e.g. cancer, neurological disease, cardiovascular disease) 2. Can bind to different types of molecules a. DNA b. Protein c. mRNA d. small molecules
mRNA ncRNAs
1. Which one of the mismatched base-pair is correct? a. The old (parental) strand is correct new strand is wrong c. But how can the cell tell which one is the old strand? i. Within cell's DNA gets _________ ii. DNA is methylated at the ________ position of ______ in ___________ sequences by the __________ enzyme iii. Right after replication only the _________ strand is methylated iv. This means that s double-stranded DNA after replication is _________ a short period of time before DAM methylase can methylate it again
methylated Adenosines 6th GATC DNA Adenine Methylase (DAM methylase) old (parental) hemimethylated
Pattern of methylation changes when we compare a normal cell to a cancerous cell. 1. This means that if we sequence a cancerous cell and compare it to normal cell, the sequence might not have changed. But the changes in _________ can change its transcriptional potential (upregulate or downregulate) making it cancerous.
methylation
DNA methylation 1. DNA _____________ adds methyl group to ___________ base (can occur on both strands) a. often happens in regions of the chromosome called ______________ 2. Methylation of CpG islands is associated with transcriptional ___________
methyltransferase cytosine CpG islands (clusters of CpG dinucleotides found at promoters) repression
Causes of mutation 1. Spontaneous mutations: a. result from i. _____________ ii. ________________ 2. Induced mutations: a. caused by environmental agents b. chemical/physical agents that are known to alter DNA are called _____________
mistakes in biological processes (DNA replication) properties of the bases in DNA themselves 1. tautomeric shift 2. deamination mutagens
1. Point mutation: individual changes of individual _________ (2 types) a. _________: one purine changes to another purine (A to G) one pyrimidine to another pyrimidine (C to T) b. __________: purine changes to pyrimidine or vice versa (C to A) c.
nucleotides Transition Transversion
Modifying transcription factors 1. Hormone can bind to transcription factor and cause it to bind to DNA (both in prokaryote and eukaryotes) 2. In response to effector molecule, it can cause changes to the _________ states of the transcription factor (eukaryotes) a. The combing of 2 transcription factor in response to an effector 3. it can also change the _________ state of the regulator Another way to control gene expression in a eukaryote is to _________ where the regulator is. If we keep the regulator in the cytoplasm, then it cannot regulate transcription. So instead of changing the regulator itself, you can change the localization of it. (eukaryotes)
oligomeric phosphorylation localize
Splicing and human diseases 1. Recent studies have shown that approximately ___________ of all disease-causing mutations are related to RNA splicing. 2. The development of new technologies in molecular biology has opened the door for research on RNA mis-splicing events and how they relate to disease.
one-third
a. Direct repair of thymine dimers by __________ ii. This repair is activated by just _________, UV light is not needed b. What happens if your expose to UV light and the sun goes down or you go inside and you do not have the light to activate this enzyme? c. There is a second mechanism called _________ of thymine dimers i. The system looks for _____________ ii. When a kink is found it recruits another protein which makes a nick _________ and __________from the dimer iii. Then ____________ come to fix it followed by ____________ iv. This system in fact can fix anything that blocks replication
photolyase BLUE light nucleotide excision repair thymine dimers upstream and downstream DNA polymerase I ligase
During translation, the poly-A tail on the 3' with a protein called ___________ will interact with a bunch of translation factors which start the translation. This makes a connection between 3' and 5' end. This tells the ribosome that the RNA is __________. It has the right thing on the 3' and the 5' end
poly-A binding protein full length
1. The tRNA in bacteria when transcribe it is not functional. It is transcribed as a _________ a. It has an extra sequence on ____________ 2. 3' (3 prime) a. To process the 3' end of the tRNA you need ___________ and _________ b. The endonuclease (RNaseF) processes the 3' end by recognizing a ___________ c. Once the structure is gone, it allows the exonuclease (RNaseD) to start working on the ________ end 3. 5' (5 prime) a. RNaseP processed the 5' end of the Trna b. RNaseP is a _________ i. Composed of RNA and proteins i. The catalytic part is made of __________ b. The more complex the animal, the less ________ is present, and the more protein is present i. This shows the evolution in process. The more complex organism has less RNA
precursor both the 5' and 3' end both an exo and endo nuclease base pair structure 3' ribozyme RNA RNA
1. DNA methylation at a _________ affects transcription factor binding. a. Most of the time b. Methyl means not activated 2. DNA methylation at an ___________ affects which gene is targeted by an enhancer. a. Since this is in an insulator region, methyl means activated
promoter insulator
mRNA splicing 1. Performed by a __________ complex called __________ 2. Spliceosome is composed of __________ and __________ 3. The parts are called ____________ a. Nuclear cause they located in nucleus b. Ribonuclear because they have RNA c. Proteins because they have protein 4. The names for the snRNPs are called U (U1, U2....) a. Named for the __________
protein-RNA spliceosome 5 proteins + RNAs small nuclear ribonuclear proteins (snRNPs) RNA
1. DNA methylation is restored after __________ a. de novo ____________ activity creates initial methylation b. _______________ methyltransferase activity propagates methylation i. meaning it methylate the hemimethylated DNA after replication i. the signal is the ________ group that is already present
replication methyltransferase maintenance methyl
Epigenetics 1. ___________ DNA sequence conferring different traits 2. phenotypic differences in organisms caused by differences in ___________ rather than differences in the genetic code itself 3. these phenotypic differences are semi-stable and sometimes heritable from one generation to the next
same gene expression
Nonsense suppression 1. _________ site mutation that reverts a __________ mutation (premature stop codon) 2. this can happen when there is a mutation in tRNA where it now bases pairs with a stop codon a. these tRNA are called _________ tRNA because it can suppress a stop codon b. the release factor can still bind to mRNA because the mRNA sequence is still a stop codon, but the tRNA will compete with it
second nonsense suppressor
1. Suppression mutation: like reversion except in a __________
second gene there is a bond between one + and one - charged protein. + is mutated to - leading to no bond. the other protein is converted from - to + leading to bond formation.
RNA editing: when you cannot trust the DNA 1. Present in only one kind of eukaryotic organism called __________ a. When they looked at their genomes there were not any genes. No protein-coding regions that make any sense in their genome. b. Cannot look at genome and predict the __________ 2. RNA editing changes the sequence of the mRNA _________. Hence the protein sequence does not match the prediction in the ________ strand of DNA 4. RNA editing in trypanosomes involves deletion and insertion of ________ 6. Many genes did not have _______ or ________ 8. They can add and subtract U residues to these pre-mRNA because they have a unique RNA called _________ a. They bind to mRNA using Watson and Crick base pair and wobble rule in an antiparallel direction via a part of the gRNA called the ________ which is located on the _________ end of the gRNA. b. Anchor makes base pairs with a specific place in __________ i. Many base pair between the anchor portion of the gRNA and pre-mRNA are _______ pair with ________ (wobble) in addition to Watson and crick c. When we go to the 3' of the gRNA there is a portion called the "middle" (aka information part) which is responsible for _____________________. d. Then the end of the gRNA there is a bunch of ____________ which is responsible for 2 things. name them?
trypanosomes AA sequence post-transcriptionally coding Uracils start codons or open reading frames (ORFs) guide RNA (gRNA) anchor 5' pre-mRNA G pair with U telling the system to add or remove U residues U's (poly-U tail) Signals this is the end of the information or the middle and also protects the gRNA from degradation on the 3' end.
